SYMBOL INDEX (9797 symbols across 1202 files)

FILE: Algorithms/2008-CliquePercolation/conradlee_clique_percolation.py
  function get_percolated_cliques (line 5) | def get_percolated_cliques(G, k):

FILE: Algorithms/2008-CliquePercolation/src_cpp/cliqueHash.h
  function class (line 27) | class cliqueHash

FILE: Algorithms/2008-CliquePercolation/src_cpp/communityTracker.h
  function class (line 33) | class CommunityTracker

FILE: Algorithms/2008-CliquePercolation/src_cpp/dendrogram.h
  function class (line 30) | class Dendrogram
  function compareNodes (line 67) | static bool compareNodes(DendrogramNode * first, DendrogramNode * second...

FILE: Algorithms/2008-CliquePercolation/src_cpp/k_clique.cpp
  type Link (line 50) | struct Link{
    method Link (line 54) | Link(size_t source=0,size_t dest=0, float weight=0.0) : source(source)...
  function determineHashSize (line 60) | size_t determineHashSize(const size_t numElements, const size_t k)
  function getNetSizeAndLinkNumbers (line 78) | bool getNetSizeAndLinkNumbers(char * fileName, size_t & netSize, size_t ...
  function readLine (line 120) | bool readLine(std::ifstream & myfile, size_t & source,  size_t & dest, f...
  function kCliquesFind (line 144) | void kCliquesFind(std::vector<weighedClique> & cliqueVector, NetType & n...
  function kCommunitiesFind (line 248) | void kCommunitiesFind(std::vector<weighedClique> & cliqueVector, Kruskal...
  function outputCommunityStructure (line 294) | void outputCommunityStructure(KruskalTree & communities, cliqueHash & k1...
  function unweightedSCP (line 323) | void unweightedSCP(NetType & net, std::list<Link> & linkList, const size...
  function weighedCliqueCmp (line 374) | bool weighedCliqueCmp(const weighedClique lhs, const weighedClique rhs)
  function kCommunitiesFindWeighted (line 379) | void kCommunitiesFindWeighted(std::vector<weighedClique> & cliqueVector,...
  function weightedSCP (line 403) | void weightedSCP(NetType & net, std::ifstream & file, const size_t numbe...
  function validateLinkList (line 434) | bool validateLinkList(std::list<Link> &linkList,size_t netSize,bool verb...
  function percolation (line 453) | int percolation(char * fileName, const size_t k, const size_t weighted, ...
  function main (line 481) | int main(int argc, char* argv[])

FILE: Algorithms/2008-CliquePercolation/src_cpp/k_clique.h
  type Set (line 51) | typedef Set<size_t> nodeSet;

FILE: Algorithms/2008-CliquePercolation/src_cpp/kruskal.h
  function class (line 28) | class KruskalTree

FILE: Algorithms/2008-CliquePercolation/src_cpp/nodeCommunities.h
  type Set (line 30) | typedef Set<size_t> nodeSet;
  function class (line 32) | class nodeCommunities

FILE: Algorithms/2008-CliquePercolation/src_cpp/script/testScp.py
  function listComp (line 8) | def listComp(l1, l2):
  function compareCommunities (line 17) | def compareCommunities(scpComms, cfComms):

FILE: Algorithms/2008-CliquePercolation/src_cpp/weighedClique.h
  function class (line 29) | class clique
  type SymmNet (line 82) | typedef  SymmNet<float> NetType;
  function class (line 86) | class weighedClique: public clique

FILE: Algorithms/2008-CliquePercolation/src_python/seq_clique_percolation.py
  class Net (line 22) | class Net(object):
    method __init__ (line 25) | def __init__(self):
    method _legaledge (line 28) | def _legaledge(self, src, dst):
    method _intsetedge (line 32) | def _intsetedge(self, src, dst, val):
    method _setedge (line 46) | def _setedge(self, src, dst, val):
    method __getitem__ (line 51) | def __getitem__(self, args):
    method __setitem__ (line 64) | def __setitem__(self, key, val):
    method __delitem__ (line 85) | def __delitem__(self, args):
    method __iter__ (line 95) | def __iter__(self):
    method isSymmetric (line 98) | def isSymmetric(self):
    method __len__ (line 101) | def __len__(self):
  class Node (line 105) | class Node(object):
    method __init__ (line 106) | def __init__(self, net, index):
    method __iter__ (line 110) | def __iter__(self):
    method __getitem__ (line 116) | def __getitem__(self, index):
    method __setitem__ (line 119) | def __setitem__(self, index, val):
    method deg (line 123) | def deg(self):
  class SymmNet (line 127) | class SymmNet(Net):
    method _legaledge (line 130) | def _legaledge(self, src, dst):
    method _intsetedge (line 139) | def _intsetedge(self, src, dst, val):
    method isSymmetric (line 144) | def isSymmetric(self):
  class Net_edges (line 149) | class Net_edges:
    method __init__ (line 150) | def __init__(self, net):
    method __iter__ (line 153) | def __iter__(self):
    method __len__ (line 160) | def __len__(self):
    method __str__ (line 169) | def __str__(self):
  function getSubnet (line 176) | def getSubnet(net, nodes):
  function loadNet_edg (line 197) | def loadNet_edg(input, mutualEdges=False, splitterChar=None, symmetricNe...
  class Enumerator (line 245) | class Enumerator:
    method __init__ (line 261) | def __init__(self):
    method _addItem (line 265) | def _addItem(self, item):
    method __getitem__ (line 271) | def __getitem__(self, item):
    method getReverse (line 277) | def getReverse(self, number):
    method __iter__ (line 280) | def __iter__(self):
    method __len__ (line 283) | def __len__(self):
  class NodeFamily (line 287) | class NodeFamily:
    method __init__ (line 292) | def __init__(self, cmap={}, inputFile=None):
    method _parseStrings (line 300) | def _parseStrings(self, input):
    method __str__ (line 306) | def __str__(self):
    method _sortBySize (line 314) | def _sortBySize(self):
    method _addCommunity (line 317) | def _addCommunity(self, newCommunity):
    method __getitem__ (line 320) | def __getitem__(self, index):
    method __len__ (line 323) | def __len__(self):
    method getSizeDist (line 326) | def getSizeDist(self):
    method getGiant (line 339) | def getGiant(self):
    method getGiantSize (line 352) | def getGiantSize(self):
    method getSusceptibility (line 362) | def getSusceptibility(self, size=None):
    method getCollapsed (line 402) | def getCollapsed(self):
    method getNew (line 421) | def getNew(self, newNodes):
    method getSetsForNodes (line 441) | def getSetsForNodes(self):
  class KtreeInteger (line 456) | class KtreeInteger:
    method __init__ (line 461) | def __init__(self, size=0):
    method __getRealParent (line 468) | def __getRealParent(self, node):
    method __setRealParent (line 478) | def __setRealParent(self, node, newParent):
    method getParent (line 488) | def getParent(self, node):
    method setParent (line 494) | def setParent(self, node, newParent):
    method __iter__ (line 497) | def __iter__(self):
    method getCommStruct (line 501) | def getCommStruct(self, separateElements=True):
    method __len__ (line 518) | def __len__(self):
    method mergeSetsWithElements (line 521) | def mergeSetsWithElements(self, elements):
    method addEdge (line 526) | def addEdge(self, edge):
    method setSize (line 529) | def setSize(self, newSize):
  class Ktree (line 534) | class Ktree(KtreeInteger):
    method __init__ (line 540) | def __init__(self, size=0):
    method getParent (line 545) | def getParent(self, node):
    method setParent (line 548) | def setParent(self, node, newParent):
    method __iter__ (line 551) | def __iter__(self):
    method getCommStruct (line 554) | def getCommStruct(self):
  class EvaluationList (line 565) | class EvaluationList:
    method __init__ (line 571) | def __init__(self, thelist, weightFunction=lambda x: x[2]):
    method setEvaluations (line 578) | def setEvaluations(self, evaluationPoints):
    method setLinearEvaluations (line 581) | def setLinearEvaluations(self, first, last, numberOfEvaluationPoints):
    method setStrengthEvaluations (line 592) | def setStrengthEvaluations(self):
    method setLastEvaluation (line 596) | def setLastEvaluation(self):
    method __iter__ (line 599) | def __iter__(self):
  function getKCliqueComponents (line 629) | def getKCliqueComponents(net, k):
  class KClique (line 646) | class KClique(object):
    method __init__ (line 652) | def __init__(self, nodelist, notSorted=True):
    method __hash__ (line 658) | def __hash__(self):
    method __iter__ (line 663) | def __iter__(self):
    method __cmp__ (line 667) | def __cmp__(self, kclique):
    method __add__ (line 673) | def __add__(self, kclique):
    method getSubcliques (line 676) | def getSubcliques(self):
    method __str__ (line 680) | def __str__(self):
    method getEdges (line 683) | def getEdges(self):
    method getK (line 689) | def getK(self):
  function getIntensity (line 693) | def getIntensity(kclique, net):
  class EvaluationEvent (line 700) | class EvaluationEvent:
    method __init__ (line 701) | def __init__(self, threshold=None, addedElements=None):
  function kcliquesAtSubnet (line 706) | def kcliquesAtSubnet(nodes, net, k):
  function kcliquesByEdges (line 727) | def kcliquesByEdges(edges, k):
  function kcliquesWeight (line 757) | def kcliquesWeight(net, k, weightFunction):
  function communitiesByKCliques (line 764) | def communitiesByKCliques(kcliques):
  function kcliquePercolator (line 783) | def kcliquePercolator(net, k, start, stop, evaluations, reverse=False, w...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Files/IOX.cc
  function fline_tr (line 15) | bool fline_tr(ifstream* fin, vector<string>* fields, string delim)
  function split_tr (line 52) | void split_tr(string input, vector < string >* fields, string delim){
  function openFile (line 87) | bool openFile(ifstream* fin, string filename)
  function openFileHarsh (line 108) | void openFileHarsh(ifstream* fin, string filename)
  function FileError (line 119) | void FileError(const string& filename){

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Files/StringEx.cc
  function trim (line 12) | const std::string trim(const std::string& pString,
  function replaceAll (line 34) | void replaceAll(string& str, const char& x, const char& y){
  function string (line 50) | string replaceStrChar(string str, const string& replace, char ch)

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/Format.cc
  function ChangeDelimiter (line 16) | void ChangeDelimiter ( const string& filein, const string& fileout, cons...
  function EncodeNetwork (line 50) | void EncodeNetwork ( const string& filein, const string& fileout, const ...
  function DecodeCommunities (line 99) | void DecodeCommunities ( const string& filein, const string& fileout, co...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/Network.h
  type cmp_str_ptr (line 9) | struct cmp_str_ptr{
  type cmp_set_str (line 15) | struct cmp_set_str{
  function class (line 31) | class Network {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/RandomNetwork.h
  function RandomNetwork (line 7) | void RandomNetwork ( const int& V, const double& dist, const int& min_de...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Network/TemporalNetwork.h
  type set (line 16) | typedef set < shared_ptr < string >, cmp_str_ptr > community;
  function class (line 22) | class TemporalNetwork{

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/Libraries/Params/Parameters.h
  type sui (line 20) | typedef short unsigned int sui;
  type lui (line 21) | typedef long unsigned int lui;
  function class (line 28) | class Parameters {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-orginal/main.cc
  function Print (line 16) | void Print( const set < shared_ptr < string >, cmp_str_ptr >& seed ){
  function CalcDensity (line 37) | double CalcDensity( const int& size, const double& Win, const double& Wo...
  function Components (line 60) | map < double, set < shared_ptr < string >, cmp_str_ptr > > Components ( ...
  function ExpandSeed (line 115) | void ExpandSeed ( set < shared_ptr < string >, cmp_str_ptr >& seed, shar...
  function Print (line 306) | void Print( const set < shared_ptr < string >, cmp_str_ptr >& seed, ofst...
  function main (line 323) | int main ( int argc, char** argv ){

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/network.h
  type cmp_str_ptr (line 11) | struct cmp_str_ptr {
  type cmp_set_str (line 17) | struct cmp_set_str {
  function class (line 34) | class network {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/graph/temporal_network.h
  type set (line 16) | typedef set<shared_ptr<string>, cmp_str_ptr> community;
  function class (line 22) | class temporal_network {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/main.cc
  function Print (line 15) | void Print(const set<shared_ptr<string>, cmp_str_ptr> &seed) {
  function CalcDensity (line 36) | double CalcDensity(const int &size, const double &Win, const double &Wou...
  function Components (line 59) | map<double, set<shared_ptr<string>, cmp_str_ptr> >
  function ExpandSeed (line 117) | void ExpandSeed(set<shared_ptr<string>, cmp_str_ptr> &seed, shared_ptr<n...
  function Print (line 316) | void Print(const set<shared_ptr<string>, cmp_str_ptr> &seed, ofstream &f...
  function main (line 333) | int main(int argc, char **argv) {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/useless/RandomNetwork.h
  function RandomNetwork (line 7) | void RandomNetwork ( const int& V, const double& dist, const int& min_de...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/graph_io_helper.cc
  function ChangeDelimiter (line 16) | void ChangeDelimiter(const string &filein, const string &fileout, const ...
  function EncodeNetwork (line 51) | void EncodeNetwork(const string &filein, const string &fileout, const ch...
  function DecodeCommunities (line 102) | void DecodeCommunities(const string &filein, const string &fileout, cons...

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/io_helper.cc
  function fline_tr (line 15) | bool fline_tr(ifstream *fin, vector<string> *fields, string delim) {
  function split_tr (line 49) | void split_tr(string input, vector<string> *fields, string delim) {
  function openFile (line 82) | bool openFile(ifstream *fin, string filename) {
  function openFileHarsh (line 101) | void openFileHarsh(ifstream *fin, string filename) {
  function FileError (line 110) | void FileError(const string &filename) {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/parameters_helper.h
  type sui (line 22) | typedef short unsigned int sui;
  type lui (line 23) | typedef long unsigned int lui;
  function class (line 30) | class parameters_helper {

FILE: Algorithms/2009-Connected-Iterative-Scan/src-refactor/util/string_helper.cc
  function trim (line 12) | const std::string trim(const std::string& pString,
  function replaceAll (line 34) | void replaceAll(string& str, const char& x, const char& y){
  function string (line 50) | string replaceStrChar(string str, const string& replace, char ch)

FILE: Algorithms/2009-EAGLE/graphs/tools/converter.py
  function asdot (line 18) | def asdot(AS):
  function select (line 25) | def select(x):
  class Converter (line 28) | class Converter:
    method reg (line 34) | def reg(self, v):
    method add (line 43) | def add(self, data, mv):
    method toFileAs (line 67) | def toFileAs(self, path):
    method toGraph (line 75) | def toGraph(self):

FILE: Algorithms/2009-EAGLE/graphs/tools/examples.py
  function example0 (line 7) | def example0():
  function example1 (line 15) | def example1():
  function example2 (line 25) | def example2():
  function example3 (line 45) | def example3():
  function example4 (line 54) | def example4():
  function example5 (line 66) | def example5():
  function example6 (line 74) | def example6():
  function example7 (line 82) | def example7():
  function example8 (line 88) | def example8():

FILE: Algorithms/2009-EAGLE/graphs/tools/progressbar.py
  class ProgressBarWidget (line 62) | class ProgressBarWidget(object):
    method update (line 69) | def update(self, pbar):
  class ProgressBarWidgetHFill (line 79) | class ProgressBarWidgetHFill(object):
    method update (line 88) | def update(self, pbar, width):
  class ETA (line 100) | class ETA(ProgressBarWidget):
    method format_time (line 102) | def format_time(self, seconds):
    method update (line 104) | def update(self, pbar):
  class FileTransferSpeed (line 114) | class FileTransferSpeed(ProgressBarWidget):
    method __init__ (line 116) | def __init__(self, unit='B'):
    method update (line 120) | def update(self, pbar):
  class RotatingMarker (line 132) | class RotatingMarker(ProgressBarWidget):
    method __init__ (line 134) | def __init__(self, markers='|/-\\'):
    method update (line 137) | def update(self, pbar):
  class Percentage (line 143) | class Percentage(ProgressBarWidget):
    method update (line 145) | def update(self, pbar):
  class SimpleProgress (line 148) | class SimpleProgress(ProgressBarWidget):
    method __init__ (line 150) | def __init__(self, sep=' of '):
    method update (line 152) | def update(self, pbar):
  class Bar (line 155) | class Bar(ProgressBarWidgetHFill):
    method __init__ (line 157) | def __init__(self, marker='#', left='|', right='|'):
    method _format_marker (line 161) | def _format_marker(self, pbar):
    method update (line 166) | def update(self, pbar, width):
  class ReverseBar (line 174) | class ReverseBar(Bar):
    method update (line 176) | def update(self, pbar, width):
  class ProgressBar (line 185) | class ProgressBar(object):
    method __init__ (line 233) | def __init__(self, maxval=None, widgets=default_widgets, term_width=None,
    method __call__ (line 258) | def __call__(self, iterable):
    method __iter__ (line 271) | def __iter__(self):
    method next (line 274) | def next(self):
    method _handle_resize (line 283) | def _handle_resize(self, signum, frame):
    method percentage (line 287) | def percentage(self):
    method _format_widgets (line 291) | def _format_widgets(self):
    method _format_line (line 313) | def _format_line(self):
    method _next_update (line 316) | def _next_update(self):
    method _need_update (line 321) | def _need_update(self):
    method update (line 341) | def update(self, value):
    method start (line 355) | def start(self):
    method finish (line 378) | def finish(self):

FILE: Algorithms/2009-EAGLE/src/communities.cpp
  function BOOST_FOREACH (line 73) | BOOST_FOREACH(CID c, keys) {
  function BOOST_FOREACH (line 84) | BOOST_FOREACH(CID c, toDelete) {
  function BOOST_FOREACH (line 190) | BOOST_FOREACH(unsigned int i, keys) {
  function CID (line 267) | CID Communities::registerCommunity(CommunityPtr c) {
  function CID (line 275) | CID Communities::addCommunity(NodeSet *s) {
  function CID (line 295) | CID Communities::addCommunity(igraph_vector_t *vector) {
  function CID (line 315) | CID Communities::addCommunity(unsigned int i) {

FILE: Algorithms/2009-EAGLE/src/communities.h
  type Community (line 27) | struct Community
  type Node (line 29) | typedef unsigned int Node;
  type CID (line 30) | typedef unsigned int CID;
  type Community (line 32) | typedef Community *CommunityPtr;
  type std (line 33) | typedef std::set<Node> NodeSet;
  type NodeSet (line 34) | typedef const NodeSet *NodeSetPtr;
  type boost (line 36) | typedef boost::unordered_map<CID, CommunityPtr> CommunitiesMap;
  type boost (line 37) | typedef boost::unordered_map<Node, std::set<CID> > MembershipMap;
  type Community (line 53) | struct Community {
  function update (line 155) | inline
  function degrees (line 184) | inline
  function CommunityPtr (line 192) | inline
  function CommunityPtr (line 203) | inline
  function igraph_vector_t (line 213) | inline
  function igraph_vs_t (line 226) | inline
  function CommunityPtr (line 234) | inline
  function class (line 250) | class Communities {
  function size (line 412) | inline
  function getDegree (line 418) | inline
  function areConnected (line 423) | inline
  function getCommunitySize (line 431) | inline
  function ownership (line 436) | inline
  function CommunityPtr (line 441) | inline
  function conductance (line 460) | inline
  function expansion (line 467) | inline
  function internalDensity (line 474) | inline
  function cutRatio (line 481) | inline
  function normalizedCut (line 488) | inline
  function linkDensity (line 497) | inline
  function scaledLinkDensity (line 504) | inline
  function maxODF (line 511) | inline
  function avgODF (line 545) | inline
  function flakeODF (line 580) | inline
  function EQ (line 614) | inline
  function similarity (line 648) | inline
  function NodeSetPtr (line 665) | inline

FILE: Algorithms/2009-EAGLE/src/eagle.cpp
  function Communities (line 67) | Communities *EAGLE::run() {

FILE: Algorithms/2009-EAGLE/src/eagle.h
  function class (line 10) | class EAGLE {

FILE: Algorithms/2009-EAGLE/src/main.cpp
  function main (line 6) | int main(int argc, char *argv[]) {

FILE: Algorithms/2009-EAGLE/src/max_cache.cpp
  function Max (line 60) | Max MaxCache::get() {

FILE: Algorithms/2009-EAGLE/src/max_cache.h
  type Max (line 14) | struct Max {
  function class (line 45) | class MaxCache {

FILE: Algorithms/2009-LineGraph/src/TseGraph.h
  function class (line 39) | class TseGraph {

FILE: Algorithms/2009-LineGraph/src/main.cpp
  function printLineGraphTypes (line 27) | void
  function printFileFormats (line 36) | void
  function usage (line 63) | void
  function usage (line 80) | void
  function parse_args (line 88) | void
  function display_time (line 137) | void
  function makeLineGraph (line 158) | void
  function main (line 261) | int main(int argc, char **argv) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/CM.java
  class CM (line 19) | public class CM {
    method CM (line 24) | public CM() {
    method main (line 27) | public static void main(String[] var0) {
    method realGraph (line 58) | private static void realGraph(String var0, String var1, int var2) {
    method benchmarkGraph (line 91) | private static void benchmarkGraph(int var0, int var1, int var2, doubl...
    method omegaResult (line 129) | private static void omegaResult(String var0, String var1, int var2) {
    method omegaBGLL (line 140) | private static double omegaBGLL(String var0, String var1, int var2) {
    method modularityResult (line 149) | private static void modularityResult(String var0, String var1) {
    method printOmega (line 155) | private static void printOmega() {
    method avgOmegaOthers (line 163) | private static void avgOmegaOthers(int var0) {
    method avgOmegaCM (line 188) | private static void avgOmegaCM(int var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/BK/BK.java
  class BK (line 18) | public class BK {
    method BK (line 27) | public BK() {
    method main (line 30) | public static void main(String[] var0) throws FileNotFoundException {
    method communityResults (line 50) | public static long communityResults(String var0, String var1, int var2...
    method saveCliques (line 78) | private static void saveCliques(ArrayList var0) {
    method printGraph (line 90) | private static void printGraph(ArrayList<HashSet<Integer>> var0) {
    method calculate (line 107) | private static void calculate(ArrayList<HashSet<Integer>> var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/BK/BronKerboschCFFast.java
  class BronKerboschCFFast (line 13) | public class BronKerboschCFFast {
    method BronKerboschCFFast (line 17) | public BronKerboschCFFast(ArrayList<HashSet<Integer>> var1) {
    method getBiggestMaximalCliques (line 21) | public Collection<Set<Integer>> getBiggestMaximalCliques() {
    method getAllMaximalCliques (line 47) | public Collection<Set<Integer>> getAllMaximalCliques() {
    method findCliques (line 63) | private Set<Integer> findCliques(List<Integer> var1, List<Integer> var...
    method check (line 129) | private void check(String var1, Set<Integer> var2, List<Integer> var3) {
    method end (line 139) | private boolean end(List<Integer> var1, List<Integer> var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/KJ/KJ.java
  class KJ (line 22) | public class KJ {
    method KJ (line 31) | public KJ() {
    method main (line 34) | public static void main(String[] var0) throws FileNotFoundException {
    method communityResults (line 54) | public static long communityResults(String var0, String var1, int var2...
    method saveCliques (line 101) | private static void saveCliques(ArrayList var0) {
    method converseTolist (line 113) | private static ArrayList converseTolist(HashSet<Integer> var0) {
    method printGraph (line 125) | private static void printGraph(ArrayList<HashSet<Integer>> var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/algorithm/MaxClique.java
  class MaxClique (line 19) | public class MaxClique {
    method MaxClique (line 29) | public MaxClique() {
    method main (line 32) | public static void main(String[] var0) {
    method mcq (line 39) | public static HashSet<Integer> mcq(String var0) {
    method mcq (line 45) | public static HashSet<Integer> mcq(ArrayList<HashSet<Integer>> var0, i...
    method mcq (line 51) | public static HashSet<Integer> mcq(ArrayList<HashSet<Integer>> var0, A...
    method readGraph (line 66) | private static int readGraph(String var0, ArrayList<HashSet<Integer>> ...
    method convert_V (line 108) | public static ARRAY2 convert_V(int var0) {
    method convert_e (line 120) | public static boolean[][] convert_e(ArrayList<HashSet<Integer>> var0) {
    method MCQ (line 134) | private static long MCQ(ArrayList<HashSet<Integer>> var0, ARRAY2 var1,...
    method vSort (line 156) | private static void vSort(ARRAY2 var0, TreeSet<ELEMENT> var1, ArrayLis...
    method initVerts (line 170) | public static TreeSet<ELEMENT> initVerts(ARRAY2 var0, ArrayList<HashSe...
    method EXPAND (line 188) | private static void EXPAND(ARRAY2 var0, boolean[][] var1, int var2) {
    method CUT2 (line 213) | private static boolean CUT2(int var0, ARRAY2 var1, ARRAY2 var2, boolea...
    method COLOR_SORT (line 227) | private static void COLOR_SORT(ARRAY2 var0, boolean[][] var1, int var2) {
    method CUT1 (line 286) | private static boolean CUT1(int var0, ARRAY_FIX var1, boolean[][] var2) {
    method COPY (line 295) | private static void COPY(ARRAY_FIX var0, ARRAY_FIX var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/input_output/ReadEdges.java
  class ReadEdges (line 12) | public class ReadEdges {
    method ReadEdges (line 13) | public ReadEdges() {
    method readGraph (line 16) | public ArrayList<HashSet<Integer>> readGraph(String var1, int var2) th...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/input_output/WriteCliques.java
  class WriteCliques (line 12) | public class WriteCliques {
    method WriteCliques (line 13) | public WriteCliques() {
    method saveGraphfile (line 16) | public static void saveGraphfile(ArrayList<HashSet<Integer>> var0, Str...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/ARRAY2.java
  class ARRAY2 (line 8) | public class ARRAY2 {
    method ARRAY2 (line 12) | public ARRAY2() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/ARRAY_FIX.java
  class ARRAY_FIX (line 8) | public class ARRAY_FIX {
    method ARRAY_FIX (line 12) | public ARRAY_FIX(int var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/Pair.java
  class Pair (line 6) | public class Pair {
    method Pair (line 10) | public Pair(int var1, int var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/Tree.java
  class Tree (line 8) | public class Tree {
    method Tree (line 14) | public Tree(HashSet<Integer> var1) {
    method Tree (line 19) | public Tree(Tree var1, Tree var2) {
    method add (line 25) | public void add(Tree var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/benchmark/GG.java
  class GG (line 26) | public class GG {
    method GG (line 32) | public GG() {
    method main (line 35) | public static void main(String[] var0) {
    method gen_benchmark (line 202) | public static int gen_benchmark(int var0, int var1, int var2, double v...
    method run_command (line 233) | private static long run_command(String var0, boolean var1) {
    method convert_bm_network (line 257) | public static void convert_bm_network(String var0, String var1) {
    method convert_bm_community (line 280) | public static int convert_bm_community(String var0, String var1) {
    method generate (line 327) | public static GGResult generate(int var0, int var1, int var2, double v...
    method gen (line 336) | private static GGResult gen(int var0, int var1, int var2, double var3,...
    method pruneGraph (line 420) | private static void pruneGraph(ArrayList<HashSet<Integer>> var0, HashS...
    method showStatsBi (line 437) | private static void showStatsBi(String var0, ArrayList<HashSet<Integer...
    method nVertices (line 506) | private static int nVertices(ArrayList<HashSet<Integer>> var0) {
    method sameGroup (line 518) | private static boolean sameGroup(int var0, int var1, ArrayList<TreeSet...
    method checkSaveGraph (line 528) | private static GGResult checkSaveGraph(ArrayList<HashSet<Integer>> var...
    method invert (line 539) | public static ArrayList<HashSet<Integer>> invert(ArrayList<HashSet<Int...
    method project (line 558) | public static ArrayList<HashSet<Integer>> project(ArrayList<HashSet<In...
    method weightedProject (line 576) | public static ArrayList<HashMap<Integer, Integer>> weightedProject(Arr...
    method averageDiameter (line 604) | private static GGResult averageDiameter(ArrayList<TreeSet<Integer>> va...
    method diameter (line 625) | private static int diameter(TreeSet<Integer> var0, ArrayList<HashSet<I...
    method maxDist (line 640) | private static int maxDist(int var0, TreeSet<Integer> var1, ArrayList<...
    method saveGroups (line 672) | private static void saveGroups(ArrayList<TreeSet<Integer>> var0, int v...
    method saveGraph (line 705) | private static void saveGraph(ArrayList<HashSet<Integer>> var0, int va...
    method saveWGraph (line 741) | private static void saveWGraph(ArrayList<HashMap<Integer, Integer>> va...
    method saveGraphCSV (line 777) | private static void saveGraphCSV(ArrayList<HashSet<Integer>> var0, int...
    method randName (line 804) | private static String randName(int var0, int var1, double var2, double...
    method minSize (line 814) | private static int minSize(ArrayList<TreeSet<Integer>> var0, int var1) {
    method makeArrayList (line 827) | private static ArrayList<HashSet<Integer>> makeArrayList(HashMap<Integ...
    method makeEdgesPA (line 847) | private static ArrayList<HashSet<Integer>> makeEdgesPA(ArrayList<TreeS...
    method randInt (line 961) | private static int randInt(double var0, Random var2) {
    method findInitVertex (line 970) | private static int findInitVertex(int var0, int var1, ArrayList<ArrayL...
    method findVertex (line 985) | private static int findVertex(int var0, int var1, ArrayList<TreeSet<In...
    method makeEdgesOld (line 1017) | private static ArrayList<HashSet<Integer>> makeEdgesOld(HashMap<Intege...
    method makeEdges (line 1055) | private static ArrayList<HashSet<Integer>> makeEdges(ArrayList<TreeSet...
    method makeEdgesBi (line 1059) | private static ArrayList<HashSet<Integer>> makeEdgesBi(ArrayList<TreeS...
    method findVertex1 (line 1159) | private static int findVertex1(int var0, double var1, TreeSet<Integer>...
    method inVertex (line 1175) | private static int inVertex(Integer[] var0, Random var1) {
    method outVertex (line 1180) | private static int outVertex(int var0, TreeSet<Integer> var1, Random v...
    method makeEdges (line 1189) | private static void makeEdges(int var0, HashSet<Integer> var1, ArrayLi...
    method makeEdge (line 1198) | private static boolean makeEdge(double var0, int var2, int var3, Array...
    method makeEdge (line 1207) | private static boolean makeEdge(int var0, int var1, ArrayList<HashSet<...
    method makeEdgesPref (line 1220) | private static HashMap<Integer, HashSet<Integer>> makeEdgesPref(HashMa...
    method makeEdgesFlat (line 1299) | private static boolean[][] makeEdgesFlat(HashSet<Pair> var0, int var1,...
    method randIntFromDouble (line 1354) | private static int randIntFromDouble(double var0, Random var2) {
    method randBoolean (line 1363) | private static boolean randBoolean(double var0, Random var2) {
    method makeSameGroup (line 1367) | private static HashMap<Integer, HashSet<Integer>> makeSameGroup(int va...
    method makeGroups (line 1394) | private static ArrayList<TreeSet<Integer>> makeGroups(int var0, int va...
    method individualName (line 1502) | private static int individualName(int var0) {
    method printBoolean (line 1506) | private static void printBoolean(boolean[][] var0, int var1) {
    method componentOf (line 1521) | private static HashSet<Integer> componentOf(int var0, ArrayList<HashSe...
    method printUsageAndExit (line 1543) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/benchmark/GGResult.java
  class GGResult (line 6) | class GGResult {
    method GGResult (line 14) | public GGResult(int var1, double var2, double var4, double var6) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CPP.java
  class CPP (line 23) | public class CPP {
    method CPP (line 24) | public CPP() {
    method main (line 27) | public static void main(String[] var0) {
    method preprocess (line 57) | public static int preprocess(String var0, String var1, String var2) {
    method process (line 69) | public static void process(String var0, String var1, String var2) {
    method convert_wakita_clusters (line 118) | public static void convert_wakita_clusters(String var0, String var1, i...
    method convert_cnm_clusters (line 186) | public static void convert_cnm_clusters(String var0, String var1) {
    method convert_cnm (line 192) | private static void convert_cnm(String var0, String var1) {
    method convert_pons_clusters (line 223) | public static void convert_pons_clusters(String var0, String var1) {
    method convert_blondel_clusters (line 260) | public static boolean convert_blondel_clusters(String var0, String var...
    method printUsageAndExit (line 312) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CommPair.java
  class CommPair (line 6) | public class CommPair {
    method CommPair (line 11) | public CommPair(int var1, int var2, double var3) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CommPairSet.java
  class CommPairSet (line 12) | public class CommPairSet {
    method compare (line 15) | public int compare(CommPair var1, CommPair var2) {
    method CommPairSet (line 20) | public CommPairSet(int var1) {
    method add (line 27) | public boolean add(CommPair var1) {
    method remove (line 33) | public void remove(int var1) {
    method best (line 49) | public CommPair best() {
    method toString (line 53) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CompleteCliques.java
  class CompleteCliques (line 13) | public class CompleteCliques {
    method CompleteCliques (line 16) | public CompleteCliques() {
    method completeCliques (line 19) | public static ArrayList<HashSet<Integer>> completeCliques(ArrayList<Ha...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/CompleteCliques1.java
  class CompleteCliques1 (line 13) | public class CompleteCliques1 {
    method CompleteCliques1 (line 14) | public CompleteCliques1() {
    method completeCliques1 (line 17) | public static ArrayList<HashSet<Integer>> completeCliques1(ArrayList<H...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/RebuildCommunities.java
  class RebuildCommunities (line 17) | public class RebuildCommunities {
    method RebuildCommunities (line 20) | public RebuildCommunities() {
    method rebuildCommunities (line 23) | public static ArrayList<HashSet<Integer>> rebuildCommunities(int var0,...
    method compareCliques_mod_fast (line 102) | private static double compareCliques_mod_fast(int var0, int var1, int[...
    method collect (line 106) | private static void collect(Tree var0, HashSet<Integer> var1) {
    method modularity (line 118) | private static double modularity(ArrayList<HashSet<Integer>> var0, int...
    method show (line 177) | public static void show(int[][] var0, ArrayList<HashSet<Integer>> var1...
    method detcomp (line 190) | public static int detcomp(double var0, int var2, int var3, double var4...
    method updateMod (line 194) | private static double updateMod(int var0, int var1, int[][] var2, Arra...
    method compareCliques_missing (line 221) | static double compareCliques_missing(int var0, int var1, ArrayList<Has...
    method compareCliques_missing2 (line 232) | static double compareCliques_missing2(int var0, int var1, ArrayList<Ha...
    method compareCliques_edgeCount (line 241) | static double compareCliques_edgeCount(int var0, int var1, ArrayList<H...
    method edgeCount (line 248) | static int edgeCount(HashSet<Integer> var0, HashSet<Integer> var1, Arr...
    method compareCliques_mod (line 267) | static double compareCliques_mod(int var0, int var1, ArrayList<HashSet...
    method getMod (line 276) | static double getMod(String var0, ArrayList<HashSet<Integer>> var1, in...
    method writeCom (line 305) | static void writeCom(HashSet<Integer> var0, PrintStream var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/community/RemoveCliques.java
  class RemoveCliques (line 15) | public class RemoveCliques {
    method RemoveCliques (line 16) | public RemoveCliques() {
    method removeCliques (line 19) | public static ArrayList<HashSet<Integer>> removeCliques(ArrayList<Hash...
    method saveNewedges (line 35) | public static void saveNewedges(ArrayList<HashSet<Integer>> var0, Stri...
    method saveUndirected (line 57) | public static void saveUndirected(ArrayList<HashSet<Integer>> var0) {
    method printGraph (line 83) | private static void printGraph(ArrayList<HashSet<Integer>> var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/graph/ELEMENT.java
  class ELEMENT (line 6) | public class ELEMENT {
    method ELEMENT (line 10) | public ELEMENT() {
    method ELEMENT (line 13) | public ELEMENT(int var1, int var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/metric/Modularity.java
  class Modularity (line 19) | public class Modularity {
    method Modularity (line 22) | public Modularity() {
    method main (line 25) | public static void main(String[] var0) {
    method modularity (line 33) | public static double modularity(String var0, String var1) {
    method modularity (line 58) | private static double modularity(int var0, List<Integer> var1, List<Pa...
    method readClusters (line 95) | private static int readClusters(List<Integer> var0, String var1, HashM...
    method numVertex (line 130) | private static int numVertex(String var0, HashMap<String, Integer> var...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/clique_modularity/util/metric/Omega.java
  class Omega (line 12) | public class Omega {
    method Omega (line 13) | public Omega() {
    method main (line 16) | public static void main(String[] var0) {
    method readCount (line 29) | public static int readCount(Vector<HashMap<Integer, Integer>> var0, St...
    method evaluateOmega (line 91) | public static double evaluateOmega(Vector<HashMap<Integer, Integer>> v...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/CONGA.java
  class CONGA (line 39) | public class CONGA {
    method CONGA (line 64) | public CONGA() {
    method main (line 67) | public static void main(String[] var0) {
    method clusterGraph (line 202) | public static Stats clusterGraph(int var0, HashSet<String> var1, Strin...
    method clusterGraph1 (line 212) | private static Stats clusterGraph1(int var0, String var1, int var2, Ha...
    method getSplitWeight (line 318) | private static float getSplitWeight(String var0, HashMap<String, HashM...
    method showOption (line 360) | private static void showOption(int var0, String var1, String var2) {
    method sameCluster (line 369) | private static boolean sameCluster(String var0, String var1, HashSet<H...
    method checkGraph (line 384) | private static int checkGraph(HashMap<String, HashSet<String>> var0) t...
    method statsGraph (line 410) | private static void statsGraph(List<HashSet<Integer>> var0) {
    method readGraphEdges (line 452) | public static HashMap<String, HashSet<String>> readGraphEdges(String v...
    method addWeight (line 538) | public static void addWeight(String var0, String var1, float var2, Has...
    method readGraph (line 554) | public static HashMap<String, HashSet<String>> readGraph(String var0, ...
    method vertex (line 633) | private static void vertex(String var0, HashMap<String, HashSet<String...
    method neighbour (line 640) | private static void neighbour(String var0, String var1, HashMap<String...
    method compactGraph (line 654) | public static void compactGraph(HashMap<String, HashSet<String>> var0,...
    method findClusters (line 713) | private static void findClusters(HashMap<String, HashSet<String>> var0...
    method writeSplitGraph (line 744) | public static void writeSplitGraph(List<HashSet<Integer>> var0, List<H...
    method sb_vs_vb (line 853) | private static float sb_vs_vb(int var0) {
    method cluster (line 877) | private static void cluster(List<HashSet<Integer>> var0, List<HashMap<...
    method wEdgeBetweenness (line 1056) | private static float wEdgeBetweenness(Edge var0, List<HashMap<Integer,...
    method wVertexBetweenness (line 1073) | private static float wVertexBetweenness(Vertex var0, float var1) {
    method updatePhase (line 1077) | private static boolean updatePhase(int var0, float var1, float var2, b...
    method addNewEdges (line 1100) | private static void addNewEdges(List<HashSet<Integer>> var0, List<Hash...
    method showStep (line 1165) | private static void showStep(int var0, int var1, int var2, float var3,...
    method setSizes (line 1204) | private static void setSizes(int var0, Between var1, List<HashSet<Inte...
    method update2Comps (line 1225) | private static boolean update2Comps(int var0, int var1, Between var2, ...
    method updateComps (line 1250) | private static void updateComps(HashSet<Integer> var0, Between var1, L...
    method compBetweenness (line 1261) | private static void compBetweenness(Between var0, List<HashSet<Integer...
    method betweenness (line 1272) | private static void betweenness(int var0, Between var1, List<HashSet<I...
    method compVertices (line 1373) | private static void compVertices(TreeSet<Integer> var0, Between var1, ...
    method detLess (line 1394) | public static boolean detLess(float var0, float var1) {
    method detLess (line 1398) | public static boolean detLess(float var0, float var1, int var2, int va...
    method detLess (line 1402) | public static boolean detLess(float var0, float var1, int var2, int va...
    method removeEdge (line 1406) | private static void removeEdge(int var0, int var1, Between var2, List<...
    method splitVertex (line 1420) | private static int splitVertex(int var0, Split var1, Between var2, Lis...
    method replaceWeight (line 1455) | private static void replaceWeight(int var0, int var1, int var2, List<H...
    method nameVertex (line 1473) | private static String nameVertex(List<String> var0, HashSet<Integer> v...
    method rootName (line 1481) | public static String rootName(String var0) {
    method compVertex (line 1486) | private static void compVertex(Integer var0, Between var1, List<HashSe...
    method tempMatrixCopy (line 1601) | private static float[][] tempMatrixCopy(float[][] var0, int var1) {
    method componentOf (line 1616) | public static TreeSet<Integer> componentOf(int var0, List<HashSet<Inte...
    method regionOf (line 1620) | private static TreeSet<Integer> regionOf(int var0, int var1, List<Hash...
    method regionOf (line 1626) | private static List<Integer> regionOf(int var0, int var1, List<HashSet...
    method smallRegion (line 1652) | private static boolean smallRegion(List<Integer> var0, TreeSet<Integer...
    method constructShowClusters (line 1675) | private static void constructShowClusters(String var0, int var1, Strin...
    method showClusters (line 1761) | private static void showClusters(List<Pair> var0, List<Pair> var1, Lis...
    method vad (line 1969) | private static double vad(HashMap<Integer, HashMap<String, Double>> va...
    method makeClusters (line 1989) | private static int makeClusters(int[] var0, HashMap<Integer, HashMap<S...
    method incWeight (line 2015) | private static void incWeight(HashMap<String, Double> var0, String var...
    method averageDiameter (line 2023) | private static GResult averageDiameter(HashMap<Integer, HashMap<String...
    method diameter (line 2047) | private static int diameter(HashMap<String, Double> var0, HashMap<Stri...
    method maxDist (line 2062) | private static int maxDist(String var0, HashMap<String, Double> var1, ...
    method modularity (line 2094) | private static double modularity(int var0, int[] var1, List<Pair> var2) {
    method rootOf (line 2131) | private static Tree rootOf(Tree var0) {
    method makeTree (line 2139) | private static Tree makeTree(Tree var0, Tree var1) {
    method clusterId (line 2149) | private static int clusterId(Tree var0) {
    method dispTree (line 2153) | private static void dispTree(Tree var0) {
    method flattenTree (line 2168) | private static HashSet<Integer> flattenTree(Tree var0) {
    method flattenTree (line 2174) | private static void flattenTree(Tree var0, HashSet<Integer> var1) {
    method printDegree (line 2184) | public static void printDegree(TreeSet<Integer> var0, List<HashSet<Int...
    method printUsageAndExit (line 2194) | private static void printUsageAndExit() {
    method cSplit (line 2219) | private static void cSplit(int var0, int var1, PrintStream var2, Clust...
    method cEdge (line 2229) | private static void cEdge(int var0, int var1, PrintStream var2, Cluste...
    method dOutput (line 2238) | private static void dOutput(String var0) {
    method sOutputN (line 2245) | private static void sOutputN(String var0) {
    method sOutput (line 2252) | private static void sOutput(String var0) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/Between.java
  class Between (line 20) | public class Between {
    method compare (line 25) | public int compare(Edge var1, Edge var2) {
    method compare (line 36) | public int compare(Vertex var1, Vertex var2) {
    method Between (line 41) | public Between(List<HashSet<Integer>> var1, HashSet<String> var2, List...
    method getPB (line 66) | public PB getPB(int var1) {
    method setSize (line 70) | public void setSize(int var1) {
    method bestEdge (line 83) | public Edge bestEdge() {
    method bestVertex (line 87) | public Vertex bestVertex() {
    method initComp (line 91) | public void initComp(TreeSet<Integer> var1, List<HashSet<Integer>> var...
    method removeEdge (line 103) | public void removeEdge(int var1, int var2) {
    method splitVertex (line 109) | public void splitVertex(int var1, int var2, HashSet<Integer> var3, Has...
    method putEdge (line 131) | public void putEdge(int var1, int var2) {
    method putVertex (line 144) | public void putVertex(int var1, float var2, Split var3) {
    method putVertex (line 148) | public void putVertex(int var1, float var2, Split var3, float var4) {
    method getVertex (line 159) | public Vertex getVertex(int var1) {
    method wBetweenness (line 164) | private float wBetweenness(Edge var1, List<HashMap<Integer, Float>> va...
    method replaceEdges (line 179) | private void replaceEdges(int var1, HashSet<Integer> var2) {
    method replaceEdge (line 203) | private void replaceEdge(int var1, int var2, int var3) {
    method deleteEdge (line 218) | private void deleteEdge(int var1, int var2) {
    method addEdge (line 232) | private void addEdge(int var1, int var2) {
    method reduceVertex (line 242) | private void reduceVertex(int var1, int var2) {
    method deleteVertex (line 250) | private void deleteVertex(int var1) {
    method addVertex (line 260) | private void addVertex(int var1, HashSet<Integer> var2) {
    method printBetweenness (line 269) | public void printBetweenness(int var1, List<String> var2) {
    method checkConsistency (line 287) | public void checkConsistency(int var1, List<HashSet<Integer>> var2) {
    method getSplitBetweenness (line 384) | public ArrayList<Float> getSplitBetweenness(List<String> var1) {
    method getVertexBetweenness (line 410) | public ArrayList<Float> getVertexBetweenness(TreeSet<Integer> var1, Li...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/CPP.java
  class CPP (line 23) | public class CPP {
    method CPP (line 24) | public CPP() {
    method main (line 27) | public static void main(String[] var0) {
    method preprocessDir (line 91) | public static void preprocessDir(String var0, String var1, String var2) {
    method preprocess (line 165) | public static int preprocess(String var0, String var1, String var2, bo...
    method alspac (line 181) | public static void alspac(String var0, String var1) {
    method process (line 214) | public static void process(String var0, String var1, String var2) {
    method convert_wakita_clusters (line 270) | public static void convert_wakita_clusters(String var0, String var1, i...
    method convert_cnm_clusters (line 338) | public static void convert_cnm_clusters(String var0, String var1) {
    method convert_cnm_network (line 344) | public static void convert_cnm_network(String var0, String var1) {
    method convert_cnm (line 366) | private static void convert_cnm(String var0, String var1) {
    method convert_pons_clusters (line 397) | public static void convert_pons_clusters(String var0, String var1) {
    method convert_lfm_clusters (line 433) | public static void convert_lfm_clusters(String var0, String var1) {
    method convert_fc_clusters (line 475) | public static void convert_fc_clusters(String var0, String var1) {
    method convert_nmf_clusters (line 534) | public static void convert_nmf_clusters(String var0, String var1) {
    method convert_eagle_clusters (line 585) | public static void convert_eagle_clusters(String var0, String var1) {
    method convert_im_clusters (line 611) | public static void convert_im_clusters(String var0, String var1) {
    method convert_oslom_clusters (line 669) | public static void convert_oslom_clusters(String var0, String var1) {
    method convert_nmf_graph (line 690) | public static int convert_nmf_graph(String var0, String var1) {
    method convert_eagle_graph (line 748) | public static void convert_eagle_graph(String var0, String var1, Strin...
    method convert_im_graph (line 784) | public static void convert_im_graph(String var0, String var1) {
    method convert_blondel_clusters (line 841) | public static boolean convert_blondel_clusters(String var0, String var...
    method printUsageAndExit (line 893) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/algorithm/PB.java
  class PB (line 13) | public class PB {
    method PB (line 21) | public PB(HashSet<Integer> var1, Vertex var2) {
    method replace (line 37) | public void replace(int var1, int var2) {
    method remove (line 43) | public int remove(int var1) {
    method print (line 70) | public void print(String var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/Pair.java
  class Pair (line 6) | public class Pair {
    method Pair (line 10) | public Pair(int var1, int var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/StrPair.java
  class StrPair (line 6) | public class StrPair {
    method StrPair (line 10) | public StrPair(String var1, String var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/Tree.java
  class Tree (line 6) | public class Tree {
    method Tree (line 12) | public Tree(int var1) {
    method Tree (line 19) | public Tree(Tree var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/benchmark/GResult.java
  class GResult (line 6) | public class GResult {
    method GResult (line 11) | public GResult(double var1, double var3, double var5) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/BP.java
  class BP (line 6) | public class BP {
    method BP (line 10) | public BP(float var1, float var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/ClusterInfo.java
  class ClusterInfo (line 10) | public class ClusterInfo {
    method ClusterInfo (line 16) | public ClusterInfo() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/community/Stats.java
  class Stats (line 12) | public class Stats {
    method Stats (line 43) | public Stats() {
    method showStats (line 46) | public void showStats(String var1) throws Exception {
    method splitVertex (line 59) | public void splitVertex(String var1, Split var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Edge.java
  class Edge (line 6) | public class Edge {
    method Edge (line 11) | public Edge(int var1, int var2) {
    method Edge (line 17) | public Edge(int var1, int var2, float var3) {
    method toString (line 23) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/LabelledEdge.java
  class LabelledEdge (line 6) | public class LabelledEdge {
    method LabelledEdge (line 11) | public LabelledEdge(float var1, int var2, int var3) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Split.java
  class Split (line 8) | public class Split {
    method Split (line 12) | public Split(HashSet<Integer> var1, HashSet<Integer> var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/graph/Vertex.java
  class Vertex (line 6) | public class Vertex {
    method Vertex (line 12) | public Vertex(int var1) {
    method Vertex (line 19) | public Vertex(int var1, float var2, Split var3, float var4) {
    method toString (line 26) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/conga/util/metric/ModOverlap.java
  class ModOverlap (line 15) | public class ModOverlap {
    method ModOverlap (line 18) | public ModOverlap() {
    method main (line 21) | public static void main(String[] var0) {
    method modOverlap (line 29) | public static double modOverlap(String var0, String var1) {
    method showClusters (line 45) | private static void showClusters(HashMap<Integer, HashMap<String, Doub...
    method invertClusters (line 51) | private static HashMap<String, HashMap<Integer, Double>> invertCluster...
    method readClusters (line 72) | private static HashMap<Integer, HashMap<String, Double>> readClusters(...
    method readGraphEdges (line 124) | public static HashMap<String, HashSet<String>> readGraphEdges(String v...
    method normalize (line 178) | public static void normalize(HashMap<Integer, HashMap<String, Double>>...
    method modOverlap (line 193) | public static double modOverlap(HashMap<Integer, HashMap<String, Doubl...
    method beta_out (line 258) | private static double beta_out(String var0, int var1, double var2, Has...
    method beta_in (line 278) | private static double beta_in(String var0, int var1, double var2, Hash...
    method F (line 298) | private static double F(String var0, String var1, int var2, HashMap<In...
    method f (line 305) | private static double f(double var0) {
    method alpha (line 309) | private static double alpha(String var0, int var1, HashMap<Integer, Ha...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/Project.java
  class Project (line 18) | public class Project {
    method Project (line 19) | public Project() {
    method main (line 22) | public static void main(String[] var0) {
    method project (line 71) | private static List<HashSet<Integer>> project(List<HashSet<Integer>> v...
    method weightedProject (line 89) | private static List<HashMap<Integer, Float>> weightedProject(List<Hash...
    method writeGraphEdges (line 117) | private static void writeGraphEdges(String var0, List<HashSet<Integer>...
    method writeWeightedEdges (line 139) | private static void writeWeightedEdges(String var0, List<HashMap<Integ...
    method printUsageAndExit (line 163) | private static void printUsageAndExit() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/algorithm/COPRA.java
  class COPRA (line 30) | public class COPRA {
    method COPRA (line 39) | public COPRA() {
    method main (line 42) | public static void main(String[] var0) {
    method showOptions (line 219) | private static void showOptions(int var0, int var1, int var2, boolean ...
    method clusterGraph (line 305) | public static VecPair clusterGraph(int var0, String var1, String var2,...
    method clusterGraph (line 314) | public static VecPair clusterGraph(int var0, String var1, String var2,...
    method clusterGraph1 (line 337) | private static VecPair clusterGraph1(int var0, String var1, List<HashS...
    method nEdges (line 515) | private static int nEdges(List<HashSet<Integer>> var0) {
    method stdDev (line 525) | private static double stdDev(double var0, int var2, double var3) {
    method minSummary (line 537) | private static Map<Integer, Float> minSummary(Map<Integer, Float> var0...
    method clusteringSummary1 (line 553) | private static Map<Integer, Float> clusteringSummary1(List<ClusterLabe...
    method clusteringSummary2 (line 572) | private static Map<Integer, Float> clusteringSummary2(List<ClusterLabe...
    method propagate (line 593) | public static void propagate(String var0, int var1, String var2, Strin...
    method propagateClusters (line 606) | private static List<ClusterLabel> propagateClusters(List<ClusterLabel>...
    method reportRes (line 629) | private static void reportRes(Vector<Double> var0, Vector<String> var1...
    method sumRes (line 640) | private static Vector<Double> sumRes(Vector<Double> var0, Vector<Doubl...
    method report (line 656) | private static void report(double var0, double var2, double var4, doub...
    method readBiGraphEdges (line 673) | public static void readBiGraphEdges(String var0, List<HashSet<Integer>...
    method copyFile (line 679) | private static void copyFile(String var0, String var1) {
    method readBiGraphEdges (line 700) | private static int readBiGraphEdges(String var0, List<HashSet<Integer>...
    method nameInt (line 768) | private static int nameInt(String var0, List<String> var1, Map<String,...
    method outputClusters (line 784) | private static Vector<Double> outputClusters(List<ClusterLabel> var0, ...
    method totSize (line 852) | private static int totSize(List<TreeSet<Integer>> var0) {
    method filterClusters (line 862) | private static List<TreeSet<Integer>> filterClusters(List<TreeSet<Inte...
    method combineGraphs (line 891) | private static List<HashSet<Integer>> combineGraphs(List<HashSet<Integ...
    method combineClusters (line 916) | private static void combineClusters(List<TreeSet<Integer>> var0, List<...
    method addSingletons (line 923) | private static void addSingletons(List<TreeSet<Integer>> var0, HashSet...
    method flatten (line 938) | private static HashSet<Integer> flatten(List<TreeSet<Integer>> var0) {
    method writeClusters (line 948) | private static void writeClusters(List<TreeSet<Integer>> var0, String ...
    method convertClusters (line 965) | private static List<TreeSet<Integer>> convertClusters(List<ClusterLabe...
    method removeEmpty (line 992) | private static List<TreeSet<Integer>> removeEmpty(List<TreeSet<Integer...
    method simpleSimplifyClusters (line 1005) | private static void simpleSimplifyClusters(List<TreeSet<Integer>> var0...
    method deletable (line 1016) | private static boolean deletable(int var0, List<TreeSet<Integer>> var1) {
    method simplifyClusters (line 1032) | private static void simplifyClusters(List<TreeSet<Integer>> var0) {
    method contiguous (line 1066) | private static List<TreeSet<Integer>> contiguous(List<TreeSet<Integer>...
    method contiguous (line 1082) | private static TreeSet<Integer> contiguous(int var0, TreeSet<Integer> ...
    method writeBiClusters (line 1100) | private static void writeBiClusters(List<TreeSet<Integer>> var0, Strin...
    method writeClusters (line 1135) | private static void writeClusters(List<TreeSet<Integer>> var0, PrintSt...
    method writeCluster (line 1147) | private static void writeCluster(TreeSet<Integer> var0, PrintStream va...
    method simpleClustering (line 1171) | private static List<ClusterLabel> simpleClustering(int var0, float var...
    method printUsageAndExit (line 1182) | private static void printUsageAndExit() {
    method readClusters (line 1198) | private static List<ClusterLabel> readClusters(String var0, int var1, ...

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/LabelPair.java
  class LabelPair (line 6) | public class LabelPair {
    method LabelPair (line 10) | public LabelPair(float var1, int var2) {
    method toString (line 15) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/SetPair.java
  class SetPair (line 8) | public class SetPair implements Comparable<SetPair> {
    method SetPair (line 12) | public SetPair(int var1, TreeSet<Integer> var2) {
    method compareTo (line 17) | public int compareTo(SetPair var1) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/VecPair.java
  class VecPair (line 8) | public class VecPair {
    method VecPair (line 12) | public VecPair(Vector<String> var1, Vector<Double> var2) {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/Vert.java
  class Vert (line 6) | public class Vert implements Comparable<Vert> {
    method Vert (line 10) | public Vert(int var1, int var2) {
    method compareTo (line 15) | @Override

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/community/ClusterLabel.java
  class ClusterLabel (line 14) | public class ClusterLabel {
    method ClusterLabel (line 20) | public ClusterLabel(int var1, float var2) {
    method ClusterLabel (line 24) | public ClusterLabel(int var1, float var2, int var3, boolean var4) {
    method initialize (line 33) | private void initialize(int var1, float var2) {
    method getLabel (line 45) | public Map<Integer, Float> getLabel() {
    method getWeight (line 49) | public float getWeight() {
    method labelSet (line 53) | public TreeSet<Integer> labelSet() {
    method labelMap (line 57) | public Map<Integer, Float> labelMap() {
    method add (line 61) | public void add(int var1) {
    method sameAs (line 71) | public boolean sameAs(ClusterLabel var1) {
    method neighbour (line 100) | public void neighbour(ClusterLabel var1, float var2) {
    method noMore (line 119) | public void noMore() {
    method reduce (line 124) | private void reduce() {
    method normalize (line 174) | public void normalize() {
    method toString (line 188) | public String toString() {

FILE: Algorithms/2010-CONGA/conga_src/src/main/java/copra/util/metric/ModOverlap.java
  class ModOverlap (line 15) | public class ModOverlap {
    method ModOverlap (line 18) | public ModOverlap() {
    method main (line 21) | public static void main(String[] var0) {
    method modOverlap (line 29) | public static double modOverlap(String var0, String var1) {
    method showClusters (line 45) | private static void showClusters(HashMap<Integer, HashMap<String, Doub...
    method invertClusters (line 51) | private static HashMap<String, HashMap<Integer, Double>> invertCluster...
    method readClusters (line 72) | private static HashMap<Integer, HashMap<String, Double>> readClusters(...
    method readGraphEdges (line 124) | public static HashMap<String, HashSet<String>> readGraphEdges(String v...
    method normalize (line 178) | public static void normalize(HashMap<Integer, HashMap<String, Double>>...
    method modOverlap (line 193) | public static double modOverlap(HashMap<Integer, HashMap<String, Doubl...
    method beta_out (line 258) | private static double beta_out(String var0, int var1, double var2, Has...
    method beta_in (line 278) | private static double beta_in(String var0, int var1, double var2, Hash...
    method F (line 298) | private static double F(String var0, String var1, int var2, HashMap<In...
    method f (line 305) | private static double f(double var0) {
    method alpha (line 309) | private static double alpha(String var0, int var1, HashMap<Integer, Ha...

FILE: Algorithms/2010-LinkCommunity/cpp/calcAndWrite_Jaccards.cpp
  function intersection_size (line 56) | int intersection_size( const set<int> &A, const set<int> &B ) {
  function main (line 76) | int main (int argc, char const *argv[]){

FILE: Algorithms/2010-LinkCommunity/cpp/clusterJaccsFile.cpp
  function main (line 65) | int main (int argc, char const *argv[]){

FILE: Algorithms/2010-LinkCommunity/cpp/edgelist2pairs.py
  function getDelimiter (line 46) | def getDelimiter(infile, expectedLength=2):

FILE: Algorithms/2010-LinkCommunity/cpp/partition_density.py
  function load_cluster_stats (line 29) | def load_cluster_stats(filename):
  function partition_density (line 33) | def partition_density(list_mc_nc):
  function partition_density_from_file (line 42) | def partition_density_from_file(filename):

FILE: Algorithms/2010-LinkCommunity/python/link_clustering.py
  function swap (line 42) | def swap(a, b):
  function Dc (line 48) | def Dc(m, n):
  class HLC (line 56) | class HLC:
    method __init__ (line 57) | def __init__(self, adj, edges):
    method initialize_edges (line 70) | def initialize_edges(self):
    method merge_comms (line 79) | def merge_comms(self, edge1, edge2, S, dendro_flag=False):
    method single_linkage (line 117) | def single_linkage(self, threshold=None, w=None, dendro_flag=False):
  function similarities_unweighted (line 156) | def similarities_unweighted(adj):
  function similarities_weighted (line 173) | def similarities_weighted(adj, ij2wij):
  function read_edgelist_unweighted (line 202) | def read_edgelist_unweighted(filename, delimiter=None, nodetype=str):
  function read_edgelist_weighted (line 218) | def read_edgelist_weighted(filename, delimiter=None, nodetype=str, weigh...
  function write_edge2cid (line 238) | def write_edge2cid(e2c, filename, delimiter="\t"):
  function write_dendro (line 271) | def write_dendro(filename, orig_cid2edge, linkage):
  class MyParser (line 283) | class MyParser(OptionParser):
    method format_epilog (line 284) | def format_epilog(self, formatter):

FILE: Algorithms/2010-LinkCommunity/python_yche_refactor/graph_io_helper.py
  function get_sorted_edge (line 9) | def get_sorted_edge(a, b):
  function read_edge_list_unweighted (line 13) | def read_edge_list_unweighted(filename, node_type=str):
  function read_edge_list_weighted (line 32) | def read_edge_list_weighted(filename, node_type=str, weight_type=float):
  function write_edge2cid (line 48) | def write_edge2cid(e2c, filename, delimiter="\t"):
  function write_dendro (line 74) | def write_dendro(filename, orig_cid2edge, linkage):

FILE: Algorithms/2010-LinkCommunity/python_yche_refactor/link_clustering.py
  class MyParser (line 10) | class MyParser(OptionParser):
    method format_epilog (line 11) | def format_epilog(self, formatter):

FILE: Algorithms/2010-LinkCommunity/python_yche_refactor/link_clustering_algo.py
  class HLC (line 10) | class HLC:
    method get_sorted_pair (line 12) | def get_sorted_pair(a, b):
    method sort_edge_pairs_by_similarity (line 16) | def sort_edge_pairs_by_similarity(adj_list_dict):
    method sort_edge_pairs_by_similarity_weighted (line 31) | def sort_edge_pairs_by_similarity_weighted(adj_list_dict, edge_weight_...
    method __init__ (line 57) | def __init__(self, adj_list_dict, edges):
    method single_linkage (line 85) | def single_linkage(self, threshold=None, w=None, dendro_flag=False):

FILE: Algorithms/2010-TopGC/src_original/Graphs/original/mkidx.c
  type list (line 7) | struct list {
  type list (line 13) | struct list
  type list (line 14) | struct list
  type list (line 21) | struct list
  function add (line 72) | void
  function dowrite (line 92) | void dowrite() {
  function outInt (line 106) | void outInt(long data) {

FILE: Algorithms/2010-TopGC/src_original/mkidx.c
  type list (line 7) | struct list
  type list (line 14) | struct list
  type list (line 15) | struct list
  type list (line 22) | struct list
  function add (line 91) | void
  function dowrite (line 114) | void
  function outInt (line 130) | void

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/FindMostProm.java
  class FindMostProm (line 16) | public class FindMostProm implements Runnable {
    method FindMostProm (line 50) | public FindMostProm(int start, int end, int threadNum, String graphFil...
    method run (line 76) | public void run() {
    method getScore2 (line 163) | public double getScore2(int currentNode, ArrayList<TempDouble2> neighb...
    method makeAndStoreWords (line 344) | public void makeAndStoreWords(int topN, ArrayList<TempDouble2> neighbo...
    method convertToList (line 441) | public LinkedList<TempDouble2> convertToList(Hashtable<Integer, Double...
    method getNumNeighborsCutoffs (line 464) | public HashSet<Integer> getNumNeighborsCutoffs(ArrayList<TempDouble2> ...
    method findIndex (line 486) | public int findIndex(double guess, TempDouble2[] neighbors) {
    method setLSH (line 503) | public void setLSH() {
    method setLSH2 (line 528) | public void setLSH2() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/HoldBucket.java
  class HoldBucket (line 9) | public class HoldBucket implements Comparable<HoldBucket> {
    method HoldBucket (line 13) | public HoldBucket(double score, Hashtable<Integer, Integer> bin) {
    method compareTo (line 18) | public int compareTo(HoldBucket other) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/HoldInt.java
  class HoldInt (line 6) | public class HoldInt {
    method HoldInt (line 9) | public HoldInt(int[] m) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/IntAndDouble.java
  class IntAndDouble (line 6) | public class IntAndDouble implements Comparable<IntAndDouble> {
    method IntAndDouble (line 10) | public IntAndDouble(int i, double d) {
    method compareTo (line 15) | public int compareTo(IntAndDouble other) {
    method toString (line 19) | public String toString() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/LSH.java
  class LSH (line 14) | public class LSH {
    method LSH (line 34) | public LSH(HashSet<Integer> bestNodes, String graphFileName, int m2, i...
    method setLSH (line 126) | public void setLSH() {
    method setLSH2 (line 151) | public void setLSH2() {
    method findLessBins (line 175) | public int findLessBins(double mult, int numToFind) {
    method findBins3 (line 245) | public int findBins3(double mult) {
    method findBins2 (line 307) | public int findBins2(double mult) {
    method findBins (line 367) | public int findBins(double mult) {
    method getCutoff (line 427) | public double getCutoff(double mult, double averageNumNeighbors) {
    method clearMem (line 436) | public void clearMem() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/LSHThread.java
  class LSHThread (line 14) | public class LSHThread implements Runnable {
    method LSHThread (line 39) | public LSHThread(int start2, int cutKey, String graphFileName, int tri...
    method run (line 66) | public void run() {
    method getNeighbors (line 113) | public LinkedList<TempDouble2> getNeighbors(Look3 look, int currentNod...
    method getNumNeighborsCutoffs (line 148) | public HashSet<Integer> getNumNeighborsCutoffs(LinkedList<TempDouble2>...
    method findIndex (line 170) | public int findIndex(double guess, TempDouble2[] neighbors) {
    method makeAndStoreWords (line 197) | public void makeAndStoreWords(int topN, LinkedList<TempDouble2> neighb...

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/LSH_Cluster.java
  class LSH_Cluster (line 11) | public class LSH_Cluster implements Comparable<LSH_Cluster> {
    method LSH_Cluster (line 18) | public LSH_Cluster(String l, Hashtable<Integer, Integer> n, Hashtable<...
    method LSH_Cluster (line 31) | public LSH_Cluster(String l, HashSet<Integer> n, Hashtable<Integer, Ha...
    method LSH_Cluster (line 44) | public LSH_Cluster(String l, HashSet<String> n, Hashtable<String, Hash...
    method compareTo (line 57) | public int compareTo(LSH_Cluster other) {
    method size (line 61) | public int size() {
    method getScore (line 65) | double getScore(Hashtable<Integer, Hashtable<Integer, Double>> smallGr...
    method getScore2 (line 94) | double getScore2(Hashtable<String, Hashtable<String, Double>> smallGra...

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/Look3.java
  class Look3 (line 10) | public class Look3 {
    method Look3 (line 24) | public Look3(String filename) throws Exception {
    method setCache (line 32) | public void setCache(int size) {
    method look (line 43) | public int[] look(int node) throws Exception {
    method getNEdges (line 86) | public int getNEdges() {
    method getNNodes (line 90) | public int getNNodes() {
    method hasWeights (line 94) | public boolean hasWeights() {
    method cacheLook (line 98) | private int[] cacheLook(int key) {
    method addCache (line 109) | public void addCache(int key, int[] entry) {
    method printCacheStats (line 120) | public static void printCacheStats() {
    method main (line 125) | public static void main(String[] args) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/MaxHeap.java
  class MaxHeap (line 8) | public class MaxHeap {
    method main (line 13) | public static void main(String[] args) {
    method MaxHeap (line 25) | public MaxHeap() {
    method MaxHeap (line 29) | public MaxHeap(int max) {
    method leftchild (line 36) | private int leftchild(int pos) {
    method rightchild (line 40) | private int rightchild(int pos) {
    method parent (line 44) | private int parent(int pos) {
    method isleaf (line 48) | private boolean isleaf(int pos) {
    method swap (line 52) | private void swap(int pos1, int pos2) {
    method insert (line 58) | public void insert(HoldBucket elem) {
    method doubleSize (line 72) | public void doubleSize() {
    method print (line 83) | public void print() {
    method peek (line 91) | public HoldBucket peek() {
    method removeMin (line 95) | public HoldBucket removeMin() {
    method pushdown (line 105) | private void pushdown(int position) {
    method size (line 122) | public int size() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/MinHeap.java
  class MinHeap (line 6) | public class MinHeap {
    method main (line 11) | public static void main(String[] args) {
    method MinHeap (line 29) | public MinHeap() {
    method MinHeap (line 33) | public MinHeap(int max) {
    method leftchild (line 40) | private int leftchild(int pos) {
    method rightchild (line 44) | private int rightchild(int pos) {
    method parent (line 48) | private int parent(int pos) {
    method isleaf (line 52) | private boolean isleaf(int pos) {
    method swap (line 56) | private void swap(int pos1, int pos2) {
    method insert (line 62) | public void insert(IntAndDouble elem) {
    method doubleSize (line 76) | public void doubleSize() {
    method print (line 87) | public void print() {
    method peek (line 95) | public IntAndDouble peek() {
    method removeMin (line 99) | public IntAndDouble removeMin() {
    method pushdown (line 109) | private void pushdown(int position) {
    method size (line 126) | public int size() {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/Prime.java
  class Prime (line 6) | public class Prime {
    method Prime (line 7) | public Prime() {
    method isPrime (line 10) | boolean isPrime(int n) {
    method getPrime (line 28) | int getPrime(int n) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/TempDouble2.java
  class TempDouble2 (line 6) | class TempDouble2 implements Comparable<TempDouble2> {
    method TempDouble2 (line 11) | public TempDouble2(int n, double w) {
    method compareTo (line 16) | public int compareTo(TempDouble2 other) {

FILE: Algorithms/2010-TopGC/src_refactor/src/main/java/TopGC.java
  class TopGC (line 20) | public class TopGC {
    method main (line 45) | public static void main(String[] argv) throws FileNotFoundException, I...
    method TopGC (line 49) | public TopGC(String[] argv) {
    method setDefaultArgs (line 329) | public void setDefaultArgs() {
    method overlapCluster (line 368) | public boolean overlapCluster(LSH_Cluster cluster, LinkedList<HashSet<...
    method getScore (line 397) | public double getScore(int currentNode, Hashtable<Integer, Double> nei...
    method checkArgsFirst (line 425) | public void checkArgsFirst(String[] argv) {
    method checkArgs (line 478) | public void checkArgs(String[] argv) {
    method makeLine (line 575) | public String makeLine(Hashtable<Integer, Integer> cluster) {
    method makeLine (line 594) | public String makeLine(HashSet<Integer> cluster) {
    method removeDupes (line 613) | public ArrayList<Hashtable<Integer, Integer>> removeDupes(ArrayList<Ha...
    method intersect (line 776) | public int intersect(HashSet<Integer> compare1, HashSet<Integer> compa...
    method overlapTooMuch (line 789) | public boolean overlapTooMuch(HashSet<Integer> compare1, HashSet<Integ...
    method convertClust (line 811) | public Hashtable<Integer, Integer> convertClust(HashSet<Integer> nodes...
    method shouldCombine (line 835) | public boolean shouldCombine(double overlapRemove, TopGC.TempCluster b...
    method removeOverlap (line 887) | public boolean removeOverlap(double overlapRemove, ArrayList<Hashtable...
    method combineBuckets (line 946) | public void combineBuckets(Hashtable<Integer, Integer> bucket1, Hashta...
    method split (line 961) | public String[] split(String str, char delim) {
    class IterateSet (line 981) | private class IterateSet {
      method IterateSet (line 986) | public IterateSet(LinkedList<Integer> var1) {
      method almostDone (line 995) | public boolean almostDone() {
      method hasNext (line 1007) | public boolean hasNext() {
      method next (line 1011) | public HashSet<Integer> next() {
      method incr (line 1024) | public void incr() {
    class TempCluster (line 1042) | private class TempCluster {
      method TempCluster (line 1054) | private TempCluster(HashSet<Integer> var1, HashSet<Integer> nodes) {
      method TempCluster (line 1060) | private TempCluster(TopGC.TempCluster clust1, TopGC.TempCluster clus...

FILE: Algorithms/2010-iLCD/src/src/main/java/CorePackage/Main.java
  class Main (line 29) | public class Main {
    method main (line 93) | public static void main(String args[]) {
    method argumentsHandling (line 132) | private void argumentsHandling(String args[]) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputCTNFhandler.java
  class InputCTNFhandler (line 16) | public class InputCTNFhandler extends InputHandlerInterface{
    method InputCTNFhandler (line 18) | public InputCTNFhandler(Network net) {
    method operationFromLine (line 25) | public Operation operationFromLine(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputHandlerInterface.java
  class InputHandlerInterface (line 6) | public abstract class InputHandlerInterface {
    method InputHandlerInterface (line 9) | InputHandlerInterface(Network net){
    method operationFromLine (line 12) | public abstract Operation operationFromLine(String line);

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputNCOLhandler.java
  class InputNCOLhandler (line 10) | public class InputNCOLhandler extends InputHandlerInterface{
    method InputNCOLhandler (line 12) | public InputNCOLhandler(Network net) {
    method operationFromLine (line 19) | public Operation operationFromLine(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/Inputs/InputOLDLNDhandler.java
  class InputOLDLNDhandler (line 17) | public class InputOLDLNDhandler extends InputHandlerInterface{
    method InputOLDLNDhandler (line 19) | public InputOLDLNDhandler(Network net) {
    method operationFromLine (line 26) | public Operation operationFromLine(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputCTNF.java
  class OutputCTNF (line 31) | public class OutputCTNF implements OutputHandlerInterface{
    method OutputCTNF (line 41) | public OutputCTNF(MyDateManager dateManager, Network theNetwork) {
    method initialise (line 46) | public void initialise(String outputFile){
    method terminate (line 56) | public void terminate(){
    method printLine (line 60) | public void printLine(String line){
    method handleGrowth (line 71) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 75) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 84) | public void handleBirth(Community c) {
    method handleDeath (line 90) | public void handleDeath(Community c) {
    method handleContraction (line 106) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 110) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 114) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 118) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 123) | public void handleDateChange(String date) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputHandlerInterface.java
  type OutputHandlerInterface (line 15) | public interface OutputHandlerInterface {
    method initialise (line 20) | public void initialise(String outputFile);
    method terminate (line 23) | public void terminate();
    method handleGrowth (line 28) | public void handleGrowth(Node n, Community c);
    method handleGrowth (line 30) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 32) | public void handleBirth(Community c);
    method handleDeath (line 34) | public void handleDeath(Community c);
    method handleContraction (line 38) | public void handleContraction(Node n, Community c);
    method handleNewEdge (line 40) | public void handleNewEdge(Node n, Node n2);
    method handleRemoveEdge (line 42) | public void handleRemoveEdge(Node n, Node n2);
    method handleFusion (line 44) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 45) | public void handleDateChange(String date);

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputMultipleHandler.java
  class OutputMultipleHandler (line 18) | public class OutputMultipleHandler implements OutputHandlerInterface{
    method OutputMultipleHandler (line 29) | public OutputMultipleHandler() {
    method addOutputHandler (line 32) | public void addOutputHandler(OutputHandlerInterface oh){
    method initialise (line 35) | public void initialise(String outputFile){
    method terminate (line 41) | public void terminate(){
    method handleGrowth (line 47) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 53) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 60) | public void handleBirth(Community c) {
    method handleDeath (line 68) | public void handleDeath(Community c) {
    method handleContraction (line 81) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 86) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 91) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 96) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 102) | public void handleDateChange(String date) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputStatic.java
  class OutputStatic (line 26) | public class OutputStatic implements OutputHandlerInterface{
    method OutputStatic (line 37) | public OutputStatic(MyDateManager dateManager, Network theNetwork) {
    method initialise (line 41) | public void initialise(String outputFile){
    method terminate (line 51) | public void terminate(){
    method printLine (line 70) | public void printLine(String line){
    method handleGrowth (line 78) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 82) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 86) | public void handleBirth(Community c) {
    method handleDeath (line 92) | public void handleDeath(Community c) {
    method handleContraction (line 105) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 109) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 113) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 117) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 121) | public void handleDateChange(String date) {

FILE: Algorithms/2010-iLCD/src/src/main/java/Outputs/OutputSummary.java
  class OutputSummary (line 27) | public class OutputSummary implements OutputHandlerInterface{
    method OutputSummary (line 42) | public OutputSummary(MyDateManager dateManager, Network theNetwork) {
    method initialise (line 47) | public void initialise(String outputFile){
    method terminate (line 57) | public void terminate(){
    method printACommunity (line 78) | private void printACommunity(CommunityToPrint ctp){
    method printLine (line 93) | public void printLine(String line){
    method handleGrowth (line 104) | public void handleGrowth(Node n, Community c){
    method handleGrowth (line 111) | public void handleGrowth(Community initialCommunity, Community resulti...
    method handleBirth (line 120) | public void handleBirth(Community c) {
    method handleDeath (line 135) | public void handleDeath(Community c) {
    method handleContraction (line 158) | public void handleContraction(Node n, Community c) {
    method handleNewEdge (line 162) | public void handleNewEdge(Node n, Node n2) {
    method handleRemoveEdge (line 166) | public void handleRemoveEdge(Node n, Node n2) {
    method handleFusion (line 170) | public void handleFusion(Community resultingCommunity, Community suppr...
    method handleDateChange (line 177) | public void handleDateChange(String date) {
    class CommunityToPrint (line 182) | private class CommunityToPrint implements Comparable<CommunityToPrint>{
      method compareTo (line 188) | @Override

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Community.java
  class Community (line 12) | public class Community implements Comparable<Community>{
    method Community (line 22) | public Community(Community c) {
    method Community (line 26) | public Community(){
    method Community (line 31) | public Community(int ID){
    method addNode (line 35) | private void addNode(Node node1) {
    method addNodeToCommunity (line 46) | public void addNodeToCommunity(Node n){
    method removeNodeFromCommunity (line 52) | protected void removeNodeFromCommunity(Node n){
    method removeNode (line 58) | protected void removeNode(Node n) {
    method getID (line 67) | public int getID() {
    method isDifferent (line 72) | public boolean isDifferent(Community otherCom) {
    method setBirthDate (line 92) | protected void setBirthDate(MyDate date){
    method getComponents (line 97) | public THashSet<Node> getComponents() {
    method youngerThan (line 101) | public boolean youngerThan(Community c2) {
    method compareTo (line 105) | @Override
    method getCommonNodes (line 110) | public THashSet<Node> getCommonNodes(Community cTested) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/CoreProcessor.java
  class CoreProcessor (line 19) | public class CoreProcessor {
    method CoreProcessor (line 28) | public CoreProcessor(Network mainNetwork) {
    method setOperationHandler (line 32) | public void setOperationHandler(OperationsHandler opHandler){
    method setInputHandler (line 36) | public void setInputHandler(InputHandlerInterface inputHandler){
    method initializeReading (line 40) | public void initializeReading(String file){
    method readALine (line 50) | public void readALine(String line){
    method readOperationStream (line 59) | public void readOperationStream(String file){
    method getOperation (line 80) | public Operation getOperation(String line){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Interface.java
  class Interface (line 13) | public class Interface {
    type PossibleOutputFormat (line 25) | public static enum PossibleOutputFormat{CTNF,SUMMARY,STATIC}
    type PossibleInputFormat (line 26) | public enum PossibleInputFormat {UNKNOWN, NCOL, TNF, CTNF, LND}
    method Interface (line 29) | public Interface(String inputFile, String inputDateF){
    method addOutput (line 61) | public void addOutput(PossibleOutputFormat format, String outputFile, ...
    method setOperationHandler (line 86) | public void setOperationHandler(OperationsHandler operationHandler){
    method readOperationStream (line 94) | public void readOperationStream() {
    method processALine (line 103) | public String processALine(String line) {
    method terminate (line 113) | public void terminate() {
    method getFileType (line 118) | public static PossibleInputFormat getFileType(String file){
    method getCurrentDate (line 138) | public String getCurrentDate(){
    method getInputFileType (line 142) | public PossibleInputFormat getInputFileType(){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/MyDate.java
  class MyDate (line 3) | public class MyDate implements Comparable{
    type dateType (line 5) | public enum dateType {YYYYMMDD,YYYYMMDDHHMMSS,NONE}
    method MyDate (line 11) | public MyDate(String date, dateType type){
    method MyDate (line 24) | public MyDate(MyDate currentTime) {
    method writeDate (line 29) | public String writeDate(dateType type){
    method before (line 42) | public boolean before(MyDate toCompare){
    method after (line 46) | public boolean after(MyDate toCompare){
    method sameDateAs (line 50) | public boolean sameDateAs(MyDate toCompare){
    method beginningOfTheUniverse (line 55) | public static MyDate beginningOfTheUniverse(){
    method increment (line 60) | public MyDate increment() {
    method compareTo (line 70) | @Override

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/MyDateManager.java
  class MyDateManager (line 5) | public class MyDateManager {
    method MyDateManager (line 12) | public MyDateManager(String inputFormat){
    method setOutputDateFormat (line 17) | public void setOutputDateFormat(String outputFormat){
    method getDate (line 22) | public MyDate getDate(String date){
    method writeDate (line 34) | public String writeDate(MyDate aDate){
    method convertDateFormat (line 38) | private MyDate.dateType convertDateFormat(String stringFormat){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Network.java
  class Network (line 17) | public class Network {
    method Network (line 26) | public Network(MyDateManager dateManager, OutputHandlerInterface outpu...
    method getNode (line 32) | public Node getNode(String nodeName) {
    method doOperation (line 43) | public void doOperation(Operation currentOperation) {
    method changeTime (line 91) | public void changeTime(MyDate newDate) {
    method getCurrentTime (line 100) | public MyDate getCurrentTime() {
    method createCommunity (line 105) | public void createCommunity(Integer c) {
    method getCommunity (line 114) | public Community getCommunity(Integer com) {
    method removeCommunity (line 122) | public void removeCommunity(Community c) {
    method addCommunity (line 131) | public void addCommunity(Community c) {
    method getCommunities (line 139) | public THashSet<Community> getCommunities() {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Node.java
  class Node (line 10) | public class Node {
    method Node (line 18) | public Node(String nodeName) {
    method getCommunities (line 22) | public THashSet<Community> getCommunities(){
    method addCommunity (line 26) | protected void addCommunity(Community c) {
    method getName (line 35) | public String getName() {
    method removeCommunity (line 39) | protected void removeCommunity(Community c) {
    method getNeighbors (line 47) | public THashSet<Node> getNeighbors() {
    method getNeighborsInCommunity (line 51) | public THashSet<Node> getNeighborsInCommunity(Community c){
    method addNeighbor (line 58) | protected void addNeighbor(Node node2) {
    method removeNeighbor (line 68) | protected void removeNeighbor(Node node2) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/AddEdgeOperation.java
  class AddEdgeOperation (line 6) | public class AddEdgeOperation extends Operation{
    method AddEdgeOperation (line 8) | public AddEdgeOperation(Node n1, Node n2) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/BirthCommunityOperation.java
  class BirthCommunityOperation (line 9) | public class BirthCommunityOperation extends Operation{
    method BirthCommunityOperation (line 13) | public BirthCommunityOperation(Community c) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/ContractCommunityOperation.java
  class ContractCommunityOperation (line 7) | public class ContractCommunityOperation extends Operation{
    method ContractCommunityOperation (line 9) | public ContractCommunityOperation(Community c, Node n) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/DeathCommunityOperation.java
  class DeathCommunityOperation (line 6) | public class DeathCommunityOperation extends Operation{
    method DeathCommunityOperation (line 8) | public DeathCommunityOperation(Community c) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/FusionCommunityOperation.java
  class FusionCommunityOperation (line 6) | public class FusionCommunityOperation extends Operation{
    method FusionCommunityOperation (line 8) | public FusionCommunityOperation(Community absorb, Community mergedIn) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/GrowthCommunityOperation.java
  class GrowthCommunityOperation (line 7) | public class GrowthCommunityOperation extends Operation{
    method GrowthCommunityOperation (line 9) | public GrowthCommunityOperation(Community c, Node n) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/Operation.java
  class Operation (line 8) | public class Operation {
    type OperationType (line 26) | public enum OperationType { ADD, REMOVE,BIRTH,DEATH,FUSION,GROWTH,CONT...
    method Operation (line 29) | public Operation(Node n1, Node n2, Community c1, Community c2, Communi...
    method getNode1 (line 37) | public Node getNode1(){
    method getNode2 (line 41) | public Node getNode2(){
    method getCommunity1 (line 45) | public Community getCommunity1(){
    method getCommunity2 (line 49) | public Community getCommunity2(){
    method getCommunity3 (line 53) | public Community getCommunity3(){
    method getNodes (line 57) | public HashSet<Node> getNodes(){

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/Operations/RemoveEdgeOperation.java
  class RemoveEdgeOperation (line 6) | public class RemoveEdgeOperation extends Operation{
    method RemoveEdgeOperation (line 8) | public RemoveEdgeOperation(Node n1, Node n2) {

FILE: Algorithms/2010-iLCD/src/src/main/java/TemporalNetworkManipulation/OperationsHandler.java
  type OperationsHandler (line 5) | public interface OperationsHandler {
    method handle (line 7) | public void handle(Operation currentOperation);

FILE: Algorithms/2010-iLCD/src/src/main/java/communityDetectionPackage/ILCDMetaAlgorithm.java
  class ILCDMetaAlgorithm (line 44) | public class ILCDMetaAlgorithm implements OperationsHandler {
    method ILCDMetaAlgorithm (line 56) | public ILCDMetaAlgorithm(Implementation implementationToUse, Network n...
    method handle (line 61) | public void handle(Operation currentOperation) {
    method addNodeToCommunity (line 248) | public void addNodeToCommunity(Node node, Community c) {
    method fusion (line 256) | private void fusion(Community resultingCommunity, Community c1, Commun...
    method deathOf (line 275) | private void deathOf(Community c) {
    method contract (line 297) | public void contract(Node n, Community community) {
    method diviseCommunity (line 308) | private void diviseCommunity(Community tempSavedCom, ArrayList<Communi...
    method addCommunity (line 315) | public void addCommunity(Community c) {

FILE: Algorithms/2010-iLCD/src/src/main/java/implementable/Implementation.java
  class Implementation (line 22) | public abstract class Implementation {
    method GROWTH (line 30) | public abstract boolean GROWTH(Node candidate, Community com);
    method BIRTH (line 40) | public abstract ArrayList<Community> BIRTH(Node n1, Node n2);
    method CONTRACTION_DIVISION (line 54) | public abstract ArrayList<Community> CONTRACTION_DIVISION(Community af...
    method DEATH (line 61) | public abstract boolean DEATH(Community testedCom);
    method FUSION (line 71) | public abstract ArrayList<Community> FUSION(Community c1, Community c2...
    method getCommunitiesForWhichIsRepresentative (line 78) | public THashSet<Community> getCommunitiesForWhichIsRepresentative(Node...

FILE: Algorithms/2010-iLCD/src/src/main/java/implementable/ImplementationRNHM.java
  class ImplementationRNHM (line 21) | public class ImplementationRNHM extends Implementation {
    method ImplementationRNHM (line 32) | public ImplementationRNHM(int intialComSize, float integrateParameter,...
    method GROWTH (line 38) | @Override
    method BIRTH (line 53) | @Override
    method CONTRACTION_DIVISION (line 80) | @Override
    method DEATH (line 118) | @Override
    method FUSION (line 128) | @Override
    method getRepresentativity (line 167) | private float getRepresentativity(Node n, Community c) {
    method getIdRelation (line 180) | private String getIdRelation(Node n, Community c) {
    method getBelongingStrength (line 184) | private float getBelongingStrength(Node n, Community c) {
    method getIntrinsicCohesion (line 204) | private float getIntrinsicCohesion(Community c) {
    method birthCase3 (line 229) | private ArrayList<Community> birthCase3(ArrayList<Community> newCommun...
    method birthCase4 (line 258) | private ArrayList<Community> birthCase4(ArrayList<Community> newCommun...

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/DebugMode.java
  class DebugMode (line 5) | public class DebugMode {
    method printDebug (line 9) | public static void printDebug(String s){
    method printBasic (line 24) | public static void printBasic(String s){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/SortEdges.java
  class SortEdges (line 8) | public class SortEdges {
    method sort (line 12) | public static void sort(String input, String output){
    method main (line 47) | public static void main(String args[]){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/Sorter.java
  class Sorter (line 7) | public class Sorter<T> {
    method Sorter (line 11) | public Sorter(){
    method add (line 16) | public void add(T el, Double val){
    method getSortedValues (line 33) | public ArrayList<T> getSortedValues(){
    method getElts (line 44) | public ArrayList<T> getElts(){
    class Element (line 50) | public class Element<T> implements Comparable{
      method compareTo (line 54) | @Override
    method modVal (line 62) | public void modVal(T el, Double val){
    method getHigher (line 68) | public T getHigher(){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/TextFileHandler.java
  class TextFileHandler (line 14) | public class TextFileHandler {
    method loadDictionary (line 19) | public static HashMap<String,String> loadDictionary(String fileName,St...
    method readFirstLine (line 53) | public static String readFirstLine(String fileName){
    method loadFile (line 74) | public static ArrayList<String> loadFile(String fileName){
    method printFile (line 97) | public static void printFile(String fileName,ArrayList<String> lines){
    method splitLine (line 117) | public static Vector<String> splitLine(String line, String separator){
    method main (line 125) | public static void main(String args[]){
    method cleanNodeName (line 158) | public static String cleanNodeName(String nodeName){

FILE: Algorithms/2010-iLCD/src/src/main/java/tools/ToolDate.java
  class ToolDate (line 7) | public class ToolDate {
    method timInDaySince (line 11) | public static long timInDaySince(Date d){
    method timInDayBetween (line 15) | public static long timInDayBetween(Date beginning, Date end){
    method dateFromString (line 19) | public static Date dateFromString(String date, String format){

FILE: Algorithms/2011-GCE/src-original/Community_Finder.cpp
  function sizeSortFunctionLargestFirst (line 26) | bool sizeSortFunctionLargestFirst (Seed * two,  Seed * one)
  function sizeSortFunctionSmallestFirst (line 31) | bool sizeSortFunctionSmallestFirst (Seed * one,  Seed * two)
  function vectorSizeSortFunctionLargestFirst (line 36) | bool vectorSizeSortFunctionLargestFirst (vector <V> two,  vector <V> one)
  function vectorSizeSortFunctionSmallestFirst (line 40) | bool vectorSizeSortFunctionSmallestFirst (vector <V> one,  vector <V> two)

FILE: Algorithms/2011-GCE/src-original/Community_Finder.h
  function class (line 26) | class Community_Finder {

FILE: Algorithms/2011-GCE/src-original/Range.hpp
  class IteratorRange (line 13) | class IteratorRange {
    method IteratorRange (line 20) | IteratorRange(const Iterator & _begin, const Iterator & _end) : curren...
    method IteratorRange (line 21) | IteratorRange(std::pair<Iterator,Iterator> be) : current(be.first), en...
    method empty (line 23) | bool empty() const { return current == end; }
    method Iterated (line 24) | Iterated & front() const { return *current; }
    method Iterator (line 25) | Iterator   frontIterator() const { return  current; }
    method popFront (line 26) | void popFront() { ++current; }
  class ContainerProperties (line 30) | class ContainerProperties {
  class ContainerRange (line 37) | class ContainerRange : public IteratorRange< typename ContainerPropertie...
    method ContainerRange (line 39) | ContainerRange(Container &c) : IteratorRange< typename ContainerProper...
  class ContainerRangeReverse (line 42) | class ContainerRangeReverse : public IteratorRange< typename ContainerPr...
    method ContainerRangeReverse (line 44) | ContainerRangeReverse(Container &c) : IteratorRange< typename Containe...
  class RangeTypes (line 50) | class RangeTypes {
  class ChainedRange (line 57) | class ChainedRange { // Chain Two together
    method ChainedRange (line 61) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 62) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 63) | bool firstEmpty() const { return first.empty(); }
    method front (line 64) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 65) | void popFront() { if (first.empty()) second.popFront(); else first.pop...

FILE: Algorithms/2011-GCE/src-original/Seed.h
  function class (line 19) | class Seed {

FILE: Algorithms/2011-GCE/src-original/aaron_utils.cpp
  function testForError (line 2) | int testForError(FILE * x) { return x==NULL; }
  function testForError (line 3) | int testForError(int x) { return x==-1; }
  function string (line 5) | string show(long x) { ostringstream s; s << x; return s.str(); }
  function string (line 6) | string show(const char * x) { ostringstream s; s << x; return s.str(); }
  function string (line 7) | string show(const string &s) { return s; }
  function string (line 15) | string runningAverage::operator() (void) const {
  function DummyOutputStream (line 21) | DummyOutputStream& DummyOutputStream::operator << (int) { return *this; }
  function DummyOutputStream (line 22) | DummyOutputStream& DummyOutputStream::operator << (const char*) { return...

FILE: Algorithms/2011-GCE/src-original/aaron_utils.hpp
  function string (line 24) | static string thousandsSeparated(unsigned long x) {
  class runningAverage (line 57) | class runningAverage {
  type RefPair (line 68) | struct RefPair {
    method RefPair (line 71) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) { }
  function make_refpair (line 75) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 80) | struct DummyOutputStream {
  type StopWatch (line 86) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 87) | struct timeval
    type timeval (line 88) | struct timeval
    method StopWatch (line 89) | StopWatch() {
    method laptime (line 93) | void laptime(void) { laptime(""); }
    method laptime (line 94) | void laptime(const string &tag) {

FILE: Algorithms/2011-GCE/src-original/cliques.cpp
  type cliques (line 3) | namespace cliques {
    function cliquesForOneNode (line 8) | void cliquesForOneNode(const SimpleIntGraph &g, CliqueFunctionAdaptor ...
    function tryCandidate (line 26) | static inline void tryCandidate (const SimpleIntGraph & g, CliqueFunct...
    function cliquesWorker (line 42) | void cliquesWorker(const SimpleIntGraph & g, CliqueFunctionAdaptor &cl...
    function create_directory (line 120) | void create_directory(const string& directory) throw() {
    function cliquesToDirectory (line 130) | void cliquesToDirectory(const bloomGraph<int> &g_, const string &outpu...

FILE: Algorithms/2011-GCE/src-original/cliques.hpp
  type cliques (line 15) | namespace cliques {
    type CliqueFunctionAdaptor (line 17) | struct CliqueFunctionAdaptor {
    function findCliques (line 30) | void findCliques(const SimpleIntGraph &g, T & cliquesOut, unsigned int...
    function findCliquesJustIDs (line 54) | void findCliquesJustIDs            (const bloomGraph<int> &g, T &cliqu...
    function findCliquesOriginalVertexNames (line 55) | void findCliquesOriginalVertexNames(const bloomGraph<int> &g, T &cliqu...
    type CliqueSink (line 57) | struct CliqueSink { // Dump the cliques to a file in the CFinder format
      method CliqueSink (line 61) | CliqueSink(const bloomGraph<int> &_g, const string& fileName) : g(_g...
      method ForeachContainer (line 65) | ForeachContainer(V v, Compsub) {

FILE: Algorithms/2011-GCE/src-original/find_communities.cpp
  function main (line 19) | int main (int argc, char **argv) {

FILE: Algorithms/2011-GCE/src-original/graph_analysis.hpp
  type graph_analysis (line 3) | namespace graph_analysis {

FILE: Algorithms/2011-GCE/src-original/graph_loading.cpp
  type graph_loading (line 15) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 16) | struct readEdgeInvalidLineInDataException : public exception { }
    class RangeOfEdges (line 19) | class RangeOfEdges {
      method read_a_row (line 25) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 27) | RangeOfEdges(const char* b, const char* e) : p(b), fileEnd(e) { if(p...
      method front (line 28) | pair<Name, Name> front() { return make_pair(l,r); }
      method empty (line 29) | bool empty() { return p == fileEnd; }
      method popFront (line 30) | void popFront() { p = updating_p ; if(p!=fileEnd) read_a_row(); }
    function loadSimpleIntGraphFromFile (line 43) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    function loadBloomGraphMMAP (line 46) | void loadBloomGraphMMAP(SimpleIntGraph &bg, const char *fileName) {
    function loadBloomGraphMMAPFastButFussy (line 110) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 151) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 219) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 230) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 251) | void populateNameToIDHash(SimpleIntGraph &bg) {
    function addNeighbour (line 267) | static void addNeighbour(VertexIDType edge_source, VertexIDType edge_t...
    function loadEdges (line 294) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 314) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-GCE/src-original/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-GCE/src-original/graph_representation.cpp
  function string (line 26) | string VertexNameToString (const int &l) {

FILE: Algorithms/2011-GCE/src-original/graph_representation.hpp
  type bloomGraph (line 14) | struct bloomGraph
    method bloomGraph (line 34) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 36) | long unsigned int vcount(void) const { return vertex_count ; }
    method ecount (line 37) | long unsigned int ecount(void) const { return edge_count / 2; }
    method degree (line 38) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 39) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 40) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 42) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 48) | pair<const VertexIDType*,const VertexIDType*> neighbours(VertexIDType ...
    method neighbours (line 54) | pair<VertexIDType*,VertexIDType*> neighbours(VertexIDType i) {
  function H (line 19) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type bloomGraph (line 27) | struct bloomGraph {
    method bloomGraph (line 34) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 36) | long unsigned int vcount(void) const { return vertex_count ; }
    method ecount (line 37) | long unsigned int ecount(void) const { return edge_count / 2; }
    method degree (line 38) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 39) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 40) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 42) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 48) | pair<const VertexIDType*,const VertexIDType*> neighbours(VertexIDType ...
    method neighbours (line 54) | pair<VertexIDType*,VertexIDType*> neighbours(VertexIDType i) {

FILE: Algorithms/2011-GCE/src-original/iterative.hpp
  type iterative (line 3) | namespace iterative {

FILE: Algorithms/2011-GCE/src-original/modularity.hpp
  type modularity (line 4) | namespace modularity {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/cliques.cpp
  type cliques (line 3) | namespace cliques {
    function cliquesForOneNode (line 9) | void cliquesForOneNode(const SimpleIntGraph &g, CliqueFunctionAdaptor ...
    function tryCandidate (line 27) | static inline void
    function cliquesWorker (line 44) | void cliquesWorker(const SimpleIntGraph &g, CliqueFunctionAdaptor &cli...
    function create_directory (line 127) | void create_directory(const string &directory) throw() {
    function cliquesToDirectory (line 137) | void

FILE: Algorithms/2011-GCE/src-refactor/algorithm/cliques.hpp
  type cliques (line 16) | namespace cliques {
    type CliqueFunctionAdaptor (line 18) | struct CliqueFunctionAdaptor {
    function findCliques (line 41) | void findCliques(const SimpleIntGraph &g, T &cliquesOut, unsigned int ...
    function findCliquesJustIDs (line 68) | void findCliquesJustIDs(const bloomGraph<int> &g, T &cliquesOut, unsig...
    function findCliquesOriginalVertexNames (line 73) | void findCliquesOriginalVertexNames(const bloomGraph<int> &g, T &cliqu...
    type CliqueSink (line 76) | struct CliqueSink { // Dump the cliques to a file in the CFinder format
      method CliqueSink (line 81) | CliqueSink(const bloomGraph<int> &_g, const string &fileName) : g(_g...
      method ForeachContainer (line 86) | ForeachContainer(V v, Compsub) {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/community_finder.cpp
  function sizeSortFunctionLargestFirst (line 27) | bool sizeSortFunctionLargestFirst(Seed *two, Seed *one) {
  function sizeSortFunctionSmallestFirst (line 31) | bool sizeSortFunctionSmallestFirst(Seed *one, Seed *two) {
  function vectorSizeSortFunctionLargestFirst (line 35) | bool vectorSizeSortFunctionLargestFirst(vector<V> two, vector<V> one) {
  function vectorSizeSortFunctionSmallestFirst (line 39) | bool vectorSizeSortFunctionSmallestFirst(vector<V> one, vector<V> two) {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/community_finder.h
  function class (line 29) | class community_finder {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/find_communities.cpp
  function main (line 17) | int main(int argc, char **argv) {

FILE: Algorithms/2011-GCE/src-refactor/algorithm/seed.h
  function class (line 22) | class Seed {

FILE: Algorithms/2011-GCE/src-refactor/useless/graph_analysis.hpp
  type graph_analysis (line 3) | namespace graph_analysis {

FILE: Algorithms/2011-GCE/src-refactor/useless/iterative.hpp
  type iterative (line 3) | namespace iterative {

FILE: Algorithms/2011-GCE/src-refactor/useless/modularity.hpp
  type modularity (line 3) | namespace modularity {

FILE: Algorithms/2011-GCE/src-refactor/util/aaron_utils.cpp
  function testForError (line 3) | int testForError(FILE *x) { return x == NULL; }
  function testForError (line 5) | int testForError(int x) { return x == -1; }
  function string (line 7) | string show(long x) {
  function string (line 13) | string show(const char *x) {
  function string (line 19) | string show(const string &s) { return s; }
  function string (line 29) | string runningAverage::operator()(void) const {
  function DummyOutputStream (line 35) | DummyOutputStream &DummyOutputStream::operator<<(int) { return *this; }
  function DummyOutputStream (line 37) | DummyOutputStream &DummyOutputStream::operator<<(const char *) { return ...

FILE: Algorithms/2011-GCE/src-refactor/util/aaron_utils.hpp
  function string (line 28) | static string thousandsSeparated(unsigned long x) {
  class runningAverage (line 65) | class runningAverage {
  type RefPair (line 79) | struct RefPair {
    method RefPair (line 83) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) {}
  function make_refpair (line 92) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 97) | struct DummyOutputStream {
  type StopWatch (line 105) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 106) | struct timeval
    type timeval (line 107) | struct timeval
    method StopWatch (line 109) | StopWatch() {
    method laptime (line 114) | void laptime(void) { laptime(""); }
    method laptime (line 116) | void laptime(const string &tag) {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_loading.cpp
  type graph_loading (line 15) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 16) | struct readEdgeInvalidLineInDataException : public exception {
    class RangeOfEdges (line 21) | class RangeOfEdges {
      method read_a_row (line 28) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 31) | RangeOfEdges(const char *b, const char *e) : p(b), fileEnd(e) { if (...
      method front (line 33) | pair<Name, Name> front() { return make_pair(l, r); }
      method empty (line 35) | bool empty() { return p == fileEnd; }
      method popFront (line 37) | void popFront() {
    function loadSimpleIntGraphFromFile (line 61) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    function loadBloomGraphMMAP (line 65) | void loadBloomGraphMMAP(SimpleIntGraph &bg, const char *fileName) {
    function loadBloomGraphMMAPFastButFussy (line 133) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 174) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 248) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 259) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 281) | void populateNameToIDHash(SimpleIntGraph &bg) {
    function addNeighbour (line 298) | static void
    function loadEdges (line 330) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 351) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_representation.cpp
  function string (line 28) | string VertexNameToString(const int &l) {

FILE: Algorithms/2011-GCE/src-refactor/util/graph/graph_representation.hpp
  type bloomGraph (line 14) | struct bloomGraph
    method bloomGraph (line 35) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 37) | long unsigned int vcount(void) const { return vertex_count; }
    method ecount (line 39) | long unsigned int ecount(void) const {
    method degree (line 42) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 44) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 46) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 50) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 57) | pair<const VertexIDType *, const VertexIDType *>
    method neighbours (line 64) | pair<VertexIDType *, VertexIDType *> neighbours(VertexIDType i) {
  function H (line 19) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type bloomGraph (line 28) | struct bloomGraph {
    method bloomGraph (line 35) | bloomGraph(void) : vertex_count(0), edge_count(0) {}
    method vcount (line 37) | long unsigned int vcount(void) const { return vertex_count; }
    method ecount (line 39) | long unsigned int ecount(void) const {
    method degree (line 42) | inline long unsigned int degree(long int v) const { return degrees.at(...
    method VertexNameType (line 44) | VertexNameType name_of_one_node(long int v) const { return vertex_mapp...
    method string (line 46) | string name_of_one_node_asString(long int v) const { return VertexName...
    method are_connected (line 50) | bool are_connected(const EdgeType &e) const {
    method neighbours (line 57) | pair<const VertexIDType *, const VertexIDType *>
    method neighbours (line 64) | pair<VertexIDType *, VertexIDType *> neighbours(VertexIDType i) {

FILE: Algorithms/2011-GCE/src-refactor/util/range.hpp
  class IteratorRange (line 13) | class IteratorRange {
    method IteratorRange (line 21) | IteratorRange(const Iterator &_begin, const Iterator &_end) : current(...
    method IteratorRange (line 23) | IteratorRange(std::pair<Iterator, Iterator> be) : current(be.first), e...
    method empty (line 25) | bool empty() const { return current == end; }
    method Iterated (line 27) | Iterated &front() const { return *current; }
    method Iterator (line 29) | Iterator frontIterator() const { return current; }
    method popFront (line 31) | void popFront() { ++current; }
  class ContainerProperties (line 35) | class ContainerProperties {
  class ContainerRange (line 43) | class ContainerRange : public IteratorRange<typename ContainerProperties...
    method ContainerRange (line 45) | ContainerRange(Container &c) : IteratorRange<typename ContainerPropert...
  class ContainerRangeReverse (line 50) | class ContainerRangeReverse : public IteratorRange<typename ContainerPro...
    method ContainerRangeReverse (line 52) | ContainerRangeReverse(Container &c) : IteratorRange<typename Container...
  class RangeTypes (line 58) | class RangeTypes {
  class ChainedRange (line 65) | class ChainedRange { // Chain Two together
    method ChainedRange (line 69) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 71) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 73) | bool firstEmpty() const { return first.empty(); }
    method front (line 75) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 77) | void popFront() { if (first.empty()) second.popFront(); else first.pop...

FILE: Algorithms/2011-MOSES/src-original/Range.cpp
  type amd (line 5) | namespace amd {
    function rangeOverStream (line 7) | std::auto_ptr< Range<std::string> > rangeOverStream(std::istream &_ist...

FILE: Algorithms/2011-MOSES/src-original/Range.hpp
  class IteratorRange (line 23) | class IteratorRange {
    method IteratorRange (line 30) | IteratorRange(const Iterator & _begin, const Iterator & _end) : curren...
    method IteratorRange (line 31) | IteratorRange(std::pair<Iterator,Iterator> be) : current(be.first), en...
    method empty (line 33) | bool empty() const { return current == end; }
    method Iterated (line 34) | Iterated & front() const { return *current; }
    method Iterator (line 35) | Iterator   frontIterator() const { return  current; }
    method popFront (line 36) | void popFront() { ++current; }
  class ContainerProperties (line 40) | class ContainerProperties {
  class ContainerRange (line 47) | class ContainerRange : public IteratorRange< typename ContainerPropertie...
    method ContainerRange (line 49) | ContainerRange(Container &c) : IteratorRange< typename ContainerProper...
  class RangeTypes (line 55) | class RangeTypes {
  class ChainedRange (line 62) | class ChainedRange { // Chain Two together
    method ChainedRange (line 66) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 67) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 68) | bool firstEmpty() const { return first.empty(); }
    method front (line 69) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 70) | void popFront() { if (first.empty()) second.popFront(); else first.pop...
  type Range (line 74) | struct Range {
  type RangeContainer (line 84) | struct RangeContainer
    method RangeContainer (line 89) | explicit RangeContainer(Iterator first, Iterator last) : _current(firs...
    method empty (line 91) | virtual bool empty() const { return _current == _last; }
    method popFront (line 92) | virtual void popFront() { ++_current; }
    method front (line 93) | virtual typename Iterator::reference front() const { return *_current; }
  type amd (line 99) | namespace amd {
    function mk_range (line 101) | std::auto_ptr< Range< typename C::iterator::reference > > mk_range(C &...
    function mk_range (line 105) | std::auto_ptr< Range< typename C::const_iterator::reference > > mk_ran...
    function mk_range_c (line 109) | std::auto_ptr< Range< typename C::const_iterator::reference > > mk_ran...
    function mk_reverse_range (line 113) | std::auto_ptr< Range< typename C::reverse_iterator::reference > > mk_r...
    function mk_reverse_range (line 117) | std::auto_ptr< Range< typename C::const_reverse_iterator::reference > ...
    class RangeOverStream (line 122) | class RangeOverStream : public Range<std::string> {
    class RangeMapper (line 137) | class RangeMapper : public Range<typename boost::result_of<F(typename ...
      method RangeMapper (line 144) | RangeMapper(const T & mapped_, F f_) : mapped(mapped_), f(f_) {}
      method empty (line 145) | bool empty() const { return mapped.empty(); }
      method popFront (line 146) | void popFront() { mapped.popFront(); }
      method value_type (line 147) | value_type front() const {
    function make_mapper_range (line 152) | RangeMapper<T, F> make_mapper_range(const T& m, F f) {
    function map_range (line 157) | RangeMapper<T, F> map_range(const F &f, const T& m) {
    class RangeFilter (line 162) | class RangeFilter : public Range<typename R::value_type> {
      method RangeFilter (line 167) | RangeFilter(const R& _r, const P& _p) : r(_r), p(_p) {
      method empty (line 172) | virtual bool empty() const { return r.empty(); }
      method popFront (line 173) | virtual void popFront() {
      method value_type (line 178) | virtual value_type front() const {
    function make_filter_range (line 183) | RangeFilter<R,P> make_filter_range(const R& r, const P& p) {
    function filter (line 188) | RangeFilter<R,P> filter(const P& p, const R& r) {
    function range_length (line 192) | int range_length(R r) {
    class RangeEnum (line 202) | class RangeEnum : public Range<I> {
      method RangeEnum (line 205) | RangeEnum(I a_) : a(a_) {}
      method empty (line 206) | virtual bool empty() const { return false; }
      method I (line 207) | virtual I front() const { return a; }
      method popFront (line 208) | virtual void popFront() { ++a; }
    function make_counter_range (line 212) | RangeEnum<I> make_counter_range(I first) {
    class RangeZipper (line 218) | class RangeZipper : public Range< std::pair<
      method RangeZipper (line 229) | RangeZipper(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 230) | virtual bool empty() const { return l.empty() || r.empty(); }
      method value_type (line 231) | virtual value_type front() const { return make_pair(l.front(), r.fro...
      method popFront (line 232) | virtual void popFront() { l.popFront(); r.popFront(); }
    function zip (line 236) | RangeZipper<L,R> zip(const L &l, const R &r) {
    class RangeChain (line 242) | class RangeChain : public Range< typename L::value_type > {
      method RangeChain (line 247) | RangeChain(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 248) | virtual bool empty() const { return l.empty() && r.empty(); }
      method value_type (line 249) | virtual value_type front() const {
      method popFront (line 255) | virtual void popFront() {
    function chain (line 263) | RangeChain<L,R> chain(const L &l, const R &r) {
  class auto_ptrWithPairedBool (line 285) | class auto_ptrWithPairedBool : public std::auto_ptr<Type> {
    method auto_ptrWithPairedBool (line 287) | auto_ptrWithPairedBool(Type *p) : std::auto_ptr<Type> (p), interrupted...

FILE: Algorithms/2011-MOSES/src-original/aaron_utils.cpp
  function testForError (line 6) | int testForError(FILE * x) { return x==NULL; }
  function testForError (line 7) | int testForError(int x) { return x==-1; }
  function string (line 9) | string show(int64 x) { ostringstream s; s << x; return s.str(); }
  function string (line 10) | string show(const char * x) { ostringstream s; s << x; return s.str(); }
  function string (line 11) | string show(const string &s) { return s; }
  function string (line 19) | string runningAverage::operator() (void) const {
  function DummyOutputStream (line 25) | DummyOutputStream& DummyOutputStream::operator << (int) { return *this; }
  function DummyOutputStream (line 26) | DummyOutputStream& DummyOutputStream::operator << (const char*) { return...
  function string (line 29) | string thousandsSeparated(uint64 x) {
  function istream (line 40) | istream *amd::zcatThis(const char *gzippedFile) {
  type stat (line 50) | struct stat

FILE: Algorithms/2011-MOSES/src-original/aaron_utils.hpp
  class runningAverage (line 60) | class runningAverage {
  type RefPair (line 71) | struct RefPair {
    method RefPair (line 74) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) { }
  function make_refpair (line 78) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 83) | struct DummyOutputStream {
  type StopWatch (line 89) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 90) | struct timeval
    type timeval (line 91) | struct timeval
    method StopWatch (line 92) | StopWatch() {
    method laptime (line 96) | void laptime(void) { laptime(""); }
    method laptime (line 97) | void laptime(const string &tag) {
  class maxOnlymap (line 111) | class maxOnlymap : public map<K, V> {
    method insert (line 113) | pair<typename map<K,V>::iterator,bool> insert ( const typename map<K,V...
  type Timer (line 125) | struct Timer {
    type timeval (line 126) | struct timeval
    method Timer (line 128) | Timer() {
    method Timer (line 131) | Timer(const string &s): _s(s) {
    method age (line 134) | double age() const {
  type amd (line 146) | namespace amd {
    type DebugCounter (line 151) | struct DebugCounter {
    function Histogram (line 160) | void Histogram(T r) {
    function TwoWayTable (line 178) | void TwoWayTable(T1 r1, T2 r2) {
    function constAt (line 227) | typename C::value_type constAt(const C &c, int i) {

FILE: Algorithms/2011-MOSES/src-original/graph_loading.cpp
  type graph_loading (line 25) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 27) | struct readEdgeInvalidLineInDataException : public exception { }
    class RangeOfEdges (line 31) | class RangeOfEdges {
      method read_a_row (line 37) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 39) | RangeOfEdges(const char* b, const char* e) : p(b), fileEnd(e) { if(p...
      method front (line 40) | pair<Name, Name> front() { return make_pair(l,r); }
      method empty (line 41) | bool empty() { return p == fileEnd; }
      method popFront (line 42) | void popFront() { p = updating_p ; if(p!=fileEnd) read_a_row(); }
    function loadSimpleStringGraphFromFile (line 56) | void loadSimpleStringGraphFromFile(SimpleStringGraph &g, const char *f...
    function loadSimpleIntGraphFromFile (line 60) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    type DegreeTag (line 65) | struct DegreeTag {}
    type NameTag (line 66) | struct NameTag {}
    function DegreeIncrementer (line 67) | void DegreeIncrementer(pair<N,V> &p) { ++p.second; }
    function DegreeDecrementer (line 68) | void DegreeDecrementer(pair<N,V> &p) { --p.second; }
    type state_flag (line 70) | enum state_flag { LOADING_NONE, LOADING_NODES, LOADING_DEGREEMAP, LOAD...
    type lsdkfj (line 71) | struct lsdkfj {
      type state_flag (line 72) | enum state_flag
    function sigUSR1_handler (line 75) | void sigUSR1_handler(int) {
    function loadBloomGraphMMAP (line 86) | static void loadBloomGraphMMAP(bloomGraph<Name> &bg, const char *fileN...
    function loadBloomGraphMMAPFastButFussy (line 273) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 321) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 390) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 401) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 422) | static void populateNameToIDHash(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 436) | static void populateNameToIDHash(SimpleStringGraph &bg) {
    function addNeighbour (line 452) | static void addNeighbour(VertexIDType edge_source, VertexIDType edge_t...
    function loadEdges (line 479) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 499) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-MOSES/src-original/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-MOSES/src-original/graph_representation.cpp
  function V (line 7) | V bloomGraph<int>::key_for_vertexName(int v) const {
  function V (line 24) | V bloomGraph<string>::key_for_vertexName(string v) const {
  function string (line 42) | string VertexNameToString (const int &l) {

FILE: Algorithms/2011-MOSES/src-original/graph_representation.hpp
  type bloomGraph (line 16) | struct bloomGraph
    method bloomGraph (line 77) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 83) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 84) | VertexNameType name(V v) const { assert(v>=0); assert(v<vcount()); ass...
    method string (line 85) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...
  function H (line 21) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  function H (line 28) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type GraphWithoutNames (line 40) | struct GraphWithoutNames { // this is useful because it doesn't need the...
    method V (line 41) | V vcount(void) const { return vertex_count ; }
    method V (line 42) | V ecount(void) const { return edge_count / 2; }
    method V (line 43) | inline V degree(V v) const { return degrees.at(v); }
    method neighbours (line 44) | pair<const VertexIDType*,const VertexIDType*> neighbours(VertexIDType ...
    method neighbours (line 50) | pair<VertexIDType*,VertexIDType*> neighbours(VertexIDType i) {
    method are_connected (line 56) | bool are_connected(const V &v, const V &v2) const { return are_connect...
    method are_connected (line 57) | bool are_connected(const EdgeType &e) const {
    method GraphWithoutNames (line 64) | GraphWithoutNames(void) : vertex_count(0), edge_count(0) {}
  type bloomGraph (line 74) | struct bloomGraph : public GraphWithoutNames {
    method bloomGraph (line 77) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 83) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 84) | VertexNameType name(V v) const { assert(v>=0); assert(v<vcount()); ass...
    method string (line 85) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...

FILE: Algorithms/2011-MOSES/src-original/groupStats.cpp
  function main (line 21) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-original/grouping.cpp
  type grouping (line 5) | namespace grouping {
    function Foreach (line 21) | Foreach(V n, ns) {
    function Group (line 46) | Group* Grouping::newG () { return this->newG(false); }
    function Group (line 47) | Group* Grouping::newG(bool randomized_p_in) {
    function ForeachContainer (line 55) | ForeachContainer (Group *grp, grps) {
    function deleteEmptyGroup (line 129) | void deleteEmptyGroup(Grouping *pging, Group *grp) { // TODO: This is ...

FILE: Algorithms/2011-MOSES/src-original/grouping.hpp
  type grouping (line 5) | namespace grouping {
    class Group (line 7) | class Group
    class Grouping (line 8) | class Grouping
      type edgeHash (line 34) | struct edgeHash {
      type EdgeCountTriple (line 44) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 47) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    type orderGroup (line 10) | struct orderGroup {
    class Grouping (line 14) | class Grouping {
      type edgeHash (line 34) | struct edgeHash {
      type EdgeCountTriple (line 44) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 47) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    class Group (line 58) | class Group {

FILE: Algorithms/2011-MOSES/src-original/iterative.hpp
  type iterative (line 3) | namespace iterative {
    type OneNode (line 11) | struct OneNode {
    type PartitionStats (line 20) | struct PartitionStats {
    type Partition (line 33) | struct Partition : public PartitionStats {

FILE: Algorithms/2011-MOSES/src-original/moses.cpp
  function main (line 21) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-original/overlapping.cpp
  function runMutual (line 66) | static void runMutual(void) {
  type overlapping (line 70) | namespace overlapping {
    function overlapping (line 74) | void overlapping(SimpleIntGraph &g) { overlappingT(g); }
    function overlapping (line 75) | void overlapping(SimpleStringGraph &g) { overlappingT(g); }
    function addSeed (line 82) | void addSeed(Grouping &ging, const set<V> &nodes, bool randomized_p_in) {
    function overlappingT (line 100) | static void overlappingT(bloomGraph<N> &g) {
    function tryAndApplyThisOne (line 237) | static bool tryAndApplyThisOne(Grouping &ging, V e, bool randomized_p_...
    function useOneNodeSeeds (line 252) | static void useOneNodeSeeds(Grouping &ging, bloomGraph<N> &g, bool ran...
    function groupStats (line 285) | static void groupStats(const Grouping &ging, bloomGraph<N> &g) {
    function seedGroupingWithPartition (line 361) | void seedGroupingWithPartition(Grouping &ging, const iterative::Partit...
    function count_intersection (line 378) | static size_t count_intersection(It it1b, It it1e, It it2b, It it2e) {
    function count_intersection (line 384) | static size_t count_intersection(const Container &container1, const Co...
    type DeltaSeed (line 393) | struct DeltaSeed {
      method deltadeltaPairEntropy (line 400) | long double deltadeltaPairEntropy() const {
      method DeltaSeed (line 403) | explicit DeltaSeed(V v, int group_size_smaller, Grouping &ging) : _v...
      method addEdge2 (line 406) | void addEdge2(V n, const V* edgeVN_ptr) { // n is connected to _v
      method addEdge (line 410) | void addEdge(V  , int sharedCommunities) { // n is connected to _v /...
      method redoEdge (line 418) | void redoEdge(V  , int previous_sharedCommunities) { // n is connect...
      method _deltaZentropy (line 424) | long double _deltaZentropy() const {
      method _deltaTotalentropy (line 443) | long double _deltaTotalentropy() const {
    type FrontierNode (line 448) | struct FrontierNode {
      method FrontierNode (line 449) | FrontierNode(long double &score, V v) : _score(score), _v(v) {}
      type Incrementer (line 452) | struct Incrementer {
        method Incrementer (line 454) | Incrementer(long double &x) : _x(x) {}
    type VertexTag (line 460) | struct VertexTag {}
    type Frontier (line 461) | struct Frontier : private multi_index_container < // TODO: Some sort o...
      method calcddEE (line 472) | static long double __attribute__ ((noinline)) calcddEE(const Groupin...
      method addNode (line 479) | void addNode(const Grouping &ging, V to, const V *edgeFT_ptr) {
      method erase_best_node (line 493) | void erase_best_node() {
      method erase_this_node (line 497) | int erase_this_node(V to) {
      method best_node_score (line 500) | long double best_node_score() const {
      method V (line 504) | V best_node_v() const {
      method Empty (line 508) | bool Empty() const {
    function logNchoose (line 513) | static long double logNchoose(int64 N, int64 n_c) {
    function growingSeed (line 543) | pair<long double, set<V> > growingSeed(Grouping &ging, int lookahead
    type ThrowingIterator (line 648) | struct ThrowingIterator {
      type Dereferenced (line 649) | struct Dereferenced {}
      method V (line 650) | V & operator *() { throw Dereferenced(); }
    function emptyIntersection (line 653) | bool emptyIntersection(const pair<const V*, const V*> &l, const pair<c...
    function growThisEdge (line 668) | static pair<long double, set<V> > growThisEdge(Grouping &ging, const V...
    function save (line 730) | static void save(Grouping &ging, bloomGraph<N> &g) {
    type hashGroup (line 745) | struct hashGroup {
    function louvainStyle (line 752) | static void louvainStyle(Grouping &ging, bloomGraph<N> &g) {
    function update_p_out (line 838) | static void update_p_out(Grouping &ging) {
    type PairGroupHash (line 846) | struct PairGroupHash {
    function tryMerges (line 851) | static void tryMerges(Grouping &ging) {
    function tryDeletions (line 991) | static void tryDeletions(Grouping &ging, bool SaveScores /*= true*/) {...
    function P_x_given_z (line 1082) | long double P_x_given_z(const Grouping &ging, long double p_o, long do...
    function MOSES_objective (line 1096) | long double MOSES_objective(const Grouping &ging) {
    function estimate_p_in_and_p_out (line 1141) | static void estimate_p_in_and_p_out(Grouping &ging) {

FILE: Algorithms/2011-MOSES/src-original/overlapping.hpp
  type overlapping (line 3) | namespace overlapping {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/group_status_exec.cpp
  function main (line 16) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/grouping.cpp
  type grouping (line 7) | namespace grouping {
    function Foreach (line 20) | Foreach(V n, ns) {
    function Group (line 48) | Group *Grouping::newG() { return this->newG(false); }
    function Group (line 50) | Group *Grouping::newG(bool randomized_p_in) {
    function ForeachContainer (line 60) | ForeachContainer (Group *grp, grps) {
    function deleteEmptyGroup (line 134) | void deleteEmptyGroup(Grouping *pging,

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/grouping.hpp
  type grouping (line 7) | namespace grouping {
    class Group (line 9) | class Group
    class Grouping (line 11) | class Grouping
      type edgeHash (line 43) | struct edgeHash {
      type EdgeCountTriple (line 55) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 59) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    type orderGroup (line 13) | struct orderGroup {
    class Grouping (line 17) | class Grouping {
      type edgeHash (line 43) | struct edgeHash {
      type EdgeCountTriple (line 55) | struct EdgeCountTriple { // TODO: make this private
        method EdgeCountTriple (line 59) | EdgeCountTriple() : shared_comms(0), other_index(0) {}
    class Group (line 72) | class Group {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/moses.cpp
  function main (line 18) | int main(int argc, char **argv) {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/overlapping.cpp
  function runMutual (line 69) | static void runMutual(void) {
  type overlapping (line 73) | namespace overlapping {
    function overlapping (line 80) | void overlapping(SimpleIntGraph &g) { overlappingT(g); }
    function overlapping (line 82) | void overlapping(SimpleStringGraph &g) { overlappingT(g); }
    function addSeed (line 95) | void addSeed(Grouping &ging, const set<V> &nodes, bool randomized_p_in) {
    function overlappingT (line 125) | static void overlappingT(bloomGraph<N> &g) {
    function tryAndApplyThisOne (line 264) | static bool tryAndApplyThisOne(Grouping &ging, V e, bool randomized_p_...
    function useOneNodeSeeds (line 281) | static void useOneNodeSeeds(Grouping &ging, bloomGraph<N> &g, bool ran...
    function groupStats (line 316) | static void groupStats(const Grouping &ging, bloomGraph<N> &g) {
    function seedGroupingWithPartition (line 395) | void seedGroupingWithPartition(Grouping &ging, const iterative::Partit...
    function count_intersection (line 412) | static size_t count_intersection(It it1b, It it1e, It it2b, It it2e) {
    function count_intersection (line 419) | static size_t count_intersection(const Container &container1, const Co...
    type DeltaSeed (line 425) | struct DeltaSeed {
      method deltadeltaPairEntropy (line 433) | long double deltadeltaPairEntropy() const {
      method DeltaSeed (line 438) | explicit DeltaSeed(V v, int group_size_smaller, Grouping &ging) : _v...
      method addEdge2 (line 445) | void addEdge2(V n, const V *edgeVN_ptr) { // n is connected to _v
      method addEdge (line 450) | void addEdge(V, int sharedCommunities) {
      method redoEdge (line 457) | void redoEdge(V,
      method _deltaZentropy (line 468) | long double _deltaZentropy() const {
      method _deltaTotalentropy (line 476) | long double _deltaTotalentropy() const {
    type FrontierNode (line 481) | struct FrontierNode {
      method FrontierNode (line 482) | FrontierNode(long double &score, V v) : _score(score), _v(v) {}
      type Incrementer (line 487) | struct Incrementer {
        method Incrementer (line 490) | Incrementer(long double &x) : _x(x) {}
    type VertexTag (line 497) | struct VertexTag {
    type Frontier (line 500) | struct Frontier : private multi_index_container< // TODO: Some sort of...
      method calcddEE (line 511) | static long double __attribute__ ((noinline)) calcddEE(const Groupin...
      method addNode (line 519) | void addNode(const Grouping &ging, V to, const V *edgeFT_ptr) {
      method erase_best_node (line 534) | void erase_best_node() {
      method erase_this_node (line 539) | int erase_this_node(V to) {
      method best_node_score (line 543) | long double best_node_score() const {
      method V (line 548) | V best_node_v() const {
      method Empty (line 553) | bool Empty() const {
    function logNchoose (line 558) | static long double logNchoose(int64 N, int64 n_c) {
    function growingSeed (line 588) | pair<long double, set<V> >
    type ThrowingIterator (line 684) | struct ThrowingIterator {
      type Dereferenced (line 685) | struct Dereferenced {
      method V (line 688) | V &operator*() { throw Dereferenced(); }
    function emptyIntersection (line 693) | bool emptyIntersection(const pair<const V *, const V *> &l, const pair...
    function growThisEdge (line 704) | static pair<long double, set<V> >
    function save (line 764) | static void save(Grouping &ging, bloomGraph<N> &g) {
    type hashGroup (line 779) | struct hashGroup {
    function louvainStyle (line 788) | static void louvainStyle(Grouping &ging, bloomGraph<N> &g) {
    function update_p_out (line 876) | static void update_p_out(Grouping &ging) {
    type PairGroupHash (line 884) | struct PairGroupHash {
    function tryMerges (line 890) | static void tryMerges(Grouping &ging) {
    function tryDeletions (line 1038) | static void tryDeletions(Grouping &ging,
    function P_x_given_z (line 1128) | long double P_x_given_z(const Grouping &ging, long double p_o, long do...
    function MOSES_objective (line 1143) | long double MOSES_objective(const Grouping &ging) {
    function estimate_p_in_and_p_out (line 1185) | static void estimate_p_in_and_p_out(Grouping &ging) {

FILE: Algorithms/2011-MOSES/src-refactor/algorithm/overlapping.hpp
  type overlapping (line 3) | namespace overlapping {

FILE: Algorithms/2011-MOSES/src-refactor/util/aaron_utils.cpp
  function testForError (line 7) | int testForError(FILE *x) { return x == NULL; }
  function testForError (line 9) | int testForError(int x) { return x == -1; }
  function string (line 11) | string show(int64 x) {
  function string (line 17) | string show(const char *x) {
  function string (line 23) | string show(const string &s) { return s; }
  function string (line 33) | string runningAverage::operator()(void) const {
  function DummyOutputStream (line 39) | DummyOutputStream &DummyOutputStream::operator<<(int) { return *this; }
  function DummyOutputStream (line 41) | DummyOutputStream &DummyOutputStream::operator<<(const char *) { return ...
  function string (line 45) | string thousandsSeparated(uint64 x) {
  function istream (line 56) | istream *amd::zcatThis(const char *gzippedFile) {
  type stat (line 67) | struct stat

FILE: Algorithms/2011-MOSES/src-refactor/util/aaron_utils.hpp
  class runningAverage (line 70) | class runningAverage {
  type RefPair (line 84) | struct RefPair {
    method RefPair (line 88) | RefPair(T1 &in1, T2 &in2) : e1(in1), e2(in2) {}
  function make_refpair (line 97) | RefPair<T1, T2> make_refpair(T1 &e1, T2 &e2) {
  type DummyOutputStream (line 102) | struct DummyOutputStream {
  type StopWatch (line 110) | struct StopWatch { // TODO: put the stopWatch in another file?
    type timeval (line 111) | struct timeval
    type timeval (line 112) | struct timeval
    method StopWatch (line 114) | StopWatch() {
    method laptime (line 119) | void laptime(void) { laptime(""); }
    method laptime (line 121) | void laptime(const string &tag) {
  class maxOnlymap (line 138) | class maxOnlymap : public map<K, V> {
    method insert (line 140) | pair<typename map<K, V>::iterator, bool> insert(const typename map<K, ...
  type Timer (line 152) | struct Timer {
    type timeval (line 153) | struct timeval
    method Timer (line 156) | Timer() {
    method Timer (line 160) | Timer(const string &s) : _s(s) {
    method age (line 164) | double age() const {
  type amd (line 178) | namespace amd {
    type DebugCounter (line 184) | struct DebugCounter {
    function Histogram (line 195) | void Histogram(T r) {
    function TwoWayTable (line 214) | void TwoWayTable(T1 r1, T2 r2) {
    function constAt (line 264) | typename C::value_type constAt(const C &c, int i) {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_loading.cpp
  type graph_loading (line 25) | namespace graph_loading {
    type readEdgeInvalidLineInDataException (line 27) | struct readEdgeInvalidLineInDataException : public exception {
    class RangeOfEdges (line 34) | class RangeOfEdges {
      method read_a_row (line 41) | void read_a_row() { updating_p = readEdge(p, l, r); }
      method RangeOfEdges (line 44) | RangeOfEdges(const char *b, const char *e) : p(b), fileEnd(e) { if (...
      method front (line 46) | pair<Name, Name> front() { return make_pair(l, r); }
      method empty (line 48) | bool empty() { return p == fileEnd; }
      method popFront (line 50) | void popFront() {
    function loadSimpleStringGraphFromFile (line 79) | void loadSimpleStringGraphFromFile(SimpleStringGraph &g, const char *f...
    function loadSimpleIntGraphFromFile (line 84) | void loadSimpleIntGraphFromFile(SimpleIntGraph &bg, const char *fileNa...
    type DegreeTag (line 89) | struct DegreeTag {
    type NameTag (line 91) | struct NameTag {
    function DegreeIncrementer (line 95) | void DegreeIncrementer(pair<N, V> &p) { ++p.second; }
    function DegreeDecrementer (line 98) | void DegreeDecrementer(pair<N, V> &p) { --p.second; }
    type state_flag (line 100) | enum state_flag {
    type lsdkfj (line 103) | struct lsdkfj {
      type state_flag (line 104) | enum state_flag
    function sigUSR1_handler (line 108) | void sigUSR1_handler(int) {
    function loadBloomGraphMMAP (line 123) | static void loadBloomGraphMMAP(bloomGraph<Name> &bg, const char *fileN...
    function loadBloomGraphMMAPFastButFussy (line 315) | void loadBloomGraphMMAPFastButFussy(SimpleIntGraph &bg, const char *fi...
    function findDistinctVertices (line 363) | void findDistinctVertices(RangeOfEdges<SimpleIntGraph::Name> roe, Simp...
    function countDegrees (line 438) | void countDegrees(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGra...
    function convertDegreesToOffsets (line 449) | void convertDegreesToOffsets(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 471) | static void populateNameToIDHash(SimpleIntGraph &bg) {
    function populateNameToIDHash (line 487) | static void populateNameToIDHash(SimpleStringGraph &bg) {
    function addNeighbour (line 504) | static void
    function loadEdges (line 536) | void loadEdges(RangeOfEdges<SimpleIntGraph::Name> roe, SimpleIntGraph ...
    function mmapFile (line 557) | pair<const char *, const char *> mmapFile(const char *fileName) {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_loading.hpp
  type graph_loading (line 5) | namespace graph_loading {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_representation.cpp
  function V (line 9) | V bloomGraph<int>::key_for_vertexName(int v) const {
  function V (line 28) | V bloomGraph<string>::key_for_vertexName(string v) const {
  function string (line 46) | string VertexNameToString(const int &l) {

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/graph_representation.hpp
  type bloomGraph (line 17) | struct bloomGraph
    method bloomGraph (line 84) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 91) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 93) | VertexNameType name(V v) const {
    method string (line 100) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...
  function H (line 22) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  function H (line 31) | H hash_integer( // This is used in populateHash and key_for_vertexName f...
  type GraphWithoutNames (line 43) | struct GraphWithoutNames { // this is useful because it doesn't need the...
    method V (line 44) | V vcount(void) const { return vertex_count; }
    method V (line 46) | V ecount(void) const { return edge_count / 2; }
    method V (line 47) | inline V degree(V v) const { return degrees.at(v); }
    method neighbours (line 49) | pair<const VertexIDType *, const VertexIDType *>
    method neighbours (line 56) | pair<VertexIDType *, VertexIDType *> neighbours(VertexIDType i) {
    method are_connected (line 62) | bool are_connected(const V &v, const V &v2) const { return are_connect...
    method are_connected (line 64) | bool are_connected(const EdgeType &e) const {
    method GraphWithoutNames (line 71) | GraphWithoutNames(void) : vertex_count(0), edge_count(0) {}
  type bloomGraph (line 81) | struct bloomGraph : public GraphWithoutNames {
    method bloomGraph (line 84) | explicit bloomGraph() : GraphWithoutNames() {}
    method VertexNameType (line 91) | VertexNameType name_of_one_node(V v) const { return vertex_mappings.at...
    method VertexNameType (line 93) | VertexNameType name(V v) const {
    method string (line 100) | string name_of_one_node_asString(V v) const { return VertexNameToStrin...

FILE: Algorithms/2011-MOSES/src-refactor/util/graph/iterative.hpp
  type iterative (line 3) | namespace iterative {
    type OneNode (line 12) | struct OneNode {
    type PartitionStats (line 22) | struct PartitionStats {
    type Partition (line 36) | struct Partition : public PartitionStats {

FILE: Algorithms/2011-MOSES/src-refactor/util/range.cpp
  type amd (line 5) | namespace amd {
    function rangeOverStream (line 7) | std::auto_ptr<range<std::string> > rangeOverStream(std::istream &_istr...

FILE: Algorithms/2011-MOSES/src-refactor/util/range.hpp
  class IteratorRange (line 23) | class IteratorRange {
    method IteratorRange (line 31) | IteratorRange(const Iterator &_begin, const Iterator &_end) : current(...
    method IteratorRange (line 33) | IteratorRange(std::pair<Iterator, Iterator> be) : current(be.first), e...
    method empty (line 35) | bool empty() const { return current == end; }
    method Iterated (line 37) | Iterated &front() const { return *current; }
    method Iterator (line 39) | Iterator frontIterator() const { return current; }
    method popFront (line 41) | void popFront() { ++current; }
  class ContainerProperties (line 45) | class ContainerProperties {
  class ContainerRange (line 53) | class ContainerRange : public IteratorRange<typename ContainerProperties...
    method ContainerRange (line 55) | ContainerRange(Container &c) : IteratorRange<typename ContainerPropert...
  class RangeTypes (line 61) | class RangeTypes {
  class ChainedRange (line 68) | class ChainedRange { // Chain Two together
    method ChainedRange (line 72) | ChainedRange(const Range &_first, const Range &_second) : first(_first...
    method empty (line 74) | bool empty() const { return first.empty() && second.empty(); }
    method firstEmpty (line 76) | bool firstEmpty() const { return first.empty(); }
    method front (line 78) | typename RangeTypes<Range>::ElementType front() const { return first.e...
    method popFront (line 80) | void popFront() { if (first.empty()) second.popFront(); else first.pop...
  type range (line 84) | struct range {
  type RangeContainer (line 98) | struct RangeContainer
    method RangeContainer (line 103) | explicit RangeContainer(Iterator first, Iterator last) : _current(firs...
    method empty (line 106) | virtual bool empty() const { return _current == _last; }
    method popFront (line 108) | virtual void popFront() { ++_current; }
    method front (line 110) | virtual typename Iterator::reference front() const { return *_current; }
  type amd (line 117) | namespace amd {
    function mk_range (line 119) | std::auto_ptr<range<typename C::iterator::reference> > mk_range(C &c) {
    function mk_range (line 125) | std::auto_ptr<range<typename C::const_iterator::reference> > mk_range(...
    function mk_range_c (line 131) | std::auto_ptr<range<typename C::const_iterator::reference> > mk_range_...
    function mk_reverse_range (line 137) | std::auto_ptr<range<typename C::reverse_iterator::reference> > mk_reve...
    function mk_reverse_range (line 143) | std::auto_ptr<range<typename C::const_reverse_iterator::reference> > m...
    class RangeOverStream (line 149) | class RangeOverStream : public range<std::string> {
    class RangeMapper (line 170) | class RangeMapper : public range<typename boost::result_of<F(
      method RangeMapper (line 179) | RangeMapper(const T &mapped_, F f_) : mapped(mapped_), f(f_) {}
      method empty (line 181) | bool empty() const { return mapped.empty(); }
      method popFront (line 183) | void popFront() { mapped.popFront(); }
      method value_type (line 185) | value_type front() const {
    function make_mapper_range (line 191) | RangeMapper<T, F> make_mapper_range(const T &m, F f) {
    function map_range (line 197) | RangeMapper<T, F> map_range(const F &f, const T &m) {
    class RangeFilter (line 202) | class RangeFilter : public range<typename R::value_type> {
      method RangeFilter (line 208) | RangeFilter(const R &_r, const P &_p) : r(_r), p(_p) {
      method empty (line 214) | virtual bool empty() const { return r.empty(); }
      method popFront (line 216) | virtual void popFront() {
      method value_type (line 222) | virtual value_type front() const {
    function make_filter_range (line 228) | RangeFilter<R, P> make_filter_range(const R &r, const P &p) {
    function filter (line 234) | RangeFilter<R, P> filter(const P &p, const R &r) {
    function range_length (line 239) | int range_length(R r) {
    class RangeEnum (line 249) | class RangeEnum : public range<I> {
      method RangeEnum (line 252) | RangeEnum(I a_) : a(a_) {}
      method empty (line 254) | virtual bool empty() const { return false; }
      method I (line 256) | virtual I front() const { return a; }
      method popFront (line 258) | virtual void popFront() { ++a; }
    function make_counter_range (line 262) | RangeEnum<I> make_counter_range(I first) {
    class RangeZipper (line 268) | class RangeZipper : public range<std::pair<
      method RangeZipper (line 278) | RangeZipper(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 280) | virtual bool empty() const { return l.empty() || r.empty(); }
      method value_type (line 282) | virtual value_type front() const { return std::make_pair(l.front(), ...
      method popFront (line 284) | virtual void popFront() {
    function zip (line 291) | RangeZipper<L, R> zip(const L &l, const R &r) {
    class RangeChain (line 297) | class RangeChain : public range<typename L::value_type> {
      method RangeChain (line 303) | RangeChain(const L &l_, const R &r_) : l(l_), r(r_) {}
      method empty (line 305) | virtual bool empty() const { return l.empty() && r.empty(); }
      method value_type (line 307) | virtual value_type front() const {
      method popFront (line 314) | virtual void popFront() {
    function chain (line 323) | RangeChain<L, R> chain(const L &l, const R &r) {
  class auto_ptrWithPairedBool (line 345) | class auto_ptrWithPairedBool : public std::auto_ptr<Type> {
    method auto_ptrWithPairedBool (line 347) | auto_ptrWithPairedBool(Type *p) : std::auto_ptr<Type>(p), interrupted(...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/dir_weighted_tabdeg.h
  type multimap (line 5) | typedef multimap<double, pair<int, double> > cup_data_struct;
  function compare_r_variables (line 14) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 47) | double right_error_function(double x) {
  function log_together (line 53) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 86) | double fitted_exponent(int N) {
  function order_statistics_left_cumulative (line 115) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function inverse_order_statistics (line 129) | double inverse_order_statistics(int sample_dim, int pos, const double  &...
  function pron_min_exp (line 171) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 185) | inline double compute_probability_to_stop(const double & a, const double...
  function equivalent_check (line 229) | bool equivalent_check(int pos_first, int pos_last, double & A_average, d...
  function equivalent_check_gather (line 272) | bool equivalent_check_gather(cup_data_struct & a, int & until, const dou...
  function hyper_table (line 327) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function compute_topologic_and_bootstrap_interval (line 332) | inline double compute_topologic_and_bootstrap_interval(int kin_node_out,...
  function compute_global_fitness (line 362) | double compute_global_fitness(int kin_node_in, int kout_g_in, int kin_no...
  function compute_topologic_step (line 492) | inline double compute_topologic_step(int kin_node_out, int kout_g_in, in...
  function compute_global_fitness_step (line 511) | double compute_global_fitness_step(int kin_node_in, int kout_g_in, int k...
  function compute_global_fitness_ofive (line 605) | inline double compute_global_fitness_ofive(int kin_node_in, int kout_g_i...
  function compute_global_fitness_randomized (line 614) | inline double compute_global_fitness_randomized(int kin_node_in, int kou...
  function compute_global_fitness_randomized_short (line 629) | double compute_global_fitness_randomized_short(int kin_node, int kout_g,...
  function class (line 659) | class facts {
  function class (line 706) | class weighted_tabdeg {
  function clear (line 746) | void weighted_tabdeg::clear() {
  function edinsert (line 756) | void weighted_tabdeg::edinsert(int a, int kpin, int kpout, int ktin, int...
  function erase (line 772) | bool weighted_tabdeg::erase(int a) {		// this function erases element a ...
  function is_internal (line 793) | bool weighted_tabdeg::is_internal(int a) {
  function set_deque (line 808) | void weighted_tabdeg::set_deque(deque<int> & vv) {
  function print_nodes (line 818) | void weighted_tabdeg::print_nodes(ostream & outb) {
  function worst_node (line 832) | int weighted_tabdeg::worst_node(int & lab, double & worst_fitness, int k...
  function best_node (line 900) | int weighted_tabdeg::best_node(int & lab, double & best_fitness, int kou...
  function _set_ (line 951) | void weighted_tabdeg::_set_(weighted_tabdeg & one)  {
  function update_group (line 967) | bool weighted_tabdeg::update_group(int a, int delta_degree_out, int delt...
  function update_neighs (line 1030) | bool weighted_tabdeg::update_neighs(int a, int delta_deg_out, int delta_...
  function set_and_update_group (line 1080) | void weighted_tabdeg::set_and_update_group(int nstar, int nn, int kout_g...
  function set_and_update_neighs (line 1105) | void weighted_tabdeg::set_and_update_neighs(int nstar, int nn, int kout_...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/directed_network.h
  function class (line 13) | class static_network {
  function clear (line 249) | void static_network::clear() {
  function set_graph (line 272) | void static_network::set_graph(map<int, map<int, pair<int, double> > > &...
  function set_oneM_etc (line 322) | void static_network::set_oneM_etc() {
  function set_graph (line 370) | bool static_network::set_graph(string file_name) {
  function set_graph (line 537) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function static_network (line 614) | int static_network::kin_m (const deque<int> & seq) {
  function kin_m (line 678) | int static_network::kin_m(const set <int> &s) {
  function draw_consecutive (line 695) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw (line 743) | int static_network::draw(string file_name) {
  function draw_with_weight_probability (line 791) | int static_network::draw_with_weight_probability(string file_name) {
  function static_network (line 840) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 848) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 856) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 866) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 877) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 886) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate (line 897) | int static_network::translate(deque<deque<int> > & ten) {
  function translate (line 942) | int static_network::translate(deque<int> & ten) {
  function set_subgraph (line 976) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function set_proper_weights (line 1023) | void static_network::set_proper_weights() {
  function set_connected_components (line 1079) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function same_component (line 1116) | void static_network::same_component(int source, set<int> & already_gone) {
  function propagate_distances (line 1156) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function translate_anyway (line 1225) | int static_network::translate_anyway(deque<deque<int> > & ten) {
  function set_upper_network (line 1265) | int static_network::set_upper_network(map<int, map<int, pair<int, double...
  function print_degree_of_homeless (line 1369) | void static_network::print_degree_of_homeless(DI & homel, ostream & outt) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/directed_oslomnet_evaluate.h
  function log_zero (line 4) | inline double log_zero(double a) {
  function class (line 16) | class oslomnet_evaluate : public oslomnet_louvain {
  function set_changendi_cum (line 86) | void oslomnet_evaluate::set_changendi_cum() {
  function set_maxbord (line 117) | int oslomnet_evaluate::set_maxbord() {
  function erase_cgroup (line 134) | void oslomnet_evaluate::erase_cgroup(int wnode) {
  function erase_the_worst (line 219) | bool oslomnet_evaluate::erase_the_worst(int & wnode) {
  function insert_cgroup (line 255) | void oslomnet_evaluate::insert_cgroup(int wnode) {
  function set_cgroup_and_neighs (line 360) | void oslomnet_evaluate::set_cgroup_and_neighs(const deque<int> & G) {
  function cup_on_list (line 381) | double oslomnet_evaluate::cup_on_list(cup_data_struct & a, deque<int> & ...
  function all_external_test (line 523) | double oslomnet_evaluate::all_external_test(int kout_g_in, int tmin, int...
  function initialize_for_evaluation (line 540) | void oslomnet_evaluate::initialize_for_evaluation(weighted_tabdeg & prev...
  function initialize_for_evaluation (line 565) | void oslomnet_evaluate::initialize_for_evaluation(const deque<int> & _c_...
  function partial_CUP (line 588) | double oslomnet_evaluate::partial_CUP(weighted_tabdeg & previous_tab_c, ...
  function CUP_runs (line 656) | double oslomnet_evaluate::CUP_runs(weighted_tabdeg & previous_tab_c, wei...
  function insert_the_best (line 823) | bool oslomnet_evaluate::insert_the_best() {
  function insertion (line 849) | void oslomnet_evaluate::insertion(int changendi) {
  function get_external_scores (line 953) | void oslomnet_evaluate::get_external_scores(weighted_tabdeg & neighs, cu...
  function try_to_assign_homeless_help (line 1011) | int oslomnet_evaluate::try_to_assign_homeless_help(module_collection & m...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/egocentric_undir.h
  function class (line 5) | class egocentric_net : public oslomnet_louvain {
  function collect_ego_groups_once (line 25) | int egocentric_net::collect_ego_groups_once(int_matrix & E) {
  function add_this_egomodules (line 44) | int egocentric_net::add_this_egomodules(int node, module_collection & Me...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/hierarchies.h
  function manipulate_string (line 5) | bool manipulate_string(string s, string netfile, string & outs) {
  function external_program_to_call (line 53) | void external_program_to_call(string network_file, oslom_net_global & ma...
  function translate_covers (line 111) | void translate_covers(string previous_tp, string new_tp, string short_tp...
  function no_singletons (line 172) | void no_singletons(char * directory_char, oslom_net_global & luca, modul...
  function write_tp_of_this_level (line 218) | bool write_tp_of_this_level(int level, oslom_net_global & luca, char * d...
  function oslom_level (line 359) | void oslom_level(oslom_net_global & luca, char * directory_char) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/log_table.h
  function class (line 8) | class log_fact_table {
  function _set_ (line 58) | void log_fact_table::_set_(int size) {
  function cum_hyper_right (line 84) | double log_fact_table::cum_hyper_right(int kin_node, int kout_g, int tm,...
  function cum_hyper_left (line 151) | double log_fact_table::cum_hyper_left(int kin_node, int kout_g, int tm, ...
  function cum_binomial_right (line 222) | double log_fact_table::cum_binomial_right(int x, int N, double prob) {
  function cum_binomial_left (line 281) | double log_fact_table::cum_binomial_left(int x, int N, double prob) {
  function slow_symmetric_eq (line 334) | double log_fact_table::slow_symmetric_eq(int k1, int k2, int H, int x) {
  function fast_right_cum_symmetric_eq (line 373) | inline double log_fact_table::fast_right_cum_symmetric_eq(int k1, int k2...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/louvain_oslomnet.h
  function class (line 6) | class oslom_module {
  type map (line 26) | typedef map<int, pair<int, double> > mapip;
  type map (line 27) | typedef map<int, oslom_module> map_int_om;
  function prints (line 31) | void prints(map_int_om & M) {
  function class (line 45) | class oslomnet_louvain : public static_network {
  function module_initializing (line 89) | void oslomnet_louvain::module_initializing() {
  function unweighted_favorite_of (line 110) | void oslomnet_louvain::unweighted_favorite_of(const int & node, int & fi...
  function weighted_favorite_of (line 167) | void oslomnet_louvain::weighted_favorite_of(const int & node, int & fi, ...
  function update_modules (line 241) | inline void oslomnet_louvain::update_modules(const int & i, const int & ...
  function single_pass_unweighted (line 275) | void oslomnet_louvain::single_pass_unweighted() {
  function single_pass_weighted (line 291) | void oslomnet_louvain::single_pass_weighted() {
  function set_partition_collected (line 305) | void oslomnet_louvain::set_partition_collected(deque<deque<int> > & ten2) {
  function collect_raw_groups_once (line 361) | int oslomnet_louvain::collect_raw_groups_once(deque<deque<int> > & P) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/louvain_oslomnet_dir.h
  function class (line 6) | class oslom_module {
  function class (line 25) | class internal_links_weights {
  type map (line 45) | typedef map<int, internal_links_weights> mapip;
  type map (line 46) | typedef map<int, oslom_module> map_int_om;
  function int_histogram (line 50) | void int_histogram(const int & c, mapip  & hist, const int & w1, const d...
  function prints (line 75) | void prints(map_int_om & M) {
  function class (line 89) | class oslomnet_louvain : public static_network {
  function module_initializing (line 133) | void oslomnet_louvain::module_initializing() {
  function unweighted_favorite_of (line 153) | void oslomnet_louvain::unweighted_favorite_of(const int & node, int & fi...
  function weighted_favorite_of (line 224) | void oslomnet_louvain::weighted_favorite_of(const int & node, int & fi, ...
  function update_modules (line 294) | inline void oslomnet_louvain::update_modules(const int & i, const int & ...
  function single_pass_unweighted (line 343) | void oslomnet_louvain::single_pass_unweighted() {
  function single_pass_weighted (line 359) | void oslomnet_louvain::single_pass_weighted() {
  function set_partition_collected (line 373) | void oslomnet_louvain::set_partition_collected(deque<deque<int> > & ten2) {
  function collect_raw_groups_once (line 428) | int oslomnet_louvain::collect_raw_groups_once(deque<deque<int> > & P) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/main_body.cpp
  function main (line 9) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/main_directed.cpp
  function program_statement (line 76) | void program_statement(char * b) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/main_undirected.cpp
  function program_statement (line 105) | void program_statement(char * b) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/module_collection.h
  function class (line 7) | class module_collection {
  function _set_ (line 68) | void module_collection::_set_(int dim) {
  function insert (line 82) | bool module_collection::insert(deque<int> & c, double bs) {
  function insert (line 93) | bool module_collection::insert(deque<int> & c, double bs, int & new_name) {
  function erase (line 126) | bool module_collection::erase(int a) {
  function print (line 160) | void module_collection::print(ostream & outt, deque<int> & netlabels, bo...
  function fill_gaps (line 199) | void module_collection::fill_gaps() {
  function put_gaps (line 215) | void module_collection::put_gaps() {
  function homeless (line 238) | void module_collection::homeless(deque<int> & h) {
  function coverage (line 260) | int module_collection::coverage() {
  function effective_groups (line 279) | int module_collection::effective_groups() {
  function set_partition (line 298) | void module_collection::set_partition(deque<deque<int> > & A) {
  function set_partition (line 307) | void module_collection::set_partition(deque<deque<int> > & A, deque<doub...
  function check_already (line 329) | bool module_collection::check_already(const deque<int> & c) {
  function compute_inclusions (line 365) | void module_collection::compute_inclusions() {
  function erase_included (line 375) | void module_collection::erase_included() {
  function erase_first_shell (line 402) | bool module_collection::erase_first_shell(map<int, deque<int> > & erase_...
  function almost_equal (line 459) | bool module_collection::almost_equal(int module_id, deque<int> & smaller) {
  function compact (line 503) | void module_collection::compact() {
  function sort_modules (line 550) | void module_collection::sort_modules(deque<int> & module_order) {
  function egomodules_to_merge (line 572) | bool module_collection::egomodules_to_merge(deque<int> & egom, deque<int...
  function merge (line 609) | void module_collection::merge(DI & c) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/oslom_net_global.h
  function class (line 5) | class oslom_net_global : public oslomnet_evaluate {
  function try_to_merge_discarded (line 83) | int oslom_net_global::try_to_merge_discarded(int_matrix & discarded, int...
  function get_single_trial_partition (line 152) | void oslom_net_global::get_single_trial_partition(int_matrix & good_modu...
  function from_matrix_to_module_collection (line 251) | void oslom_net_global::from_matrix_to_module_collection(int_matrix & goo...
  function get_cover (line 271) | void oslom_net_global::get_cover(module_collection & minimal_modules) {
  function check_minimality_all (line 296) | void oslom_net_global::check_minimality_all(int_matrix & A, DD & bss, mo...
  function check_minimality_matrix (line 344) | void oslom_net_global::check_minimality_matrix(int_matrix & A, DD & bss,...
  function check_minimality (line 372) | bool oslom_net_global::check_minimality(deque<int> & group, double & bs_...
  function print_modules (line 445) | void oslom_net_global::print_modules(bool not_homeless, string tp, modul...
  function print_modules (line 461) | void oslom_net_global::print_modules(bool not_homeless, ostream & out1, ...
  function load (line 484) | void oslom_net_global::load(string filename, module_collection & Mall) {
  function get_covers (line 515) | void oslom_net_global::get_covers(string cover_file, int & soft_partitio...
  function ultimate_cover (line 570) | void oslom_net_global::ultimate_cover(string cover_file, int soft_partit...
  function hint (line 614) | void oslom_net_global::hint(module_collection & minimal_modules, string ...
  function print_statistics (line 661) | void oslom_net_global::print_statistics(ostream & outt, module_collectio...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/oslom_net_unions.cpp
  function from_int_matrix_and_deque_to_deque (line 3) | void from_int_matrix_and_deque_to_deque(int_matrix & its_submodules, con...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/set_parameters.h
  function general_program_statement (line 13) | void general_program_statement(char * b) {
  function error_statement (line 67) | void error_statement(char * b) {
  function class (line 81) | class Parameters {
  function print (line 161) | void Parameters::print() {
  function set_flag_and_number (line 207) | bool Parameters::set_flag_and_number(double & number_to_set, int & argct...
  function set_flag_and_number (line 239) | bool Parameters::set_flag_and_number(int & number_to_set, int & argct, i...
  function set_flag_and_number_external_program (line 360) | bool Parameters::set_flag_and_number_external_program(string program_nam...
  function _set_ (line 410) | bool Parameters::_set_(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 193) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 217) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 240) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 257) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 273) | double poisson (int x, double mu) {
  function shuffle_and_set (line 283) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 304) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 332) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 360) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 375) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 406) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 475) | int random_from_set(set<int> & s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function deque_to_set_app (line 168) | void deque_to_set_app(const deque<int> & a, set<int> & s) {
  function norm_one (line 180) | double norm_one(const deque<double> & a) {
  function normalize_one (line 195) | int normalize_one(deque<double> & a) {
  function jaccard (line 210) | double jaccard(set<int> & a1,  set<int> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 139) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 265) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 275) | void compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 301) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 428) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 525) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 620) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 721) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 824) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 925) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1025) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1123) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1225) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1326) | void int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1355) | void int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1384) | void int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1399) | void int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1414) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1440) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1466) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1493) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1523) | void int_histogram(string infile, string outfile) {
  function int_histogram (line 1550) | void int_histogram(int c, map<int, int> & hist, int w) {
  function int_histogram (line 1567) | void int_histogram(const int & c, map<int, pair<int, double> >  & hist, ...
  function int_histogram (line 1586) | void int_histogram(int c, map<int, pair<double, double> > & hist, double...
  function int_histogram (line 1604) | void int_histogram(int c, map<int, pair<int, int> > & hist, int w1, int ...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 541) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/pajek.cpp
  function number_together (line 4) | int number_together(deque<int> & a) {
  function get_partition_from_file_list_pajek (line 36) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function set_partition_from_list (line 90) | void set_partition_from_list(deque<int> & mems, deque<deque<int> > & ten) {
  function get_partition_from_file_list_pajek_tree (line 129) | int get_partition_from_file_list_pajek_tree(string s, deque<deque<deque<...
  function pajek_format (line 228) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/partition.cpp
  function get_partition_from_file_tp_format_with_homeless (line 51) | int get_partition_from_file_tp_format_with_homeless(string S, deque<dequ...
  function get_partition_from_file_tp_format (line 95) | int get_partition_from_file_tp_format(string S, map<int, deque<int> > & ...
  function get_partition_from_file_tp_format (line 137) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 198) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 236) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M) {
  function get_partition_from_file (line 242) | int get_partition_from_file(string s, deque<deque<int> > & M, int min) {
  function get_partition_from_file (line 271) | int get_partition_from_file(string s, deque<deque<int> > & M) {
  function get_partition_from_file_list (line 277) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {
  function get_data_from_file_string (line 311) | void get_data_from_file_string(string s, deque<string> & a1, int col) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/undir_weighted_tabdeg.h
  type multimap (line 6) | typedef multimap<double, pair<int, double> > cup_data_struct;
  function compare_r_variables (line 15) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 48) | double right_error_function(double x) {
  function log_together (line 56) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 89) | double fitted_exponent(int N) {
  function order_statistics_left_cumulative (line 118) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function inverse_order_statistics (line 132) | double inverse_order_statistics(int sample_dim, int pos, const double  &...
  function pron_min_exp (line 174) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 188) | inline double compute_probability_to_stop(const double & a, const double...
  function equivalent_check (line 206) | bool equivalent_check(int pos_first, int pos_last, double & A_average, d...
  function equivalent_check_gather (line 249) | bool equivalent_check_gather(cup_data_struct & a, int & until, const dou...
  function hyper_table (line 302) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function topological_05 (line 314) | inline double topological_05(int kin_node, int kout_g, int tm, int degre...
  function compute_global_fitness (line 322) | double compute_global_fitness(int kin_node, int kout_g, int tm, int degr...
  function compute_global_fitness_step (line 392) | double compute_global_fitness_step(int kin_node, int kout_g, int tm, int...
  function compute_global_fitness_ofive (line 416) | inline double compute_global_fitness_ofive(int kin_node, int kout_g, int...
  function compute_global_fitness_randomized (line 423) | inline double compute_global_fitness_randomized(int kin_node, int kout_g...
  function compute_global_fitness_randomized_short (line 431) | double compute_global_fitness_randomized_short(int kin_node, int kout_g,...
  function class (line 461) | class facts {
  function class (line 481) | class weighted_tabdeg {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/undirected_network.h
  function class (line 13) | class static_network {
  function kplus_global_and_quick (line 139) | void static_network::vertex::kplus_global_and_quick(deque<int> & a, int ...
  function kplus_m (line 173) | int static_network::vertex::kplus_m(const deque<int> &a) {
  function kplus_w (line 192) | double static_network::vertex::kplus_w(const deque<int> &a) {
  function kplus_m (line 214) | int static_network::vertex::kplus_m(const set<int> &a) {
  function clear (line 242) | void static_network::clear() {
  function set_graph (line 265) | void static_network::set_graph(map<int, map<int, pair<int, double> > > &...
  function set_graph (line 314) | bool static_network::set_graph(string file_name) {
  function set_graph (line 547) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function static_network (line 631) | int static_network::kin_m (const deque<int> & seq) {
  function static_network (line 654) | int static_network::ktot_m (const deque<int> &seq) {
  function ktot_m (line 664) | int static_network::ktot_m(const set <int> &s) {
  function kin_m (line 677) | int static_network::kin_m(const set <int> &s) {
  function draw (line 693) | int static_network::draw(string file_name) {
  function static_network (line 732) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 740) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 748) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 758) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 769) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 778) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate_anyway (line 790) | int static_network::translate_anyway(deque<deque<int> > & ten) {
  function translate (line 826) | int static_network::translate(deque<deque<int> > & ten) {
  function set_subgraph (line 870) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function set_proper_weights (line 917) | void static_network::set_proper_weights() {
  function set_connected_components (line 963) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function same_component (line 999) | void static_network::same_component(int source, set<int> & already_gone) {
  function propagate_distances (line 1030) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function draw_consecutive (line 1092) | int static_network::draw_consecutive(string file_name1, string file_name...
  function set_upper_network (line 1132) | int static_network::set_upper_network(map<int, map<int, pair<int, double...
  function draw_with_weight_probability (line 1218) | int static_network::draw_with_weight_probability(string file_name) {
  function print_degree_of_homeless (line 1252) | void static_network::print_degree_of_homeless(DI & homel, ostream & outt) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/undirected_oslomnet_evaluate.h
  function log_zero (line 4) | inline double log_zero(double a) {
  function class (line 16) | class oslomnet_evaluate : public oslomnet_louvain {
  function set_changendi_cum (line 83) | void oslomnet_evaluate::set_changendi_cum() {
  function set_maxbord (line 113) | int oslomnet_evaluate::set_maxbord() {
  function erase_cgroup (line 126) | void oslomnet_evaluate::erase_cgroup(int wnode) {
  function erase_the_worst (line 169) | bool oslomnet_evaluate::erase_the_worst(int & wnode) {
  function insert_cgroup (line 201) | void oslomnet_evaluate::insert_cgroup(int wnode) {
  function set_cgroup_and_neighs (line 264) | void oslomnet_evaluate::set_cgroup_and_neighs(const deque<int> & G) {
  function cup_on_list (line 285) | double oslomnet_evaluate::cup_on_list(cup_data_struct & a, deque<int> & ...
  function all_external_test (line 427) | double oslomnet_evaluate::all_external_test(int kout_g, int tm, int Nsta...
  function initialize_for_evaluation (line 443) | void oslomnet_evaluate::initialize_for_evaluation(weighted_tabdeg & prev...
  function initialize_for_evaluation (line 462) | void oslomnet_evaluate::initialize_for_evaluation(const deque<int> & _c_...
  function partial_CUP (line 481) | double oslomnet_evaluate::partial_CUP(weighted_tabdeg & previous_tab_c, ...
  function CUP_runs (line 522) | double oslomnet_evaluate::CUP_runs(weighted_tabdeg & previous_tab_c, wei...
  function insert_the_best (line 677) | bool oslomnet_evaluate::insert_the_best() {
  function insertion (line 700) | void oslomnet_evaluate::insertion(int changendi) {
  function get_external_scores (line 787) | void oslomnet_evaluate::get_external_scores(weighted_tabdeg& neighs, cup...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/OSLOM_files/wsarray.h
  function class (line 17) | class wsarray {
  function find (line 88) | int wsarray::find(int a) {
  function push_back (line 128) | void wsarray::push_back(int a, int bb, double b) {
  function freeze (line 139) | void wsarray::freeze() {
  function prints (line 195) | void prints(wsarray &a) {
  function prints (line 207) | void prints(wsarray &a, ostream & pout) {
  function prints (line 219) | void prints(wsarray *a, ostream & pout) {
  function prints (line 230) | void prints(wsarray *a) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/Greedy.h
  function class (line 19) | class Greedy : public GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/GreedyBase.h
  function class (line 9) | class GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/MersenneTwister.h
  function class (line 54) | class MTRand {
  function MTRand (line 115) | inline MTRand::MTRand( const uint32& oneSeed )
  function MTRand (line 118) | inline MTRand::MTRand( uint32 *const bigSeed )
  function MTRand (line 121) | inline MTRand::MTRand()
  function rand (line 124) | inline double MTRand::rand()
  function rand (line 127) | inline double MTRand::rand( const double& n )
  function randExc (line 130) | inline double MTRand::randExc()
  function randExc (line 133) | inline double MTRand::randExc( const double& n )
  function randDblExc (line 136) | inline double MTRand::randDblExc()
  function randDblExc (line 139) | inline double MTRand::randDblExc( const double& n )
  function seed (line 172) | inline void MTRand::seed( uint32 oneSeed )
  function seed (line 186) | inline void MTRand::seed( uint32 *const bigSeed )
  function seed (line 202) | inline void MTRand::seed()
  function reload (line 235) | inline void MTRand::reload()
  function save (line 277) | inline void MTRand::save( uint32* saveArray ) const
  function load (line 287) | inline void MTRand::load( uint32 *const loadArray )

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/Node.h
  function class (line 18) | class Node{

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/infomap.cc
  function stou (line 8) | unsigned stou(char *s){
  function main (line 17) | int main(int argc,char *argv[]){
  function partition (line 344) | void partition(MTRand *R, Node ***node, GreedyBase *greedy, bool silent){
  function repeated_partition (line 544) | void repeated_partition(MTRand *R, Node ***node, GreedyBase *greedy, boo...
  function printTree (line 600) | void printTree(string s,multimap<double,treeNode,greater<double> >::iter...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/infomap.h
  function class (line 19) | class treeNode{
  function cpyNode (line 33) | void cpyNode(Node *newNode,Node *oldNode){

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/infomap_scr.cpp
  function main (line 10) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 302) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 330) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 358) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 373) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 404) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 473) | int random_from_set(set<int> & s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function norm_one (line 167) | double norm_one(const deque<double> & a) {
  function normalize_one (line 182) | int normalize_one(deque<double> & a) {
  function jaccard (line 197) | double jaccard(set<int> & a1,  set<int> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 141) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 267) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 277) | double compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 303) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 430) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 527) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 624) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 725) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 828) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 929) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1029) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1127) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1229) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1330) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1359) | int int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1388) | int int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1403) | int int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1418) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1444) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1470) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1497) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1527) | int int_histogram(string infile, string outfile) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 542) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/pajek.cpp
  function number_together (line 4) | int number_together(deque<int> & a) {
  function get_partition_from_file_list_pajek (line 36) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function set_partition_from_list (line 90) | int set_partition_from_list(deque<int> & mems, deque<deque<int> > & ten) {
  function get_partition_from_file_list_pajek_tree (line 137) | int get_partition_from_file_list_pajek_tree(string s, deque<deque<deque<...
  function pajek_format (line 236) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/partition.cpp
  function get_partition_from_file_tp_format (line 56) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 117) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 155) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M) {
  function get_partition_from_file (line 161) | int get_partition_from_file(string s, deque<deque<int> > & M, int min) {
  function get_partition_from_file (line 190) | int get_partition_from_file(string s, deque<deque<int> > & M) {
  function get_partition_from_file_list (line 196) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_dir/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/Greedy.h
  function class (line 19) | class Greedy : public GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/GreedyBase.h
  function class (line 9) | class GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/MersenneTwister.h
  function class (line 54) | class MTRand {
  function MTRand (line 115) | inline MTRand::MTRand( const uint32& oneSeed )
  function MTRand (line 118) | inline MTRand::MTRand( uint32 *const bigSeed )
  function MTRand (line 121) | inline MTRand::MTRand()
  function rand (line 124) | inline double MTRand::rand()
  function rand (line 127) | inline double MTRand::rand( const double& n )
  function randExc (line 130) | inline double MTRand::randExc()
  function randExc (line 133) | inline double MTRand::randExc( const double& n )
  function randDblExc (line 136) | inline double MTRand::randDblExc()
  function randDblExc (line 139) | inline double MTRand::randDblExc( const double& n )
  function seed (line 172) | inline void MTRand::seed( uint32 oneSeed )
  function seed (line 186) | inline void MTRand::seed( uint32 *const bigSeed )
  function seed (line 202) | inline void MTRand::seed()
  function reload (line 235) | inline void MTRand::reload()
  function save (line 277) | inline void MTRand::save( uint32* saveArray ) const
  function load (line 287) | inline void MTRand::load( uint32 *const loadArray )

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/Node.h
  function class (line 18) | class Node{

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/infomap.cc
  function stou (line 8) | unsigned stou(char *s){
  function main (line 17) | int main(int argc,char *argv[]){
  function partition (line 323) | void partition(MTRand *R,Node ***node, GreedyBase *greedy, bool silent){
  function repeated_partition (line 523) | void repeated_partition(MTRand *R, Node ***node, GreedyBase *greedy, boo...
  function printTree (line 576) | void printTree(string s,multimap<double,treeNode,greater<double> >::iter...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/infomap.h
  function class (line 19) | class treeNode{
  function cpyNode (line 33) | void cpyNode(Node *newNode,Node *oldNode){

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/infomap_scr.cpp
  function main (line 10) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 302) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 330) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 358) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 373) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 404) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 473) | int random_from_set(set<int> & s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function norm_one (line 167) | double norm_one(const deque<double> & a) {
  function normalize_one (line 182) | int normalize_one(deque<double> & a) {
  function jaccard (line 197) | double jaccard(set<int> & a1,  set<int> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 141) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 267) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 277) | double compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 303) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 430) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 527) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 624) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 725) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 828) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 929) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1029) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1127) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1229) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1330) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1359) | int int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1388) | int int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1403) | int int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1418) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1444) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1470) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1497) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1527) | int int_histogram(string infile, string outfile) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 542) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/pajek.cpp
  function number_together (line 4) | int number_together(deque<int> & a) {
  function get_partition_from_file_list_pajek (line 36) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function set_partition_from_list (line 90) | int set_partition_from_list(deque<int> & mems, deque<deque<int> > & ten) {
  function get_partition_from_file_list_pajek_tree (line 137) | int get_partition_from_file_list_pajek_tree(string s, deque<deque<deque<...
  function pajek_format (line 236) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/partition.cpp
  function get_partition_from_file_tp_format (line 56) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 117) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 155) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M) {
  function get_partition_from_file (line 161) | int get_partition_from_file(string s, deque<deque<int> > & M, int min) {
  function get_partition_from_file (line 190) | int get_partition_from_file(string s, deque<deque<int> > & M) {
  function get_partition_from_file_list (line 196) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/infomap_undir/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/community.cpp
  function Graph (line 150) | Graph

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/community.h
  function class (line 32) | class Community {
  function remove (line 103) | inline void
  function insert (line 112) | inline void
  function modularity_gain (line 121) | inline double

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/graph.h
  function class (line 35) | class Graph {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/graph_binary.h
  function class (line 36) | class Graph {
  function nb_neighbors (line 79) | inline int
  function nb_selfloops (line 89) | inline int
  function weighted_degree (line 105) | inline int

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/graph_binary_linux.h
  function class (line 36) | class Graph {
  function nb_neighbors (line 79) | inline int
  function nb_selfloops (line 89) | inline int
  function weighted_degree (line 105) | inline int

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/graph_binary_mac.h
  function class (line 36) | class Graph {
  function nb_neighbors (line 79) | inline int
  function nb_selfloops (line 89) | inline int
  function weighted_degree (line 105) | inline int

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/main_community.cpp
  function usage (line 38) | void
  function parse_args (line 50) | void
  function display_time (line 85) | void
  function main (line 94) | int

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/main_convert.cpp
  function usage (line 25) | void
  function parse_args (line 35) | void
  function main (line 66) | int

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/main_hierarchy.cpp
  function usage (line 32) | void
  function parse_args (line 46) | void
  function main (line 74) | int

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/order.cpp
  function main (line 12) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/script_to_compile.cpp
  function main (line 12) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 302) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 330) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 358) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 373) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 404) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 473) | int random_from_set(set<int> & s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function norm_one (line 167) | double norm_one(const deque<double> & a) {
  function normalize_one (line 182) | int normalize_one(deque<double> & a) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 141) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 267) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 277) | double compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 303) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 430) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 527) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 624) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 725) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 828) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 929) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1029) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1127) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1229) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1330) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1359) | int int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1388) | int int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1403) | int int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1418) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1444) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1470) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1497) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1527) | int int_histogram(string infile, string outfile) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 542) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/pajek.cpp
  function get_partition_from_file_list_pajek (line 4) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function pajek_format (line 62) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/partition.cpp
  function get_partition_from_file_list (line 38) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/static_network.h
  function statement (line 13) | void statement() {
  function parse_command_line (line 21) | int parse_command_line(bool & value, string & s, string & s2, int argc, ...
  function get_id_label (line 125) | void get_id_label(map <int, int> &);
  function edges (line 129) | double edges() {return tstrength;}
  function id_of (line 148) | int id_of(int a) {return vertices[a]->id_num;}
  function knn (line 155) | int knn(map <int, double> & );
  function kplus (line 249) | double static_network::vertex::kplus(const deque<int> &a) {
  function kplus (line 266) | double static_network::vertex::kplus(const set<int> &a) {
  function clear (line 337) | void static_network::clear() {
  function set_graph (line 357) | void static_network::set_graph(multimap<int, int> & A) {
  function set_graph (line 396) | void static_network::set_graph(map<int, map<int, double> > & A) {
  function set_graph (line 440) | bool static_network::set_graph(string file_name) {
  function set_graph (line 603) | void static_network::set_graph(bool weighted_, deque<deque<int> > & link...
  function set_graph (line 674) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function get_degree (line 751) | int static_network::get_degree(deque<int> &d) {
  function newman_modularity (line 763) | double static_network::newman_modularity(const double kin_g, const doubl...
  function newman_modularity (line 769) | double static_network::newman_modularity(set<int> & s) {
  function newman_modularity (line 777) | double static_network::newman_modularity(deque<set<int> > & Comps) {
  function newman_modularity (line 788) | double static_network::newman_modularity(deque<int> & s) {
  function newman_modularity (line 796) | double static_network::newman_modularity(deque<deque<int> > & Comps) {
  function erase_link (line 809) | void static_network::erase_link(int a, int b) {
  function static_network (line 831) | int static_network::connected (string str) {
  function static_network (line 921) | double static_network::kin (const deque<int> & seq) {
  function static_network (line 944) | double static_network::ktot (const deque<int> &seq) {
  function ktot (line 954) | double static_network::ktot(const set <int> &s) {
  function kin (line 967) | double static_network::kin(const set <int> &s) {
  function draw (line 985) | int static_network::draw(string file_name) {
  function draw_consecutive (line 991) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw_consecutive (line 996) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw (line 1040) | int static_network::draw(string file_name, bool _weighted_) {
  function rewiring (line 1078) | void static_network::rewiring(deque<set<int> >& en) {
  function print_random_version (line 1164) | void static_network::print_random_version(string file_name) {
  function static_network (line 1282) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 1290) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 1298) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 1308) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 1319) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 1328) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate (line 1339) | int static_network::translate(deque<deque<int> > & ten) {
  function print_component (line 1371) | void static_network::print_component(string file_name, const deque<int> ...
  function print_subgraph (line 1393) | void static_network::print_subgraph(string file_name, const deque<int> &...
  function next_shell (line 1426) | void static_network::next_shell(const set<int> & shell0, set<int> & shel...
  function pajek_print_cluster (line 1440) | void static_network::pajek_print_cluster(string file_name, deque<int> gr...
  function set_subgraph (line 1541) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function same_component (line 1585) | void static_network::same_component(int source, set<int> & already_gone) {
  function set_connected_components (line 1618) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function set_connected_components (line 1659) | void static_network::set_connected_components(deque<set<int> > & comps) {
  function print_connected_components (line 1688) | void static_network::print_connected_components(ostream & outb) {
  function propagate_bw (line 1755) | void static_network::propagate_bw(int* distances, int* weights, int sour...
  function compute_betweeness_single_source (line 1796) | int static_network::compute_betweeness_single_source(int source, map<pai...
  function component_betweeness (line 1945) | int static_network::component_betweeness(int source, map<pair<int, int>,...
  function all_betweeness (line 1993) | int static_network::all_betweeness(map<pair<int, int>, double> & tot_edg...
  function static_network (line 2033) | int static_network::set_mem_adj (deque<deque<int> > & mem_adj) {		// unw...
  function propagate_distances (line 2054) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function distances_from_i (line 2110) | int static_network::distances_from_i(int node, double & average, deque<d...
  function diameter_and_asp (line 2167) | int static_network::diameter_and_asp(double & averageall, int & diameter...
  function knn (line 2218) | int static_network::knn(map <int, deque<double > > & knn_hist) {
  function knn (line 2257) | int static_network::knn(map <int, double> & knn_hist) {
  function clustering_coefficient (line 2322) | double static_network::clustering_coefficient() {
  function clustering_coefficient (line 2347) | void static_network::clustering_coefficient(map <int, deque<double> > & ...
  function GN_bench (line 2386) | bool static_network::GN_bench(int nodes, int modules, double kout, doubl...
  function set_binary_random (line 2481) | bool static_network::set_binary_random(const deque<int> & degrees) {
  function integral (line 2578) | double integral (double a, double b) {
  function integer_average (line 2591) | double integer_average (int n, int min, double tau) {
  function average_degree (line 2609) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 2617) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function set_random_powlaw (line 2669) | bool static_network::set_random_powlaw(int num_nodes, double tau, double...
  function set_multiple_random (line 2710) | bool static_network::set_multiple_random(const deque<int> & degrees, boo...
  function set_random_powlaw_multiple (line 2888) | bool static_network::set_random_powlaw_multiple(int num_nodes, double ta...
  function community_netknn (line 2927) | void static_network::community_netknn(deque<deque<int> > & ten) {
  function community_net (line 3020) | void static_network::community_net(deque<deque<int> > & ten) {
  function monte_carlo_asp (line 3087) | double static_network::monte_carlo_asp() {
  function add_isolated (line 3126) | void static_network::add_isolated(int id_iso) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/louvain/wsarray.h
  function class (line 18) | class wsarray {
  function find (line 91) | int wsarray::find(int a) {
  function push_back (line 131) | void wsarray::push_back(int a, double b) {
  function erase (line 140) | bool wsarray::erase(int y) {
  function freeze (line 194) | void wsarray::freeze() {
  function prints (line 250) | void prints(wsarray &a) {
  function prints (line 262) | void prints(wsarray &a, ostream &out) {
  function prints (line 274) | void prints(wsarray *a, ostream & out) {
  function prints (line 285) | void prints(wsarray *a) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/hier.h
  function check_position (line 9) | int check_position(map<int, double> & lab_x, map<int, double> & lab_y, m...
  function get_partition_from_file_tp_format (line 24) | int get_partition_from_file_tp_format(string S, map<int, deque<int> > & ...
  function get_sizes (line 63) | int get_sizes(string file_for_sizes, map<int, int> & sizes) {
  function insert_isolated (line 94) | int insert_isolated(visual_network & luca, map<int, int> & sizes) {
  function o_level (line 118) | int o_level(double origin_x, double origin_y, double radius, visual_netw...
  function another_level (line 157) | int another_level(string short_tpn, string netn, string tpn, map<int, do...
  function all_levels (line 399) | int all_levels(int levels, string network_file) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/main.cpp
  function get_tp_files (line 37) | int get_tp_files(string network_file) {
  function main (line 70) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/main_pajek.cpp
  function get_tp_files (line 36) | int get_tp_files(string network_file) {
  function main (line 70) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/main_pajek_directed.cpp
  function get_tp_files (line 36) | int get_tp_files(string network_file) {
  function main (line 70) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/netvi.h
  function class (line 7) | class netvi : public static_network {
  function print_module_names (line 43) | int netvi::print_module_names(int module, map<int, string> & names) {
  function print_module_id (line 56) | int netvi::print_module_id(int module) {
  function print_positions (line 78) | int netvi::print_positions(ostream & go, int color, double siz, string o...
  function print_internal (line 93) | int netvi::print_internal(ostream & go, int color, string outfile, int l...
  function print_external (line 112) | int netvi::print_external(ostream & go, int color, string outfile, int l...
  function print_label (line 131) | int netvi::print_label(ostream & go, int color, string outfile, int leve...
  function print_names_file (line 147) | int netvi::print_names_file(ostream & go, int color, string outfile, int...
  function print_names_file (line 162) | int netvi::print_names_file(ostream & go, int color, string outfile, int...
  function set_all (line 179) | int netvi::set_all(int level, string network_file) {
  function class (line 402) | class netgnu {
  function set_networks (line 470) | int netgnu::set_networks(int levels, string network_file) {
  function set_labs (line 498) | int netgnu::set_labs(int net, double siz) {
  function erase_labs (line 509) | int netgnu::erase_labs(int net) {
  function set_position (line 518) | int netgnu::set_position(int net, int color, double siz) {
  function erase_position (line 530) | int netgnu::erase_position(int net) {
  function set_internal (line 539) | int netgnu::set_internal(int net, double edge_width) {
  function erase_internal (line 550) | int netgnu::erase_internal(int net) {
  function set_external (line 559) | int netgnu::set_external(int net, double edge_width) {
  function erase_external (line 570) | int netgnu::erase_external(int net) {
  function print_id (line 578) | int netgnu::print_id(int net, int module) {
  function print_names (line 587) | int netgnu::print_names(int net, int module) {
  function print_names_on_graph (line 604) | int netgnu::print_names_on_graph(double siz) {
  function interface (line 624) | int netgnu::interface() {
  function plot_commands (line 936) | int netgnu::plot_commands() {
  function read_names (line 1024) | int netgnu::read_names(string s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/position.h
  type multimap (line 8) | typedef multimap<double, int>::iterator map_idi;
  type pair (line 9) | typedef pair<map_idi, map_idi> pmap_idi;
  function class (line 18) | class xypos {
  function set_all (line 58) | void xypos::set_all(map<int, double> & lab_x, map<int, double> & lab_y, ...
  function clear (line 93) | void xypos::clear() {
  function erase (line 103) | bool xypos::erase(int a) {		// this function erases element a if exists ...
  function edinsert (line 125) | void xypos::edinsert(int a, double x, double y) {		// this function inse...
  function print_points (line 139) | void xypos::print_points(ostream & outb) {
  function get_new_pos (line 149) | void xypos::get_new_pos(map<int, double> & lab_x, map<int, double> & lab...
  function neighbors (line 166) | int xypos::neighbors(int a, deque<int> & group_intsec) {
  function xy_close (line 208) | int xypos::xy_close(multimap<double, int> & m, double x, double dx, set<...
  function move (line 275) | int xypos::move(int a) {
  function move_all (line 395) | int xypos::move_all() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 302) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 330) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 358) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 373) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 404) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 473) | int random_from_set(set<int> & s) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function norm_one (line 167) | double norm_one(const deque<double> & a) {
  function normalize_one (line 182) | int normalize_one(deque<double> & a) {
  function jaccard (line 197) | double jaccard(set<int> & a1,  set<int> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 141) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 267) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 277) | double compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 303) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 430) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 527) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 624) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 725) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 828) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 929) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1029) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1127) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1229) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1330) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1359) | int int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1388) | int int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1403) | int int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1418) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1444) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1470) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1497) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1527) | int int_histogram(string infile, string outfile) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 542) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/pajek.cpp
  function get_partition_from_file_list_pajek (line 4) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function pajek_format (line 62) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/partition.cpp
  function get_partition_from_file_tp_format (line 50) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M) {
  function get_partition_from_file (line 87) | int get_partition_from_file(string s, deque<deque<int> > & M, int min) {
  function get_partition_from_file (line 116) | int get_partition_from_file(string s, deque<deque<int> > & M) {
  function get_partition_from_file_list (line 122) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/static_network.h
  function statement (line 13) | void statement() {
  function parse_command_line (line 21) | int parse_command_line(bool & value, string & s, string & s2, int argc, ...
  function get_id_label (line 125) | void get_id_label(map <int, int> &);
  function edges (line 129) | double edges() {return tstrength;}
  function id_of (line 148) | int id_of(int a) {return vertices[a]->id_num;}
  function knn (line 155) | int knn(map <int, double> & );
  function kplus (line 254) | double static_network::vertex::kplus(const deque<int> &a) {
  function kplus (line 271) | double static_network::vertex::kplus(const set<int> &a) {
  function clear (line 342) | void static_network::clear() {
  function set_graph (line 362) | void static_network::set_graph(multimap<int, int> & A) {
  function set_graph (line 401) | void static_network::set_graph(map<int, map<int, double> > & A) {
  function set_graph (line 445) | bool static_network::set_graph(string file_name) {
  function set_graph (line 608) | void static_network::set_graph(bool weighted_, deque<deque<int> > & link...
  function set_graph (line 679) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function get_degree (line 756) | int static_network::get_degree(deque<int> &d) {
  function newman_modularity (line 768) | double static_network::newman_modularity(const double kin_g, const doubl...
  function newman_modularity (line 774) | double static_network::newman_modularity(set<int> & s) {
  function newman_modularity (line 782) | double static_network::newman_modularity(deque<set<int> > & Comps) {
  function newman_modularity (line 793) | double static_network::newman_modularity(deque<int> & s) {
  function newman_modularity (line 801) | double static_network::newman_modularity(deque<deque<int> > & Comps) {
  function erase_link (line 814) | void static_network::erase_link(int a, int b) {
  function static_network (line 836) | int static_network::connected (string str) {
  function static_network (line 926) | double static_network::kin (const deque<int> & seq) {
  function static_network (line 949) | double static_network::ktot (const deque<int> &seq) {
  function ktot (line 959) | double static_network::ktot(const set <int> &s) {
  function kin (line 972) | double static_network::kin(const set <int> &s) {
  function draw (line 990) | int static_network::draw(string file_name) {
  function draw_consecutive (line 996) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw_consecutive (line 1001) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw (line 1045) | int static_network::draw(string file_name, bool _weighted_) {
  function rewiring (line 1083) | void static_network::rewiring(deque<set<int> >& en) {
  function print_random_version (line 1169) | void static_network::print_random_version(string file_name) {
  function static_network (line 1287) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 1295) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 1303) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 1313) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 1324) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 1333) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate (line 1344) | int static_network::translate(deque<deque<int> > & ten) {
  function print_component (line 1376) | void static_network::print_component(string file_name, const deque<int> ...
  function print_subgraph (line 1398) | void static_network::print_subgraph(string file_name, const deque<int> &...
  function next_shell (line 1431) | void static_network::next_shell(const set<int> & shell0, set<int> & shel...
  function draw_pajek_directed (line 1449) | void static_network::draw_pajek_directed(map<int, double> & lab_x, map<i...
  function draw_pajek (line 1668) | void static_network::draw_pajek(map<int, double> & lab_x, map<int, doubl...
  function pajek_print_cluster (line 1864) | void static_network::pajek_print_cluster(string file_name, deque<int> gr...
  function set_subgraph (line 1965) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function same_component (line 2009) | void static_network::same_component(int source, set<int> & already_gone) {
  function set_connected_components (line 2042) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function set_connected_components (line 2083) | void static_network::set_connected_components(deque<set<int> > & comps) {
  function print_connected_components (line 2112) | void static_network::print_connected_components(ostream & outb) {
  function propagate_bw (line 2179) | void static_network::propagate_bw(int* distances, int* weights, int sour...
  function compute_betweeness_single_source (line 2220) | int static_network::compute_betweeness_single_source(int source, map<pai...
  function component_betweeness (line 2369) | int static_network::component_betweeness(int source, map<pair<int, int>,...
  function all_betweeness (line 2417) | int static_network::all_betweeness(map<pair<int, int>, double> & tot_edg...
  function static_network (line 2457) | int static_network::set_mem_adj (deque<deque<int> > & mem_adj) {		// unw...
  function propagate_distances (line 2478) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function distances_from_i (line 2534) | int static_network::distances_from_i(int node, double & average, deque<d...
  function diameter_and_asp (line 2591) | int static_network::diameter_and_asp(double & averageall, int & diameter...
  function knn (line 2642) | int static_network::knn(map <int, deque<double > > & knn_hist) {
  function knn (line 2681) | int static_network::knn(map <int, double> & knn_hist) {
  function clustering_coefficient (line 2746) | double static_network::clustering_coefficient() {
  function clustering_coefficient (line 2771) | void static_network::clustering_coefficient(map <int, deque<double> > & ...
  function GN_bench (line 2810) | bool static_network::GN_bench(int nodes, int modules, double kout, doubl...
  function set_binary_random (line 2905) | bool static_network::set_binary_random(const deque<int> & degrees) {
  function integral (line 3002) | double integral (double a, double b) {
  function integer_average (line 3015) | double integer_average (int n, int min, double tau) {
  function average_degree (line 3033) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 3041) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function set_random_powlaw (line 3093) | bool static_network::set_random_powlaw(int num_nodes, double tau, double...
  function set_multiple_random (line 3134) | bool static_network::set_multiple_random(const deque<int> & degrees, boo...
  function set_random_powlaw_multiple (line 3312) | bool static_network::set_random_powlaw_multiple(int num_nodes, double ta...
  function community_netknn (line 3351) | void static_network::community_netknn(deque<deque<int> > & ten) {
  function community_net (line 3444) | void static_network::community_net(deque<deque<int> > & ten) {
  function monte_carlo_asp (line 3511) | double static_network::monte_carlo_asp() {
  function add_isolated (line 3550) | void static_network::add_isolated(int id_iso) {
  function mate (line 3560) | bool mate(deque<set<int> > & node_member, int i, int j) {
  function draw_gnuplot (line 3579) | double static_network::draw_gnuplot(map<int, double> & lab_x, map<int, d...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/visual_net.h
  function class (line 12) | class visual_network : public static_network {
  function distance_node (line 56) | inline double visual_network::distance_node(int node1) {
  function swap (line 75) | inline bool visual_network::swap() {
  function find_position_goniometric (line 119) | int visual_network::find_position_goniometric(int secs) {
  function draw_pajek (line 194) | double visual_network::draw_pajek(deque<double> & angles, deque<double> ...
  function draw_pajek (line 230) | double visual_network::draw_pajek(map<int, double> & lab_x, map<int, dou...
  function internal_link_map (line 290) | void visual_network:: internal_link_map(multimap<int, int> & int_edges, ...
  function draw_gnuplot (line 339) | double visual_network::draw_gnuplot(map<int, double> & lab_x, map<int, d...
  function draw_gnuplot (line 365) | double visual_network::draw_gnuplot(map<int, double> & lab_x, map<int, d...
  function draw_gnuplot (line 439) | double visual_network::draw_gnuplot(map<int, double> & lab_x, map<int, d...
  function relabel (line 508) | double visual_network::relabel(map<int, double> & lab_x, map<int, double...
  function with_colors (line 549) | double visual_network::with_colors(deque<deque<int> >  & ten) {
  function circles (line 610) | int visual_network::circles(int secs, map<int, int> & lab_sizes, deque<d...

FILE: Algorithms/2011-OSLOM-v2/Sources_2_5/visualSources/wsarray.h
  function class (line 18) | class wsarray {
  function find (line 91) | int wsarray::find(int a) {
  function push_back (line 131) | void wsarray::push_back(int a, double b) {
  function erase (line 140) | bool wsarray::erase(int y) {
  function freeze (line 194) | void wsarray::freeze() {
  function prints (line 250) | void prints(wsarray &a) {
  function prints (line 262) | void prints(wsarray &a, ostream &out) {
  function prints (line 274) | void prints(wsarray *a, ostream & out) {
  function prints (line 285) | void prints(wsarray *a) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/Greedy.h
  function class (line 19) | class Greedy : public GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/GreedyBase.h
  function class (line 9) | class GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/MersenneTwister.h
  function class (line 54) | class MTRand {
  function MTRand (line 115) | inline MTRand::MTRand( const uint32& oneSeed )
  function MTRand (line 118) | inline MTRand::MTRand( uint32 *const bigSeed )
  function MTRand (line 121) | inline MTRand::MTRand()
  function rand (line 124) | inline double MTRand::rand()
  function rand (line 127) | inline double MTRand::rand( const double& n )
  function randExc (line 130) | inline double MTRand::randExc()
  function randExc (line 133) | inline double MTRand::randExc( const double& n )
  function randDblExc (line 136) | inline double MTRand::randDblExc()
  function randDblExc (line 139) | inline double MTRand::randDblExc( const double& n )
  function seed (line 172) | inline void MTRand::seed( uint32 oneSeed )
  function seed (line 186) | inline void MTRand::seed( uint32 *const bigSeed )
  function seed (line 202) | inline void MTRand::seed()
  function reload (line 235) | inline void MTRand::reload()
  function save (line 277) | inline void MTRand::save( uint32* saveArray ) const
  function load (line 287) | inline void MTRand::load( uint32 *const loadArray )

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/Node.h
  function class (line 18) | class Node{

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/doc/infomap_scr.cpp
  function main (line 10) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/infomap.cc
  function stou (line 8) | unsigned stou(char *s){
  function main (line 17) | int main(int argc,char *argv[]){
  function partition (line 344) | void partition(MTRand *R, Node ***node, GreedyBase *greedy, bool silent){
  function repeated_partition (line 544) | void repeated_partition(MTRand *R, Node ***node, GreedyBase *greedy, boo...
  function printTree (line 600) | void printTree(string s,multimap<double,treeNode,greater<double> >::iter...

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/dir/infomap.h
  function class (line 19) | class treeNode{
  function cpyNode (line 33) | void cpyNode(Node *newNode,Node *oldNode){

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/Greedy.h
  function class (line 19) | class Greedy : public GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/GreedyBase.h
  function class (line 9) | class GreedyBase{

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/MersenneTwister.h
  function class (line 54) | class MTRand {
  function MTRand (line 115) | inline MTRand::MTRand( const uint32& oneSeed )
  function MTRand (line 118) | inline MTRand::MTRand( uint32 *const bigSeed )
  function MTRand (line 121) | inline MTRand::MTRand()
  function rand (line 124) | inline double MTRand::rand()
  function rand (line 127) | inline double MTRand::rand( const double& n )
  function randExc (line 130) | inline double MTRand::randExc()
  function randExc (line 133) | inline double MTRand::randExc( const double& n )
  function randDblExc (line 136) | inline double MTRand::randDblExc()
  function randDblExc (line 139) | inline double MTRand::randDblExc( const double& n )
  function seed (line 172) | inline void MTRand::seed( uint32 oneSeed )
  function seed (line 186) | inline void MTRand::seed( uint32 *const bigSeed )
  function seed (line 202) | inline void MTRand::seed()
  function reload (line 235) | inline void MTRand::reload()
  function save (line 277) | inline void MTRand::save( uint32* saveArray ) const
  function load (line 287) | inline void MTRand::load( uint32 *const loadArray )

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/Node.h
  function class (line 18) | class Node{

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/doc/infomap_scr.cpp
  function main (line 10) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/infomap.cc
  function stou (line 8) | unsigned stou(char *s){
  function main (line 17) | int main(int argc,char *argv[]){
  function partition (line 323) | void partition(MTRand *R,Node ***node, GreedyBase *greedy, bool silent){
  function repeated_partition (line 523) | void repeated_partition(MTRand *R, Node ***node, GreedyBase *greedy, boo...
  function printTree (line 576) | void printTree(string s,multimap<double,treeNode,greater<double> >::iter...

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/infomap/undir/infomap.h
  function class (line 19) | class treeNode{
  function cpyNode (line 33) | void cpyNode(Node *newNode,Node *oldNode){

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/community.cpp
  function Graph (line 150) | Graph

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/community.h
  function class (line 32) | class Community {
  function remove (line 103) | inline void
  function insert (line 112) | inline void
  function modularity_gain (line 121) | inline double

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/doc/order.cpp
  function main (line 12) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/doc/script_to_compile.cpp
  function main (line 12) | int main(int argc, char * argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/doc/static_network.h
  function statement (line 6) | void statement() {
  function parse_command_line (line 14) | int parse_command_line(bool & value, string & s, string & s2, int argc, ...
  function get_id_label (line 118) | void get_id_label(map <int, int> &);
  function edges (line 122) | double edges() {return tstrength;}
  function id_of (line 141) | int id_of(int a) {return vertices[a]->id_num;}
  function knn (line 148) | int knn(map <int, double> & );
  function kplus (line 242) | double static_network::vertex::kplus(const deque<int> &a) {
  function kplus (line 259) | double static_network::vertex::kplus(const set<int> &a) {
  function clear (line 330) | void static_network::clear() {
  function set_graph (line 350) | void static_network::set_graph(multimap<int, int> & A) {
  function set_graph (line 389) | void static_network::set_graph(map<int, map<int, double> > & A) {
  function set_graph (line 433) | bool static_network::set_graph(string file_name) {
  function set_graph (line 596) | void static_network::set_graph(bool weighted_, deque<deque<int> > & link...
  function set_graph (line 667) | void static_network::set_graph(deque<deque<int> > & link_per_node, deque...
  function get_degree (line 744) | int static_network::get_degree(deque<int> &d) {
  function newman_modularity (line 756) | double static_network::newman_modularity(const double kin_g, const doubl...
  function newman_modularity (line 762) | double static_network::newman_modularity(set<int> & s) {
  function newman_modularity (line 770) | double static_network::newman_modularity(deque<set<int> > & Comps) {
  function newman_modularity (line 781) | double static_network::newman_modularity(deque<int> & s) {
  function newman_modularity (line 789) | double static_network::newman_modularity(deque<deque<int> > & Comps) {
  function erase_link (line 802) | void static_network::erase_link(int a, int b) {
  function static_network (line 824) | int static_network::connected (string str) {
  function static_network (line 914) | double static_network::kin (const deque<int> & seq) {
  function static_network (line 937) | double static_network::ktot (const deque<int> &seq) {
  function ktot (line 947) | double static_network::ktot(const set <int> &s) {
  function kin (line 960) | double static_network::kin(const set <int> &s) {
  function draw (line 978) | int static_network::draw(string file_name) {
  function draw_consecutive (line 984) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw_consecutive (line 989) | int static_network::draw_consecutive(string file_name1, string file_name...
  function draw (line 1033) | int static_network::draw(string file_name, bool _weighted_) {
  function rewiring (line 1071) | void static_network::rewiring(deque<set<int> >& en) {
  function print_random_version (line 1157) | void static_network::print_random_version(string file_name) {
  function static_network (line 1275) | void static_network::get_id_label (map <int, int> &a) {
  function deque_id (line 1283) | void static_network::deque_id(deque<int> & a) {
  function print_id (line 1291) | void static_network::print_id(const deque<int> & a, ostream & pout) {
  function print_id (line 1301) | void static_network::print_id(const set<int> & a, ostream & pout) {
  function print_id (line 1312) | void static_network::print_id(const deque<deque<int> > & a, ostream & po...
  function print_id (line 1321) | void static_network::print_id(const deque<set<int> > & a, ostream & pout) {
  function translate (line 1332) | int static_network::translate(deque<deque<int> > & ten) {
  function print_component (line 1364) | void static_network::print_component(string file_name, const deque<int> ...
  function print_subgraph (line 1386) | void static_network::print_subgraph(string file_name, const deque<int> &...
  function next_shell (line 1419) | void static_network::next_shell(const set<int> & shell0, set<int> & shel...
  function pajek_print_cluster (line 1433) | void static_network::pajek_print_cluster(string file_name, deque<int> gr...
  function set_subgraph (line 1534) | void static_network::set_subgraph(deque<int> & group, deque<deque<int> >...
  function same_component (line 1578) | void static_network::same_component(int source, set<int> & already_gone) {
  function set_connected_components (line 1611) | void static_network::set_connected_components(deque<deque<int> > & comps) {
  function set_connected_components (line 1652) | void static_network::set_connected_components(deque<set<int> > & comps) {
  function print_connected_components (line 1681) | void static_network::print_connected_components(ostream & outb) {
  function propagate_bw (line 1748) | void static_network::propagate_bw(int* distances, int* weights, int sour...
  function compute_betweeness_single_source (line 1789) | int static_network::compute_betweeness_single_source(int source, map<pai...
  function component_betweeness (line 1938) | int static_network::component_betweeness(int source, map<pair<int, int>,...
  function all_betweeness (line 1986) | int static_network::all_betweeness(map<pair<int, int>, double> & tot_edg...
  function static_network (line 2026) | int static_network::set_mem_adj (deque<deque<int> > & mem_adj) {		// unw...
  function propagate_distances (line 2047) | int static_network::propagate_distances(deque<int> & new_shell, set<int>...
  function distances_from_i (line 2103) | int static_network::distances_from_i(int node, double & average, deque<d...
  function diameter_and_asp (line 2160) | int static_network::diameter_and_asp(double & averageall, int & diameter...
  function knn (line 2211) | int static_network::knn(map <int, deque<double > > & knn_hist) {
  function knn (line 2250) | int static_network::knn(map <int, double> & knn_hist) {
  function clustering_coefficient (line 2315) | double static_network::clustering_coefficient() {
  function clustering_coefficient (line 2340) | void static_network::clustering_coefficient(map <int, deque<double> > & ...
  function GN_bench (line 2379) | bool static_network::GN_bench(int nodes, int modules, double kout, doubl...
  function set_binary_random (line 2474) | bool static_network::set_binary_random(const deque<int> & degrees) {
  function integral (line 2571) | double integral (double a, double b) {
  function integer_average (line 2584) | double integer_average (int n, int min, double tau) {
  function average_degree (line 2602) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 2610) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function set_random_powlaw (line 2662) | bool static_network::set_random_powlaw(int num_nodes, double tau, double...
  function set_multiple_random (line 2703) | bool static_network::set_multiple_random(const deque<int> & degrees, boo...
  function set_random_powlaw_multiple (line 2881) | bool static_network::set_random_powlaw_multiple(int num_nodes, double ta...
  function community_netknn (line 2920) | void static_network::community_netknn(deque<deque<int> > & ten) {
  function community_net (line 3013) | void static_network::community_net(deque<deque<int> > & ten) {
  function monte_carlo_asp (line 3080) | double static_network::monte_carlo_asp() {
  function add_isolated (line 3119) | void static_network::add_isolated(int id_iso) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/graph.h
  function class (line 36) | class Graph {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/graph_binary.h
  function class (line 35) | class Graph {
  function nb_neighbors (line 78) | inline int
  function nb_selfloops (line 88) | inline int
  function weighted_degree (line 104) | inline int

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/graph_binary_linux.h
  function class (line 36) | class Graph {
  function nb_neighbors (line 79) | inline int
  function nb_selfloops (line 89) | inline int
  function weighted_degree (line 105) | inline int

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/graph_binary_mac.h
  function class (line 36) | class Graph {
  function nb_neighbors (line 79) | inline int
  function nb_selfloops (line 89) | inline int
  function weighted_degree (line 105) | inline int

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/main_community.cpp
  function usage (line 32) | void
  function parse_args (line 44) | void
  function display_time (line 79) | void
  function main (line 88) | int

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/main_convert.cpp
  function usage (line 25) | void
  function parse_args (line 35) | void
  function main (line 66) | int

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/louvain/main_hierarchy.cpp
  function usage (line 31) | void
  function parse_args (line 45) | void
  function main (line 73) | int

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/oslom/hierarchies.cpp
  function manipulate_string (line 6) | bool manipulate_string(string s, string netfile, string &outs) {
  function external_program_to_call (line 31) | void external_program_to_call(string network_file, oslom_net_global &mat...
  function translate_covers (line 58) | void translate_covers(string previous_tp, string new_tp, string short_tp...
  function no_singletons (line 92) | void no_singletons(char *directory_char, oslom_net_global &luca, module_...
  function write_tp_of_this_level (line 119) | bool write_tp_of_this_level(int level, oslom_net_global &luca, char *dir...
  function oslom_level (line 205) | void oslom_level(oslom_net_global &luca, char *directory_char) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/oslom/main_directed.cpp
  function program_statement (line 37) | void program_statement(char *b) {
  function main (line 42) | int main(int argc, char *argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/algorithm/oslom/main_undirected.cpp
  function program_statement (line 54) | void program_statement(char *b) {
  function main (line 59) | int main(int argc, char *argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/directed/dir_weighted_tabdeg.cpp
  function compare_r_variables (line 7) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 33) | double right_error_function(double x) {
  function log_together (line 39) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 66) | double fitted_exponent(int N) {
  function order_statistics_left_cumulative (line 91) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function inverse_order_statistics (line 103) | double inverse_order_statistics(int sample_dim, int pos, const double &z...
  function pron_min_exp (line 143) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 155) | inline double
  function equivalent_check (line 198) | bool equivalent_check(int pos_first, int pos_last, double &A_average, do...
  function equivalent_check_gather (line 241) | bool equivalent_check_gather(cup_data_struct &a, int &until, const doubl...
  function hyper_table (line 295) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function compute_topologic_and_bootstrap_interval (line 300) | inline double compute_topologic_and_bootstrap_interval(int kin_node_out,...
  function compute_global_fitness (line 324) | double compute_global_fitness(int kin_node_in, int kout_g_in, int kin_no...
  function compute_topologic_step (line 461) | inline double
  function compute_global_fitness_step (line 479) | double
  function compute_global_fitness_ofive (line 571) | inline double
  function compute_global_fitness_randomized (line 584) | inline double
  function compute_global_fitness_randomized_short (line 600) | double
  class facts (line 626) | class facts {
    method facts (line 632) | facts(int in_id, int in_od, double in_iw, double in_ow, multimap<doubl...
  class weighted_tabdeg (line 668) | class weighted_tabdeg {
    method weighted_tabdeg (line 673) | weighted_tabdeg() {}
    method size (line 689) | int size() { return lab_facts.size(); }

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/directed/dir_weighted_tabdeg.h
  type multimap (line 4) | typedef multimap<double, pair<int, double> > cup_data_struct;
  function compare_r_variables (line 10) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 36) | double right_error_function(double x) {
  function log_together (line 42) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 69) | double fitted_exponent(int N) {
  function order_statistics_left_cumulative (line 94) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function inverse_order_statistics (line 106) | double inverse_order_statistics(int sample_dim, int pos, const double &z...
  function pron_min_exp (line 146) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 158) | inline double
  function equivalent_check (line 201) | bool equivalent_check(int pos_first, int pos_last, double &A_average, do...
  function equivalent_check_gather (line 244) | bool equivalent_check_gather(cup_data_struct &a, int &until, const doubl...
  function hyper_table (line 298) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function compute_topologic_and_bootstrap_interval (line 303) | inline double compute_topologic_and_bootstrap_interval(int kin_node_out,...
  function compute_global_fitness (line 327) | double compute_global_fitness(int kin_node_in, int kout_g_in, int kin_no...
  function compute_topologic_step (line 464) | inline double
  function compute_global_fitness_step (line 482) | double
  function compute_global_fitness_ofive (line 574) | inline double
  function compute_global_fitness_randomized (line 587) | inline double
  function compute_global_fitness_randomized_short (line 603) | double
  function class (line 629) | class facts {
  function class (line 671) | class weighted_tabdeg {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/directed/directed_network.h
  function class (line 19) | class static_network {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/directed/directed_oslomnet_evaluate.h
  function log_zero (line 7) | inline double log_zero(double a) {
  function class (line 14) | class oslomnet_evaluate : public oslomnet_louvain {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/directed/louvain_oslomnet_dir.h
  function class (line 6) | class oslom_module {
  function class (line 24) | class internal_links_weights {
  type map (line 40) | typedef map<int, internal_links_weights> mapip;
  type map (line 41) | typedef map<int, oslom_module> map_int_om;
  function int_histogram (line 43) | void
  function prints (line 57) | void prints(map_int_om &M) {
  function class (line 64) | class oslomnet_louvain : public static_network {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/oslom_net_global.cpp
  function from_int_matrix_and_deque_to_deque (line 484) | void from_int_matrix_and_deque_to_deque(int_matrix &its_submodules, cons...

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/oslom_net_global.h
  function class (line 5) | class oslom_net_global : public oslomnet_evaluate {
  function class (line 83) | class oslom_module {
  type map (line 97) | typedef map<int, pair<int, double> > mapip;
  type map (line 98) | typedef map<int, oslom_module> map_int_om;
  function prints (line 100) | void prints(map_int_om &M) {
  function class (line 106) | class oslomnet_louvain : public static_network {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/undirected/egocentric_undir.h
  function class (line 8) | class egocentric_net : public oslomnet_louvain {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/undirected/undir_weighted_tabdeg.cpp
  function compare_r_variables (line 6) | double compare_r_variables(double a, double b, double c, double d) {
  function right_error_function (line 21) | double right_error_function(double x) {
  function log_together (line 25) | double log_together(double minus_log_total, int number) {
  function fitted_exponent (line 39) | double fitted_exponent(int N) {
  function inverse_order_statistics (line 52) | double inverse_order_statistics(int sample_dim, int pos, const double &z...
  function equivalent_check (line 73) | bool equivalent_check(int pos_first, int pos_last, double &A_average, do...
  function equivalent_check_gather (line 98) | bool equivalent_check_gather(cup_data_struct &a, int &until, const doubl...
  function compute_global_fitness (line 136) | double
  function compute_global_fitness_step (line 178) | double compute_global_fitness_step(int kin_node, int kout_g, int tm, int...
  function compute_global_fitness_randomized_short (line 193) | double

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/undirected/undir_weighted_tabdeg.h
  type multimap (line 15) | typedef multimap<double, pair<int, double> > cup_data_struct;
  function hyper_table (line 33) | inline double hyper_table(int kin_node, int kout_g, int tm, int degree_n...
  function topological_05 (line 37) | inline double topological_05(int kin_node, int kout_g, int tm, int degre...
  function order_statistics_left_cumulative (line 52) | inline double order_statistics_left_cumulative(int N, int pos, double x) {
  function pron_min_exp (line 58) | inline double pron_min_exp(int N, double xi) {
  function compute_probability_to_stop (line 64) | inline double
  function compute_global_fitness_ofive (line 73) | inline double compute_global_fitness_ofive(int kin_node, int kout_g, int...
  function compute_global_fitness_randomized (line 79) | inline double
  function class (line 86) | class facts {
  function size (line 118) | int size() { return lab_facts.size(); }

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/undirected/undirected_network.h
  function class (line 19) | class static_network {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/graph/undirected/undirected_oslomnet_evaluate.h
  function log_zero (line 8) | inline double log_zero(double a) {
  function class (line 15) | class oslomnet_evaluate : public oslomnet_louvain {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/collection/module_collection.h
  type UI (line 14) | typedef unsigned int UI;
  type deque (line 15) | typedef deque<double> DD;
  type deque (line 16) | typedef deque<int> DI;
  type deque (line 17) | typedef deque<deque<int> > int_matrix;
  function class (line 20) | class module_collection {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/collection/wsarray.cpp
  function prints (line 7) | void prints(wsarray &a) {
  function prints (line 13) | void prints(wsarray &a, ostream &pout) {
  function prints (line 19) | void prints(wsarray *a, ostream &pout) {
  function prints (line 25) | void prints(wsarray *a) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/collection/wsarray.h
  function class (line 15) | class wsarray {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/cast.cpp
  function cast_string_to_double (line 6) | bool cast_string_to_double(string &b, double &h) {
  function cast_int (line 43) | int cast_int(double u) {
  function cast_string_to_char (line 50) | int cast_string_to_char(string &file_name, char *b) {
  function cast_string_to_doubles (line 57) | bool cast_string_to_doubles(string &b, deque<double> &v) {
  function cast_string_to_doubles (line 81) | bool cast_string_to_doubles(string &b, deque<int> &v) {
  function separate_strings (line 90) | bool separate_strings(string &b, deque<string> &v) {
  function approx (line 109) | double approx(double a, int digits) {
  function cast_string_to_double (line 132) | double cast_string_to_double(string &b) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/cc.cpp
  function they_are_mate (line 3) | bool they_are_mate(int a, int b, const deque<deque<int>> &member_list) {
  function common_neighbors (line 11) | int common_neighbors(int a, int b, deque<set<int>> &en) {
  function compute_cc (line 21) | double compute_cc(deque<set<int>> &en, int i) {
  function compute_cc (line 29) | double compute_cc(deque<set<int>> &en) {
  function compute_tot_t (line 42) | double compute_tot_t(deque<set<int>> &en) {
  function choose_the_least (line 50) | int choose_the_least(deque<set<int>> &en, deque<int> &A, int a, int &cn_...
  function cclu (line 66) | int cclu(deque<set<int>> &en, const deque<deque<int>> &member_list,

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/combinatorics.cpp
  function log_factorial (line 7) | double log_factorial(int num) {
  function log_combination (line 14) | double log_combination(int n, int k) {
  function binomial (line 30) | double binomial(int n, int x, double p) {
  function binomial_cumulative (line 51) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 64) | int powerlaw(int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 78) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 89) | int cumulative_from_distribution(deque<double> &cum, const deque<double>...
  function poisson (line 99) | double poisson(int x, double mu) {
  function shuffle_and_set (line 103) | int shuffle_and_set(int *due, int dim) {        // it sets due as a rand...
  function shuffle_s (line 114) | int shuffle_s(deque<int> &sq) {
  function compute_r (line 128) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 135) | int add_factors(deque<double> &num, deque<double> &den, int n, int k) {
  function compute_hypergeometric (line 149) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 192) | int random_from_set(set<int> &s) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/deque_numeric.cpp
  function compare (line 3) | bool compare(deque<double> &one, deque<double> &two) {
  function Euclidean_norm (line 13) | double Euclidean_norm(const deque<double> &a) {
  function Euclidean_normalize (line 21) | int Euclidean_normalize(deque<double> &a) {
  function scalar_product (line 29) | double scalar_product(deque<double> &a, deque<double> &b) {
  function orthogonalize (line 37) | int orthogonalize(deque<double> &a, deque<deque<double> > &M) {
  function matrix_time_vector (line 48) | int matrix_time_vector(deque<deque<double> > &Q, deque<double> &v, deque...
  function set_to_deque (line 59) | void set_to_deque(const set<int> &s, deque<int> &a) {
  function set_to_deque (line 65) | void set_to_deque(const set<double> &s, deque<double> &a) {
  function deque_to_set (line 71) | void deque_to_set(const deque<double> &a, set<double> &s) {
  function deque_to_set (line 77) | void deque_to_set(const deque<int> &a, set<int> &s) {
  function deque_to_set_app (line 83) | void deque_to_set_app(const deque<int> &a, set<int> &s) {
  function norm_one (line 88) | double norm_one(const deque<double> &a) {
  function normalize_one (line 96) | int normalize_one(deque<double> &a) {
  function jaccard (line 104) | double jaccard(set<int> &a1, set<int> &a2) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/histograms.cpp
  function intlog_binning (line 6) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> &Xs, ...
  function xybinning (line 71) | int
  function xybinning (line 130) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 136) | void compute_quantiles(double q, deque<double> &y, deque<double> &qs) {
  function xybinning_quantiles (line 152) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 216) | int log_histogram(deque<type> &c, ostream &out,
  function log_histogram (line 268) | int log_histogram(deque<double> &c, deque<double> &c2, ostream &out,
  function histogram (line 317) | int histogram(vector<type> &c, ostream &out, int number_of_bins, double ...
  function not_norm_histogram_correlated (line 363) | int
  function histogram (line 412) | int histogram(deque<type> &c, ostream &out, int number_of_bins, double b...
  function not_norm_histogram (line 460) | int not_norm_histogram(vector<type> &c, ostream &out, int number_of_bins...
  function not_norm_histogram (line 506) | int not_norm_histogram(deque<type> &c, ostream &out, int number_of_bins,...
  function histogram (line 551) | int histogram(deque<double> &c, deque<double> &c2, ostream &out, int num...
  function not_norm_histogram (line 599) | int not_norm_histogram(deque<double> &c, deque<double> &c2, ostream &out...
  function int_histogram (line 647) | void int_histogram(vector<int> &c, ostream &out) {
  function int_histogram (line 662) | void int_histogram(deque<int> &c, ostream &out) {
  function int_histogram (line 677) | void int_histogram(int c, map<int, int> &hist) {
  function int_histogram (line 685) | void int_histogram(int c, map<int, double> &hist, double w) {
  function print_cumulative (line 693) | int print_cumulative(deque<double> &kws, string file, int number_of_step) {
  function print_cumulative (line 706) | int print_cumulative(deque<int> &kws, string file, int number_of_step) {
  function print_cumulative (line 719) | int print_cumulative(vector<double> &kws, string file, int number_of_ste...
  function print_cumulative (line 732) | int print_cumulative(vector<int> &kws, string file, int number_of_step) {
  function int_histogram (line 745) | void int_histogram(string infile, string outfile) {
  function int_histogram (line 759) | void int_histogram(int c, map<int, int> &hist, int w) {
  function int_histogram (line 767) | void int_histogram(const int &c, map<int, pair<int, double> > &hist, con...
  function int_histogram (line 777) | void int_histogram(int c, map<int, pair<double, double> > &hist, double ...
  function int_histogram (line 787) | void int_histogram(int c, map<int, pair<int, int> > &hist, int w1, int w...

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/log_table.h
  function class (line 10) | class log_fact_table {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/common/random.cpp
  function ran2 (line 8) | double ran2(long *idum) {
  function ran4 (line 41) | double ran4(bool t, long s) {
  function ran4 (line 51) | double ran4() {
  function srand4 (line 55) | void srand4(void) {
  function srand5 (line 60) | void srand5(int rank) {
  function irand (line 65) | int irand(int n) {
  function srand_file (line 69) | void srand_file(void) {
  function configuration_model (line 83) | int configuration_model(deque<set<int>> &en, deque<int> &degrees) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/input_output/pajek.cpp
  function get_partition_from_file_list_pajek (line 10) | int get_partition_from_file_list_pajek(string s, deque<deque<int>> &ten,...
  function pajek_format (line 37) | int pajek_format(string filename, bool directed) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/input_output/partition.cpp
  function get_partition_from_file (line 3) | int get_partition_from_file(string s, deque<deque<int>> &M) {
  function get_partition_from_file_list (line 19) | int get_partition_from_file_list(string s, deque<deque<int>> &ten) {
  function get_partition_from_file_tp_format (line 46) | int get_partition_from_file_tp_format(string S, deque<deque<int> > &M, b...
  function get_partition_from_file_tp_format (line 69) | int get_partition_from_file_tp_format(string S, deque<deque<int> > &M) {
  function get_partition_from_file (line 91) | int get_partition_from_file(string s, deque<deque<int> > &M, int min) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/input_output/pretty_print.h
  function namespace (line 25) | namespace pretty_print {
  type custom_delims_base (line 360) | struct custom_delims_base {
  type T (line 404) | typedef const T *const_iterator;
  type T (line 405) | typedef T value_type;
  type typename (line 424) | typedef typename T::const_local_iterator const_iterator;
  type typename (line 425) | typedef typename T::size_type size_type;
  function namespace (line 462) | namespace std {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/input_output/tab_degree.h
  type multiset (line 20) | typedef multiset<pair<double, int>> muspi;
  function class (line 22) | class TabDegree {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/metric/mutual.cpp
  function H (line 6) | double H(double a) {
  function H (line 10) | double H(deque<double> &p) {
  function overlap_grouping (line 17) | int overlap_grouping(deque<deque<int>> ten, int unique) {        //hrepi...
  function mutual (line 30) | double mutual(deque<deque<int>> en, deque<deque<int>> ten) {
  function H_x_given_y (line 91) | double H_x_given_y(deque<deque<int>> &en, deque<deque<int>> &ten, int di...
  function mutual2 (line 145) | double mutual2(deque<deque<int>> en, deque<deque<int>> ten) {
  function H_x_given_y3 (line 178) | double H_x_given_y3(deque<deque<int>> &en, deque<deque<int>> &ten, int d...
  function mutual3 (line 241) | double mutual3(deque<deque<int>> en, deque<deque<int>> ten) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/program_options/set_parameters.cpp
  function general_program_statement (line 6) | void general_program_statement(char *b) {
  function error_statement (line 66) | void error_statement(char *b) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/util/program_options/set_parameters.h
  function class (line 18) | class Parameters {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/main.cpp
  function get_tp_files (line 31) | int get_tp_files(string network_file) {
  function main (line 49) | int main(int argc, char *argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/main_pajek.cpp
  function get_tp_files (line 39) | int get_tp_files(string network_file) {
  function main (line 57) | int main(int argc, char *argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/main_pajek_directed.cpp
  function get_tp_files (line 33) | int get_tp_files(string network_file) {
  function main (line 51) | int main(int argc, char *argv[]) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/unused/netvi.h
  function class (line 12) | class netvi : public static_network {
  function class (line 49) | class netgnu {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/hier.cpp
  function check_position (line 12) | int check_position(map<int, double> &lab_x, map<int, double> &lab_y, map...
  function get_partition_from_file_tp_format (line 20) | int get_partition_from_file_tp_format(string S, map<int, deque<int> > &M...
  function get_sizes (line 41) | int get_sizes(string file_for_sizes, map<int, int> &sizes) {
  function insert_isolated (line 57) | int insert_isolated(visual_network &luca, map<int, int> &sizes) {
  function o_level (line 70) | int o_level(double origin_x, double origin_y, double radius, visual_netw...
  function another_level (line 95) | int another_level(string short_tpn, string netn, string tpn, map<int, do...
  function all_levels (line 230) | int all_levels(int levels, string network_file) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/position.h
  type multimap (line 13) | typedef multimap<double, int>::iterator map_idi;
  type pair (line 14) | typedef pair<map_idi, map_idi> pmap_idi;
  function class (line 16) | class xypos {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/static_network.cpp
  function statement (line 12) | void statement() {
  function parse_command_line (line 19) | int parse_command_line(bool &value, string &s, string &s2, int argc, cha...
  function integral (line 2954) | double integral(double a, double b) {
  function integer_average (line 2967) | double integer_average(int n, int min, double tau) {
  function average_degree (line 2985) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 2994) | double solve_dmin(const double &dmax, const double &dmed, const double &...
  function mate (line 3474) | bool mate(deque<set<int> > &node_member, int i, int j) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/static_network.h
  function class (line 20) | class static_network {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/visual_net.h
  function class (line 6) | class visual_network : public static_network {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/wsarray.cpp
  function prints (line 116) | void prints(wsarray &a) {
  function prints (line 122) | void prints(wsarray &a, ostream &out) {
  function prints (line 128) | void prints(wsarray *a, ostream &out) {
  function prints (line 134) | void prints(wsarray *a) {

FILE: Algorithms/2011-OSLOM-v2/src-refactor/visualization/util/wsarray.h
  function class (line 17) | class wsarray {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/CommonFuns.cpp
  function printVect_INT (line 24) | void printVect_INT(vector<int>& vect){
  function printVectVect_INT (line 30) | void printVectVect_INT(vector<vector<int> >& cpm){
  function printVectVect_INT_pointer (line 39) | void printVectVect_INT_pointer(vector<vector<int>* >& cpm_ptr){
  function sort_cpm_pointer (line 48) | void sort_cpm_pointer(vector<vector<int>* >& cpm){
  function dist_euclidean (line 63) | double dist_euclidean(vector<double>& A,vector<double>& B){
  function dist_cosine (line 78) | double dist_cosine(vector<double>& A,vector<double>& B){
  function dist_euclidean_sparse_unorderMap (line 146) | double dist_euclidean_sparse_unorderMap(UOrderedH_INT_DBL& A,UOrderedH_I...
  function dist_cosine_sparse_unorderMap (line 162) | double dist_cosine_sparse_unorderMap(UOrderedH_INT_DBL& A,UOrderedH_INT_...
  function rndPropotional2Length_INT (line 197) | int rndPropotional2Length_INT(vector<int>& input){
  function sortMapInt_DBL (line 238) | void sortMapInt_DBL(map<int,double> & words, vector<pair<int,double> > &...
  function sortMapInt_DBL_unorderMap (line 250) | void sortMapInt_DBL_unorderMap( UOrderedH_INT_DBL & words, vector<pair<i...
  function myround (line 264) | double myround( double value ){
  function createHistogram (line 268) | void createHistogram(map<int,double>& hist, const vector<int>& wordsList){
  function string (line 293) | string int2str(int i){
  function string (line 302) | string dbl2str(double f){
  function string (line 312) | string bool2str(bool flag){

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/CommonFuns.h
  type std (line 31) | typedef std::tr1::unordered_map<int, double> UOrderedH_INT_DBL;
  type sort_pair_INT_DBL (line 34) | struct sort_pair_INT_DBL {
  type sort_INT_DEC (line 40) | struct sort_INT_DEC {
  type sort_INT_INC (line 46) | struct sort_INT_INC {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/CommonFuns_Measure.cpp
  function sort_cpm_vectINT (line 20) | void sort_cpm_vectINT(vector<vector<int> >& cpm){
  function sortMapInt_Int (line 31) | void sortMapInt_Int(map<int,int> & words, vector<pair<int,int> > & words...
  function createHistogram (line 48) | void createHistogram(map<int,int>& hist, const vector<int>& wordsList){
  function nchoosek (line 93) | double nchoosek(double n,double k){

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/CommonFuns_Measure.h
  type sort_pair_INT_INT (line 31) | struct sort_pair_INT_INT {
  type sort_INT_DEC (line 37) | struct sort_INT_DEC {
  type sort_INT_INC (line 43) | struct sort_INT_INC {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/ComputeSnapshotChange.cpp
  function UOrderedSet_INT (line 195) | UOrderedSet_INT ComputeSnapshotChange:: mySet_Union_int(UOrderedSet_INT ...

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/ComputeSnapshotChange.h
  type std (line 29) | typedef std::tr1::unordered_set<int> UOrderedSet_INT;
  function class (line 31) | class ComputeSnapshotChange {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/DisjointM.cpp
  function Net (line 29) | Net* DisjointM::INIT_readNetwork(string fileName_net,bool isUseLargestCo...

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/DisjointM.h
  function class (line 24) | class DisjointM {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/LPA.h
  type std (line 25) | typedef std::tr1::unordered_map<int, int> UOrderedH_INT_INT;
  type std (line 26) | typedef std::tr1::unordered_map<int, double> UOrderedH_INT_DBL;
  function class (line 28) | class LPA {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/LRTPrama.h
  function class (line 17) | class LRTPrama{

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/LabelRank.cpp
  function UOrderedH_INT_DBL (line 860) | UOrderedH_INT_DBL LabelRank:: calNewBelongingCoefficients_w(NODE* v, int...

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/LabelRank.h
  type std (line 22) | typedef std::tr1::unordered_map<int, int> UOrderedH_INT_INT;
  type std (line 23) | typedef std::tr1::unordered_map<int, double> UOrderedH_INT_DBL;
  type thread_data (line 28) | struct thread_data{
  function class (line 40) | class LabelRank {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/MersenneTwister.h
  function class (line 70) | class MTRand {
  function initialize (line 167) | inline void MTRand::initialize( const uint32 seed )
  function reload (line 184) | inline void MTRand::reload()
  function seed (line 200) | inline void MTRand::seed( const uint32 oneSeed )
  function seed (line 207) | inline void MTRand::seed( uint32 *const bigSeed, const uint32 seedLength )
  function seed (line 242) | inline void MTRand::seed()
  function MTRand (line 265) | inline MTRand::MTRand( const uint32 oneSeed )
  function MTRand (line 268) | inline MTRand::MTRand( uint32 *const bigSeed, const uint32 seedLength )
  function MTRand (line 271) | inline MTRand::MTRand()
  function MTRand (line 274) | inline MTRand::MTRand( const MTRand& o )
  function rand (line 319) | inline double MTRand::rand()
  function rand (line 322) | inline double MTRand::rand( const double n )
  function randExc (line 325) | inline double MTRand::randExc()
  function randExc (line 328) | inline double MTRand::randExc( const double n )
  function randDblExc (line 331) | inline double MTRand::randDblExc()
  function randDblExc (line 334) | inline double MTRand::randDblExc( const double n )
  function rand53 (line 337) | inline double MTRand::rand53()
  function randNorm (line 343) | inline double MTRand::randNorm( const double mean, const double stddev )
  function save (line 364) | inline void MTRand::save( uint32* saveArray ) const
  function load (line 373) | inline void MTRand::load( uint32 *const loadArray )

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/NODE.h
  type std (line 25) | typedef std::tr1::unordered_set<int> UOrderedSet_INT;
  type std (line 26) | typedef std::tr1::unordered_map<int, double> UOrderedH_INT_DBL;
  function class (line 29) | class NODE {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/Net.cpp
  type sortIDs (line 32) | struct sortIDs {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/Net.h
  type std (line 29) | typedef std::tr1::unordered_set<int> UOrderedSet_INT;
  function class (line 32) | class Net {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/TieLabel.cpp
  type sort_TieLabel_by_measureINT_DEC (line 16) | struct sort_TieLabel_by_measureINT_DEC {
  type sort_TieLabel_by_measureINT_INC (line 21) | struct sort_TieLabel_by_measureINT_INC {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/TieLabel.h
  function class (line 23) | class TieLabel {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/fileOpts.cpp
  function isFileExist (line 23) | bool isFileExist(const char* fileName){
  function writeToTxt (line 34) | void writeToTxt(string fileName, bool isappend, vector<string>& data){
  function extractFileName_Extention (line 58) | void extractFileName_Extention(const string& str,string& file,string& ext){
  function extractFileName_FullPath (line 71) | void extractFileName_FullPath (const string& str,string& file, string& e...

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/main_LabelRank_release.cpp
  function main (line 38) | int main(int argc, char* argv[]) {

FILE: Algorithms/2011-SLPA/src_original/GANXiS-S_v1.0/rndNumbers.cpp
  function rndDblBtw01 (line 15) | double rndDblBtw01(){
  function rndDblBtw0Nminus1 (line 22) | int rndDblBtw0Nminus1(int N){ //****NOT GOOD ***

FILE: Algorithms/2011-SLPA/src_python/romain-fontugne/slpa.py
  function find_communities (line 6) | def find_communities(G, T, r):

FILE: Algorithms/2011-SLPA/src_python/ying_nus/nmi.py
  function usage (line 15) | def usage():
  function main (line 19) | def main(argv):

FILE: Algorithms/2011-SLPA/src_python/ying_nus/slpa.py
  class Slpa (line 12) | class Slpa:
    method __init__ (line 28) | def __init__(self, input_file):
    method perform_slpa (line 63) | def perform_slpa(self, ITERATION):
    method post_processing (line 99) | def post_processing(self, THRESHHOLD):
  function main (line 121) | def main():

FILE: Algorithms/2011-SLPA/src_python/ying_nus/test_slpa.py
  function usage (line 16) | def usage():
  function main (line 20) | def main(argv):

FILE: Algorithms/2011-SLPA/src_refactor/src/main/java/CollectionFuns.java
  class CollectionFuns (line 15) | public class CollectionFuns {
    method CollectionFuns (line 16) | public CollectionFuns() {
    method roundTwoDecimals (line 19) | public static double roundTwoDecimals(double d) {
    method Ascii2Str (line 24) | public static String Ascii2Str(int i) {
    method sortString (line 28) | public static String sortString(String str) {
    method intArrayToString (line 35) | public static String intArrayToString(int[] narray) {
    method String2intArray (line 45) | public static int[] String2intArray(String str) {
    method int2intArray (line 55) | public static int[] int2intArray(Integer aInt) {
    method intArray2int (line 60) | public static int intArray2int(int[] intarray) {
    method printAHashtablebyKey (line 65) | public void printAHashtablebyKey(Hashtable ht) {
    method doGC (line 76) | public static void doGC(int n) {
    method getSizeofUsedHeap (line 85) | public static long getSizeofUsedHeap() {
    method getSizeofAvailableHeap (line 90) | public static long getSizeofAvailableHeap() {
    method getTotalHeapSize (line 95) | public static void getTotalHeapSize() {
    method addArray2ToArray1_Double (line 100) | public static void addArray2ToArray1_Double(ArrayList<Double> al1, Arr...
    method AvgArray_Double (line 107) | public static void AvgArray_Double(ArrayList<Double> al, Double times) {
    method sumArray_Double (line 114) | public static double sumArray_Double(ArrayList<Double> al) {
    method ExpandArrayByLastE_Double (line 124) | public static void ExpandArrayByLastE_Double(ArrayList<Double> al, Dou...
    method FindMaxBetween2Array_Double (line 131) | public static void FindMaxBetween2Array_Double(ArrayList<Double> al1, ...
    method FindMinBetween2Array_Double (line 140) | public static void FindMinBetween2Array_Double(ArrayList<Double> al1, ...
    method unionSet (line 149) | public static Set unionSet(Set s1, Set s2) {
    method interSet (line 156) | public static Set interSet(Set s1, Set s2) {
    method diffSet (line 163) | public static Set diffSet(Set s1, Set s2) {
    method round2nDecimal (line 170) | public static double round2nDecimal(double v, double p) {
    method makeListUnique (line 176) | public static void makeListUnique(ArrayList AList) {
    method Lookup_Hashtable_getputID_Str_Long (line 187) | public static Long Lookup_Hashtable_getputID_Str_Long(Hashtable<String...
    method main (line 195) | public static void main(String[] args) {

FILE: Algorithms/2011-SLPA/src_refactor/src/main/java/NODE.java
  class NODE (line 12) | public class NODE {
    method compare (line 35) | public int compare(NODE v1, NODE v2) {
    method NODE (line 42) | public NODE(Long ID) {
    method main (line 52) | public static void main(String[] args) {

FILE: Algorithms/2011-SLPA/src_refactor/src/main/java/Net.java
  class Net (line 21) | public class Net {
    method compare (line 31) | public int compare(ArrayList<Long> o1, ArrayList<Long> o2) {
    method Net (line 38) | public Net(String networkPath, String netName) {
    method readNetwork_EdgesList (line 43) | public void readNetwork_EdgesList(String fileName, boolean isUseLarges...
    method post_UseLargestComponent (line 145) | public void post_UseLargestComponent() {
    method pre_ReadInOneEdge (line 174) | public void pre_ReadInOneEdge(Long fromID, Long toID, String fromID_s,...
    method pre_convert_nbSet2_nbList (line 200) | public void pre_convert_nbSet2_nbList() {
    method pre_convert_nbList2_nbSet (line 240) | public void pre_convert_nbList2_nbSet() {
    method pre_findAllConnectedComponents_InOneCluster_CPM (line 248) | public ArrayList<ArrayList<Long>> pre_findAllConnectedComponents_InOne...
    method getFirstElemnetInSet (line 294) | public Long getFirstElemnetInSet(HashSet<Long> set) {
    method readCPM (line 304) | public ArrayList<ArrayList<Long>> readCPM(String cpmPath, String fileN...
    method write2Txt_WQ_nameS (line 366) | public void write2Txt_WQ_nameS(String fileName, int st) {
    method applyEvolutionCutoff (line 387) | public void applyEvolutionCutoff(int T, double EC) {
    method calNumDistinctLabelAtT (line 418) | public double calNumDistinctLabelAtT(int t) {
    method main (line 431) | public static void main(String[] args) {

FILE: Algorithms/2011-SLPA/src_refactor/src/main/java/SLPAw.java
  class SLPAw (line 17) | public class SLPAw {
    method compare (line 51) | public int compare(Entry e1, Entry e2) {
    method compare (line 58) | public int compare(Entry e1, Entry e2) {
    method SLPAw (line 65) | public SLPAw(String fileName_net, ArrayList<Double> THRS, int maxRun, ...
    method printNodesInfo_Directed (line 77) | public void printNodesInfo_Directed() {
    method printSingleDeg_NodesInfo (line 100) | public void printSingleDeg_NodesInfo() {
    method isSingleDegNode_directed (line 119) | public int isSingleDegNode_directed(NODE v) {
    method identify_singleDegNode_directed (line 123) | public void identify_singleDegNode_directed(Net net) {
    method start (line 158) | public void start() {
    method copyHist2Histr (line 240) | public void copyHist2Histr() {
    method identify_NodeCommTable_fromCPM (line 254) | public void identify_NodeCommTable_fromCPM(ArrayList<NODE> NODES, Arra...
    method getUDUW_nbSet_from_nbList_InOut (line 356) | public static void getUDUW_nbSet_from_nbList_InOut(Net net) {
    method post_separate_disconnect_subcomponent (line 366) | public ArrayList<ArrayList<Long>> post_separate_disconnect_subcomponen...
    method post_processing (line 375) | public ArrayList<ArrayList<Long>> post_processing(ArrayList<ArrayList<...
    method post_smallComs_mergeAndFindconnectedComponent (line 388) | public ArrayList<ArrayList<Long>> post_smallComs_mergeAndFindconnected...
    method post_threshold_createCPM (line 424) | public void post_threshold_createCPM(int thrc, String fileName, double...
    method write2txt_histInfo_nameS (line 519) | public void write2txt_histInfo_nameS(String fileName, int Level) {
    method write2txt_smallCom_nameS (line 585) | public void write2txt_smallCom_nameS(String fileName, ArrayList<ArrayL...
    method update_WQHistgram_r_fromEmbeddedSLPAw_WQHistgram (line 602) | public void update_WQHistgram_r_fromEmbeddedSLPAw_WQHistgram(ArrayList...
    method post_applymaxC (line 619) | public ArrayList<ArrayList<Long>> post_applymaxC(double thrp, ArrayLis...
    method post_sameLabelDisconnectedComponents (line 693) | public ArrayList<ArrayList<Long>> post_sameLabelDisconnectedComponents...
    method show_cpm (line 698) | public void show_cpm(ArrayList<ArrayList<Integer>> cpm) {
    method create_sortedMapEntryList_fromHistogram_IntInt_dec (line 706) | public ArrayList<Entry<Integer, Integer>> create_sortedMapEntryList_fr...
    method post_mergeSmallComms (line 712) | public ArrayList<ArrayList<Long>> post_mergeSmallComms(ArrayList<Array...
    method post_reassign_singledeg_shallow (line 800) | public ArrayList<ArrayList<Long>> post_reassign_singledeg_shallow(Arra...
    method post_removeSubset (line 852) | public ArrayList<ArrayList<Long>> post_removeSubset(ArrayList<ArrayLis...
    method write2txt_CPM_nameS (line 891) | public void write2txt_CPM_nameS(String fileName, ArrayList<ArrayList<L...
    method pre_initial_THRCS (line 911) | public void pre_initial_THRCS() {
    method post_createWQHistogram_MapEntryList (line 920) | public void post_createWQHistogram_MapEntryList() {
    method post_thresholding (line 931) | public ArrayList<Long> post_thresholding(ArrayList<Entry<Long, Integer...
    method SLPAw_asyn (line 960) | public void SLPAw_asyn() {
    method collect_labels_from_nbs_weightedDirected_randomThr (line 990) | public long collect_labels_from_nbs_weightedDirected_randomThr(NODE v) {
    method collect_labels_from_nbs_weightedDirected_sumprob (line 1023) | public long collect_labels_from_nbs_weightedDirected_sumprob(NODE v) {
    method collect_labels_from_nbs_weightedDirected_maxprob (line 1030) | public Long collect_labels_from_nbs_weightedDirected_maxprob(NODE v) {
    method getNbs_label_weight_Hist_Incoming (line 1037) | public ArrayList<Entry<Long, Double>> getNbs_label_weight_Hist_Incomin...
    method selectOneLabel_withAccumuatedProb (line 1058) | public Long selectOneLabel_withAccumuatedProb(ArrayList<Entry<Long, Do...
    method initWQueue (line 1079) | public void initWQueue() {
    method ceateHistogram_selRandMax (line 1088) | public Long ceateHistogram_selRandMax(ArrayList<Long> wordsList) {
    method createHistogram (line 1119) | public Hashtable<Long, Integer> createHistogram(ArrayList<Long> wordsL...
    method pre_load_THRS (line 1134) | public static ArrayList<Double> pre_load_THRS() {
    method printCitation (line 1150) | static final void printCitation() {
    method printUsage (line 1171) | static final void printUsage(String usage) {
    method main (line 1177) | public static void main(String[] args) {
    method embededSLPAw_on_OneCOM_start (line 1439) | public SLPAw embededSLPAw_on_OneCOM_start(double thrp, ArrayList<Long>...

FILE: Algorithms/2011-SLPA/src_refactor/src/main/java/fileOpts.java
  class fileOpts (line 22) | public class fileOpts {
    method fileOpts (line 23) | public fileOpts() {
    method extractFileName (line 26) | public static String extractFileName(String fullName) {
    method extractFileName_FullPath (line 38) | public static String extractFileName_FullPath(String fullName) {
    method readFromTxt (line 62) | public static ArrayList<String> readFromTxt(String filename) {
    method writeToTxt (line 93) | public static void writeToTxt(String filename, boolean append, ArrayLi...
    method isFileExist (line 123) | public static boolean isFileExist(String name) {
    method createDirectory (line 128) | public static void createDirectory(String strDirectoy) {
    method createEmptyTxt (line 138) | public static void createEmptyTxt(String filename) {
    method writeObj2File (line 144) | public static void writeObj2File(Object oriObj, String fileName) {
    method readObjfromFile (line 156) | public static Object readObjfromFile(String fileName) {
    method writeObj2ByteArray (line 172) | public static byte[] writeObj2ByteArray(Object oriObj) {
    method readObjfromwByteArray (line 188) | public static Object readObjfromwByteArray(byte[] buf) {
    method main (line 204) | public static void main(String[] args) {

FILE: Algorithms/2012-CPMOnSteroids/src_original/cliques.c
  function cliques_init (line 8) | int cliques_init(cliques **c) {
  function cliques_load_unordered_maximal_cliques_list (line 16) | int cliques_load_unordered_maximal_cliques_list(cliques *c, const char *...
  function cliques_init_member_vectors (line 67) | static int cliques_init_member_vectors(cliques *c, int max_size){
  function cliques_count_maximal_cliques (line 90) | static int cliques_count_maximal_cliques(cliques *c) {
  function cliques_order_cliques_by_decreasing_k (line 107) | static int cliques_order_cliques_by_decreasing_k(cliques *c, const char ...
  function cliques_rows_to_be_read (line 153) | int cliques_rows_to_be_read(const cliques *c, unsigned int k, unsigned l...
  function igraph_vector_t (line 164) | igraph_vector_t* cliques_get_clique(cliques* c, int i){
  function cliques_get_clique_size (line 168) | uint8_t cliques_get_clique_size(cliques* c, int i){
  function cliques_overlap_cliques (line 173) | uint8_t cliques_overlap_cliques(cliques* c, int i, int j){

FILE: Algorithms/2012-CPMOnSteroids/src_original/cos.c
  function constructor_thread_body (line 17) | static void constructor_thread_body(void* params){
  function community_thread_epilogue (line 34) | static int community_thread_epilogue(dsforest_t *thread_dsf, unsigned in...
  function community_thread_body (line 66) | static void community_thread_body(void* params){
  function cos_ (line 127) | int cos_() {

FILE: Algorithms/2012-CPMOnSteroids/src_original/cospoc.c
  function cospoc_thread_epilogue (line 14) | static int cospoc_thread_epilogue(dsforest_t **thread_dsfs){
  function cospoc_thread_body (line 52) | static void cospoc_thread_body(void* params){
  function cospoc (line 127) | int cospoc() {

FILE: Algorithms/2012-CPMOnSteroids/src_original/dsforest.c
  function clear_node (line 3) | static int clear_node(forest_node_t* node){
  function forest_node_t (line 10) | static forest_node_t* make_set(int label) {
  function forest_node_t (line 17) | static forest_node_t* find(forest_node_t* node) {
  function union_ (line 27) | static int union_(forest_node_t* node1, forest_node_t* node2) {
  function dsforest_init (line 39) | extern int dsforest_init(dsforest_t **dsf, unsigned int num_elements){
  function dsforest_clear (line 51) | extern int dsforest_clear(dsforest_t *dsf){
  function dsforest_destroy (line 58) | extern int dsforest_destroy(dsforest_t *dsf){
  function dsforest_find (line 67) | extern int dsforest_find(dsforest_t *dsf, unsigned int node_label){
  function dsforest_union (line 78) | extern int dsforest_union(dsforest_t *dsf, unsigned int root1_label, uns...
  function dsforest_is_root (line 93) | extern int dsforest_is_root(dsforest_t *dsf, unsigned int label){

FILE: Algorithms/2012-CPMOnSteroids/src_original/extras/maximal_cliques.c
  function main (line 10) | int main(int argc, char **argv){
  function usage (line 100) | static void usage(const char* progname){

FILE: Algorithms/2012-CPMOnSteroids/src_original/include/cliques.h
  type cliques (line 12) | struct cliques{
  type cliques (line 22) | typedef struct cliques cliques;

FILE: Algorithms/2012-CPMOnSteroids/src_original/include/common.h
  type constructor_thread_data (line 6) | struct constructor_thread_data {
  type constructor_thread_data (line 10) | typedef struct constructor_thread_data constructor_thread_data;
  type community_thread_data (line 12) | struct community_thread_data {
  type community_thread_data (line 17) | typedef struct community_thread_data community_thread_data;

FILE: Algorithms/2012-CPMOnSteroids/src_original/include/dsforest.h
  type forest_node_t (line 9) | typedef struct forest_node {
  type dsforest_t (line 16) | typedef struct dsforest {

FILE: Algorithms/2012-CPMOnSteroids/src_original/include/matrix.h
  type boolean (line 12) | enum boolean{
  type errors (line 17) | enum errors{
  type info (line 26) | enum info{
  type matrix (line 34) | struct matrix{
  type matrix (line 44) | typedef struct matrix matrix;

FILE: Algorithms/2012-CPMOnSteroids/src_original/main.c
  function main (line 23) | int main(int argc, char** argv) {
  function debug__ (line 82) | void
  function usage (line 104) | static void usage(const char* progname){

FILE: Algorithms/2012-CPMOnSteroids/src_original/matrix.c
  function matrix_ends_at (line 4) | static int matrix_ends_at(matrix *m){
  function matrix_offsets (line 67) | static int matrix_offsets(matrix *m){
  function matrix_init (line 96) | int matrix_init(matrix **m, long int matrix_diagonal_size){
  function matrix_slide_forward (line 119) | int matrix_slide_forward(matrix *m){
  function matrix_set (line 138) | int matrix_set(matrix *m, int i, int j, uint8_t value){
  function matrix_get (line 150) | int matrix_get(const matrix *m, int i, int j, uint8_t *value){
  function matrix_row_in_window (line 162) | int matrix_row_in_window(const matrix *m, int i){
  function matrix_col_in_matrix_bounds (line 166) | int matrix_col_in_matrix_bounds(const matrix *m, int j){
  function matrix_get_num_rows_in_window (line 170) | int matrix_get_num_rows_in_window(const matrix *m, int *rows_in_window){
  function matrix_destroy (line 177) | int matrix_destroy(matrix *m){

FILE: Algorithms/2012-CPMOnSteroids/src_original/output_communities.c
  function write_found_communities_to_file_thread (line 13) | static int write_found_communities_to_file_thread(void *k_param){
  function write_found_communities_to_file (line 79) | int write_found_communities_to_file(){

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/cliques.c
  function cliques_init (line 8) | int cliques_init(cliques **c) {
  function cliques_load_unordered_maximal_cliques_list (line 16) | int cliques_load_unordered_maximal_cliques_list(cliques *c, const char *...
  function cliques_init_member_vectors (line 67) | static int cliques_init_member_vectors(cliques *c, int max_size){
  function cliques_count_maximal_cliques (line 90) | static int cliques_count_maximal_cliques(cliques *c) {
  function cliques_order_cliques_by_decreasing_k (line 107) | static int cliques_order_cliques_by_decreasing_k(cliques *c, const char ...
  function cliques_rows_to_be_read (line 153) | int cliques_rows_to_be_read(const cliques *c, unsigned int k, unsigned l...
  function igraph_vector_t (line 164) | igraph_vector_t* cliques_get_clique(cliques* c, int i){
  function cliques_get_clique_size (line 168) | uint8_t cliques_get_clique_size(cliques* c, int i){
  function cliques_overlap_cliques (line 173) | uint8_t cliques_overlap_cliques(cliques* c, int i, int j){

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/cliques.h
  type cliques (line 12) | struct cliques{
  type cliques (line 22) | typedef struct cliques cliques;

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/common.h
  type constructor_thread_data (line 6) | struct constructor_thread_data {
  type constructor_thread_data (line 10) | typedef struct constructor_thread_data constructor_thread_data;
  type community_thread_data (line 12) | struct community_thread_data {
  type community_thread_data (line 17) | typedef struct community_thread_data community_thread_data;

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/cos.c
  function constructor_thread_body (line 17) | static void constructor_thread_body(void* params){
  function community_thread_epilogue (line 34) | static int community_thread_epilogue(dsforest_t *thread_dsf, unsigned in...
  function community_thread_body (line 66) | static void community_thread_body(void* params){
  function cos_ (line 127) | int cos_() {

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/cospoc.c
  function cospoc_thread_epilogue (line 14) | static int cospoc_thread_epilogue(dsforest_t **thread_dsfs){
  function cospoc_thread_body (line 52) | static void cospoc_thread_body(void* params){
  function cospoc (line 127) | int cospoc() {

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/dsforest.c
  function clear_node (line 3) | static int clear_node(forest_node_t* node){
  function forest_node_t (line 10) | static forest_node_t* make_set(int label) {
  function forest_node_t (line 17) | static forest_node_t* find(forest_node_t* node) {
  function union_ (line 27) | static int union_(forest_node_t* node1, forest_node_t* node2) {
  function dsforest_init (line 39) | extern int dsforest_init(dsforest_t **dsf, unsigned int num_elements){
  function dsforest_clear (line 51) | extern int dsforest_clear(dsforest_t *dsf){
  function dsforest_destroy (line 58) | extern int dsforest_destroy(dsforest_t *dsf){
  function dsforest_find (line 67) | extern int dsforest_find(dsforest_t *dsf, unsigned int node_label){
  function dsforest_union (line 78) | extern int dsforest_union(dsforest_t *dsf, unsigned int root1_label, uns...
  function dsforest_is_root (line 93) | extern int dsforest_is_root(dsforest_t *dsf, unsigned int label){

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/dsforest.h
  type forest_node_t (line 9) | typedef struct forest_node {
  type dsforest_t (line 16) | typedef struct dsforest {

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/extras/maximal_cliques.c
  function main (line 10) | int main(int argc, char **argv){
  function usage (line 100) | static void usage(const char* progname){

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/main.c
  function main (line 23) | int main(int argc, char** argv) {
  function debug__ (line 82) | void
  function usage (line 104) | static void usage(const char* progname){

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/matrix.c
  function matrix_ends_at (line 4) | static int matrix_ends_at(matrix *m){
  function matrix_offsets (line 67) | static int matrix_offsets(matrix *m){
  function matrix_init (line 96) | int matrix_init(matrix **m, long int matrix_diagonal_size){
  function matrix_slide_forward (line 119) | int matrix_slide_forward(matrix *m){
  function matrix_set (line 138) | int matrix_set(matrix *m, int i, int j, uint8_t value){
  function matrix_get (line 150) | int matrix_get(const matrix *m, int i, int j, uint8_t *value){
  function matrix_row_in_window (line 162) | int matrix_row_in_window(const matrix *m, int i){
  function matrix_col_in_matrix_bounds (line 166) | int matrix_col_in_matrix_bounds(const matrix *m, int j){
  function matrix_get_num_rows_in_window (line 170) | int matrix_get_num_rows_in_window(const matrix *m, int *rows_in_window){
  function matrix_destroy (line 177) | int matrix_destroy(matrix *m){

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/matrix.h
  type boolean (line 12) | enum boolean{
  type errors (line 17) | enum errors{
  type info (line 26) | enum info{
  type matrix (line 34) | struct matrix{
  type matrix (line 44) | typedef struct matrix matrix;

FILE: Algorithms/2012-CPMOnSteroids/src_refactor/src/output_communities.c
  function write_found_communities_to_file_thread (line 13) | static int write_found_communities_to_file_thread(void *k_param){
  function write_found_communities_to_file (line 79) | int write_found_communities_to_file(){

FILE: Algorithms/2012-DEMON/Demon.py
  class Demon (line 11) | class Demon(object):
    method __init__ (line 18) | def __init__(self):
    method execute (line 23) | def execute(self, G, epsilon=0.25, weighted=False, min_community_size=3):
    method __overlapping_label_propagation (line 74) | def __overlapping_label_propagation(self, ego_minus_ego, ego, max_iter...
    method __merge_communities (line 177) | def __merge_communities(self, communities, actual_community):
    method __generalized_inclusion (line 208) | def __generalized_inclusion(self, c1, c2):

FILE: Algorithms/2012-DEMON/HDemon.py
  class HDemon (line 9) | class HDemon(object):
    method __init__ (line 17) | def __init__(self, g, min_community_size=0, epsilon=0.25):
    method execute (line 30) | def execute(self):
    method __build_graph_from_communities (line 87) | def __build_graph_from_communities(self, communities):
    method __overlapping_label_propagation (line 105) | def __overlapping_label_propagation(self, ego_minus_ego, ego, actual_c...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/cliques.cpp
  type cliques (line 15) | namespace cliques {
    type list_of_ints (line 19) | struct list_of_ints : private list<int32_t> {
      method list_of_ints (line 25) | explicit list_of_ints() : list<int32_t>(), sz(0) {
      method push_back (line 31) | void push_back(int32_t v) {
      method size (line 35) | size_t size() const {
      method empty (line 39) | bool empty() const {
      method iterator (line 42) | iterator begin() {
      method iterator (line 45) | iterator end() {
      method iterator (line 48) | iterator erase(iterator i) {
      method insert (line 52) | void insert(iterator i, int32_t v) {
      method list_of_ints (line 57) | list_of_ints(const list<int32_t> &) {}
    type CliqueReceiver (line 62) | struct CliqueReceiver
    type CliqueReceiver (line 75) | struct CliqueReceiver {
    function cliquesForOneNode (line 80) | static void cliquesForOneNode(const SimpleIntGraph &g, CliqueReceiver ...
    function tryCandidate (line 115) | static inline void tryCandidate (const SimpleIntGraph & g, CliqueRecei...
    function cliquesWorker (line 136) | static void cliquesWorker(const SimpleIntGraph &g, CliqueReceiver *sen...
    type CliquesToStdout (line 202) | struct CliquesToStdout : public CliqueReceiver {
      method CliquesToStdout (line 206) | CliquesToStdout(const graph :: NetworkInterfaceConvertedToString *_g...
    type SelfLoopsNotSupportedException (line 225) | struct SelfLoopsNotSupportedException {
    function findCliques (line 227) | static void findCliques(const SimpleIntGraph &g, CliqueReceiver *send_...
    function cliquesToStdout (line 242) | void cliquesToStdout(const graph :: NetworkInterfaceConvertedToString ...
    function count_disconnections (line 257) | static int32_t count_disconnections(const set<int> &cands, const int32...
    function find_node_with_fewest_discs (line 282) | static void find_node_with_fewest_discs(int &fewestDisc, int &fewestDi...
    type StoreCliquesInVector (line 313) | struct StoreCliquesInVector : public CliqueReceiver {
      method StoreCliquesInVector (line 316) | StoreCliquesInVector(all_cliques_by_orig_name_t &x, graph :: Network...
    function cliquesToVector (line 330) | void cliquesToVector(vector< vector<int64_t> > &all_cliques_by_orig_na...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/cliques.hpp
  type cliques (line 9) | namespace cliques {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/cmdline.c
  type cmdline_parser_arg_type (line 42) | typedef enum {ARG_NO
  type gengetopt_args_info (line 48) | struct gengetopt_args_info
  type gengetopt_args_info (line 50) | struct gengetopt_args_info
  type gengetopt_args_info (line 53) | struct gengetopt_args_info
  type cmdline_parser_params (line 54) | struct cmdline_parser_params
  function clear_given (line 60) | static
  function clear_args (line 69) | static
  function init_args_info (line 79) | static
  function cmdline_parser_print_version (line 91) | void
  function print_help_common (line 99) | static void print_help_common(void) {
  function cmdline_parser_print_help (line 114) | void
  function cmdline_parser_init (line 123) | void
  function cmdline_parser_params_init (line 134) | void
  type cmdline_parser_params (line 147) | struct cmdline_parser_params
  type cmdline_parser_params (line 150) | struct cmdline_parser_params
  type cmdline_parser_params (line 151) | struct cmdline_parser_params
  type cmdline_parser_params (line 151) | struct cmdline_parser_params
  function free_string_field (line 156) | static void
  function cmdline_parser_release (line 167) | static void
  function write_into_file (line 184) | static void
  function cmdline_parser_dump (line 196) | int
  function cmdline_parser_file_save (line 221) | int
  function cmdline_parser_free (line 241) | void
  function cmdline_parser (line 262) | int
  function cmdline_parser_ext (line 268) | int
  function cmdline_parser2 (line 284) | int
  function cmdline_parser_required (line 307) | int
  function update_arg (line 336) | static
  function cmdline_parser_internal (line 423) | int

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/cmdline.h
  type gengetopt_args_info (line 38) | struct gengetopt_args_info
  type cmdline_parser_params (line 58) | struct cmdline_parser_params
  type gengetopt_args_info (line 82) | struct gengetopt_args_info
  type gengetopt_args_info (line 96) | struct gengetopt_args_info
  type gengetopt_args_info (line 108) | struct gengetopt_args_info
  type cmdline_parser_params (line 109) | struct cmdline_parser_params
  type gengetopt_args_info (line 118) | struct gengetopt_args_info
  type gengetopt_args_info (line 128) | struct gengetopt_args_info
  type cmdline_parser_params (line 144) | struct cmdline_parser_params
  type cmdline_parser_params (line 151) | struct cmdline_parser_params
  type gengetopt_args_info (line 158) | struct gengetopt_args_info
  type gengetopt_args_info (line 164) | struct gengetopt_args_info
  type gengetopt_args_info (line 173) | struct gengetopt_args_info

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/bloom.cpp
  type graph (line 4) | namespace graph {
    type bloom (line 5) | namespace bloom {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/bloom.hpp
  type graph (line 3) | namespace graph {
    type bloom (line 4) | namespace bloom {
      class BloomAreConnected (line 7) | class BloomAreConnected
        method test (line 15) | bool test( const int32_t node_id_1, const int32_t node_id_2 ) const {
      class BloomAreConnected (line 9) | class BloomAreConnected {
        method test (line 15) | bool test( const int32_t node_id_1, const int32_t node_id_2 ) const {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/graph.cpp
  type graph (line 2) | namespace graph {
    function neighbouring_node_id_iterator (line 4) | neighbouring_node_id_iterator neighbouring_node_id_iterator :: end_mar...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/graph.hpp
  type graph (line 11) | namespace graph {
    class VerySimpleGraphInterface (line 13) | class VerySimpleGraphInterface
      method degree (line 23) | virtual int32_t degree(const int32_t node_id) const { return int32_t...
      method are_connected (line 24) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) con...
    class VerySimpleGraphInterface (line 15) | class VerySimpleGraphInterface { // consecutive ints. No attributes, o...
      method degree (line 23) | virtual int32_t degree(const int32_t node_id) const { return int32_t...
      method are_connected (line 24) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) con...
    class neighbouring_rel_id_iterator (line 33) | class neighbouring_rel_id_iterator : public std :: iterator< std :: fo...
      method neighbouring_rel_id_iterator (line 38) | neighbouring_rel_id_iterator(const VerySimpleGraphInterface * vsg, c...
      method neighbouring_rel_id_iterator (line 43) | neighbouring_rel_id_iterator & operator++() {
      method neighbouring_rel_id_iterator (line 56) | neighbouring_rel_id_iterator   operator++(int) { // postfix. Should ...
      method at_end (line 61) | bool at_end() const {
    class neighbouring_node_id_iterator (line 70) | class neighbouring_node_id_iterator : public std :: iterator< std :: f...
      method neighbouring_node_id_iterator (line 77) | neighbouring_node_id_iterator() : vsg(NULL), node_id(0) { // constru...
      method neighbouring_node_id_iterator (line 79) | neighbouring_node_id_iterator(const VerySimpleGraphInterface * _vsg,...
      method neighbouring_node_id_iterator (line 84) | neighbouring_node_id_iterator & operator++() {
      method neighbouring_node_id_iterator (line 98) | neighbouring_node_id_iterator   operator++(int) { // postfix. Should...
      method at_end (line 104) | bool at_end() const {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/loading.cpp
  type graph (line 22) | namespace graph {
    type loading (line 23) | namespace loading {
      type ModifiableNetwork (line 28) | struct ModifiableNetwork
        method ModifiableNetwork (line 95) | ModifiableNetwork(const bool directed, const bool weighted) : Netw...
        method find_ordered_node_names_offset (line 99) | int32_t find_ordered_node_names_offset(const t &node_name) {
      class MyVSG (line 37) | class MyVSG
        method MyVSG (line 61) | MyVSG () {
        method numNodes (line 64) | int numNodes() const { return this->N; }
        method numRels (line 65) | int numRels() const { return this->R; }
        method are_connected (line 74) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) c...
      type hash_pair_of_ints (line 42) | struct hash_pair_of_ints {
      class MyVSG (line 50) | class MyVSG : public VerySimpleGraphInterface {
        method MyVSG (line 61) | MyVSG () {
        method numNodes (line 64) | int numNodes() const { return this->N; }
        method numRels (line 65) | int numRels() const { return this->R; }
        method are_connected (line 74) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) c...
      type ModifiableNetwork (line 92) | struct ModifiableNetwork : public NetworkInterface<NodeNameT> { // N...
        method ModifiableNetwork (line 95) | ModifiableNetwork(const bool directed, const bool weighted) : Netw...
        method find_ordered_node_names_offset (line 99) | int32_t find_ordered_node_names_offset(const t &node_name) {
      type ModifiableNetwork<graph :: NodeNameIsInt64> (line 118) | struct ModifiableNetwork<graph :: NodeNameIsInt64>
      type ModifiableNetwork<graph :: NodeNameIsString> (line 119) | struct ModifiableNetwork<graph :: NodeNameIsString>
      function ThreeStrings (line 121) | static ThreeStrings parseLine(const string &lineOrig) {
      function read_edge_list_from_file (line 151) | static void read_edge_list_from_file(ModifiableNetwork<NodeNameT> *m...
      function make_Network_from_edge_list_int64 (line 289) | std :: auto_ptr< graph :: NetworkInt64 > make_Network_from_edge_list...
      function make_Network_from_edge_list_string (line 293) | std :: auto_ptr< graph :: NetworkString > make_Network_from_edge_lis...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/loading.hpp
  type graph (line 7) | namespace graph {
    type loading (line 8) | namespace loading {
      type BadlyFormattedLine (line 10) | struct BadlyFormattedLine : public std :: exception {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/network.cpp
  type graph (line 2) | namespace graph {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/network.hpp
  type graph (line 11) | namespace graph {
    type NetworkInterface (line 14) | struct NetworkInterface
    type NetworkInterfaceConvertedToString (line 15) | struct NetworkInterfaceConvertedToString
      method numNodes (line 65) | virtual int32_t numNodes() const { return this->get_plain_graph()->n...
      method numRels (line 66) | virtual int32_t numRels()  const { return this->get_plain_graph()->n...
      method degree (line 67) | virtual int32_t degree(const int32_t node_id) const { return this->g...
    type NetworkInterfaceConvertedToStringWithWeights (line 16) | struct NetworkInterfaceConvertedToStringWithWeights
    type NodeNameIsInt64 (line 18) | struct NodeNameIsInt64
      method value_type (line 39) | inline static value_type fromString(const std :: string &s) {
    type NodeNameIsString (line 19) | struct NodeNameIsString
      method value_type (line 55) | inline static value_type fromString(const std :: string &s) {
    type BadlyFormattedNodeName (line 20) | struct BadlyFormattedNodeName : public std :: exception { // if the te...
      method BadlyFormattedNodeName (line 22) | BadlyFormattedNodeName(const char * type_name, const std :: string &...
    type NodeNameIsInt64 (line 37) | struct NodeNameIsInt64 {
      method value_type (line 39) | inline static value_type fromString(const std :: string &s) {
    type NodeNameIsString (line 53) | struct NodeNameIsString {
      method value_type (line 55) | inline static value_type fromString(const std :: string &s) {
    type NetworkInterfaceConvertedToString (line 62) | struct NetworkInterfaceConvertedToString  { // Any NodeNameT (int or s...
      method numNodes (line 65) | virtual int32_t numNodes() const { return this->get_plain_graph()->n...
      method numRels (line 66) | virtual int32_t numRels()  const { return this->get_plain_graph()->n...
      method degree (line 67) | virtual int32_t degree(const int32_t node_id) const { return this->g...
    type NetworkInterfaceConvertedToStringWithWeights (line 71) | struct NetworkInterfaceConvertedToStringWithWeights : public NetworkIn...
    type NetworkInterface (line 76) | struct NetworkInterface : public NetworkInterfaceConvertedToStringWith...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/saving.cpp
  type graph (line 8) | namespace graph {
    type saving (line 9) | namespace saving {
      function print_Network_to_screen (line 11) | void print_Network_to_screen( const graph :: NetworkInterfaceConvert...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/saving.hpp
  type graph (line 5) | namespace graph {
    type saving (line 6) | namespace saving {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/strings.cpp
  type strings (line 4) | namespace strings {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/strings.hpp
  type strings (line 4) | namespace strings {
    class StrH (line 5) | class StrH { // string handle. It just wraps an int that refers to the...
      type hasher (line 10) | struct hasher
    type StrH :: hasher (line 13) | struct StrH :: hasher {
    class StringArray (line 16) | class StringArray {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/weights.cpp
  type graph (line 7) | namespace graph {
    type weights (line 8) | namespace weights {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/graph/weights.hpp
  type graph (line 9) | namespace graph {
    type weights (line 10) | namespace weights {
      type EdgeDetailsInterface (line 12) | struct EdgeDetailsInterface {
      type EdgeDetails (line 22) | struct EdgeDetails : public EdgeDetailsInterface {
        method is_directed (line 29) | virtual bool is_directed() const { return W :: is_directed; }
        method is_weighted (line 30) | virtual bool is_weighted() const { return W :: is_weighted; }
      type NoDetails (line 33) | struct NoDetails { // unweighted, undirected
        method inform (line 37) | void inform(const bool, const std :: string) const {
        method getl2h (line 39) | long double getl2h() const {
        method geth2l (line 42) | long double geth2l() const {
      type DirectedLDoubleWeights (line 47) | struct DirectedLDoubleWeights {
        type LdblPair (line 50) | struct LdblPair : public std :: pair<long double,long double> {
          method LdblPair (line 51) | LdblPair() {
          type DuplicateWeightedEdge (line 54) | struct DuplicateWeightedEdge : public std :: exception {
          method inform (line 56) | void inform(const bool highToLow, const std :: string weight) { ...
          method getl2h (line 71) | long double getl2h() const {
          method geth2l (line 74) | long double geth2l() const {
      type DirectedNoWeights (line 79) | struct DirectedNoWeights {
        type IntPair (line 82) | struct IntPair : public std :: pair<int,int> {
          method IntPair (line 83) | IntPair() {
          method inform (line 86) | void inform(const bool highToLow, const std :: string) { // the ...
          method getl2h (line 93) | long double getl2h() const {
          method geth2l (line 96) | long double geth2l() const {
      type WeightNoDir (line 101) | struct WeightNoDir {
        type LdblPair (line 104) | struct LdblPair {
          method LdblPair (line 106) | LdblPair() {
          type DuplicateWeightedEdge (line 109) | struct DuplicateWeightedEdge : public std :: exception {
          method inform (line 111) | void inform(const bool , const std :: string weight) { // the we...
          method getl2h (line 122) | long double getl2h() const {
          method geth2l (line 125) | long double geth2l() const {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_original/percolateCliques.cpp
  function main (line 25) | int main(int argc, char **argv) {
  function percolateCliques (line 48) | void percolateCliques(const char * edgeListFileName, const int k, const ...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_python/clique_percoaltion_naive.py
  function get_percolated_cliques (line 8) | def get_percolated_cliques(G, k):

FILE: Algorithms/2012-Fast-Clique-Percolation/src_python/clique_percolation_fast.py
  function get_adjacent_cliques (line 12) | def get_adjacent_cliques(clique, membership_dict):
  function get_fast_percolated_cliques (line 22) | def get_fast_percolated_cliques(G, k):
  function print_sorted_res (line 90) | def print_sorted_res(result):

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/cliques.cpp
  type cliques (line 15) | namespace cliques {
    type list_of_ints (line 20) | struct list_of_ints : public list<int32_t> {
      method list_of_ints (line 26) | explicit list_of_ints() : list<int32_t>(), sz(0) {
      method push_back (line 33) | void push_back(int32_t v) {
      method size (line 38) | size_t size() const {
      method empty (line 43) | bool empty() const {
      method iterator (line 47) | iterator begin() {
      method iterator (line 51) | iterator end() {
      method iterator (line 55) | iterator erase(iterator i) {
      method insert (line 60) | void insert(iterator i, int32_t v) {
      method list_of_ints (line 66) | list_of_ints(
    type CliqueReceiver (line 73) | struct CliqueReceiver
    type CliqueReceiver (line 94) | struct CliqueReceiver {
    function cliquesForOneNode (line 100) | static void cliquesForOneNode(const SimpleIntGraph &g, CliqueReceiver ...
    function tryCandidate (line 135) | static inline void
    function cliquesWorker (line 157) | static void cliquesWorker(const SimpleIntGraph &g, CliqueReceiver *sen...
    type CliquesToStdout (line 225) | struct CliquesToStdout : public CliqueReceiver {
      method CliquesToStdout (line 230) | CliquesToStdout(const graph::NetworkInterfaceConvertedToString *_g) ...
    type SelfLoopsNotSupportedException (line 250) | struct SelfLoopsNotSupportedException {
    function findCliques (line 253) | static void findCliques(const SimpleIntGraph &g, CliqueReceiver *send_...
    function cliquesToStdout (line 269) | void cliquesToStdout(const graph::NetworkInterfaceConvertedToString *n...
    function count_disconnections (line 284) | static int32_t count_disconnections(const set<int> &cands, const int32...
    function find_node_with_fewest_discs (line 308) | static void
    type StoreCliquesInVector (line 344) | struct StoreCliquesInVector : public CliqueReceiver {
      method StoreCliquesInVector (line 348) | StoreCliquesInVector(all_cliques_by_orig_name_t &x, graph::NetworkIn...
    function cliquesToVector (line 365) | void

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/cliques.hpp
  type cliques (line 9) | namespace cliques {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/cmdline.c
  type cmdline_parser_arg_type (line 42) | typedef enum {ARG_NO
  type gengetopt_args_info (line 48) | struct gengetopt_args_info
  type gengetopt_args_info (line 50) | struct gengetopt_args_info
  type gengetopt_args_info (line 53) | struct gengetopt_args_info
  type cmdline_parser_params (line 54) | struct cmdline_parser_params
  function clear_given (line 60) | static
  function clear_args (line 69) | static
  function init_args_info (line 79) | static
  function cmdline_parser_print_version (line 91) | void
  function print_help_common (line 99) | static void print_help_common(void) {
  function cmdline_parser_print_help (line 114) | void
  function cmdline_parser_init (line 123) | void
  function cmdline_parser_params_init (line 134) | void
  type cmdline_parser_params (line 147) | struct cmdline_parser_params
  type cmdline_parser_params (line 150) | struct cmdline_parser_params
  type cmdline_parser_params (line 151) | struct cmdline_parser_params
  type cmdline_parser_params (line 151) | struct cmdline_parser_params
  function free_string_field (line 156) | static void
  function cmdline_parser_release (line 167) | static void
  function write_into_file (line 184) | static void
  function cmdline_parser_dump (line 196) | int
  function cmdline_parser_file_save (line 221) | int
  function cmdline_parser_free (line 241) | void
  function cmdline_parser (line 262) | int
  function cmdline_parser_ext (line 268) | int
  function cmdline_parser2 (line 284) | int
  function cmdline_parser_required (line 307) | int
  function update_arg (line 336) | static
  function cmdline_parser_internal (line 423) | int

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/cmdline.h
  type gengetopt_args_info (line 38) | struct gengetopt_args_info
  type cmdline_parser_params (line 58) | struct cmdline_parser_params
  type gengetopt_args_info (line 82) | struct gengetopt_args_info
  type gengetopt_args_info (line 96) | struct gengetopt_args_info
  type gengetopt_args_info (line 108) | struct gengetopt_args_info
  type cmdline_parser_params (line 109) | struct cmdline_parser_params
  type gengetopt_args_info (line 118) | struct gengetopt_args_info
  type gengetopt_args_info (line 128) | struct gengetopt_args_info
  type cmdline_parser_params (line 144) | struct cmdline_parser_params
  type cmdline_parser_params (line 151) | struct cmdline_parser_params
  type gengetopt_args_info (line 158) | struct gengetopt_args_info
  type gengetopt_args_info (line 164) | struct gengetopt_args_info
  type gengetopt_args_info (line 173) | struct gengetopt_args_info

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/bloom.cpp
  type graph (line 4) | namespace graph {
    type bloom (line 5) | namespace bloom {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/bloom.hpp
  type graph (line 3) | namespace graph {
    type bloom (line 4) | namespace bloom {
      class BloomAreConnected (line 7) | class BloomAreConnected
        method test (line 15) | bool test( const int32_t node_id_1, const int32_t node_id_2 ) const {
      class BloomAreConnected (line 9) | class BloomAreConnected {
        method test (line 15) | bool test( const int32_t node_id_1, const int32_t node_id_2 ) const {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/graph.cpp
  type graph (line 2) | namespace graph {
    function neighbouring_node_id_iterator (line 4) | neighbouring_node_id_iterator neighbouring_node_id_iterator :: end_mar...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/graph.hpp
  type graph (line 11) | namespace graph {
    class VerySimpleGraphInterface (line 13) | class VerySimpleGraphInterface
      method degree (line 23) | virtual int32_t degree(const int32_t node_id) const { return int32_t...
      method are_connected (line 24) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) con...
    class VerySimpleGraphInterface (line 15) | class VerySimpleGraphInterface { // consecutive ints. No attributes, o...
      method degree (line 23) | virtual int32_t degree(const int32_t node_id) const { return int32_t...
      method are_connected (line 24) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) con...
    class neighbouring_rel_id_iterator (line 33) | class neighbouring_rel_id_iterator : public std :: iterator< std :: fo...
      method neighbouring_rel_id_iterator (line 38) | neighbouring_rel_id_iterator(const VerySimpleGraphInterface * vsg, c...
      method neighbouring_rel_id_iterator (line 43) | neighbouring_rel_id_iterator & operator++() {
      method neighbouring_rel_id_iterator (line 56) | neighbouring_rel_id_iterator   operator++(int) { // postfix. Should ...
      method at_end (line 61) | bool at_end() const {
    class neighbouring_node_id_iterator (line 70) | class neighbouring_node_id_iterator : public std :: iterator< std :: f...
      method neighbouring_node_id_iterator (line 77) | neighbouring_node_id_iterator() : vsg(NULL), node_id(0) { // constru...
      method neighbouring_node_id_iterator (line 79) | neighbouring_node_id_iterator(const VerySimpleGraphInterface * _vsg,...
      method neighbouring_node_id_iterator (line 84) | neighbouring_node_id_iterator & operator++() {
      method neighbouring_node_id_iterator (line 98) | neighbouring_node_id_iterator   operator++(int) { // postfix. Should...
      method at_end (line 104) | bool at_end() const {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/loading.cpp
  type graph (line 22) | namespace graph {
    type loading (line 23) | namespace loading {
      type ModifiableNetwork (line 28) | struct ModifiableNetwork
        method ModifiableNetwork (line 95) | ModifiableNetwork(const bool directed, const bool weighted) : Netw...
        method find_ordered_node_names_offset (line 99) | int32_t find_ordered_node_names_offset(const t &node_name) {
      class MyVSG (line 37) | class MyVSG
        method MyVSG (line 61) | MyVSG () {
        method numNodes (line 64) | int numNodes() const { return this->N; }
        method numRels (line 65) | int numRels() const { return this->R; }
        method are_connected (line 74) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) c...
      type hash_pair_of_ints (line 42) | struct hash_pair_of_ints {
      class MyVSG (line 50) | class MyVSG : public VerySimpleGraphInterface {
        method MyVSG (line 61) | MyVSG () {
        method numNodes (line 64) | int numNodes() const { return this->N; }
        method numRels (line 65) | int numRels() const { return this->R; }
        method are_connected (line 74) | virtual bool are_connected(int32_t node_id_1, int32_t node_id_2) c...
      type ModifiableNetwork (line 92) | struct ModifiableNetwork : public NetworkInterface<NodeNameT> { // N...
        method ModifiableNetwork (line 95) | ModifiableNetwork(const bool directed, const bool weighted) : Netw...
        method find_ordered_node_names_offset (line 99) | int32_t find_ordered_node_names_offset(const t &node_name) {
      type ModifiableNetwork<graph :: NodeNameIsInt64> (line 118) | struct ModifiableNetwork<graph :: NodeNameIsInt64>
      type ModifiableNetwork<graph :: NodeNameIsString> (line 119) | struct ModifiableNetwork<graph :: NodeNameIsString>
      function ThreeStrings (line 121) | static ThreeStrings parseLine(const string &lineOrig) {
      function read_edge_list_from_file (line 151) | static void read_edge_list_from_file(ModifiableNetwork<NodeNameT> *m...
      function make_Network_from_edge_list_int64 (line 289) | std :: auto_ptr< graph :: NetworkInt64 > make_Network_from_edge_list...
      function make_Network_from_edge_list_string (line 293) | std :: auto_ptr< graph :: NetworkString > make_Network_from_edge_lis...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/loading.hpp
  type graph (line 7) | namespace graph {
    type loading (line 8) | namespace loading {
      type BadlyFormattedLine (line 10) | struct BadlyFormattedLine : public std :: exception {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/network.cpp
  type graph (line 2) | namespace graph {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/network.hpp
  type graph (line 11) | namespace graph {
    type NetworkInterface (line 14) | struct NetworkInterface
    type NetworkInterfaceConvertedToString (line 15) | struct NetworkInterfaceConvertedToString
      method numNodes (line 65) | virtual int32_t numNodes() const { return this->get_plain_graph()->n...
      method numRels (line 66) | virtual int32_t numRels()  const { return this->get_plain_graph()->n...
      method degree (line 67) | virtual int32_t degree(const int32_t node_id) const { return this->g...
    type NetworkInterfaceConvertedToStringWithWeights (line 16) | struct NetworkInterfaceConvertedToStringWithWeights
    type NodeNameIsInt64 (line 18) | struct NodeNameIsInt64
      method value_type (line 39) | inline static value_type fromString(const std :: string &s) {
    type NodeNameIsString (line 19) | struct NodeNameIsString
      method value_type (line 55) | inline static value_type fromString(const std :: string &s) {
    type BadlyFormattedNodeName (line 20) | struct BadlyFormattedNodeName : public std :: exception { // if the te...
      method BadlyFormattedNodeName (line 22) | BadlyFormattedNodeName(const char * type_name, const std :: string &...
    type NodeNameIsInt64 (line 37) | struct NodeNameIsInt64 {
      method value_type (line 39) | inline static value_type fromString(const std :: string &s) {
    type NodeNameIsString (line 53) | struct NodeNameIsString {
      method value_type (line 55) | inline static value_type fromString(const std :: string &s) {
    type NetworkInterfaceConvertedToString (line 62) | struct NetworkInterfaceConvertedToString  { // Any NodeNameT (int or s...
      method numNodes (line 65) | virtual int32_t numNodes() const { return this->get_plain_graph()->n...
      method numRels (line 66) | virtual int32_t numRels()  const { return this->get_plain_graph()->n...
      method degree (line 67) | virtual int32_t degree(const int32_t node_id) const { return this->g...
    type NetworkInterfaceConvertedToStringWithWeights (line 71) | struct NetworkInterfaceConvertedToStringWithWeights : public NetworkIn...
    type NetworkInterface (line 76) | struct NetworkInterface : public NetworkInterfaceConvertedToStringWith...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/saving.cpp
  type graph (line 8) | namespace graph {
    type saving (line 9) | namespace saving {
      function print_Network_to_screen (line 11) | void print_Network_to_screen( const graph :: NetworkInterfaceConvert...

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/saving.hpp
  type graph (line 5) | namespace graph {
    type saving (line 6) | namespace saving {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/strings.cpp
  type strings (line 4) | namespace strings {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/strings.hpp
  type strings (line 4) | namespace strings {
    class StrH (line 5) | class StrH { // string handle. It just wraps an int that refers to the...
      type hasher (line 10) | struct hasher
    type StrH :: hasher (line 13) | struct StrH :: hasher {
    class StringArray (line 16) | class StringArray {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/weights.cpp
  type graph (line 7) | namespace graph {
    type weights (line 8) | namespace weights {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/graph/weights.hpp
  type graph (line 9) | namespace graph {
    type weights (line 10) | namespace weights {
      type EdgeDetailsInterface (line 12) | struct EdgeDetailsInterface {
      type EdgeDetails (line 22) | struct EdgeDetails : public EdgeDetailsInterface {
        method is_directed (line 29) | virtual bool is_directed() const { return W :: is_directed; }
        method is_weighted (line 30) | virtual bool is_weighted() const { return W :: is_weighted; }
      type NoDetails (line 33) | struct NoDetails { // unweighted, undirected
        method inform (line 37) | void inform(const bool, const std :: string) const {
        method getl2h (line 39) | long double getl2h() const {
        method geth2l (line 42) | long double geth2l() const {
      type DirectedLDoubleWeights (line 47) | struct DirectedLDoubleWeights {
        type LdblPair (line 50) | struct LdblPair : public std :: pair<long double,long double> {
          method LdblPair (line 51) | LdblPair() {
          type DuplicateWeightedEdge (line 54) | struct DuplicateWeightedEdge : public std :: exception {
          method inform (line 56) | void inform(const bool highToLow, const std :: string weight) { ...
          method getl2h (line 71) | long double getl2h() const {
          method geth2l (line 74) | long double geth2l() const {
      type DirectedNoWeights (line 79) | struct DirectedNoWeights {
        type IntPair (line 82) | struct IntPair : public std :: pair<int,int> {
          method IntPair (line 83) | IntPair() {
          method inform (line 86) | void inform(const bool highToLow, const std :: string) { // the ...
          method getl2h (line 93) | long double getl2h() const {
          method geth2l (line 96) | long double geth2l() const {
      type WeightNoDir (line 101) | struct WeightNoDir {
        type LdblPair (line 104) | struct LdblPair {
          method LdblPair (line 106) | LdblPair() {
          type DuplicateWeightedEdge (line 109) | struct DuplicateWeightedEdge : public std :: exception {
          method inform (line 111) | void inform(const bool , const std :: string weight) { // the we...
          method getl2h (line 122) | long double getl2h() const {
          method geth2l (line 125) | long double geth2l() const {

FILE: Algorithms/2012-Fast-Clique-Percolation/src_refactor/percolateCliques.cpp
  function main (line 25) | int main(int argc, char **argv) {
  function percolateCliques (line 48) | void percolateCliques(const char * edgeListFileName, const int k, const ...

FILE: Algorithms/2013-MSCD/src/analyse_main.cpp
  function print_usage (line 19) | void print_usage(const char * command) {
  function main (line 40) | int main (int argc, char * const argv[]) {

FILE: Algorithms/2013-MSCD/src/conv_main.cpp
  function print_usage (line 19) | void print_usage(const char * command) {
  function main (line 57) | int main (int argc, char * const argv[]) {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_afg.cpp
  type mscd (line 23) | namespace mscd {
    type alg (line 24) | namespace alg {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_afg.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_algorithm.h
  function namespace (line 37) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_hslsw.cpp
  type mscd (line 19) | namespace mscd {
    type alg (line 20) | namespace alg {
      type great_sim (line 359) | struct great_sim {
      function comp_key (line 366) | bool comp_key(const std::pair<long,preal> & p1, const std::pair<long...

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_hslsw.h
  function namespace (line 27) | namespace mscd {
  function class (line 50) | class MSCD_HSLSW: public MSCDAlgorithm {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_lfk.cpp
  type mscd (line 19) | namespace mscd {
    type alg (line 20) | namespace alg {
      type great_sim (line 360) | struct great_sim {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_lfk.h
  function namespace (line 25) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_lfk2.cpp
  type mscd (line 27) | namespace mscd {
    type alg (line 28) | namespace alg {
      function thread_grow_func (line 33) | void thread_grow_func(MSCD_LFK2 & inst, MSCD_LFK2::ThreadGrowData & ...
      function thread_check_func (line 41) | void thread_check_func(MSCD_LFK2 & inst, MSCD_LFK2::ThreadCheckData ...
      function thread_merge_func (line 48) | void thread_merge_func(MSCD_LFK2 & inst, MSCD_LFK2::ThreadMergeData ...
      type great_sim (line 367) | struct great_sim {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_lfk2.h
  function namespace (line 29) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_rb.cpp
  type mscd (line 23) | namespace mscd {
    type alg (line 24) | namespace alg {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_rb.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_rn.cpp
  type mscd (line 23) | namespace mscd {
    type alg (line 24) | namespace alg {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_rn.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_so.cpp
  type mscd (line 25) | namespace mscd {
    type alg (line 26) | namespace alg {
      function computeALpart (line 473) | void computeALpart(const long begin, const long end, preal min_edge,...

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_so.h
  function namespace (line 19) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_som.cpp
  type mscd (line 20) | namespace mscd {
    type alg (line 21) | namespace alg {
      function MAT_TYPE (line 445) | MAT_TYPE const * MSCD_SOM::getMt(const ds::Graph::adjlist & al, cons...

FILE: Algorithms/2013-MSCD/src/mscd/alg/mscd_som.h
  function namespace (line 28) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/ds/communities.h
  function namespace (line 20) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/ds/graph.h
  function namespace (line 17) | namespace mscd {
  function insert_edge (line 103) | inline bool insert_edge(const long s, const long t, const preal w) {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/community_list_reader.cpp
  type mscd (line 18) | namespace mscd {
    type io (line 19) | namespace io {
      type in (line 20) | namespace in {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/community_list_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/community_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/edge_list_graph_reader.cpp
  type mscd (line 17) | namespace mscd {
    type io (line 18) | namespace io {
      type in (line 19) | namespace in {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/edge_list_graph_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/graph_reader copy.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/graph_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/lf_community_reader.cpp
  type mscd (line 18) | namespace mscd {
    type io (line 19) | namespace io {
      type in (line 20) | namespace in {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/lf_community_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/pajek_community_reader.cpp
  type mscd (line 20) | namespace mscd {
    type io (line 21) | namespace io {
      type in (line 22) | namespace in {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/pajek_community_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/pajek_graph_reader.cpp
  type mscd (line 16) | namespace mscd {
    type io (line 17) | namespace io {
      type in (line 18) | namespace in {

FILE: Algorithms/2013-MSCD/src/mscd/io/in/pajek_graph_reader.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/community_list_writer.cpp
  type mscd (line 18) | namespace mscd {
    type io (line 19) | namespace io {
      type out (line 20) | namespace out {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/community_list_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/community_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/edge_list_graph_writer.cpp
  type mscd (line 17) | namespace mscd {
    type io (line 18) | namespace io {
      type out (line 19) | namespace out {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/edge_list_graph_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/graph_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/lf_community_writer.cpp
  type mscd (line 18) | namespace mscd {
    type io (line 19) | namespace io {
      type out (line 20) | namespace out {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/lf_community_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/pajek_community_writer.cpp
  type mscd (line 18) | namespace mscd {
    type io (line 19) | namespace io {
      type out (line 20) | namespace out {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/pajek_community_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/pajek_graph_writer.cpp
  type mscd (line 17) | namespace mscd {
    type io (line 18) | namespace io {
      type out (line 19) | namespace out {

FILE: Algorithms/2013-MSCD/src/mscd/io/out/pajek_graph_writer.h
  function namespace (line 16) | namespace mscd {

FILE: Algorithms/2013-MSCD/src/mscd_main.cpp
  function print_usage (line 24) | void print_usage(const char * command) {
  function main (line 55) | int main (int argc, char * const argv[]) {

FILE: Algorithms/2013-MSCD/src/speedtest_main.cpp
  class DummyCommunityListWriter (line 21) | class DummyCommunityListWriter: public mscd::io::out::CommunityWriter {
    method GetName (line 23) | virtual std::string GetName() const { return ""; }
    method ToFile (line 24) | virtual bool ToFile(const std::string &, const mscd::ds::Communities &...
  function print_usage (line 31) | void print_usage(const char * command) {
  function main (line 60) | int main (int argc, char * const argv[]) {

FILE: Algorithms/2013-MSCD/src/toolkit/atomic_set.h
  function namespace (line 17) | namespace toolkit {

FILE: Algorithms/2013-MSCD/src/toolkit/nmi.h
  function namespace (line 21) | namespace toolkit {

FILE: Algorithms/2013-MSCD/src/toolkit/registry.h
  function namespace (line 17) | namespace toolkit {

FILE: Algorithms/2013-MSCD/src/toolkit/tokeniser.cpp
  type toolkit (line 6) | namespace toolkit {

FILE: Algorithms/2013-MSCD/src/toolkit/tokeniser.h
  function namespace (line 20) | namespace toolkit {

FILE: Algorithms/2013-MSCD/src/toolkit/tools.h
  function namespace (line 20) | namespace toolkit {

FILE: Algorithms/2013-SVINET/src-cmake/src/collection/fastqueue.hh
  class FastQueue (line 22) | class FastQueue {
    method FastQueue (line 24) | FastQueue() :
    method length (line 31) | unsigned length() const { return _list.size(); }
    method total (line 54) | double total() const { return _total; }
    method KVList (line 58) | const KVList &list() const { return _list; }
    method K (line 64) | static uint32_t K() { return _K; }
  function string (line 293) | inline string

FILE: Algorithms/2013-SVINET/src-cmake/src/collection/matrix.hh
  class Edge (line 16) | class Edge: public std::pair<uint32_t, uint32_t> {
    method Edge (line 19) | Edge(): inherited() { }
    method Edge (line 20) | Edge(uint32_t a, uint32_t b): inherited(a,b) { }
  class D1Array (line 37) | class D1Array {
    method n (line 43) | uint32_t n() const { return _n; }
    method size (line 44) | uint32_t size() const { return _n; }
    method T (line 54) | T *data() { return _data; }
    method T (line 55) | const T * const data() const {return (const T *)_data;}
    method T (line 56) | const T * const const_data() const {return (const T *)_data;}
    method lognormalize (line 67) | void lognormalize() { }
    method lognormalize (line 68) | void lognormalize(double log_sum) { }
  function cmpdouble (line 210) | static int
  function cmpuint32 (line 218) | static int
  function cmppairval (line 226) | static int
  function cmppairedgeval (line 234) | static int
  function T (line 257) | inline T
  function sub (line 410) | inline void
  function prod (line 421) | inline void
  function dot (line 432) | inline double
  function dotverb (line 443) | inline double
  function inner_prod_max (line 459) | inline double
  function inner_prod (line 478) | inline void
  function inner_prod_max2 (line 489) | inline double
  function T (line 547) | inline T &
  function T (line 554) | inline T
  function string (line 561) | inline string
  function string (line 579) | inline string
  function string (line 593) | inline string
  class D2Array (line 609) | class D2Array {
    method m (line 615) | uint32_t m() const { return _m; }
    method n (line 616) | uint32_t n() const { return _n; }
    method T (line 627) | T **data() { return _data; }
    method T (line 628) | const T ** const data() const {return (const T **)_data;}
    method T (line 629) | const T ** const const_data() const {return (const T **)_data;}
  function T (line 693) | inline T
  function T (line 821) | inline T
  function string (line 897) | inline string
  function string (line 925) | inline string
  function sub (line 979) | inline void
  class D3Array (line 1003) | class D3Array {
    method m (line 1008) | uint32_t m() const { return _m; }
    method n (line 1009) | uint32_t n() const { return _n; }
    method k (line 1010) | uint32_t k() const { return _k; }
    method T (line 1012) | T ***data() { return _data; }
    method T (line 1013) | const T *** const data() const { return (const T ***)_data; }
    method T (line 1014) | const T *** const const_data() const { return (const T ***)_data; }
  function T (line 1059) | inline T
  function string (line 1109) | inline string

FILE: Algorithms/2013-SVINET/src-cmake/src/collection/tsqueue.hh
  class TSQueue (line 9) | class TSQueue : public std::queue<T *>
    method TSQueue (line 14) | TSQueue() { }
  function T (line 35) | inline T *

FILE: Algorithms/2013-SVINET/src-cmake/src/community.hh
  class Community (line 6) | class Community {
    method Community (line 8) | Community() { }
    method Community (line 9) | Community(uint32_t id)
    method nodes (line 17) | uint32_t nodes() const { return _network.size(); }

FILE: Algorithms/2013-SVINET/src-cmake/src/env.hh
  class Env (line 52) | class Env {
  function string (line 270) | inline string
  function string (line 277) | inline string
  function timeval_subtract (line 636) | inline int
  function timeval_add (line 660) | inline void

FILE: Algorithms/2013-SVINET/src-cmake/src/fastamm.cc
  function string (line 358) | string
  type timeval (line 552) | struct timeval
  type timeval (line 569) | struct timeval
  type timeval (line 956) | struct timeval
  type timeval (line 1019) | struct timeval

FILE: Algorithms/2013-SVINET/src-cmake/src/fastamm.hh
  class FPhiComp (line 27) | class FPhiComp {
    method FPhiComp (line 29) | FPhiComp(const Env &env, gsl_rng **r,
    method Array (line 53) | const Array& phi1() const { return _phi1; }
    method Array (line 54) | const Array& phi2() const { return _phi2; }
    method Array (line 56) | Array& mutable_phi1()  { return _phi1; }
    method Array (line 57) | Array& mutable_phi2()  { return _phi2; }
    method iter (line 59) | uint32_t iter() const { return _iter; }
  class FastAMM (line 213) | class FastAMM {
    type timeval (line 375) | struct timeval
  function yval_t (line 773) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/fastamm2.cc
  function string (line 343) | string
  type timeval (line 539) | struct timeval
  type timeval (line 569) | struct timeval
  type timeval (line 977) | struct timeval
  type timeval (line 1042) | struct timeval

FILE: Algorithms/2013-SVINET/src-cmake/src/fastamm2.hh
  class PhiCompute (line 25) | class PhiCompute {
    method PhiCompute (line 27) | PhiCompute(const Env &env, gsl_rng **r,
    method Array (line 51) | const Array& phi1() const { return _phi1; }
    method Array (line 52) | const Array& phi2() const { return _phi2; }
    method Array (line 54) | Array& mutable_phi1()  { return _phi1; }
    method Array (line 55) | Array& mutable_phi2()  { return _phi2; }
    method iter (line 57) | uint32_t iter() const { return _iter; }
  class FastAMM2 (line 211) | class FastAMM2 {
    type timeval (line 364) | struct timeval
  function yval_t (line 739) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/fastinit.cc
  function string (line 166) | string

FILE: Algorithms/2013-SVINET/src-cmake/src/fastinit.hh
  class FastInit (line 27) | class FastInit {
    type timeval (line 145) | struct timeval
  function yval_t (line 435) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/linksampling.cc
  function string (line 190) | string

FILE: Algorithms/2013-SVINET/src-cmake/src/linksampling.hh
  class LinkSampling (line 21) | class LinkSampling {
    type timeval (line 131) | struct timeval
  function yval_t (line 351) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/log.cc
  function string (line 55) | string
  function string (line 66) | string
  type stat (line 109) | struct stat

FILE: Algorithms/2013-SVINET/src-cmake/src/log.hh
  class Logger (line 22) | class Logger {
    method string (line 29) | static string log_fname() { return dirname() + string("/") + _log_fnam...
    method string (line 30) | static string dirname()   { return _prefix; }

FILE: Algorithms/2013-SVINET/src-cmake/src/main.cc
  function term_handler (line 29) | void
  function main (line 42) | int
  function usage (line 380) | void
  function test (line 408) | void

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsbgen.cc
  type stat (line 893) | struct stat

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsbgen.hh
  class MMSBGen (line 10) | class MMSBGen {
  function string (line 135) | inline string

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsbinfer.cc
  function string (line 230) | string
  type timeval (line 479) | struct timeval
  type timeval (line 525) | struct timeval
  type timeval (line 539) | struct timeval
  type timeval (line 559) | struct timeval
  type timeval (line 657) | struct timeval
  type timeval (line 672) | struct timeval
  type timeval (line 673) | struct timeval
  type timeval (line 688) | struct timeval
  type timeval (line 1323) | struct timeval
  type timeval (line 1359) | struct timeval
  type timeval (line 1424) | struct timeval
  type timeval (line 1707) | struct timeval
  type timeval (line 1752) | struct timeval
  type timeval (line 2419) | struct timeval
  type timeval (line 2641) | struct timeval

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsbinfer.hh
  class PhiComp (line 25) | class PhiComp {
    method PhiComp (line 27) | PhiComp(const Env &env, const uint32_t &iter,
    method static_initialize (line 45) | static void static_initialize(uint32_t n, uint32_t k) { }
    method static_uninitialize (line 46) | static void static_uninitialize() { }
    method Array (line 50) | const Array& phi1() const { return _phi1; }
    method Array (line 51) | const Array& phi2() const { return _phi2; }
    method Array (line 53) | Array& mutable_phi1()  { return _phi1; }
    method Array (line 54) | Array& mutable_phi2()  { return _phi2; }
    method iter (line 56) | uint32_t iter() const { return _iter; }
  type MRStats (line 201) | struct MRStats  {
    type timeval (line 204) | struct timeval
    type timeval (line 205) | struct timeval
    type timeval (line 206) | struct timeval
    type timeval (line 209) | struct timeval
    type timeval (line 210) | struct timeval
    type timeval (line 211) | struct timeval
    type timeval (line 214) | struct timeval
    type timeval (line 215) | struct timeval
    type timeval (line 216) | struct timeval
  type timeval (line 230) | struct timeval
  type timeval (line 231) | struct timeval
  type timeval (line 232) | struct timeval
  type timeval (line 234) | struct timeval
  type timeval (line 235) | struct timeval
  type timeval (line 236) | struct timeval
  type timeval (line 238) | struct timeval
  type timeval (line 239) | struct timeval
  type timeval (line 240) | struct timeval
  class PhiRunner (line 245) | class PhiRunner : public Thread {
    method PhiRunner (line 247) | PhiRunner(const Env &env, Network &network,
    method set_done (line 277) | void set_done()   { _done = true; }
    method done (line 278) | bool done() const { return _done; }
    method EdgeList (line 281) | const EdgeList &sample() const { assert(_sample); return *_sample; }
    method Matrix (line 283) | const Matrix &gammat() const  { return _gammat; }
    method Matrix (line 284) | const Matrix &lambdat() const { return _lambdat; }
    method Array (line 285) | const Array &count() const    { return _count; }
    method MRStats (line 287) | const MRStats *rt() const { return &_rt; }
  class MMSBInfer (line 337) | class MMSBInfer {
    type timeval (line 471) | struct timeval
  function yval_t (line 844) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsbinferorig.cc
  function string (line 589) | string

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsbinferorig.hh
  class PhiComp2 (line 22) | class PhiComp2 {
    method PhiComp2 (line 24) | PhiComp2(const Env &env, const uint32_t &iter,
    method Array (line 47) | const Array& phi1() const { return _phi1; }
    method Array (line 48) | const Array& phi2() const { return _phi2; }
    method iter (line 50) | uint32_t iter() const { return _iter; }
    method D3 (line 55) | static const D3 &gphi1() { assert(_gphi1); return *_gphi1; }
    method D3 (line 56) | static const D3 &gphi2() { assert(_gphi2); return *_gphi2; }
  class MMSBInferOrig (line 229) | class MMSBInferOrig {
    type timeval (line 291) | struct timeval
  function yval_t (line 336) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/mmsborig.hh
  class MMSBOrig (line 17) | class MMSBOrig {

FILE: Algorithms/2013-SVINET/src-cmake/src/network.cc
  function string (line 161) | string

FILE: Algorithms/2013-SVINET/src-cmake/src/network.hh
  class Network (line 22) | class Network {
    method Network (line 24) | Network(Env &env):
    method SparseMatrix (line 33) | const SparseMatrix &sparse_y() const { return _sparse_y; }
    method SparseMatrix (line 34) | SparseMatrix &sparse_y() { return _sparse_y; }
    method SparseMatrix (line 35) | SparseMatrix &sparse_zeros() { return _sparse_zeros; }
    method EdgeList (line 42) | const EdgeList &edges() const { return _edges; }
    method EdgeList (line 43) | EdgeList &edgelist() { return _edges; }
    method nlinks (line 45) | uint32_t nlinks() const { return _edges.size(); }
    method Array (line 47) | const Array &deg() const { assert(_env.undirected); return _deg; }
    method Array (line 48) | Array &deg() { assert(_env.undirected); return _deg; }
    method MapVec (line 52) | const MapVec &gt_communities() const { return _gt_communities; }
    method MapVec (line 53) | const MapVec &gt_communities_seq() const { return _gt_communities_seq; }
    method MapVec (line 55) | const MapVec &init_communities() const { return _init_communities; }
    method MapVec (line 56) | const MapVec &init_communities_seq() const { return _init_communities_...
    method MapVec (line 58) | const MapVec &init_community_to_nodes() const { return _init_community...
    method MapVec (line 59) | const MapVec &init_community_to_nodes_seq() const { return _init_commu...
    method ones (line 61) | uint32_t ones() const { return _ones; }
    method singles (line 62) | uint32_t singles() const { return _single_nodes; }
    method IDMap (line 81) | const IDMap &id2seq() const { return _id2seq; }
    method IDMap (line 82) | const IDMap &seq2id() const { return _seq2id; }
    method StrMap (line 84) | const StrMap &str2id() const { return _str2id; }
    method StrMapInv (line 85) | const StrMapInv &id2str() const { return _id2str; }
  function yval_t (line 158) | inline yval_t
  function string (line 207) | inline string

FILE: Algorithms/2013-SVINET/src-cmake/src/sbm.cc
  function string (line 187) | string

FILE: Algorithms/2013-SVINET/src-cmake/src/sbm.hh
  class SBM (line 24) | class SBM {
    type timeval (line 144) | struct timeval
  function yval_t (line 362) | inline yval_t

FILE: Algorithms/2013-SVINET/src-cmake/src/thread.hh
  class Thread (line 12) | class Thread {
    method pthread_t (line 19) | pthread_t id() const { return _tid; }
    method do_work (line 21) | virtual int do_work() { return 0; }
  class Mutex (line 35) | class Mutex {
  class CondMutex (line 86) | class CondMutex {
    method lock (line 94) | int lock() { return _mutex.lock(); }
    method unlock (line 95) | int unlock() { return _mutex.unlock(); }

FILE: Algorithms/2013-SVINET/svinet-master/src/community.hh
  class Community (line 6) | class Community {
    method Community (line 8) | Community() { }
    method Community (line 9) | Community(uint32_t id)
    method nodes (line 17) | uint32_t nodes() const { return _network.size(); }

FILE: Algorithms/2013-SVINET/svinet-master/src/env.hh
  class Env (line 52) | class Env {
  function string (line 270) | inline string
  function string (line 277) | inline string
  function timeval_subtract (line 636) | inline int
  function timeval_add (line 660) | inline void

FILE: Algorithms/2013-SVINET/svinet-master/src/fastamm.cc
  function string (line 358) | string
  type timeval (line 552) | struct timeval
  type timeval (line 569) | struct timeval
  type timeval (line 956) | struct timeval
  type timeval (line 1019) | struct timeval

FILE: Algorithms/2013-SVINET/svinet-master/src/fastamm.hh
  class FPhiComp (line 27) | class FPhiComp {
    method FPhiComp (line 29) | FPhiComp(const Env &env, gsl_rng **r,
    method Array (line 53) | const Array& phi1() const { return _phi1; }
    method Array (line 54) | const Array& phi2() const { return _phi2; }
    method Array (line 56) | Array& mutable_phi1()  { return _phi1; }
    method Array (line 57) | Array& mutable_phi2()  { return _phi2; }
    method iter (line 59) | uint32_t iter() const { return _iter; }
  class FastAMM (line 213) | class FastAMM {
    type timeval (line 375) | struct timeval
  function yval_t (line 773) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/fastamm2.cc
  function string (line 343) | string
  type timeval (line 539) | struct timeval
  type timeval (line 569) | struct timeval
  type timeval (line 977) | struct timeval
  type timeval (line 1042) | struct timeval

FILE: Algorithms/2013-SVINET/svinet-master/src/fastamm2.hh
  class PhiCompute (line 25) | class PhiCompute {
    method PhiCompute (line 27) | PhiCompute(const Env &env, gsl_rng **r,
    method Array (line 51) | const Array& phi1() const { return _phi1; }
    method Array (line 52) | const Array& phi2() const { return _phi2; }
    method Array (line 54) | Array& mutable_phi1()  { return _phi1; }
    method Array (line 55) | Array& mutable_phi2()  { return _phi2; }
    method iter (line 57) | uint32_t iter() const { return _iter; }
  class FastAMM2 (line 211) | class FastAMM2 {
    type timeval (line 364) | struct timeval
  function yval_t (line 739) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/fastinit.cc
  function string (line 166) | string

FILE: Algorithms/2013-SVINET/svinet-master/src/fastinit.hh
  class FastInit (line 27) | class FastInit {
    type timeval (line 145) | struct timeval
  function yval_t (line 435) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/fastqueue.hh
  class FastQueue (line 22) | class FastQueue {
    method FastQueue (line 24) | FastQueue():
    method length (line 30) | unsigned length() const      		{ return _list.size(); }
    method total (line 45) | double total() const                  { return _total; }
    method KVList (line 47) | const KVList &list() const { return _list; }
    method K (line 51) | static uint32_t K() { return _K; }
  function string (line 291) | inline string

FILE: Algorithms/2013-SVINET/svinet-master/src/linksampling.cc
  function string (line 190) | string

FILE: Algorithms/2013-SVINET/svinet-master/src/linksampling.hh
  class LinkSampling (line 21) | class LinkSampling {
    type timeval (line 131) | struct timeval
  function yval_t (line 351) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/log.cc
  function string (line 55) | string
  function string (line 66) | string
  type stat (line 109) | struct stat

FILE: Algorithms/2013-SVINET/svinet-master/src/log.hh
  class Logger (line 22) | class Logger {
    method string (line 29) | static string log_fname() { return dirname() + string("/") + _log_fnam...
    method string (line 30) | static string dirname()   { return _prefix; }

FILE: Algorithms/2013-SVINET/svinet-master/src/main.cc
  function term_handler (line 29) | void
  function main (line 42) | int
  function usage (line 380) | void
  function test (line 408) | void

FILE: Algorithms/2013-SVINET/svinet-master/src/matrix.hh
  class Edge (line 16) | class Edge: public std::pair<uint32_t, uint32_t> {
    method Edge (line 19) | Edge(): inherited() { }
    method Edge (line 20) | Edge(uint32_t a, uint32_t b): inherited(a,b) { }
  class D1Array (line 37) | class D1Array {
    method n (line 43) | uint32_t n() const { return _n; }
    method size (line 44) | uint32_t size() const { return _n; }
    method T (line 54) | T *data() { return _data; }
    method T (line 55) | const T * const data() const {return (const T *)_data;}
    method T (line 56) | const T * const const_data() const {return (const T *)_data;}
    method lognormalize (line 67) | void lognormalize() { }
    method lognormalize (line 68) | void lognormalize(double log_sum) { }
  function cmpdouble (line 210) | static int
  function cmpuint32 (line 218) | static int
  function cmppairval (line 226) | static int
  function cmppairedgeval (line 234) | static int
  function T (line 257) | inline T
  function sub (line 410) | inline void
  function prod (line 421) | inline void
  function dot (line 432) | inline double
  function dotverb (line 443) | inline double
  function inner_prod_max (line 459) | inline double
  function inner_prod (line 478) | inline void
  function inner_prod_max2 (line 489) | inline double
  function T (line 547) | inline T &
  function T (line 554) | inline T
  function string (line 561) | inline string
  function string (line 579) | inline string
  function string (line 593) | inline string
  class D2Array (line 609) | class D2Array {
    method m (line 615) | uint32_t m() const { return _m; }
    method n (line 616) | uint32_t n() const { return _n; }
    method T (line 627) | T **data() { return _data; }
    method T (line 628) | const T ** const data() const {return (const T **)_data;}
    method T (line 629) | const T ** const const_data() const {return (const T **)_data;}
  function T (line 693) | inline T
  function T (line 821) | inline T
  function string (line 897) | inline string
  function string (line 925) | inline string
  function sub (line 979) | inline void
  class D3Array (line 1003) | class D3Array {
    method m (line 1008) | uint32_t m() const { return _m; }
    method n (line 1009) | uint32_t n() const { return _n; }
    method k (line 1010) | uint32_t k() const { return _k; }
    method T (line 1012) | T ***data() { return _data; }
    method T (line 1013) | const T *** const data() const { return (const T ***)_data; }
    method T (line 1014) | const T *** const const_data() const { return (const T ***)_data; }
  function T (line 1059) | inline T
  function string (line 1109) | inline string

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsbgen.cc
  type stat (line 893) | struct stat

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsbgen.hh
  class MMSBGen (line 10) | class MMSBGen {
  function string (line 135) | inline string

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsbinfer.cc
  function string (line 230) | string
  type timeval (line 479) | struct timeval
  type timeval (line 525) | struct timeval
  type timeval (line 539) | struct timeval
  type timeval (line 559) | struct timeval
  type timeval (line 657) | struct timeval
  type timeval (line 672) | struct timeval
  type timeval (line 673) | struct timeval
  type timeval (line 688) | struct timeval
  type timeval (line 1323) | struct timeval
  type timeval (line 1359) | struct timeval
  type timeval (line 1424) | struct timeval
  type timeval (line 1707) | struct timeval
  type timeval (line 1752) | struct timeval
  type timeval (line 2419) | struct timeval
  type timeval (line 2641) | struct timeval

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsbinfer.hh
  class PhiComp (line 25) | class PhiComp {
    method PhiComp (line 27) | PhiComp(const Env &env, const uint32_t &iter,
    method static_initialize (line 45) | static void static_initialize(uint32_t n, uint32_t k) { }
    method static_uninitialize (line 46) | static void static_uninitialize() { }
    method Array (line 50) | const Array& phi1() const { return _phi1; }
    method Array (line 51) | const Array& phi2() const { return _phi2; }
    method Array (line 53) | Array& mutable_phi1()  { return _phi1; }
    method Array (line 54) | Array& mutable_phi2()  { return _phi2; }
    method iter (line 56) | uint32_t iter() const { return _iter; }
  type MRStats (line 201) | struct MRStats  {
    type timeval (line 204) | struct timeval
    type timeval (line 205) | struct timeval
    type timeval (line 206) | struct timeval
    type timeval (line 209) | struct timeval
    type timeval (line 210) | struct timeval
    type timeval (line 211) | struct timeval
    type timeval (line 214) | struct timeval
    type timeval (line 215) | struct timeval
    type timeval (line 216) | struct timeval
  type timeval (line 230) | struct timeval
  type timeval (line 231) | struct timeval
  type timeval (line 232) | struct timeval
  type timeval (line 234) | struct timeval
  type timeval (line 235) | struct timeval
  type timeval (line 236) | struct timeval
  type timeval (line 238) | struct timeval
  type timeval (line 239) | struct timeval
  type timeval (line 240) | struct timeval
  class PhiRunner (line 245) | class PhiRunner : public Thread {
    method PhiRunner (line 247) | PhiRunner(const Env &env, Network &network,
    method set_done (line 277) | void set_done()   { _done = true; }
    method done (line 278) | bool done() const { return _done; }
    method EdgeList (line 281) | const EdgeList &sample() const { assert(_sample); return *_sample; }
    method Matrix (line 283) | const Matrix &gammat() const  { return _gammat; }
    method Matrix (line 284) | const Matrix &lambdat() const { return _lambdat; }
    method Array (line 285) | const Array &count() const    { return _count; }
    method MRStats (line 287) | const MRStats *rt() const { return &_rt; }
  class MMSBInfer (line 337) | class MMSBInfer {
    type timeval (line 471) | struct timeval
  function yval_t (line 844) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsbinferorig.cc
  function string (line 589) | string

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsbinferorig.hh
  class PhiComp2 (line 22) | class PhiComp2 {
    method PhiComp2 (line 24) | PhiComp2(const Env &env, const uint32_t &iter,
    method Array (line 47) | const Array& phi1() const { return _phi1; }
    method Array (line 48) | const Array& phi2() const { return _phi2; }
    method iter (line 50) | uint32_t iter() const { return _iter; }
    method D3 (line 55) | static const D3 &gphi1() { assert(_gphi1); return *_gphi1; }
    method D3 (line 56) | static const D3 &gphi2() { assert(_gphi2); return *_gphi2; }
  class MMSBInferOrig (line 229) | class MMSBInferOrig {
    type timeval (line 291) | struct timeval
  function yval_t (line 336) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/mmsborig.hh
  class MMSBOrig (line 17) | class MMSBOrig {

FILE: Algorithms/2013-SVINET/svinet-master/src/network.cc
  function string (line 161) | string

FILE: Algorithms/2013-SVINET/svinet-master/src/network.hh
  class Network (line 22) | class Network {
    method Network (line 24) | Network(Env &env):
    method SparseMatrix (line 33) | const SparseMatrix &sparse_y() const { return _sparse_y; }
    method SparseMatrix (line 34) | SparseMatrix &sparse_y() { return _sparse_y; }
    method SparseMatrix (line 35) | SparseMatrix &sparse_zeros() { return _sparse_zeros; }
    method EdgeList (line 42) | const EdgeList &edges() const { return _edges; }
    method EdgeList (line 43) | EdgeList &edgelist() { return _edges; }
    method nlinks (line 45) | uint32_t nlinks() const { return _edges.size(); }
    method Array (line 47) | const Array &deg() const { assert(_env.undirected); return _deg; }
    method Array (line 48) | Array &deg() { assert(_env.undirected); return _deg; }
    method MapVec (line 52) | const MapVec &gt_communities() const { return _gt_communities; }
    method MapVec (line 53) | const MapVec &gt_communities_seq() const { return _gt_communities_seq; }
    method MapVec (line 55) | const MapVec &init_communities() const { return _init_communities; }
    method MapVec (line 56) | const MapVec &init_communities_seq() const { return _init_communities_...
    method MapVec (line 58) | const MapVec &init_community_to_nodes() const { return _init_community...
    method MapVec (line 59) | const MapVec &init_community_to_nodes_seq() const { return _init_commu...
    method ones (line 61) | uint32_t ones() const { return _ones; }
    method singles (line 62) | uint32_t singles() const { return _single_nodes; }
    method IDMap (line 81) | const IDMap &id2seq() const { return _id2seq; }
    method IDMap (line 82) | const IDMap &seq2id() const { return _seq2id; }
    method StrMap (line 84) | const StrMap &str2id() const { return _str2id; }
    method StrMapInv (line 85) | const StrMapInv &id2str() const { return _id2str; }
  function yval_t (line 158) | inline yval_t
  function string (line 207) | inline string

FILE: Algorithms/2013-SVINET/svinet-master/src/sbm.cc
  function string (line 187) | string

FILE: Algorithms/2013-SVINET/svinet-master/src/sbm.hh
  class SBM (line 24) | class SBM {
    type timeval (line 144) | struct timeval
  function yval_t (line 362) | inline yval_t

FILE: Algorithms/2013-SVINET/svinet-master/src/thread.hh
  class Thread (line 12) | class Thread {
    method pthread_t (line 19) | pthread_t id() const { return _tid; }
    method do_work (line 21) | virtual int do_work() { return 0; }
  class Mutex (line 35) | class Mutex {
  class CondMutex (line 86) | class CondMutex {
    method lock (line 94) | int lock() { return _mutex.lock(); }
    method unlock (line 95) | int unlock() { return _mutex.unlock(); }

FILE: Algorithms/2013-SVINET/svinet-master/src/tsqueue.hh
  class TSQueue (line 9) | class TSQueue : public std::queue<T *>
    method TSQueue (line 14) | TSQueue() { }
  function T (line 35) | inline T *

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/matlab/graclus_mex.cpp
  function mexFunction (line 28) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/matlab/io.cpp
  function readClustering (line 20) | int readClustering(char *filename, int *part, int nvtex){
  function WriteCoarsestGraph (line 39) | void WriteCoarsestGraph(GraphType *graph, char *filename, int *wgtflag)
  function ReadCoarsestInit (line 68) | void ReadCoarsestInit(GraphType *graph, char *filename, int *wgtflag)
  function CreateGraph_Matlab (line 91) | void CreateGraph_Matlab(GraphType *graph, double* idata, double* jdata, ...
  function ReadGraph (line 135) | void ReadGraph(GraphType *graph, char *filename, int *wgtflag)
  function WritePartition (line 264) | void WritePartition(char *fname, idxtype *part, int n, int nparts)
  function WriteMeshPartition (line 288) | void WriteMeshPartition(char *fname, int nparts, int ne, idxtype *epart,...
  function WritePermutation (line 322) | void WritePermutation(char *fname, idxtype *iperm, int n)
  function CheckGraph (line 345) | int CheckGraph(GraphType *graph)
  function idxtype (line 392) | idxtype *ReadMesh(char *filename, int *ne, int *nn, int *etype)
  function WriteGraph (line 440) | void WriteGraph(char *filename, int nvtxs, idxtype *xadj, idxtype *adjncy)
  function WriteMocGraph (line 465) | void WriteMocGraph(GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/matlab/mlkkm.cpp
  function MLKKM_PartGraphKway (line 25) | void MLKKM_PartGraphKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, idx...
  function MLKKM_WPartGraphKway (line 46) | void MLKKM_WPartGraphKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function MLKKMPartitioning (line 183) | int MLKKMPartitioning(CtrlType *ctrl, GraphType *graph, int nparts, int ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/matlab/wkkm.cpp
  function Compute_Weights (line 19) | void Compute_Weights(CtrlType *ctrl, GraphType *graph, idxtype *w)
  function transform_matrix (line 43) | void transform_matrix(CtrlType *ctrl, GraphType *graph, idxtype *w, floa...
  function transform_matrix_half (line 90) | void transform_matrix_half(CtrlType *ctrl, GraphType *graph, idxtype *w,...
  function pingpong (line 138) | void pingpong(CtrlType *ctrl, GraphType *graph, int nparts, int chain_le...
  function Weighted_kernel_k_means (line 187) | void Weighted_kernel_k_means(CtrlType *ctrl, GraphType *graph, int npart...
  function local_search (line 352) | int local_search(CtrlType *ctrl, GraphType *graph, int nparts, int chain...
  function onePoint_move (line 551) | float onePoint_move(GraphType *graph, int nparts, idxtype *sum, idxtype ...
  function move1Point2EmptyCluster (line 679) | void move1Point2EmptyCluster(GraphType *graph, int nparts, idxtype *sum,...
  function remove_empty_clusters_l1 (line 855) | void remove_empty_clusters_l1(CtrlType *ctrl, GraphType *graph, int npar...
  function remove_empty_clusters_l2 (line 872) | void remove_empty_clusters_l2(CtrlType *ctrl, GraphType *graph, int npar...
  function MLKKMRefine (line 955) | void MLKKMRefine(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/balance.c
  function Balance2Way (line 21) | void Balance2Way(CtrlType *ctrl, GraphType *graph, int *tpwgts, float ub...
  function Bnd2WayBalance (line 48) | void Bnd2WayBalance(CtrlType *ctrl, GraphType *graph, int *tpwgts)
  function General2WayBalance (line 174) | void General2WayBalance(CtrlType *ctrl, GraphType *graph, int *tpwgts)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/bucketsort.c
  function BucketSortKeysInc (line 25) | void BucketSortKeysInc(int n, int max, idxtype *keys, idxtype *tperm, id...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/ccgraph.c
  function CreateCoarseGraph (line 22) | void CreateCoarseGraph(CtrlType *ctrl, GraphType *graph, int cnvtxs, idx...
  function CreateCoarseGraphNoMask (line 195) | void CreateCoarseGraphNoMask(CtrlType *ctrl, GraphType *graph, int cnvtx...
  function CreateCoarseGraph_NVW (line 330) | void CreateCoarseGraph_NVW(CtrlType *ctrl, GraphType *graph, int cnvtxs,...
  function GraphType (line 479) | GraphType *SetUpCoarseGraph(GraphType *graph, int cnvtxs, int dovsize)
  function ReAdjustMemory (line 548) | void ReAdjustMemory(GraphType *graph, GraphType *cgraph, int dovsize)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/coarsen.c
  function GraphType (line 19) | GraphType *Coarsen2Way(CtrlType *ctrl, GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/compress.c
  function CompressGraph (line 21) | void CompressGraph(CtrlType *ctrl, GraphType *graph, int nvtxs, idxtype ...
  function PruneGraph (line 160) | void PruneGraph(CtrlType *ctrl, GraphType *graph, int nvtxs, idxtype *xa...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/debug.c
  function ComputeRAsso (line 20) | float ComputeRAsso(GraphType *graph, idxtype *where, int npart)
  function ComputeNCut (line 67) | float ComputeNCut(GraphType *graph, idxtype *where, int npart)
  function ComputeCut (line 119) | int ComputeCut(GraphType *graph, idxtype *where)
  function CheckBnd (line 145) | int CheckBnd(GraphType *graph)
  function CheckBnd2 (line 181) | int CheckBnd2(GraphType *graph)
  function CheckNodeBnd (line 216) | int CheckNodeBnd(GraphType *graph, int onbnd)
  function CheckRInfo (line 252) | int CheckRInfo(RInfoType *rinfo)
  function CheckNodePartitionParams (line 269) | int CheckNodePartitionParams(GraphType *graph)
  function IsSeparable (line 316) | int IsSeparable(GraphType *graph)
  function ComputeCenterNode (line 344) | void ComputeCenterNode(GraphType *graph, int nparts, idxtype * where, ch...
  function WriteCenterNodes (line 458) | void WriteCenterNodes(char *fname, idxtype *center, int nparts)
  function WriteDistances (line 479) | void WriteDistances(char *fname, float *distance2center, int nparts, int...
  function ComputeAllDistance (line 501) | void ComputeAllDistance(GraphType *graph, int nparts, idxtype * where, i...
  function ComputeWithinEdges (line 630) | float ComputeWithinEdges(GraphType *graph, int numParts, idxtype* parts){
  function PrintClusterSizes (line 654) | void PrintClusterSizes(GraphType *graph, int numParts, idxtype* parts)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/estmem.c
  function METIS_EstimateMemory (line 22) | void METIS_EstimateMemory(int *nvtxs, idxtype *xadj, idxtype *adjncy, in...
  function EstimateCFraction (line 66) | void EstimateCFraction(int nvtxs, idxtype *xadj, idxtype *adjncy, float ...
  function ComputeCoarseGraphSize (line 111) | int ComputeCoarseGraphSize(int nvtxs, idxtype *xadj, idxtype *adjncy, in...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/fm.c
  function FM_2WayEdgeRefine (line 20) | void FM_2WayEdgeRefine(CtrlType *ctrl, GraphType *graph, int *tpwgts, in...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/fortran.c
  function Change2CNumbering (line 21) | void Change2CNumbering(int nvtxs, idxtype *xadj, idxtype *adjncy)
  function Change2FNumbering (line 36) | void Change2FNumbering(int nvtxs, idxtype *xadj, idxtype *adjncy, idxtyp...
  function Change2FNumbering2 (line 54) | void Change2FNumbering2(int nvtxs, idxtype *xadj, idxtype *adjncy)
  function Change2FNumberingOrder (line 71) | void Change2FNumberingOrder(int nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function ChangeMesh2CNumbering (line 94) | void ChangeMesh2CNumbering(int n, idxtype *mesh)
  function ChangeMesh2FNumbering (line 107) | void ChangeMesh2FNumbering(int n, idxtype *mesh, int nvtxs, idxtype *xad...
  function ChangeMesh2FNumbering2 (line 127) | void ChangeMesh2FNumbering2(int n, idxtype *mesh, int ne, int nn, idxtyp...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/frename.c
  function METIS_PARTGRAPHRECURSIVE (line 18) | void METIS_PARTGRAPHRECURSIVE(int *nvtxs, idxtype *xadj, idxtype *adjncy...
  function metis_partgraphrecursive (line 22) | void metis_partgraphrecursive(int *nvtxs, idxtype *xadj, idxtype *adjncy...
  function metis_partgraphrecursive_ (line 26) | void metis_partgraphrecursive_(int *nvtxs, idxtype *xadj, idxtype *adjnc...
  function metis_partgraphrecursive__ (line 30) | void metis_partgraphrecursive__(int *nvtxs, idxtype *xadj, idxtype *adjn...
  function METIS_WPARTGRAPHRECURSIVE (line 36) | void METIS_WPARTGRAPHRECURSIVE(int *nvtxs, idxtype *xadj, idxtype *adjnc...
  function metis_wpartgraphrecursive (line 40) | void metis_wpartgraphrecursive(int *nvtxs, idxtype *xadj, idxtype *adjnc...
  function metis_wpartgraphrecursive_ (line 44) | void metis_wpartgraphrecursive_(int *nvtxs, idxtype *xadj, idxtype *adjn...
  function metis_wpartgraphrecursive__ (line 48) | void metis_wpartgraphrecursive__(int *nvtxs, idxtype *xadj, idxtype *adj...
  function METIS_PARTGRAPHKWAY (line 55) | void METIS_PARTGRAPHKWAY(int *nvtxs, idxtype *xadj, idxtype *adjncy, idx...
  function metis_partgraphkway (line 59) | void metis_partgraphkway(int *nvtxs, idxtype *xadj, idxtype *adjncy, idx...
  function metis_partgraphkway_ (line 63) | void metis_partgraphkway_(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function metis_partgraphkway__ (line 67) | void metis_partgraphkway__(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function METIS_WPARTGRAPHKWAY (line 74) | void METIS_WPARTGRAPHKWAY(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function metis_wpartgraphkway (line 78) | void metis_wpartgraphkway(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function metis_wpartgraphkway_ (line 82) | void metis_wpartgraphkway_(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function metis_wpartgraphkway__ (line 86) | void metis_wpartgraphkway__(int *nvtxs, idxtype *xadj, idxtype *adjncy, ...
  function METIS_EDGEND (line 93) | void METIS_EDGEND(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numfl...
  function metis_edgend (line 97) | void metis_edgend(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numfl...
  function metis_edgend_ (line 101) | void metis_edgend_(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numf...
  function metis_edgend__ (line 105) | void metis_edgend__(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *num...
  function METIS_NODEND (line 112) | void METIS_NODEND(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numfl...
  function metis_nodend (line 116) | void metis_nodend(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numfl...
  function metis_nodend_ (line 120) | void metis_nodend_(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numf...
  function metis_nodend__ (line 124) | void metis_nodend__(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *num...
  function METIS_NODEWND (line 131) | void METIS_NODEWND(int *nvtxs, idxtype *xadj, idxtype *adjncy, idxtype *...
  function metis_nodewnd (line 135) | void metis_nodewnd(int *nvtxs, idxtype *xadj, idxtype *adjncy, idxtype *...
  function metis_nodewnd_ (line 139) | void metis_nodewnd_(int *nvtxs, idxtype *xadj, idxtype *adjncy, idxtype ...
  function metis_nodewnd__ (line 143) | void metis_nodewnd__(int *nvtxs, idxtype *xadj, idxtype *adjncy, idxtype...
  function METIS_PARTMESHNODAL (line 150) | void METIS_PARTMESHNODAL(int *ne, int *nn, idxtype *elmnts, int *etype, ...
  function metis_partmeshnodal (line 154) | void metis_partmeshnodal(int *ne, int *nn, idxtype *elmnts, int *etype, ...
  function metis_partmeshnodal_ (line 158) | void metis_partmeshnodal_(int *ne, int *nn, idxtype *elmnts, int *etype,...
  function metis_partmeshnodal__ (line 162) | void metis_partmeshnodal__(int *ne, int *nn, idxtype *elmnts, int *etype...
  function METIS_PARTMESHDUAL (line 168) | void METIS_PARTMESHDUAL(int *ne, int *nn, idxtype *elmnts, int *etype, i...
  function metis_partmeshdual (line 172) | void metis_partmeshdual(int *ne, int *nn, idxtype *elmnts, int *etype, i...
  function metis_partmeshdual_ (line 176) | void metis_partmeshdual_(int *ne, int *nn, idxtype *elmnts, int *etype, ...
  function metis_partmeshdual__ (line 180) | void metis_partmeshdual__(int *ne, int *nn, idxtype *elmnts, int *etype,...
  function METIS_MESHTONODAL (line 186) | void METIS_MESHTONODAL(int *ne, int *nn, idxtype *elmnts, int *etype, in...
  function metis_meshtonodal (line 190) | void metis_meshtonodal(int *ne, int *nn, idxtype *elmnts, int *etype, in...
  function metis_meshtonodal_ (line 194) | void metis_meshtonodal_(int *ne, int *nn, idxtype *elmnts, int *etype, i...
  function metis_meshtonodal__ (line 198) | void metis_meshtonodal__(int *ne, int *nn, idxtype *elmnts, int *etype, ...
  function METIS_MESHTODUAL (line 204) | void METIS_MESHTODUAL(int *ne, int *nn, idxtype *elmnts, int *etype, int...
  function metis_meshtodual (line 208) | void metis_meshtodual(int *ne, int *nn, idxtype *elmnts, int *etype, int...
  function metis_meshtodual_ (line 212) | void metis_meshtodual_(int *ne, int *nn, idxtype *elmnts, int *etype, in...
  function metis_meshtodual__ (line 216) | void metis_meshtodual__(int *ne, int *nn, idxtype *elmnts, int *etype, i...
  function METIS_ESTIMATEMEMORY (line 222) | void METIS_ESTIMATEMEMORY(int *nvtxs, idxtype *xadj, idxtype *adjncy, in...
  function metis_estimatememory (line 226) | void metis_estimatememory(int *nvtxs, idxtype *xadj, idxtype *adjncy, in...
  function metis_estimatememory_ (line 230) | void metis_estimatememory_(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function metis_estimatememory__ (line 234) | void metis_estimatememory__(int *nvtxs, idxtype *xadj, idxtype *adjncy, ...
  function METIS_MCPARTGRAPHRECURSIVE (line 241) | void METIS_MCPARTGRAPHRECURSIVE(int *nvtxs, int *ncon, idxtype *xadj, id...
  function metis_mcpartgraphrecursive (line 245) | void metis_mcpartgraphrecursive(int *nvtxs, int *ncon, idxtype *xadj, id...
  function metis_mcpartgraphrecursive_ (line 249) | void metis_mcpartgraphrecursive_(int *nvtxs, int *ncon, idxtype *xadj, i...
  function metis_mcpartgraphrecursive__ (line 253) | void metis_mcpartgraphrecursive__(int *nvtxs, int *ncon, idxtype *xadj, ...
  function METIS_MCPARTGRAPHKWAY (line 259) | void METIS_MCPARTGRAPHKWAY(int *nvtxs, int *ncon, idxtype *xadj, idxtype...
  function metis_mcpartgraphkway (line 263) | void metis_mcpartgraphkway(int *nvtxs, int *ncon, idxtype *xadj, idxtype...
  function metis_mcpartgraphkway_ (line 267) | void metis_mcpartgraphkway_(int *nvtxs, int *ncon, idxtype *xadj, idxtyp...
  function metis_mcpartgraphkway__ (line 271) | void metis_mcpartgraphkway__(int *nvtxs, int *ncon, idxtype *xadj, idxty...
  function METIS_PARTGRAPHVKWAY (line 277) | void METIS_PARTGRAPHVKWAY(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function metis_partgraphvkway (line 281) | void metis_partgraphvkway(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function metis_partgraphvkway_ (line 285) | void metis_partgraphvkway_(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function metis_partgraphvkway__ (line 289) | void metis_partgraphvkway__(int *nvtxs, idxtype *xadj, idxtype *adjncy, ...
  function METIS_WPARTGRAPHVKWAY (line 294) | void METIS_WPARTGRAPHVKWAY(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function metis_wpartgraphvkway (line 298) | void metis_wpartgraphvkway(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function metis_wpartgraphvkway_ (line 302) | void metis_wpartgraphvkway_(int *nvtxs, idxtype *xadj, idxtype *adjncy, ...
  function metis_wpartgraphvkway__ (line 306) | void metis_wpartgraphvkway__(int *nvtxs, idxtype *xadj, idxtype *adjncy,...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/graph.c
  function SetUpGraph (line 21) | void SetUpGraph(GraphType *graph, int OpType, int nvtxs, int ncon,
  function SetUpGraphKway (line 142) | void SetUpGraphKway(GraphType *graph, int nvtxs, idxtype *xadj, idxtype ...
  function SetUpGraph2 (line 171) | void SetUpGraph2(GraphType *graph, int nvtxs, int ncon, idxtype *xadj,
  function VolSetUpGraph (line 211) | void VolSetUpGraph(GraphType *graph, int OpType, int nvtxs, int ncon, id...
  function RandomizeGraph (line 352) | void RandomizeGraph(GraphType *graph)
  function IsConnectedSubdomain (line 376) | int IsConnectedSubdomain(CtrlType *ctrl, GraphType *graph, int pid, int ...
  function IsConnected (line 454) | int IsConnected(CtrlType *ctrl, GraphType *graph, int report)
  function IsConnected2 (line 491) | int IsConnected2(GraphType *graph, int report)
  function FindComponents (line 554) | int FindComponents(CtrlType *ctrl, GraphType *graph, idxtype *cptr, idxt...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/initpart.c
  function Init2WayPartition (line 21) | void Init2WayPartition(CtrlType *ctrl, GraphType *graph, int *tpwgts, fl...
  function InitSeparator (line 55) | void InitSeparator(CtrlType *ctrl, GraphType *graph, float ubfactor)
  function GrowBisection (line 82) | void GrowBisection(CtrlType *ctrl, GraphType *graph, int *tpwgts, float ...
  function GrowBisectionNode (line 210) | void GrowBisectionNode(CtrlType *ctrl, GraphType *graph, float ubfactor)
  function RandomBisection (line 346) | void RandomBisection(CtrlType *ctrl, GraphType *graph, int *tpwgts, floa...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/kmetis.c
  function METIS_PartGraphKway (line 22) | void METIS_PartGraphKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, idx...
  function METIS_WPartGraphKway (line 43) | void METIS_WPartGraphKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function MlevelKWayPartitioning (line 94) | int MlevelKWayPartitioning(CtrlType *ctrl, GraphType *graph, int nparts,...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/kvmetis.c
  function METIS_PartGraphVKway (line 22) | void METIS_PartGraphVKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function METIS_WPartGraphVKway (line 43) | void METIS_WPartGraphVKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function MlevelVolKWayPartitioning (line 94) | int MlevelVolKWayPartitioning(CtrlType *ctrl, GraphType *graph, int npar...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/kwayfm.c
  function Random_KWayEdgeRefine (line 19) | void Random_KWayEdgeRefine(CtrlType *ctrl, GraphType *graph, int nparts,...
  function Greedy_KWayEdgeRefine (line 222) | void Greedy_KWayEdgeRefine(CtrlType *ctrl, GraphType *graph, int nparts,...
  function Greedy_KWayEdgeBalance (line 452) | void Greedy_KWayEdgeBalance(CtrlType *ctrl, GraphType *graph, int nparts...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/kwayrefine.c
  function RefineKWay (line 20) | void RefineKWay(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, i...
  function AllocateKWayPartitionMemory (line 115) | void AllocateKWayPartitionMemory(CtrlType *ctrl, GraphType *graph, int n...
  function ComputeKWayPartitionParams (line 141) | void ComputeKWayPartitionParams(CtrlType *ctrl, GraphType *graph, int np...
  function ProjectKWayPartition (line 222) | void ProjectKWayPartition(CtrlType *ctrl, GraphType *graph, int nparts)
  function IsBalanced (line 329) | int IsBalanced(idxtype *pwgts, int nparts, float *tpwgts, float ubfactor)
  function ComputeKWayBoundary (line 346) | void ComputeKWayBoundary(CtrlType *ctrl, GraphType *graph, int nparts)
  function ComputeKWayBalanceBoundary (line 371) | void ComputeKWayBalanceBoundary(CtrlType *ctrl, GraphType *graph, int np...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/kwayvolfm.c
  function Random_KWayVolRefine (line 19) | void Random_KWayVolRefine(CtrlType *ctrl, GraphType *graph, int nparts, ...
  function Random_KWayVolRefineMConn (line 163) | void Random_KWayVolRefineMConn(CtrlType *ctrl, GraphType *graph, int npa...
  function Greedy_KWayVolBalance (line 402) | void Greedy_KWayVolBalance(CtrlType *ctrl, GraphType *graph, int nparts,...
  function Greedy_KWayVolBalanceMConn (line 556) | void Greedy_KWayVolBalanceMConn(CtrlType *ctrl, GraphType *graph, int np...
  function KWayVolUpdate (line 805) | void KWayVolUpdate(CtrlType *ctrl, GraphType *graph, int v, int from, in...
  function ComputeKWayVolume (line 1089) | void ComputeKWayVolume(GraphType *graph, int nupd, idxtype *updind, idxt...
  function ComputeVolume (line 1180) | int ComputeVolume(GraphType *graph, idxtype *where)
  function CheckVolKWayPartitionParams (line 1219) | void CheckVolKWayPartitionParams(CtrlType *ctrl, GraphType *graph, int n...
  function ComputeVolSubDomainGraph (line 1345) | void ComputeVolSubDomainGraph(GraphType *graph, int nparts, idxtype *pma...
  function EliminateVolSubDomainEdges (line 1387) | void EliminateVolSubDomainEdges(CtrlType *ctrl, GraphType *graph, int np...
  function EliminateVolComponents (line 1614) | void EliminateVolComponents(CtrlType *ctrl, GraphType *graph, int nparts...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/kwayvolrefine.c
  function RefineVolKWay (line 20) | void RefineVolKWay(CtrlType *ctrl, GraphType *orggraph, GraphType *graph...
  function AllocateVolKWayPartitionMemory (line 107) | void AllocateVolKWayPartitionMemory(CtrlType *ctrl, GraphType *graph, in...
  function ComputeVolKWayPartitionParams (line 129) | void ComputeVolKWayPartitionParams(CtrlType *ctrl, GraphType *graph, int...
  function ComputeKWayVolGains (line 209) | void ComputeKWayVolGains(CtrlType *ctrl, GraphType *graph, int nparts)
  function ProjectVolKWayPartition (line 309) | void ProjectVolKWayPartition(CtrlType *ctrl, GraphType *graph, int nparts)
  function ComputeVolKWayBoundary (line 414) | void ComputeVolKWayBoundary(CtrlType *ctrl, GraphType *graph, int nparts)
  function ComputeVolKWayBalanceBoundary (line 439) | void ComputeVolKWayBalanceBoundary(CtrlType *ctrl, GraphType *graph, int...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/match.c
  function Match_SHEMN (line 21) | void Match_SHEMN(CtrlType *ctrl, GraphType *graph)
  function Match_HEMN (line 116) | void Match_HEMN(CtrlType *ctrl, GraphType *graph)
  function Match_RM (line 175) | void Match_RM(CtrlType *ctrl, GraphType *graph)
  function Match_RM_NVW (line 228) | void Match_RM_NVW(CtrlType *ctrl, GraphType *graph)
  function Match_HEM (line 281) | void Match_HEM(CtrlType *ctrl, GraphType *graph)
  function Match_SHEM (line 337) | void Match_SHEM(CtrlType *ctrl, GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mbalance.c
  function MocBalance2Way (line 22) | void MocBalance2Way(CtrlType *ctrl, GraphType *graph, float *tpwgts, flo...
  function MocGeneral2WayBalance (line 36) | void MocGeneral2WayBalance(CtrlType *ctrl, GraphType *graph, float *tpwg...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mbalance2.c
  function MocBalance2Way2 (line 22) | void MocBalance2Way2(CtrlType *ctrl, GraphType *graph, float *tpwgts, fl...
  function MocGeneral2WayBalance2 (line 37) | void MocGeneral2WayBalance2(CtrlType *ctrl, GraphType *graph, float *tpw...
  function SelectQueue3 (line 266) | void SelectQueue3(int ncon, float *npwgts, float *tpwgts, int *from, int...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mcoarsen.c
  function GraphType (line 19) | GraphType *MCCoarsen2Way(CtrlType *ctrl, GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/memory.c
  function AllocateWorkSpace (line 21) | void AllocateWorkSpace(CtrlType *ctrl, GraphType *graph, int nparts)
  function FreeWorkSpace (line 88) | void FreeWorkSpace(CtrlType *ctrl, GraphType *graph)
  function WspaceAvail (line 96) | int WspaceAvail(CtrlType *ctrl)
  function idxtype (line 105) | idxtype *idxwspacemalloc(CtrlType *ctrl, int n)
  function idxwspacefree (line 117) | void idxwspacefree(CtrlType *ctrl, int n)
  function fwspacefree (line 141) | void fwspacefree(CtrlType *ctrl, int n)
  function GraphType (line 155) | GraphType *CreateGraph(void)
  function InitGraph (line 171) | void InitGraph(GraphType *graph)
  function FreeGraph (line 203) | void FreeGraph(GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mesh.c
  function METIS_MeshToDual (line 23) | void METIS_MeshToDual(int *ne, int *nn, idxtype *elmnts, int *etype, int...
  function METIS_MeshToNodal (line 42) | void METIS_MeshToNodal(int *ne, int *nn, idxtype *elmnts, int *etype, in...
  function GENDUALMETIS (line 74) | void GENDUALMETIS(int nelmnts, int nvtxs, int etype, idxtype *elmnts, id...
  function TRINODALMETIS (line 169) | void TRINODALMETIS(int nelmnts, int nvtxs, idxtype *elmnts, idxtype *dxa...
  function TETNODALMETIS (line 218) | void TETNODALMETIS(int nelmnts, int nvtxs, idxtype *elmnts, idxtype *dxa...
  function HEXNODALMETIS (line 267) | void HEXNODALMETIS(int nelmnts, int nvtxs, idxtype *elmnts, idxtype *dxa...
  function QUADNODALMETIS (line 340) | void QUADNODALMETIS(int nelmnts, int nvtxs, idxtype *elmnts, idxtype *dx...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/meshpart.c
  function METIS_PartMeshNodal (line 22) | void METIS_PartMeshNodal(int *ne, int *nn, idxtype *elmnts, int *etype, ...
  function METIS_PartMeshDual (line 110) | void METIS_PartMeshDual(int *ne, int *nn, idxtype *elmnts, int *etype, i...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mfm.c
  function MocFM_2WayEdgeRefine (line 20) | void MocFM_2WayEdgeRefine(CtrlType *ctrl, GraphType *graph, float *tpwgt...
  function SelectQueue (line 238) | void SelectQueue(int ncon, float *npwgts, float *tpwgts, int *from, int ...
  function BetterBalance (line 303) | int BetterBalance(int ncon, float *npwgts, float *tpwgts, float *diff)
  function Compute2WayHLoadImbalance (line 319) | float Compute2WayHLoadImbalance(int ncon, float *npwgts, float *tpwgts)
  function Compute2WayHLoadImbalanceVec (line 337) | void Compute2WayHLoadImbalanceVec(int ncon, float *npwgts, float *tpwgts...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mfm2.c
  function MocFM_2WayEdgeRefine2 (line 20) | void MocFM_2WayEdgeRefine2(CtrlType *ctrl, GraphType *graph, float *tpwg...
  function SelectQueue2 (line 263) | void SelectQueue2(int ncon, float *npwgts, float *tpwgts, int *from, int...
  function IsBetter2wayBalance (line 326) | int IsBetter2wayBalance(int ncon, float *newbal, float *oldbal, float *u...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mincover.c
  function MinCover (line 42) | void MinCover(idxtype *xadj, idxtype *adjncy, int asize, int bsize, idxt...
  function MinCover_Augment (line 126) | int MinCover_Augment(idxtype *xadj, idxtype *adjncy, int col, idxtype *m...
  function MinCover_Decompose (line 163) | void MinCover_Decompose(idxtype *xadj, idxtype *adjncy, int asize, int b...
  function MinCover_ColDFS (line 212) | void MinCover_ColDFS(idxtype *xadj, idxtype *adjncy, int root, idxtype *...
  function MinCover_RowDFS (line 237) | void MinCover_RowDFS(idxtype *xadj, idxtype *adjncy, int root, idxtype *...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/minitpart.c
  function MocInit2WayPartition (line 21) | void MocInit2WayPartition(CtrlType *ctrl, GraphType *graph, float *tpwgt...
  function MocGrowBisection (line 57) | void MocGrowBisection(CtrlType *ctrl, GraphType *graph, float *tpwgts, f...
  function MocRandomBisection (line 105) | void MocRandomBisection(CtrlType *ctrl, GraphType *graph, float *tpwgts,...
  function MocInit2WayBalance (line 178) | void MocInit2WayBalance(CtrlType *ctrl, GraphType *graph, float *tpwgts)
  function SelectQueueOneWay (line 339) | int SelectQueueOneWay(int ncon, float *npwgts, float *tpwgts, int from, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/minitpart2.c
  function MocInit2WayPartition2 (line 21) | void MocInit2WayPartition2(CtrlType *ctrl, GraphType *graph, float *tpwg...
  function MocGrowBisection2 (line 57) | void MocGrowBisection2(CtrlType *ctrl, GraphType *graph, float *tpwgts, ...
  function MocGrowBisectionNew2 (line 108) | void MocGrowBisectionNew2(CtrlType *ctrl, GraphType *graph, float *tpwgt...
  function MocInit2WayBalance2 (line 156) | void MocInit2WayBalance2(CtrlType *ctrl, GraphType *graph, float *tpwgts...
  function SelectQueueOneWay2 (line 330) | int SelectQueueOneWay2(int ncon, float *pto, PQueueType queues[MAXNCON][...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mkmetis.c
  function METIS_mCPartGraphKway (line 23) | void METIS_mCPartGraphKway(int *nvtxs, int *ncon, idxtype *xadj, idxtype...
  function MCMlevelKWayPartitioning (line 76) | int MCMlevelKWayPartitioning(CtrlType *ctrl, GraphType *graph, int npart...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mkwayfmh.c
  function MCRandom_KWayEdgeRefineHorizontal (line 20) | void MCRandom_KWayEdgeRefineHorizontal(CtrlType *ctrl, GraphType *graph,...
  function MCGreedy_KWayEdgeBalanceHorizontal (line 257) | void MCGreedy_KWayEdgeBalanceHorizontal(CtrlType *ctrl, GraphType *graph...
  function AreAllHVwgtsBelow (line 512) | int AreAllHVwgtsBelow(int ncon, float alpha, float *vwgt1, float beta, f...
  function AreAllHVwgtsAbove (line 529) | int AreAllHVwgtsAbove(int ncon, float alpha, float *vwgt1, float beta, f...
  function ComputeHKWayLoadImbalance (line 545) | void ComputeHKWayLoadImbalance(int ncon, int nparts, float *npwgts, floa...
  function MocIsHBalanced (line 565) | int MocIsHBalanced(int ncon, int nparts, float *npwgts, float *ubvec)
  function IsHBalanceBetterFT (line 593) | int IsHBalanceBetterFT(int ncon, int nparts, float *pfrom, float *pto, f...
  function IsHBalanceBetterTT (line 641) | int IsHBalanceBetterTT(int ncon, int nparts, float *pt1, float *pt2, flo...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mkwayrefine.c
  function MocRefineKWayHorizontal (line 20) | void MocRefineKWayHorizontal(CtrlType *ctrl, GraphType *orggraph, GraphT...
  function MocAllocateKWayPartitionMemory (line 67) | void MocAllocateKWayPartitionMemory(CtrlType *ctrl, GraphType *graph, in...
  function MocComputeKWayPartitionParams (line 89) | void MocComputeKWayPartitionParams(CtrlType *ctrl, GraphType *graph, int...
  function MocProjectKWayPartition (line 172) | void MocProjectKWayPartition(CtrlType *ctrl, GraphType *graph, int nparts)
  function MocComputeKWayBalanceBoundary (line 278) | void MocComputeKWayBalanceBoundary(CtrlType *ctrl, GraphType *graph, int...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mmatch.c
  function MCMatch_RM (line 22) | void MCMatch_RM(CtrlType *ctrl, GraphType *graph)
  function MCMatch_HEM (line 79) | void MCMatch_HEM(CtrlType *ctrl, GraphType *graph)
  function MCMatch_SHEM (line 138) | void MCMatch_SHEM(CtrlType *ctrl, GraphType *graph)
  function MCMatch_SHEBM (line 232) | void MCMatch_SHEBM(CtrlType *ctrl, GraphType *graph, int norm)
  function MCMatch_SBHEM (line 333) | void MCMatch_SBHEM(CtrlType *ctrl, GraphType *graph, int norm)
  function BetterVBalance (line 435) | float BetterVBalance(int ncon, int norm, float *vwgt, float *u1wgt, floa...
  function AreAllVwgtsBelowFast (line 496) | int AreAllVwgtsBelowFast(int ncon, float *vwgt1, float *vwgt2, float limit)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mmd.c
  function genmmd (line 53) | void genmmd(int neqns, idxtype *xadj, idxtype *adjncy, idxtype *invp, id...
  function mmdelm (line 171) | void mmdelm(int mdeg_node, idxtype *xadj, idxtype *adjncy, idxtype *head...
  function mmdint (line 305) | int  mmdint(int neqns, idxtype *xadj, idxtype *adjncy, idxtype *head, id...
  function mmdnum (line 348) | void mmdnum(int neqns, idxtype *perm, idxtype *invp, idxtype *qsize)
  function mmdupd (line 412) | void mmdupd(int ehead, int neqns, idxtype *xadj, idxtype *adjncy, int de...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mpmetis.c
  function METIS_mCPartGraphRecursive (line 24) | void METIS_mCPartGraphRecursive(int *nvtxs, int *ncon, idxtype *xadj, id...
  function METIS_mCHPartGraphRecursive (line 78) | void METIS_mCHPartGraphRecursive(int *nvtxs, int *ncon, idxtype *xadj, i...
  function METIS_mCPartGraphRecursiveInternal (line 137) | void METIS_mCPartGraphRecursiveInternal(int *nvtxs, int *ncon, idxtype *...
  function METIS_mCHPartGraphRecursiveInternal (line 184) | void METIS_mCHPartGraphRecursiveInternal(int *nvtxs, int *ncon, idxtype ...
  function MCMlevelRecursiveBisection (line 238) | int MCMlevelRecursiveBisection(CtrlType *ctrl, GraphType *graph, int npa...
  function MCHMlevelRecursiveBisection (line 290) | int MCHMlevelRecursiveBisection(CtrlType *ctrl, GraphType *graph, int np...
  function MCMlevelEdgeBisection (line 366) | void MCMlevelEdgeBisection(CtrlType *ctrl, GraphType *graph, float *tpwg...
  function MCHMlevelEdgeBisection (line 383) | void MCHMlevelEdgeBisection(CtrlType *ctrl, GraphType *graph, float *tpw...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mrefine.c
  function MocRefine2Way (line 20) | void MocRefine2Way(CtrlType *ctrl, GraphType *orggraph, GraphType *graph...
  function MocAllocate2WayPartitionMemory (line 70) | void MocAllocate2WayPartitionMemory(CtrlType *ctrl, GraphType *graph)
  function MocCompute2WayPartitionParams (line 91) | void MocCompute2WayPartitionParams(CtrlType *ctrl, GraphType *graph)
  function MocProject2WayPartition (line 149) | void MocProject2WayPartition(CtrlType *ctrl, GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mrefine2.c
  function MocRefine2Way2 (line 20) | void MocRefine2Way2(CtrlType *ctrl, GraphType *orggraph, GraphType *grap...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/mutil.c
  function AreAllVwgtsBelow (line 21) | int AreAllVwgtsBelow(int ncon, float alpha, float *vwgt1, float beta, fl...
  function AreAnyVwgtsBelow (line 37) | int AreAnyVwgtsBelow(int ncon, float alpha, float *vwgt1, float beta, fl...
  function AreAllVwgtsAbove (line 54) | int AreAllVwgtsAbove(int ncon, float alpha, float *vwgt1, float beta, fl...
  function ComputeLoadImbalance (line 70) | float ComputeLoadImbalance(int ncon, int nparts, float *npwgts, float *t...
  function AreAllBelow (line 92) | int AreAllBelow(int ncon, float *v1, float *v2)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/myqsort.c
  function iidxsort (line 32) | void iidxsort(int n, idxtype *base)
  function siqst (line 77) | static void siqst(idxtype *base, idxtype *max)
  function iintsort (line 161) | void iintsort(int n, int *base)
  function iiqst (line 207) | static void iiqst(int *base, int *max)
  function ikeysort (line 291) | void ikeysort(int n, KeyValueType *base)
  function keyiqst (line 345) | static void keyiqst(KeyValueType *base, KeyValueType *max)
  function ikeyvalsort (line 427) | void ikeyvalsort(int n, KeyValueType *base)
  function keyvaliqst (line 473) | static void keyvaliqst(KeyValueType *base, KeyValueType *max)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/ometis.c
  function METIS_EdgeND (line 22) | void METIS_EdgeND(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numfl...
  function METIS_NodeND (line 79) | void METIS_NodeND(int *nvtxs, idxtype *xadj, idxtype *adjncy, int *numfl...
  function METIS_NodeWND (line 204) | void METIS_NodeWND(int *nvtxs, idxtype *xadj, idxtype *adjncy, idxtype *...
  function MlevelNestedDissection (line 263) | void MlevelNestedDissection(CtrlType *ctrl, GraphType *graph, idxtype *o...
  function MlevelNestedDissectionCC (line 323) | void MlevelNestedDissectionCC(CtrlType *ctrl, GraphType *graph, idxtype ...
  function MlevelNodeBisectionMultiple (line 386) | void MlevelNodeBisectionMultiple(CtrlType *ctrl, GraphType *graph, int *...
  function MlevelNodeBisection (line 468) | void MlevelNodeBisection(CtrlType *ctrl, GraphType *graph, int *tpwgts, ...
  function SplitGraphOrder (line 508) | void SplitGraphOrder(CtrlType *ctrl, GraphType *graph, GraphType *lgraph...
  function MMDOrder (line 617) | void MMDOrder(CtrlType *ctrl, GraphType *graph, idxtype *order, int last...
  function SplitGraphOrderCC (line 663) | int SplitGraphOrderCC(CtrlType *ctrl, GraphType *graph, GraphType *sgrap...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/parmetis.c
  function METIS_PartGraphKway2 (line 22) | void METIS_PartGraphKway2(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function METIS_WPartGraphKway2 (line 44) | void METIS_WPartGraphKway2(int *nvtxs, idxtype *xadj, idxtype *adjncy, i...
  function METIS_NodeNDP (line 95) | void METIS_NodeNDP(int nvtxs, idxtype *xadj, idxtype *adjncy, int npes,
  function MlevelNestedDissectionP (line 193) | void MlevelNestedDissectionP(CtrlType *ctrl, GraphType *graph, idxtype *...
  function METIS_NodeComputeSeparator (line 262) | void METIS_NodeComputeSeparator(int *nvtxs, idxtype *xadj, idxtype *adjn...
  function METIS_EdgeComputeSeparator (line 320) | void METIS_EdgeComputeSeparator(int *nvtxs, idxtype *xadj, idxtype *adjn...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/pmetis.c
  function METIS_PartGraphRecursive (line 22) | void METIS_PartGraphRecursive(int *nvtxs, idxtype *xadj, idxtype *adjncy...
  function METIS_WPartGraphRecursive (line 45) | void METIS_WPartGraphRecursive(int *nvtxs, idxtype *xadj, idxtype *adjnc...
  function MlevelRecursiveBisection (line 103) | int MlevelRecursiveBisection(CtrlType *ctrl, GraphType *graph, int npart...
  function MlevelEdgeBisection (line 168) | void MlevelEdgeBisection(CtrlType *ctrl, GraphType *graph, int *tpwgts, ...
  function SplitGraphPart (line 190) | void SplitGraphPart(CtrlType *ctrl, GraphType *graph, GraphType *lgraph,...
  function SetUpSplitGraph (line 309) | void SetUpSplitGraph(GraphType *graph, GraphType *sgraph, int snvtxs, in...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/pqueue.c
  function PQueueInit (line 23) | void PQueueInit(CtrlType *ctrl, PQueueType *queue, int maxnodes, int max...
  function PQueueReset (line 80) | void PQueueReset(PQueueType *queue)
  function PQueueFree (line 104) | void PQueueFree(CtrlType *ctrl, PQueueType *queue)
  function PQueueGetSize (line 129) | int PQueueGetSize(PQueueType *queue)
  function PQueueInsert (line 138) | int PQueueInsert(PQueueType *queue, int node, int gain)
  function PQueueDelete (line 197) | int PQueueDelete(PQueueType *queue, int node, int gain)
  function PQueueUpdate (line 293) | int PQueueUpdate(PQueueType *queue, int node, int oldgain, int newgain)
  function PQueueUpdateUp (line 367) | void PQueueUpdateUp(PQueueType *queue, int node, int oldgain, int newgain)
  function PQueueGetMax (line 440) | int PQueueGetMax(PQueueType *queue)
  function PQueueSeeMax (line 511) | int PQueueSeeMax(PQueueType *queue)
  function PQueueGetKey (line 530) | int PQueueGetKey(PQueueType *queue)
  function CheckHeap (line 551) | int CheckHeap(PQueueType *queue)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/refine.c
  function Refine2Way (line 20) | void Refine2Way(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, i...
  function Allocate2WayPartitionMemory (line 58) | void Allocate2WayPartitionMemory(CtrlType *ctrl, GraphType *graph)
  function Compute2WayPartitionParams (line 77) | void Compute2WayPartitionParams(CtrlType *ctrl, GraphType *graph)
  function Project2WayPartition (line 134) | void Project2WayPartition(CtrlType *ctrl, GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/separator.c
  function ConstructSeparator (line 21) | void ConstructSeparator(CtrlType *ctrl, GraphType *graph, float ubfactor)
  function ConstructMinCoverSeparator0 (line 63) | void ConstructMinCoverSeparator0(CtrlType *ctrl, GraphType *graph, float...
  function ConstructMinCoverSeparator (line 178) | void ConstructMinCoverSeparator(CtrlType *ctrl, GraphType *graph, float ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/sfm.c
  function FM_2WayNodeRefine (line 21) | void FM_2WayNodeRefine(CtrlType *ctrl, GraphType *graph, float ubfactor,...
  function FM_2WayNodeRefine2 (line 256) | void FM_2WayNodeRefine2(CtrlType *ctrl, GraphType *graph, float ubfactor...
  function FM_2WayNodeRefineEqWgt (line 493) | void FM_2WayNodeRefineEqWgt(CtrlType *ctrl, GraphType *graph, int npasses)
  function FM_2WayNodeRefine_OneSided (line 717) | void FM_2WayNodeRefine_OneSided(CtrlType *ctrl, GraphType *graph, float ...
  function FM_2WayNodeBalance (line 918) | void FM_2WayNodeBalance(CtrlType *ctrl, GraphType *graph, float ubfactor)
  function ComputeMaxNodeGain (line 1051) | int ComputeMaxNodeGain(int nvtxs, idxtype *xadj, idxtype *adjncy, idxtyp...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/srefine.c
  function Refine2WayNode (line 21) | void Refine2WayNode(CtrlType *ctrl, GraphType *orggraph, GraphType *grap...
  function Allocate2WayNodePartitionMemory (line 68) | void Allocate2WayNodePartitionMemory(CtrlType *ctrl, GraphType *graph)
  function Compute2WayNodePartitionParams (line 89) | void Compute2WayNodePartitionParams(CtrlType *ctrl, GraphType *graph)
  function Project2WayNodePartition (line 144) | void Project2WayNodePartition(CtrlType *ctrl, GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/stat.c
  function ComputePartitionInfo (line 21) | void ComputePartitionInfo(GraphType *graph, int nparts, idxtype *where)
  function ComputePartitionInfoBipartite (line 130) | void ComputePartitionInfoBipartite(GraphType *graph, int nparts, idxtype...
  function ComputePartitionBalance (line 235) | void ComputePartitionBalance(GraphType *graph, int nparts, idxtype *wher...
  function ComputeElementBalance (line 270) | float ComputeElementBalance(int ne, int nparts, idxtype *where)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/struct.h
  type idxtype (line 22) | typedef long long idxtype;
  type idxtype (line 24) | typedef int idxtype;
  type ChainType (line 32) | struct ChainType {
  type Chains (line 39) | typedef struct ChainType Chains;
  type KeyValueType (line 45) | struct KeyValueType {
  type KeyValueType (line 50) | typedef struct KeyValueType KeyValueType;
  type ListNodeType (line 56) | struct ListNodeType {
  type ListNodeType (line 61) | typedef struct ListNodeType ListNodeType;
  type PQueueType (line 69) | struct PQueueType {
  type PQueueType (line 86) | typedef struct PQueueType PQueueType;
  type edegreedef (line 92) | struct edegreedef {
  type EDegreeType (line 98) | typedef struct edegreedef EDegreeType;
  type vedegreedef (line 104) | struct vedegreedef {
  type VEDegreeType (line 109) | typedef struct vedegreedef VEDegreeType;
  type workspacedef (line 115) | struct workspacedef {
  type WorkSpaceType (line 129) | typedef struct workspacedef WorkSpaceType;
  type rinfodef (line 136) | struct rinfodef {
  type RInfoType (line 142) | typedef struct rinfodef RInfoType;
  type vrinfodef (line 149) | struct vrinfodef {
  type VRInfoType (line 156) | typedef struct vrinfodef VRInfoType;
  type nrinfodef (line 163) | struct nrinfodef {
  type NRInfoType (line 167) | typedef struct nrinfodef NRInfoType;
  type graphdef (line 173) | struct graphdef {
  type GraphType (line 218) | typedef struct graphdef GraphType;
  type timer (line 225) | typedef double timer;
  type controldef (line 231) | struct controldef {
  type CtrlType (line 253) | typedef struct controldef CtrlType;
  type vpwgtdef (line 260) | struct vpwgtdef {
  type VPInfoType (line 265) | typedef struct vpwgtdef VPInfoType;

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/subdomains.c
  function Random_KWayEdgeRefineMConn (line 22) | void Random_KWayEdgeRefineMConn(CtrlType *ctrl, GraphType *graph, int np...
  function Greedy_KWayEdgeBalanceMConn (line 312) | void Greedy_KWayEdgeBalanceMConn(CtrlType *ctrl, GraphType *graph, int n...
  function PrintSubDomainGraph (line 625) | void PrintSubDomainGraph(GraphType *graph, int nparts, idxtype *where)
  function ComputeSubDomainGraph (line 676) | void ComputeSubDomainGraph(GraphType *graph, int nparts, idxtype *pmat, ...
  function EliminateSubDomainEdges (line 721) | void EliminateSubDomainEdges(CtrlType *ctrl, GraphType *graph, int npart...
  function MoveGroupMConn (line 892) | void MoveGroupMConn(CtrlType *ctrl, GraphType *graph, idxtype *ndoms, id...
  function EliminateComponents (line 1048) | void EliminateComponents(CtrlType *ctrl, GraphType *graph, int nparts, f...
  function MoveGroup (line 1174) | void MoveGroup(CtrlType *ctrl, GraphType *graph, int nparts, int to, int...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/timing.c
  function InitTimers (line 21) | void InitTimers(CtrlType *ctrl)
  function PrintTimers (line 46) | void PrintTimers(CtrlType *ctrl)
  function seconds (line 69) | double seconds(void)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/metisLib/util.c
  function print_help (line 19) | void print_help(char *program_name){
  function clusterSize (line 33) | void clusterSize(GraphType * graph, int *clustersize){
  function sparse2dense (line 46) | void sparse2dense(GraphType * graph, double * dense, float *m_adjwgt)
  function extractfilename (line 73) | void extractfilename(char *path, char *name)
  function errexit (line 98) | void errexit(char *f_str,...)
  function Chains (line 121) | Chains *chainmalloc(int n, char *msg)
  function idxtype (line 176) | idxtype *idxmalloc(int n, char *msg)
  function idxtype (line 185) | idxtype *idxmalloc_long(long long n, char *msg)
  function idxtype (line 221) | idxtype *idxsmalloc(int n, idxtype ival, char *msg)
  function GKfree (line 266) | void GKfree(void **ptr1,...)
  function idxtype (line 305) | idxtype *idxset(int n, idxtype val, idxtype *x)
  function iamax (line 334) | int iamax(int n, int *x)
  function idxamax (line 348) | int idxamax(int n, idxtype *x)
  function idxamax_strd (line 361) | int idxamax_strd(int n, idxtype *x, int incx)
  function samax (line 377) | int samax(int n, float *x)
  function samax2 (line 390) | int samax2(int n, float *x)
  function idxamin (line 419) | int idxamin(int n, idxtype *x)
  function samin (line 433) | int samin(int n, float *x)
  function idxsum (line 447) | int idxsum(int n, idxtype *x)
  function idxsum_strd (line 461) | int idxsum_strd(int n, idxtype *x, int incx)
  function idxadd (line 476) | void idxadd(int n, idxtype *x, idxtype *y)
  function charsum (line 486) | int charsum(int n, char *x)
  function isum (line 499) | int isum(int n, int *x)
  function ssum (line 512) | float ssum(int n, float *x)
  function ssum_strd (line 526) | float ssum_strd(int n, float *x, int incx)
  function sscale (line 540) | void sscale(int n, float alpha, float *x)
  function snorm2 (line 552) | float snorm2(int n, float *v)
  function sdot (line 568) | float sdot(int n, float *x, float *y)
  function saxpy (line 583) | void saxpy(int n, float alpha, float *x, int incx, float *y, int incy)
  function RandomPermute (line 599) | void RandomPermute(int n, idxtype *p, int flag)
  function RandomInit (line 641) | void RandomInit(int n, int k, idxtype *label)
  function ispow2 (line 663) | int ispow2(int a)
  function InitRandom (line 673) | void InitRandom(int seed)
  function log2_metis (line 692) | int log2_metis(int a)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/multilevelLib/mlkkm.c
  function MLKKM_PartGraphKway (line 25) | void MLKKM_PartGraphKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, idx...
  function MLKKM_WPartGraphKway (line 46) | void MLKKM_WPartGraphKway(int *nvtxs, idxtype *xadj, idxtype *adjncy, id...
  function MLKKMPartitioning (line 183) | int MLKKMPartitioning(CtrlType *ctrl, GraphType *graph, int nparts, int ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/multilevelLib/wkkm.c
  function Compute_Weights (line 19) | void Compute_Weights(CtrlType *ctrl, GraphType *graph, idxtype *w)
  function transform_matrix (line 43) | void transform_matrix(CtrlType *ctrl, GraphType *graph, idxtype *w, floa...
  function transform_matrix_half (line 90) | void transform_matrix_half(CtrlType *ctrl, GraphType *graph, idxtype *w,...
  function pingpong (line 138) | void pingpong(CtrlType *ctrl, GraphType *graph, int nparts, int chain_le...
  function Weighted_kernel_k_means (line 187) | void Weighted_kernel_k_means(CtrlType *ctrl, GraphType *graph, int npart...
  function local_search (line 352) | int local_search(CtrlType *ctrl, GraphType *graph, int nparts, int chain...
  function onePoint_move (line 551) | float onePoint_move(GraphType *graph, int nparts, idxtype *sum, idxtype ...
  function move1Point2EmptyCluster (line 679) | void move1Point2EmptyCluster(GraphType *graph, int nparts, idxtype *sum,...
  function remove_empty_clusters_l1 (line 855) | void remove_empty_clusters_l1(CtrlType *ctrl, GraphType *graph, int npar...
  function remove_empty_clusters_l2 (line 872) | void remove_empty_clusters_l2(CtrlType *ctrl, GraphType *graph, int npar...
  function MLKKMRefine (line 955) | void MLKKMRefine(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/multilevelLib/wkkm_boundary_only.c
  function Compute_Weights (line 19) | void Compute_Weights(CtrlType *ctrl, GraphType *graph, idxtype *w)
  function transform_matrix (line 43) | void transform_matrix(CtrlType *ctrl, GraphType *graph, idxtype *w, floa...
  function pingpong (line 90) | void pingpong(CtrlType *ctrl, GraphType *graph, int nparts, int chain_le...
  function Weighted_kernel_k_means (line 135) | void Weighted_kernel_k_means(CtrlType *ctrl, GraphType *graph, int npart...
  function onePoint_move (line 543) | float onePoint_move(GraphType *graph, int nparts, idxtype *sum, idxtype ...
  function move1Point2EmptyCluster (line 642) | void move1Point2EmptyCluster(GraphType *graph, int nparts, idxtype *sum,...
  function local_search (line 699) | int local_search(CtrlType *ctrl, GraphType *graph, int nparts, int chain...
  function remove_empty_clusters_l1 (line 785) | void remove_empty_clusters_l1(CtrlType *ctrl, GraphType *graph, int npar...
  function remove_empty_clusters_l2 (line 802) | void remove_empty_clusters_l2(CtrlType *ctrl, GraphType *graph, int npar...
  function MLKKMRefine (line 877) | void MLKKMRefine(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/multilevelLib/wkkm_experiment.c
  function Compute_Weights (line 19) | void Compute_Weights(CtrlType *ctrl, GraphType *graph, idxtype *w)
  function transform_matrix (line 43) | void transform_matrix(CtrlType *ctrl, GraphType *graph, idxtype *w, floa...
  function pingpong (line 90) | void pingpong(CtrlType *ctrl, GraphType *graph, int nparts, int chain_le...
  function Weighted_kernel_k_means (line 132) | void Weighted_kernel_k_means(CtrlType *ctrl, GraphType *graph, int npart...
  function onePoint_move (line 540) | float onePoint_move(GraphType *graph, int nparts, idxtype *sum, idxtype ...
  function move1Point2EmptyCluster (line 642) | void move1Point2EmptyCluster(GraphType *graph, int nparts, idxtype *sum,...
  function local_search (line 707) | int local_search(CtrlType *ctrl, GraphType *graph, int nparts, int chain...
  function remove_empty_clusters_l1 (line 813) | void remove_empty_clusters_l1(CtrlType *ctrl, GraphType *graph, int npar...
  function remove_empty_clusters_l2 (line 830) | void remove_empty_clusters_l2(CtrlType *ctrl, GraphType *graph, int npar...
  function MLKKMRefine (line 913) | void MLKKMRefine(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/multilevelLib/wkkm_old.c
  function Compute_Weights (line 19) | void Compute_Weights(CtrlType *ctrl, GraphType *graph, idxtype *w)
  function transform_matrix (line 43) | void transform_matrix(CtrlType *ctrl, GraphType *graph, idxtype *w, floa...
  function transform_matrix_half (line 90) | void transform_matrix_half(CtrlType *ctrl, GraphType *graph, idxtype *w,...
  function pingpong (line 138) | void pingpong(CtrlType *ctrl, GraphType *graph, int nparts, int chain_le...
  function Weighted_kernel_k_means (line 170) | void Weighted_kernel_k_means(CtrlType *ctrl, GraphType *graph, int npart...
  function local_search (line 312) | int local_search(CtrlType *ctrl, GraphType *graph, int nparts, int chain...
  function MLKKMRefine (line 464) | void MLKKMRefine(CtrlType *ctrl, GraphType *orggraph, GraphType *graph, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/GraclusSeeds/graclus1.2/programs/io.c
  function readClustering (line 20) | int readClustering(char *filename, int *part, int nvtex){
  function WriteCoarsestGraph (line 39) | void WriteCoarsestGraph(GraphType *graph, char *filename, int *wgtflag)
  function ReadCoarsestInit (line 68) | void ReadCoarsestInit(GraphType *graph, char *filename, int *wgtflag)
  function ReadGraph (line 91) | void ReadGraph(GraphType *graph, char *filename, int *wgtflag)
  function WritePartition (line 219) | void WritePartition(char *fname, idxtype *part, int n, int nparts)
  function WriteMeshPartition (line 243) | void WriteMeshPartition(char *fname, int nparts, int ne, idxtype *epart,...
  function WritePermutation (line 277) | void WritePermutation(char *fname, idxtype *iperm, int n)
  function CheckGraph (line 300) | int CheckGraph(GraphType *graph)
  function idxtype (line 347) | idxtype *ReadMesh(char *filename, int *ne, int *nn, int *etype)
  function WriteGraph (line 395) | void WriteGraph(char *filename, int nvtxs, idxtype *xadj, idxtype *adjncy)
  function WriteMocGraph (line 420) | void WriteMocGraph(GraphType *graph)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/components.cc
  function strong_components (line 20) | int strong_components(
  function biconnected_components (line 54) | int biconnected_components(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/crm_graph.hpp
  type boost (line 15) | namespace boost
    type yasmic_compressed_row_matrix_traversal_category (line 17) | struct yasmic_compressed_row_matrix_traversal_category :
    type impl (line 26) | namespace impl
      class crm_graph_edge_iter (line 29) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 143) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 145) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 158) | crm_graph_edge_iter(
        method increment (line 168) | void increment()
        method equal (line 188) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 193) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_edge (line 30) | struct crm_graph_edge
      type crm_graph (line 33) | struct crm_graph
      type nonzero_to_adjacency_transform (line 55) | struct nonzero_to_adjacency_transform
        method result_type (line 62) | result_type operator() (argument_type arg) const
      class crm_graph_edge_type (line 111) | class crm_graph_edge_type :
        method crm_graph_edge_type (line 115) | crm_graph_edge_type() { }
        method crm_graph_edge_type (line 116) | crm_graph_edge_type(V s, V d, S id)
        method S (line 119) | S id() { return (_id); }
      type crm_graph_edge (line 126) | struct crm_graph_edge
      class crm_graph_edge_iter (line 135) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 143) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 145) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 158) | crm_graph_edge_iter(
        method increment (line 168) | void increment()
        method equal (line 188) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 193) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_ret (line 209) | struct crm_graph_ret
    type graph_traits< yasmic::compressed_row_matrix<RowIter, ColIter, ValIter> > (line 71) | struct graph_traits< yasmic::compressed_row_matrix<RowIter, ColIter, V...
      method vertex_descriptor (line 100) | static vertex_descriptor null_vertex()
    type impl (line 106) | namespace impl
      class crm_graph_edge_iter (line 29) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 143) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 145) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 158) | crm_graph_edge_iter(
        method increment (line 168) | void increment()
        method equal (line 188) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 193) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_edge (line 30) | struct crm_graph_edge
      type crm_graph (line 33) | struct crm_graph
      type nonzero_to_adjacency_transform (line 55) | struct nonzero_to_adjacency_transform
        method result_type (line 62) | result_type operator() (argument_type arg) const
      class crm_graph_edge_type (line 111) | class crm_graph_edge_type :
        method crm_graph_edge_type (line 115) | crm_graph_edge_type() { }
        method crm_graph_edge_type (line 116) | crm_graph_edge_type(V s, V d, S id)
        method S (line 119) | S id() { return (_id); }
      type crm_graph_edge (line 126) | struct crm_graph_edge
      class crm_graph_edge_iter (line 135) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 143) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 145) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 158) | crm_graph_edge_iter(
        method increment (line 168) | void increment()
        method equal (line 188) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 193) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_ret (line 209) | struct crm_graph_ret
    function num_vertices (line 231) | inline typename boost::graph_traits< yasmic::compressed_row_matrix<Row...
    function num_edges (line 238) | inline typename boost::graph_traits< yasmic::compressed_row_matrix<Row...
    function source (line 245) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::g_trai...
    function target (line 254) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::g_trai...
    function out_edges (line 264) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::out_ed...
    function out_degree (line 289) | typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::g_traits::deg...
    function adjacent_vertices (line 309) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::adjace...
    function vertices (line 326) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::vertic...
    function edges (line 336) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::edges_ret
    class compressed_row_matrix_graph_id_map (line 348) | class compressed_row_matrix_graph_id_map
      method compressed_row_matrix_graph_id_map (line 361) | compressed_row_matrix_graph_id_map() { }
      method S (line 362) | S operator [] (T x) const { return x._nzi; }
    function identity_property_map (line 368) | inline identity_property_map get(vertex_index_t,
    function get (line 376) | inline compressed_row_matrix_graph_id_map<RowIter, ColIter, ValIter> g...
    type compressed_row_matrix_graph_property_map (line 387) | struct compressed_row_matrix_graph_property_map { }
    type compressed_row_matrix_graph_property_map<vertex_index_t> (line 390) | struct compressed_row_matrix_graph_property_map<vertex_index_t> {
      type bind_ (line 392) | struct bind_ {
    type compressed_row_matrix_graph_property_map<edge_index_t> (line 399) | struct compressed_row_matrix_graph_property_map<edge_index_t> {
      type bind_ (line 401) | struct bind_ {
    type compressed_row_matrix_graph_property_map<edge_weight_t> (line 408) | struct compressed_row_matrix_graph_property_map<edge_weight_t> {
      type bind_ (line 410) | struct bind_ {
    type property_map<yasmic::compressed_row_matrix<RowIter, ColIter, ValIter>, Tag> (line 417) | struct property_map<yasmic::compressed_row_matrix<RowIter, ColIter, Va...
    function get (line 425) | inline typename property_map<yasmic::compressed_row_matrix<RowIter, Co...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/include/matlab_bgl.h
  type bfs_visitor_funcs_t (line 27) | typedef struct {
  type dfs_visitor_funcs_t (line 43) | typedef struct {
  type dijkstra_visitor_funcs_t (line 57) | typedef struct {
  type astar_visitor_funcs_t (line 70) | typedef struct {
  type bellman_ford_visitor_funcs_t (line 85) | typedef struct {
  type gursoy_atun_layout_topology_t (line 301) | typedef enum  {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/include/matlab_bgl_types.h
  type mbglIndex (line 27) | typedef size_t mbglIndex;
  type mbglIndex (line 28) | typedef mbglIndex mbglDegreeType;
  type mbglIndex (line 30) | typedef int mbglIndex;
  type mbglDegreeType (line 31) | typedef unsigned int mbglDegreeType;

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/layouts.cc
  class layout_and_iteration_tolerance (line 44) | class layout_and_iteration_tolerance
    method layout_and_iteration_tolerance (line 47) | layout_and_iteration_tolerance(const T& tolerance=0.001, int maxiter =...
  function kamada_kawai_spring_layout (line 117) | int kamada_kawai_spring_layout(
  function fruchterman_reingold_force_directed_layout (line 195) | int fruchterman_reingold_force_directed_layout(
  function gursoy_atun_layout_helper (line 247) | int gursoy_atun_layout_helper(const Graph& g, bool weighted,
  function gursoy_atun_layout (line 293) | int gursoy_atun_layout(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/fr_layout_test.cc
  function main (line 5) | int main(int argc, char **argv) {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/layout_funcs_test.cc
  function test_layout_1 (line 7) | int test_layout_1() {
  function layout_funcs_test (line 23) | int layout_funcs_test()

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/libmbgl_funcs_test.cc
  function main (line 10) | int main(int argc, char **argv) {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/libmbgl_test.cc
  function main (line 19) | int main(int argc, char **argv)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/planar_funcs_test.cc
  function test_1 (line 7) | int test_1() {
  function test_2 (line 38) | int test_2() {
  function test_3 (line 70) | int test_3() {
  function test_4 (line 103) | int test_4() {
  function test_5 (line 137) | int test_5() {
  function planar_funcs_test (line 161) | int planar_funcs_test() {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/planar_is_straight_line_test.cc
  function main (line 5) | int main(int argc, char **argv) {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/planar_ksubgraph_test.cc
  function main (line 5) | int main(int argc, char **argv) {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/property_map_test.cc
  function test_edge_index_map_impl (line 8) | void test_edge_index_map_impl(const EdgeIndexMap& m, Graph& g, Edge& e)
  function test_edge_index_map (line 16) | void test_edge_index_map(EdgeIndexMap m, Graph& g) {
  function test_edge_property_map (line 25) | void test_edge_property_map(EdgeComponentPropertyMap m, Graph& g)
  function main (line 37) | int main(int argc, char **argv)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/simple_prop_map_test.cc
  type yasmic (line 4) | namespace yasmic {
    type impl (line 5) | namespace impl {
      class simple_csr_edge (line 7) | class simple_csr_edge {
        method simple_csr_edge (line 11) | simple_csr_edge(Index row, EdgeIndex ind) : r(row), i(ind) {}
        method simple_csr_edge (line 12) | simple_csr_edge() : r(0), i(0) {}
  type boost (line 19) | namespace boost {
    type detail (line 20) | namespace detail {
      type simple_csr_edge_index_map (line 23) | struct simple_csr_edge_index_map {
    function EdgeIndex (line 32) | inline EdgeIndex
  function test_edge_index_map_impl (line 42) | void test_edge_index_map_impl(const EdgeIndexMap& m, Edge& e)
  function test_edge_index_map (line 50) | void test_edge_index_map(EdgeIndexMap m) {
  function test_edge_property_map (line 59) | void test_edge_property_map(EdgeComponentPropertyMap m)
  function main (line 70) | int main(int argc, char **argv)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/simple_prop_map_test_2.cc
  class simple_csr_edge (line 5) | class simple_csr_edge {
    method simple_csr_edge (line 9) | simple_csr_edge(Index row, EdgeIndex ind) : r(row), i(ind) {}
    method simple_csr_edge (line 10) | simple_csr_edge() : r(0), i(0) {}
  type simple_csr_edge_index_map (line 17) | struct simple_csr_edge_index_map {
  function EdgeIndex (line 25) | inline EdgeIndex
  function test_edge_index_map_impl (line 34) | void test_edge_index_map_impl(const EdgeIndexMap& m, Edge& e)
  function test_edge_index_map (line 42) | void test_edge_index_map(EdgeIndexMap m) {
  function test_edge_property_map (line 51) | void test_edge_property_map(EdgeComponentPropertyMap m)
  function main (line 62) | int main(int argc, char **argv)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/simple_prop_map_test_3.cc
  type yasmic (line 4) | namespace yasmic {
    type impl (line 5) | namespace impl {
      class simple_csr_edge (line 7) | class simple_csr_edge {
        method simple_csr_edge (line 11) | simple_csr_edge(Index row, EdgeIndex ind) : r(row), i(ind) {}
        method simple_csr_edge (line 12) | simple_csr_edge() : r(0), i(0) {}
  type boost (line 17) | namespace boost {
    type simple_csr_edge_index_map (line 21) | struct simple_csr_edge_index_map {
    function EdgeIndex (line 29) | inline EdgeIndex
  function test_edge_index_map_impl (line 39) | void test_edge_index_map_impl(const EdgeIndexMap& m, Edge& e)
  function test_edge_index_map (line 47) | void test_edge_index_map(EdgeIndexMap m) {
  function test_edge_property_map (line 56) | void test_edge_property_map(EdgeComponentPropertyMap m)
  function main (line 67) | int main(int argc, char **argv)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_test/simple_prop_map_test_4.cc
  type yasmic (line 4) | namespace yasmic {
    type impl (line 5) | namespace impl {
      class simple_csr_edge (line 7) | class simple_csr_edge {
        method simple_csr_edge (line 11) | simple_csr_edge(Index row, EdgeIndex ind) : r(row), i(ind) {}
        method simple_csr_edge (line 12) | simple_csr_edge() : r(0), i(0) {}
  type boost (line 19) | namespace boost {
    type detail (line 20) | namespace detail {
      type simple_csr_edge_index_map (line 23) | struct simple_csr_edge_index_map {
      function EdgeIndex (line 31) | inline EdgeIndex
  function test_edge_index_map_impl (line 44) | void test_edge_index_map_impl(const EdgeIndexMap& m, Edge& e)
  function test_edge_index_map (line 52) | void test_edge_index_map(EdgeIndexMap m) {
  function test_edge_property_map (line 61) | void test_edge_property_map(EdgeComponentPropertyMap m)
  function main (line 72) | int main(int argc, char **argv)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/libmbgl_util.hpp
  type row_matrix (line 15) | struct row_matrix {
    method value_type (line 19) | const value_type* operator[](std::size_t i) const {
    method value_type (line 23) | value_type* operator[](std::size_t i) {
    method row_matrix (line 27) | row_matrix(value_type* _head, std::size_t _nrows, std::size_t _ncols)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/max_flow.cc
  type reverse_edge_pmap_helper (line 34) | struct reverse_edge_pmap_helper
  class reverse_edge_pmap (line 62) | class reverse_edge_pmap
    method reference (line 80) | inline reference
    method reverse_edge_pmap (line 90) | inline
  function make_reverse_edge_pmap (line 97) | inline reverse_edge_pmap<Index, Value, EdgeIndex>
  function push_relabel_max_flow (line 128) | int push_relabel_max_flow(
  function edmunds_karp_max_flow (line 176) | int edmunds_karp_max_flow(
  function kolmogorov_max_flow (line 221) | int kolmogorov_max_flow(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/planar.cc
  function mbglIndex (line 43) | mbglIndex copy_to_ij(Graph& g, Iterator oi,
  function copy_embedding (line 61) | void copy_embedding(Graph& g, PlanarEmbedding e, mbglIndex *eip, mbglInd...
  function boyer_myrvold_planarity_test (line 110) | int boyer_myrvold_planarity_test(
  type upper_triangle_edge_filter (line 193) | struct upper_triangle_edge_filter {
    method upper_triangle_edge_filter (line 194) | upper_triangle_edge_filter() : _g(NULL) {}
    method upper_triangle_edge_filter (line 195) | upper_triangle_edge_filter(const Graph& g_) : _g(&g_) {}
  function is_kuratowski_subgraph (line 213) | int is_kuratowski_subgraph(
  function is_straight_line_drawing (line 246) | int is_straight_line_drawing(
  function copy_crs_to_graph (line 276) | void copy_crs_to_graph(
  type record_add_edge_visitor (line 306) | struct record_add_edge_visitor {
    method record_add_edge_visitor (line 311) | record_add_edge_visitor(EdgeSrcOutIterator soi_, EdgeSrcOutIterator so...
    method visit_vertex_pair (line 317) | void visit_vertex_pair(Vertex u, Vertex v, Graph& g) {
  function triangulate_bgl_graph (line 331) | int triangulate_bgl_graph(
  function triangulate_graph (line 417) | int triangulate_graph(
  function chrobak_payne_straight_line_drawing_on_maximal_graph (line 441) | int chrobak_payne_straight_line_drawing_on_maximal_graph(const Graph& g,
  function chrobak_payne_straight_line_drawing (line 534) | int chrobak_payne_straight_line_drawing(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/searches.cc
  type stop_bfs (line 38) | struct stop_bfs {}
  function breadth_first_search (line 61) | int breadth_first_search(
  function breadth_first_search_visitor (line 130) | int breadth_first_search_visitor(
  type stop_dfs (line 164) | struct stop_dfs {}
  function depth_first_search (line 191) | int depth_first_search(
  function depth_first_search_visitor (line 279) | int depth_first_search_visitor(
  type stop_astar (line 322) | struct stop_astar {}
  class astar_heuristic_data (line 341) | class astar_heuristic_data : public std::unary_function<
    method astar_heuristic_data (line 349) | astar_heuristic_data(CostType *data) : _data(data) {}
    method CostType (line 350) | CostType operator()(Vertex u) { return _data[u]; }
  class astar_heuristic_func (line 354) | class astar_heuristic_func : public std::unary_function<
    method astar_heuristic_func (line 363) | astar_heuristic_func(CostType (*hfunc)(void* pdata, mbglIndex u), void...
    method CostType (line 364) | CostType operator()(Vertex u) { return _func(_pdata, u); }
  function astar_search (line 368) | int astar_search(
  function astar_search_hfunc (line 405) | int astar_search_hfunc(
  function astar_search_hfunc_visitor (line 441) | int astar_search_hfunc_visitor(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/shortest_path.cc
  type stop_dijkstra (line 36) | struct stop_dijkstra {}
  function dijkstra_sp (line 38) | int dijkstra_sp(
  function dijkstra_sp_visitor (line 79) | int dijkstra_sp_visitor(
  type stop_bellman_ford (line 105) | struct stop_bellman_ford {}
  function bellman_ford_sp (line 107) | int bellman_ford_sp(
  function bellman_ford_sp_visitor (line 147) | int bellman_ford_sp_visitor(
  type stop_dag (line 174) | struct stop_dag {}
  function dag_sp (line 176) | int dag_sp(
  function johnson_all_sp (line 202) | int johnson_all_sp(
  function floyd_warshall_all_sp (line 226) | int floyd_warshall_all_sp(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/spanning_trees.cc
  function mbglIndex (line 70) | mbglIndex copy_to_ijval(Graph& g, EdgeWeightPropMap ewpm, Iterator oi,
  function kruskal_mst (line 86) | int kruskal_mst(
  function prim_mst_rooted (line 122) | int prim_mst_rooted(mbglIndex nverts, mbglIndex *ja, mbglIndex *ia,
  function prim_mst (line 168) | int prim_mst(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/statistics.cc
  type in_indicator_pred (line 40) | struct in_indicator_pred
    method in_indicator_pred (line 43) | in_indicator_pred(IndMap indmap, Vertex src)
  function cluster_coefficients (line 58) | void cluster_coefficients(const Graph& g, CCMap cc, IndMap ind)
  function undirected_clustering_coefficients (line 117) | void undirected_clustering_coefficients(const Graph& g, CCMap cc, EdgeWe...
  function directed_clustering_coefficients (line 169) | void directed_clustering_coefficients(const Graph& g,
  function clustering_coefficients (line 305) | int clustering_coefficients(
  function weighted_clustering_coefficients (line 341) | int weighted_clustering_coefficients(
  function directed_clustering_coefficients (line 363) | int directed_clustering_coefficients(
  function betweenness_centrality (line 400) | int betweenness_centrality(
  function topological_order (line 460) | int topological_order(
  function matching_help (line 506) | bool matching_help(const Graph& g, MateMap mate, VertexIndexMap vm,
  function maximum_cardinality_matching (line 631) | int maximum_cardinality_matching(
  function verify_matching_help (line 666) | bool verify_matching_help(const Graph& g, MateMap mate, VertexIndexMap vm)
  function test_maximum_cardinality_matching (line 675) | int test_maximum_cardinality_matching(
  function core_numbers (line 712) | int core_numbers(
  function weighted_core_numbers (line 752) | int weighted_core_numbers(
  function dominator_tree (line 775) | int dominator_tree(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/stop_visitors.hpp
  type vertex_search_stopper (line 16) | struct vertex_search_stopper
    method vertex_search_stopper (line 20) | vertex_search_stopper(Vertex v)
  function stop_search_on_vertex_target (line 30) | vertex_search_stopper<Vertex, Exception, Tag>

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/bgl_kcore.hpp
  type boost (line 30) | namespace boost
    function core_numbers (line 34) | void core_numbers(const Graph& g, KCoreMap kcm, PositionMap pos)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/binary_ifstream_graph.hpp
  type yasmic (line 21) | namespace yasmic
    type impl (line 23) | namespace impl
      class binary_ifstream_graph_const_iterator (line 27) | class binary_ifstream_graph_const_iterator
        method binary_ifstream_graph_const_iterator (line 37) | binary_ifstream_graph_const_iterator()
        method binary_ifstream_graph_const_iterator (line 41) | binary_ifstream_graph_const_iterator(std::istream &str)
        method increment (line 49) | void increment()
        method equal (line 60) | bool equal(binary_ifstream_graph_const_iterator const& other) const
        method dereference (line 65) | boost::tuple<
    type binary_ifstream_graph (line 82) | struct binary_ifstream_graph
      method binary_ifstream_graph (line 86) | binary_ifstream_graph(std::istream& f)
      method binary_ifstream_graph (line 90) | binary_ifstream_graph(const binary_ifstream_graph& bifm)
    type smatrix_traits<binary_ifstream_graph<i_index_type, i_value_type, i_size_type> > (line 96) | struct smatrix_traits<binary_ifstream_graph<i_index_type, i_value_type...
    function dimensions (line 115) | inline std::pair<typename smatrix_traits<binary_ifstream_graph<i_index...
    function nnz (line 132) | typename smatrix_traits<binary_ifstream_graph<i_index_type, i_value_ty...
    function nonzeros (line 150) | std::pair<typename smatrix_traits<binary_ifstream_graph<i_index_type, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/binary_ifstream_matrix.hpp
  type yasmic (line 21) | namespace yasmic
    type impl (line 23) | namespace impl
      class binary_ifstream_matrix_const_iterator (line 27) | class binary_ifstream_matrix_const_iterator
        method binary_ifstream_matrix_const_iterator (line 37) | binary_ifstream_matrix_const_iterator()
        method binary_ifstream_matrix_const_iterator (line 41) | binary_ifstream_matrix_const_iterator(std::istream &str)
        method increment (line 49) | void increment()
        method equal (line 61) | bool equal(binary_ifstream_matrix_const_iterator const& other) const
        method dereference (line 66) | boost::tuple<
    type binary_ifstream_matrix (line 83) | struct binary_ifstream_matrix
      method binary_ifstream_matrix (line 87) | binary_ifstream_matrix(std::istream& f)
      method binary_ifstream_matrix (line 91) | binary_ifstream_matrix(const binary_ifstream_matrix& bifm)
    type smatrix_traits<binary_ifstream_matrix<i_index_type, i_value_type, i_size_type> > (line 97) | struct smatrix_traits<binary_ifstream_matrix<i_index_type, i_value_typ...
    function dimensions (line 116) | inline std::pair<typename smatrix_traits<binary_ifstream_matrix<i_inde...
    function nnz (line 133) | typename smatrix_traits<binary_ifstream_matrix<i_index_type, i_value_t...
    function nonzeros (line 151) | std::pair<typename smatrix_traits<binary_ifstream_matrix<i_index_type,...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/bind_utility.hpp
  type boost (line 14) | namespace boost {
    class binder1st (line 17) | class binder1st
      method binder1st (line 24) | binder1st() { }
      method binder1st (line 25) | binder1st(const Operation& x,
    function bind1st (line 35) | inline binder1st<Operation> bind1st(const Operation& op, const T& x) {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/bellman_ford_shortest_paths.hpp
  type boost (line 33) | namespace boost {
    type BellmanFordVisitorConcept (line 36) | struct BellmanFordVisitorConcept {
      method constraints (line 37) | void constraints() {
    class bellman_visitor (line 51) | class bellman_visitor {
      method bellman_visitor (line 53) | bellman_visitor() { }
      method bellman_visitor (line 54) | bellman_visitor(Visitors vis) : m_vis(vis) { }
      method examine_edge (line 57) | void examine_edge(Edge u, Graph& g) {
      method edge_relaxed (line 61) | void edge_relaxed(Edge u, Graph& g) {
      method edge_not_relaxed (line 65) | void edge_not_relaxed(Edge u, Graph& g) {
      method edge_minimized (line 69) | void edge_minimized(Edge u, Graph& g) {
      method edge_not_minimized (line 73) | void edge_not_minimized(Edge u, Graph& g) {
    function make_bellman_visitor (line 80) | bellman_visitor<Visitors>
    function bellman_ford_shortest_paths (line 90) | bool bellman_ford_shortest_paths(EdgeListGraph& g, Size N,
    type detail (line 135) | namespace detail {
      function bellman_dispatch2 (line 140) | bool
      function bellman_dispatch2 (line 175) | bool
      function bellman_dispatch (line 197) | bool bellman_dispatch(EdgeListGraph& g, Size N,
    function bellman_ford_shortest_paths (line 214) | bool bellman_ford_shortest_paths
    function bellman_ford_shortest_paths (line 226) | bool bellman_ford_shortest_paths(EdgeListGraph& g, Size N)
    function bellman_ford_shortest_paths (line 233) | bool bellman_ford_shortest_paths

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/betweenness_centrality.hpp
  type boost (line 26) | namespace boost {
    type brandes_dijkstra_visitor (line 37) | struct brandes_dijkstra_visitor : public bfs_visitor<>
      method brandes_dijkstra_visitor (line 42) | brandes_dijkstra_visitor(std::stack<vertex_descriptor>& ordered_vert...
      method edge_relaxed (line 57) | void edge_relaxed(edge_descriptor e, const Graph& g)
      method edge_not_relaxed (line 71) | void edge_not_relaxed(edge_descriptor e, const Graph& g)
      method examine_vertex (line 87) | void examine_vertex(vertex_descriptor w, const Graph&)
    type brandes_dijkstra_shortest_paths (line 106) | struct brandes_dijkstra_shortest_paths
      method brandes_dijkstra_shortest_paths (line 108) | brandes_dijkstra_shortest_paths(WeightMap weight_map)
    type brandes_unweighted_shortest_paths (line 141) | struct brandes_unweighted_shortest_paths
      type visitor_type (line 150) | struct visitor_type : public bfs_visitor<>
        method visitor_type (line 156) | visitor_type(IncomingMap incoming, DistanceMap distance,
        method examine_vertex (line 163) | void examine_vertex(vertex_descriptor v, const Graph&)
        method tree_edge (line 173) | void tree_edge(edge_descriptor e, const Graph& g)
        method non_tree_edge (line 189) | void non_tree_edge(edge_descriptor e, const Graph& g)
    function init_centrality_map (line 235) | inline void
    function init_centrality_map (line 241) | void
    function update_centrality (line 255) | inline void
    function update_centrality (line 260) | inline void
    function divide_centrality_by_two (line 265) | inline void
    function divide_centrality_by_two (line 269) | inline void
    function brandes_betweenness_centrality_impl (line 284) | void
    function brandes_betweenness_centrality (line 360) | void
    function brandes_betweenness_centrality (line 384) | void
    function brandes_betweenness_centrality_dispatch2 (line 408) | void
    function brandes_betweenness_centrality_dispatch2 (line 445) | void
    type brandes_betweenness_centrality_dispatch1 (line 479) | struct brandes_betweenness_centrality_dispatch1
      method run (line 483) | static void
    type brandes_betweenness_centrality_dispatch1<detail::error_property_not_found> (line 494) | struct brandes_betweenness_centrality_dispatch1<detail::error_property...
      method run (line 498) | static void
    function brandes_betweenness_centrality (line 511) | void
    function brandes_betweenness_centrality (line 529) | void
    function brandes_betweenness_centrality (line 537) | void
    function relative_betweenness_centrality (line 552) | void
    function central_point_dominance (line 568) | typename property_traits<CentralityMap>::value_type

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/chrobak_payne_drawing.hpp
  type boost (line 20) | namespace boost
    type graph (line 23) | namespace graph { namespace detail
      type detail (line 23) | namespace detail
        function accumulate_offsets (line 29) | void accumulate_offsets(typename graph_traits<Graph>::vertex_descr...
    function chrobak_payne_straight_line_drawing (line 56) | void chrobak_payne_straight_line_drawing(const Graph& g,
    function chrobak_payne_straight_line_drawing (line 251) | inline void chrobak_payne_straight_line_drawing(const Graph& g,

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/core_numbers.hpp
  type boost (line 34) | namespace boost {
    type CoreNumbersVisitorConcept (line 47) | struct CoreNumbersVisitorConcept {
      method constraints (line 48) | void constraints()
    class core_numbers_visitor (line 62) | class core_numbers_visitor : public bfs_visitor<Visitors> {
      method core_numbers_visitor (line 64) | core_numbers_visitor() {}
      method core_numbers_visitor (line 65) | core_numbers_visitor(Visitors vis)
      method initialize_vertex (line 70) | void initialize_vertex(Vertex, Graph&) {}
      method discover_vertex (line 72) | void discover_vertex(Vertex , Graph&) {}
      method gray_target (line 74) | void gray_target(Vertex, Graph&) {}
      method black_target (line 76) | void black_target(Vertex, Graph&) {}
      method tree_edge (line 78) | void tree_edge(Edge, Graph&) {}
      method non_tree_edge (line 80) | void non_tree_edge(Edge, Graph&) {}
    function make_core_numbers_visitor (line 84) | core_numbers_visitor<Visitors>
    type detail (line 91) | namespace detail {
      class constant_value_property_map (line 97) | class constant_value_property_map
        method constant_value_property_map (line 106) | inline constant_value_property_map(ValueType cc) : c(cc) { }
        method constant_value_property_map (line 107) | inline constant_value_property_map(const constant_value_property_m...
        method reference (line 110) | inline reference operator[](Vertex) const { return c; }
      function compute_in_degree_map (line 119) | void compute_in_degree_map(Graph& g, CoreMap d, EdgeWeightMap wm)
      function core_numbers_impl (line 137) | typename property_traits<CoreMap>::value_type
      function core_numbers_dispatch (line 169) | typename property_traits<CoreMap>::value_type
      function core_numbers_impl (line 194) | typename property_traits<CoreMap>::value_type
    function core_numbers (line 283) | typename property_traits<CoreMap>::value_type
    function core_numbers (line 299) | typename property_traits<CoreMap>::value_type
    function core_numbers (line 308) | typename property_traits<CoreMap>::value_type
    function weighted_core_numbers (line 329) | typename property_traits<CoreMap>::value_type
    function weighted_core_numbers (line 336) | typename property_traits<CoreMap>::value_type

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/floyd_warshall_shortest.hpp
  type boost (line 40) | namespace boost
    type detail (line 42) | namespace detail {
      class dummy_predecessor_matrix (line 44) | class dummy_predecessor_matrix {
        method dummy_predecessor_matrix (line 46) | inline dummy_predecessor_matrix() {}
        method dummy_predecessor_matrix (line 47) | inline dummy_predecessor_matrix(const dummy_predecessor_matrix& x)
        method reference (line 51) | inline reference operator[](K) const { return p; }
      function T (line 57) | T min_with_compare(const T& x, const T& y, const BinaryPredicate& co...
      function min_with_compare_and_choice (line 64) | std::pair<T,bool>
      function floyd_warshall_dispatch (line 76) | bool floyd_warshall_dispatch(const VertexListGraph& g,
      function floyd_warshall_init_dispatch (line 213) | bool floyd_warshall_init_dispatch(const VertexListGraph& g,
      function floyd_warshall_noninit_dispatch (line 237) | bool floyd_warshall_noninit_dispatch(const VertexAndEdgeListGraph& g,
    function floyd_warshall_initialized_all_pairs_shortest_paths (line 109) | bool floyd_warshall_initialized_all_pairs_shortest_paths(
    function floyd_warshall_all_pairs_shortest_paths (line 124) | bool floyd_warshall_all_pairs_shortest_paths(
    function floyd_warshall_all_pairs_shortest_paths (line 198) | bool floyd_warshall_all_pairs_shortest_paths(
    type detail (line 210) | namespace detail {
      class dummy_predecessor_matrix (line 44) | class dummy_predecessor_matrix {
        method dummy_predecessor_matrix (line 46) | inline dummy_predecessor_matrix() {}
        method dummy_predecessor_matrix (line 47) | inline dummy_predecessor_matrix(const dummy_predecessor_matrix& x)
        method reference (line 51) | inline reference operator[](K) const { return p; }
      function T (line 57) | T min_with_compare(const T& x, const T& y, const BinaryPredicate& co...
      function min_with_compare_and_choice (line 64) | std::pair<T,bool>
      function floyd_warshall_dispatch (line 76) | bool floyd_warshall_dispatch(const VertexListGraph& g,
      function floyd_warshall_init_dispatch (line 213) | bool floyd_warshall_init_dispatch(const VertexListGraph& g,
      function floyd_warshall_noninit_dispatch (line 237) | bool floyd_warshall_noninit_dispatch(const VertexAndEdgeListGraph& g,
    function floyd_warshall_initialized_all_pairs_shortest_paths (line 264) | bool floyd_warshall_initialized_all_pairs_shortest_paths(
    function floyd_warshall_initialized_all_pairs_shortest_paths (line 274) | bool floyd_warshall_initialized_all_pairs_shortest_paths(
    function floyd_warshall_all_pairs_shortest_paths (line 287) | bool floyd_warshall_all_pairs_shortest_paths(
    function floyd_warshall_all_pairs_shortest_paths (line 297) | bool floyd_warshall_all_pairs_shortest_paths(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/fruchterman_reingold.hpp
  type boost (line 20) | namespace boost {
    type square_distance_attractive_force (line 22) | struct square_distance_attractive_force {
      method T (line 24) | T
    type square_distance_repulsive_force (line 34) | struct square_distance_repulsive_force {
      method T (line 36) | T
    type linear_cooling (line 48) | struct linear_cooling {
      method linear_cooling (line 51) | linear_cooling(std::size_t iterations)
      method linear_cooling (line 54) | linear_cooling(std::size_t iterations, T temp)
      method T (line 57) | T operator()()
    type all_force_pairs (line 70) | struct all_force_pairs
    type grid_force_pairs (line 88) | struct grid_force_pairs
      method grid_force_pairs (line 91) | explicit
    function make_grid_force_pairs (line 161) | inline grid_force_pairs<Dim, PositionMap>
    function scale_graph (line 167) | void
    type detail (line 202) | namespace detail {
      type fr_apply_force (line 205) | struct fr_apply_force
        method fr_apply_force (line 209) | fr_apply_force(const PositionMap& position,
      type fr_force_directed_layout (line 325) | struct fr_force_directed_layout
        method run (line 331) | static void
      type fr_force_directed_layout<error_property_not_found> (line 350) | struct fr_force_directed_layout<error_property_not_found>
        method run (line 356) | static void
    function fruchterman_reingold_force_directed_layout (line 244) | void
    type detail (line 323) | namespace detail {
      type fr_apply_force (line 205) | struct fr_apply_force
        method fr_apply_force (line 209) | fr_apply_force(const PositionMap& position,
      type fr_force_directed_layout (line 325) | struct fr_force_directed_layout
        method run (line 331) | static void
      type fr_force_directed_layout<error_property_not_found> (line 350) | struct fr_force_directed_layout<error_property_not_found>
        method run (line 356) | static void
    function fruchterman_reingold_force_directed_layout (line 384) | void
    function fruchterman_reingold_force_directed_layout (line 410) | void

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/gzip.hpp
  type std (line 46) | namespace std { using ::time_t; }
  type boost (line 49) | namespace boost { namespace iostreams {
    type iostreams (line 49) | namespace iostreams {
      type gzip (line 51) | namespace gzip {
        type magic (line 63) | namespace magic {
        type method (line 72) | namespace method {
        type flags (line 80) | namespace flags {
        type extra_flags (line 92) | namespace extra_flags {
      type gzip_params (line 126) | struct gzip_params : zlib_params {
        method gzip_params (line 129) | gzip_params( int level              = gzip::default_compression,
      class gzip_error (line 150) | class gzip_error : public BOOST_IOSTREAMS_FAILURE {
        method gzip_error (line 152) | explicit gzip_error(int error)
        method gzip_error (line 155) | explicit gzip_error(const zlib_error& e)
        method error (line 159) | int error() const { return error_; }
        method zlib_error_code (line 160) | int zlib_error_code() const { return zlib_error_code_; }
      class basic_gzip_compressor (line 172) | class basic_gzip_compressor : basic_zlib_compressor<Alloc> {
        type category (line 177) | struct category
        method read (line 187) | std::streamsize read(Source& src, char_type* s, std::streamsize n)
        method write (line 221) | std::streamsize write(Sink& snk, const char_type* s, std::streamsi...
        method close (line 236) | void close(Sink& snk, BOOST_IOS::openmode m)
        method write_long (line 269) | static void write_long(long n, Sink& next)
        type flag_type (line 277) | enum flag_type {
      class basic_gzip_decompressor (line 297) | class basic_gzip_decompressor : basic_zlib_decompressor<Alloc> {
        type category (line 300) | struct category
        method seek (line 312) | std::streampos seek(Source &src, stream_offset off,
        method read (line 356) | std::streamsize read(Source& src, char_type* s, std::streamsize n)
        method close (line 390) | void close(Source& src)
        method file_name (line 400) | std::string file_name() const { return file_name_; }
        method comment (line 401) | std::string comment() const { return comment_; }
        method text (line 402) | bool text() const { return (flags_ & gzip::flags::text) != 0; }
        method os (line 403) | int os() const { return os_; }
        method mtime (line 404) | std::time_t mtime() const { return mtime_; }
        method is_eof (line 408) | static bool is_eof(int c) { return traits_type::eq_int_type(c, EOF...
        method read_uint8 (line 412) | static uint8_t read_uint8(Source& src, int error)
        method read_uint32 (line 421) | static uint32_t read_uint32(Source& src, int error)
        method read_string (line 431) | std::string read_string(Source& src)
        method read_header (line 446) | void read_header(Source& src) // Source is non-blocking.
        method read_footer (line 500) | void read_footer(Source& src)
        type flag_type (line 514) | enum flag_type {
      function gzip_params (line 579) | gzip_params basic_gzip_compressor<Alloc>::normalize_params(gzip_para...
        method gzip_params (line 129) | gzip_params( int level              = gzip::default_compression,
      function gzip_params (line 626) | gzip_params basic_gzip_decompressor<Alloc>::make_params(int window_b...
        method gzip_params (line 129) | gzip_params( int level              = gzip::default_compression,

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/integer_extra.hpp
  type boost (line 12) | namespace boost {
    type int_t<64> (line 14) | struct int_t<64> {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/is_straight_line_drawing.hpp
  type boost (line 25) | namespace boost
    function intersects (line 37) | bool intersects(double x1, double y1,
    function is_straight_line_drawing (line 101) | bool is_straight_line_drawing(const Graph& g,
    function is_straight_line_drawing (line 245) | bool is_straight_line_drawing(const Graph& g, GridPositionMap drawing)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/johnson_all_pairs_shortest.hpp
  type boost (line 33) | namespace boost {
    type detail (line 136) | namespace detail {
      type single_source_vertex_graph (line 139) | struct single_source_vertex_graph {
        method single_source_vertex_graph (line 144) | single_source_vertex_graph(VertexAndEdgeListGraph& g,
      type ssv_graph_edge (line 149) | struct ssv_graph_edge
        method ssv_graph_edge (line 152) | ssv_graph_edge() {}
        method ssv_graph_edge (line 153) | ssv_graph_edge(Vertex s, Vertex t, Weight w) :
      class ssv_edge_iter (line 159) | class ssv_edge_iter :
        method ssv_edge_iter (line 176) | ssv_edge_iter() {}
        method ssv_edge_iter (line 177) | ssv_edge_iter(bool iter_source, src_iter si, src_iter siend,
        method ssv_edge_iter (line 182) | ssv_edge_iter(const ssv_edge_iter& sei)
        method increment (line 189) | inline void increment() {
        method Edge (line 197) | inline Edge dereference() const {
        method equal (line 201) | inline bool equal(const ssv_edge_iter& other) const {
      type ssv_graph_help (line 208) | struct ssv_graph_help {
      class ssv_edge_weight_map (line 221) | class ssv_edge_weight_map {}
      function johnson_dispatch (line 437) | bool
    type graph_traits< detail::single_source_vertex_graph<
      VertexAndEdgeListGraph, VertexIDMap, WeightMap, DistanceZero> > (line 226) | struct graph_traits< detail::single_source_vertex_graph<
      method vertex_descriptor (line 240) | static vertex_descriptor null_vertex() {
    function edges (line 252) | typename detail::ssv_graph_help<
    function num_edges (line 270) | typename detail::ssv_graph_help<
    function Weight (line 279) | Weight get(const detail::ssv_edge_weight_map<Vertex,Weight>&,
    type property_traits<detail::ssv_edge_weight_map<Vertex,Weight> > (line 284) | struct property_traits<detail::ssv_edge_weight_map<Vertex,Weight> > {
    function johnson_all_pairs_shortest_paths (line 294) | bool
    function johnson_all_pairs_shortest_paths (line 419) | bool
    type detail (line 432) | namespace detail {
      type single_source_vertex_graph (line 139) | struct single_source_vertex_graph {
        method single_source_vertex_graph (line 144) | single_source_vertex_graph(VertexAndEdgeListGraph& g,
      type ssv_graph_edge (line 149) | struct ssv_graph_edge
        method ssv_graph_edge (line 152) | ssv_graph_edge() {}
        method ssv_graph_edge (line 153) | ssv_graph_edge(Vertex s, Vertex t, Weight w) :
      class ssv_edge_iter (line 159) | class ssv_edge_iter :
        method ssv_edge_iter (line 176) | ssv_edge_iter() {}
        method ssv_edge_iter (line 177) | ssv_edge_iter(bool iter_source, src_iter si, src_iter siend,
        method ssv_edge_iter (line 182) | ssv_edge_iter(const ssv_edge_iter& sei)
        method increment (line 189) | inline void increment() {
        method Edge (line 197) | inline Edge dereference() const {
        method equal (line 201) | inline bool equal(const ssv_edge_iter& other) const {
      type ssv_graph_help (line 208) | struct ssv_graph_help {
      class ssv_edge_weight_map (line 221) | class ssv_edge_weight_map {}
      function johnson_dispatch (line 437) | bool
    function johnson_all_pairs_shortest_paths (line 460) | bool
    function johnson_all_pairs_shortest_paths (line 474) | bool

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/kolmogorov_max_flow.hpp
  type boost (line 50) | namespace boost {
    type detail (line 51) | namespace detail {
      class kolmogorov (line 61) | class kolmogorov{
        method kolmogorov (line 75) | kolmogorov(Graph& g,
        method tEdgeVal (line 126) | tEdgeVal max_flow(){
        method augment_direct_paths (line 147) | void augment_direct_paths(){
        method grow (line 229) | std::pair<edge_descriptor, bool> grow(){
        method augment (line 312) | void augment(edge_descriptor e){
        method tEdgeVal (line 358) | inline tEdgeVal find_bottleneck(edge_descriptor e){
        method adopt (line 382) | void adopt(){
        method vertex_descriptor (line 481) | inline vertex_descriptor get_next_active_node(){
        method add_active_node (line 500) | inline void add_active_node(vertex_descriptor v){
        method finish_node (line 513) | inline void finish_node(vertex_descriptor v){
        method remove_active_node (line 524) | inline void remove_active_node(vertex_descriptor v){
        method tColorValue (line 531) | inline tColorValue get_tree(vertex_descriptor v) const {
        method set_tree (line 538) | inline void set_tree(vertex_descriptor v, tColorValue t){
        method edge_descriptor (line 545) | inline edge_descriptor get_edge_to_parent(vertex_descriptor v) const{
        method has_parent (line 552) | inline bool has_parent(vertex_descriptor v) const{
        method set_edge_to_parent (line 559) | inline void set_edge_to_parent(vertex_descriptor v, edge_descripto...
        method set_no_parent (line 568) | inline void set_no_parent(vertex_descriptor v){
        method has_sink_connect (line 577) | inline bool has_sink_connect(vertex_descriptor v){
        method has_source_connect (line 613) | inline bool has_source_connect(vertex_descriptor v){
        method is_closer_to_terminal (line 647) | inline bool is_closer_to_terminal(vertex_descriptor p, vertex_desc...
    function kolmogorov_max_flow (line 692) | typename property_traits<CapacityEdgeMap>::value_type
    function kolmogorov_max_flow (line 729) | typename property_traits<CapacityEdgeMap>::value_type
    function kolmogorov_max_flow (line 756) | typename property_traits<CapacityEdgeMap>::value_type
    function kolmogorov_max_flow (line 783) | typename property_traits<typename property_map<Graph, edge_capacity_t>...
    function kolmogorov_max_flow (line 805) | typename property_traits<typename property_map<Graph, edge_capacity_t>...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/kruskal_min_spanning_tree.hpp
  type boost (line 33) | namespace boost {
    type detail (line 42) | namespace detail {
      function OutputIterator (line 46) | OutputIterator
    function OutputIterator (line 100) | inline OutputIterator
    function OutputIterator (line 121) | inline OutputIterator

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/boost_mod/zlib.cpp
  type boost (line 23) | namespace boost { namespace iostreams {
    type iostreams (line 23) | namespace iostreams {
      type zlib (line 25) | namespace zlib {
      type detail (line 89) | namespace detail {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/bvgraph_matrix.hpp
  type yasmic (line 38) | namespace yasmic
    type impl (line 41) | namespace impl {
      class bit_istream (line 42) | class bit_istream
        method bit_istream (line 202) | bit_istream(std::istream& is, const int buffer_size)
        method flush (line 216) | void flush() {
        method close (line 226) | void close() {
        method read_bit (line 231) | int read_bit()
        method read_int (line 239) | int read_int(int len)
        method read_unary (line 259) | int read_unary()
        method read_gamma (line 282) | int read_gamma()
        method read_zeta (line 288) | int read_zeta(const int k)
        method read (line 324) | int read()
        method refill16 (line 346) | int refill16()
        method refill (line 362) | int refill()
        method read_from_current (line 382) | int read_from_current(const int len)
      class bvgraph_sequential_iterator (line 43) | class bvgraph_sequential_iterator
        method read_offset (line 421) | int read_offset() { return (bis.read_gamma()); }
        method read_outdegree (line 422) | int read_outdegree() { return (bis.read_gamma()); }
        method read_reference (line 423) | int read_reference() { return (bis.read_unary()); }
        method read_block (line 424) | int read_block() { return (bis.read_gamma()); }
        method read_block_count (line 425) | int read_block_count() { return (bis.read_gamma()); }
        method read_residual (line 426) | int read_residual() { return (bis.read_zeta(zeta_k)); }
        method nat2int (line 428) | int nat2int(const int x) { return x % 2 == 0 ? x >> 1 : -( ( x + 1...
        method load_successors (line 430) | void load_successors()
        method bvgraph_sequential_iterator (line 635) | bvgraph_sequential_iterator(
        method reset (line 655) | void reset()
        method next_row (line 667) | void next_row()
        method cur_row (line 690) | int cur_row() { return (curr); }
        method cur_row_outdegree (line 692) | int cur_row_outdegree() { return (curr_outd); }
        method rows_end (line 694) | bool rows_end() { return (_rows_end); }
        method next_row_arc (line 697) | void next_row_arc()
        method cur_row_arc_target (line 703) | int cur_row_arc_target() { return (arcs[curr_arc]); }
        method row_arcs_end (line 705) | bool row_arcs_end() { return (_row_arcs_end); }
      class bit_istream (line 199) | class bit_istream
        method bit_istream (line 202) | bit_istream(std::istream& is, const int buffer_size)
        method flush (line 216) | void flush() {
        method close (line 226) | void close() {
        method read_bit (line 231) | int read_bit()
        method read_int (line 239) | int read_int(int len)
        method read_unary (line 259) | int read_unary()
        method read_gamma (line 282) | int read_gamma()
        method read_zeta (line 288) | int read_zeta(const int k)
        method read (line 324) | int read()
        method refill16 (line 346) | int refill16()
        method refill (line 362) | int refill()
        method read_from_current (line 382) | int read_from_current(const int len)
      class bvgraph_sequential_iterator (line 392) | class bvgraph_sequential_iterator
        method read_offset (line 421) | int read_offset() { return (bis.read_gamma()); }
        method read_outdegree (line 422) | int read_outdegree() { return (bis.read_gamma()); }
        method read_reference (line 423) | int read_reference() { return (bis.read_unary()); }
        method read_block (line 424) | int read_block() { return (bis.read_gamma()); }
        method read_block_count (line 425) | int read_block_count() { return (bis.read_gamma()); }
        method read_residual (line 426) | int read_residual() { return (bis.read_zeta(zeta_k)); }
        method nat2int (line 428) | int nat2int(const int x) { return x % 2 == 0 ? x >> 1 : -( ( x + 1...
        method load_successors (line 430) | void load_successors()
        method bvgraph_sequential_iterator (line 635) | bvgraph_sequential_iterator(
        method reset (line 655) | void reset()
        method next_row (line 667) | void next_row()
        method cur_row (line 690) | int cur_row() { return (curr); }
        method cur_row_outdegree (line 692) | int cur_row_outdegree() { return (curr_outd); }
        method rows_end (line 694) | bool rows_end() { return (_rows_end); }
        method next_row_arc (line 697) | void next_row_arc()
        method cur_row_arc_target (line 703) | int cur_row_arc_target() { return (arcs[curr_arc]); }
        method row_arcs_end (line 705) | bool row_arcs_end() { return (_row_arcs_end); }
    class bvgraph_matrix (line 46) | class bvgraph_matrix
      method load_internal (line 71) | void load_internal()
      method bvgraph_matrix (line 133) | bvgraph_matrix(const char* filename)
      method num_nodes (line 142) | int num_nodes() const  { return (n); }
      method num_arcs (line 143) | int num_arcs() const { return (m); }
      method graph_filename (line 145) | std::string graph_filename() const { return (basename + ".graph"); }
      method max_ref_count (line 146) | int max_ref_count() const  { return (_max_ref_count); }
      method window_size (line 147) | int window_size() const { return (_window_size); }
      method min_interval_length (line 148) | int min_interval_length() const { return (_min_interval_length); }
      method zeta_k (line 149) | int zeta_k() const { return (_zeta_k); }
    type impl (line 156) | namespace impl
      class bit_istream (line 42) | class bit_istream
        method bit_istream (line 202) | bit_istream(std::istream& is, const int buffer_size)
        method flush (line 216) | void flush() {
        method close (line 226) | void close() {
        method read_bit (line 231) | int read_bit()
        method read_int (line 239) | int read_int(int len)
        method read_unary (line 259) | int read_unary()
        method read_gamma (line 282) | int read_gamma()
        method read_zeta (line 288) | int read_zeta(const int k)
        method read (line 324) | int read()
        method refill16 (line 346) | int refill16()
        method refill (line 362) | int refill()
        method read_from_current (line 382) | int read_from_current(const int len)
      class bvgraph_sequential_iterator (line 43) | class bvgraph_sequential_iterator
        method read_offset (line 421) | int read_offset() { return (bis.read_gamma()); }
        method read_outdegree (line 422) | int read_outdegree() { return (bis.read_gamma()); }
        method read_reference (line 423) | int read_reference() { return (bis.read_unary()); }
        method read_block (line 424) | int read_block() { return (bis.read_gamma()); }
        method read_block_count (line 425) | int read_block_count() { return (bis.read_gamma()); }
        method read_residual (line 426) | int read_residual() { return (bis.read_zeta(zeta_k)); }
        method nat2int (line 428) | int nat2int(const int x) { return x % 2 == 0 ? x >> 1 : -( ( x + 1...
        method load_successors (line 430) | void load_successors()
        method bvgraph_sequential_iterator (line 635) | bvgraph_sequential_iterator(
        method reset (line 655) | void reset()
        method next_row (line 667) | void next_row()
        method cur_row (line 690) | int cur_row() { return (curr); }
        method cur_row_outdegree (line 692) | int cur_row_outdegree() { return (curr_outd); }
        method rows_end (line 694) | bool rows_end() { return (_rows_end); }
        method next_row_arc (line 697) | void next_row_arc()
        method cur_row_arc_target (line 703) | int cur_row_arc_target() { return (arcs[curr_arc]); }
        method row_arcs_end (line 705) | bool row_arcs_end() { return (_row_arcs_end); }
      class bit_istream (line 199) | class bit_istream
        method bit_istream (line 202) | bit_istream(std::istream& is, const int buffer_size)
        method flush (line 216) | void flush() {
        method close (line 226) | void close() {
        method read_bit (line 231) | int read_bit()
        method read_int (line 239) | int read_int(int len)
        method read_unary (line 259) | int read_unary()
        method read_gamma (line 282) | int read_gamma()
        method read_zeta (line 288) | int read_zeta(const int k)
        method read (line 324) | int read()
        method refill16 (line 346) | int refill16()
        method refill (line 362) | int refill()
        method read_from_current (line 382) | int read_from_current(const int len)
      class bvgraph_sequential_iterator (line 392) | class bvgraph_sequential_iterator
        method read_offset (line 421) | int read_offset() { return (bis.read_gamma()); }
        method read_outdegree (line 422) | int read_outdegree() { return (bis.read_gamma()); }
        method read_reference (line 423) | int read_reference() { return (bis.read_unary()); }
        method read_block (line 424) | int read_block() { return (bis.read_gamma()); }
        method read_block_count (line 425) | int read_block_count() { return (bis.read_gamma()); }
        method read_residual (line 426) | int read_residual() { return (bis.read_zeta(zeta_k)); }
        method nat2int (line 428) | int nat2int(const int x) { return x % 2 == 0 ? x >> 1 : -( ( x + 1...
        method load_successors (line 430) | void load_successors()
        method bvgraph_sequential_iterator (line 635) | bvgraph_sequential_iterator(
        method reset (line 655) | void reset()
        method next_row (line 667) | void next_row()
        method cur_row (line 690) | int cur_row() { return (curr); }
        method cur_row_outdegree (line 692) | int cur_row_outdegree() { return (curr_outd); }
        method rows_end (line 694) | bool rows_end() { return (_rows_end); }
        method next_row_arc (line 697) | void next_row_arc()
        method cur_row_arc_target (line 703) | int cur_row_arc_target() { return (arcs[curr_arc]); }
        method row_arcs_end (line 705) | bool row_arcs_end() { return (_row_arcs_end); }

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/cluto_ifstream_matrix.hpp
  type yasmic (line 25) | namespace yasmic
    type impl (line 27) | namespace impl
      class cluto_ifstream_matrix_const_iterator (line 97) | class cluto_ifstream_matrix_const_iterator
        method cluto_ifstream_matrix_const_iterator (line 107) | cluto_ifstream_matrix_const_iterator()
        method cluto_ifstream_matrix_const_iterator (line 111) | cluto_ifstream_matrix_const_iterator(std::ifstream &str, std::istr...
        method increment (line 128) | void increment()
        method equal (line 181) | bool equal(cluto_ifstream_matrix_const_iterator const& other) const
        method dereference (line 186) | boost::tuple<
    type cluto_ifstream_matrix (line 208) | struct cluto_ifstream_matrix
      method cluto_ifstream_matrix (line 216) | cluto_ifstream_matrix(std::ifstream& f)
      method cluto_ifstream_matrix (line 222) | cluto_ifstream_matrix(std::ifstream& f, bool graph)
      method cluto_ifstream_matrix (line 228) | cluto_ifstream_matrix(std::ifstream& f, bool graph, bool dense)
      method detect_graph_and_dense (line 247) | void detect_graph_and_dense()
      method detect_dense (line 315) | void detect_dense()
      method detect_graph_and_dense_check_line (line 351) | bool detect_graph_and_dense_check_line(index_type maybe_nrows, index...
    type smatrix_traits<cluto_ifstream_matrix<i_index_type, i_value_type, i_size_type> > (line 433) | struct smatrix_traits<cluto_ifstream_matrix<i_index_type, i_value_type...
    function dimensions (line 454) | inline std::pair<typename smatrix_traits<cluto_ifstream_matrix<i_index...
    function nnz (line 478) | typename smatrix_traits<cluto_ifstream_matrix<i_index_type, i_value_ty...
    function nonzeros (line 520) | std::pair<typename smatrix_traits<cluto_ifstream_matrix<i_index_type, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/compressed_row_matrix.hpp
  type yasmic (line 26) | namespace yasmic
    type impl (line 28) | namespace impl
      class compressed_row_nonzero_const_iterator (line 35) | class compressed_row_nonzero_const_iterator
        method compressed_row_nonzero_const_iterator (line 49) | compressed_row_nonzero_const_iterator() {}
        method compressed_row_nonzero_const_iterator (line 51) | compressed_row_nonzero_const_iterator(
        method compressed_row_nonzero_const_iterator (line 64) | compressed_row_nonzero_const_iterator(
        method increment (line 76) | inline void increment()
        method equal (line 96) | bool equal(compressed_row_nonzero_const_iterator const& other) const
        method dereference (line 101) | yasmic::simple_nonzero<
      class crm_row_nonzero_const_iterator (line 123) | class crm_row_nonzero_const_iterator
        method crm_row_nonzero_const_iterator (line 137) | crm_row_nonzero_const_iterator() {}
        method crm_row_nonzero_const_iterator (line 139) | crm_row_nonzero_const_iterator(
        method increment (line 153) | void increment()
        method equal (line 160) | bool equal(crm_row_nonzero_const_iterator const& other) const
        method dereference (line 165) | yasmic::simple_nonzero<
      type crm_row_nonzero_iter_help (line 176) | struct crm_row_nonzero_iter_help
      type crm_col_val_iter_helper_type (line 423) | struct crm_col_val_iter_helper_type
      class crm_col_val_iter (line 439) | class crm_col_val_iter
        method crm_col_val_iter (line 448) | crm_col_val_iter()
        method crm_col_val_iter (line 451) | crm_col_val_iter(ColIter ci, ValIter vi)
        method increment (line 465) | void increment()
        method decrement (line 470) | void decrement()
        method equal (line 475) | bool equal(crm_col_val_iter const& other) const
        method dereference (line 480) | typename crm_col_val_iter_helper_type<ColIter, ValIter>::ref_type ...
        method advance (line 487) | void advance(my_difference_type n)
        method my_difference_type (line 493) | my_difference_type distance_to(crm_col_val_iter const& other) const
      type crm_col_val_iter_tuple_compare (line 502) | struct crm_col_val_iter_tuple_compare
      function crm_make_col_val_iter (line 516) | crm_col_val_iter<ColIter, ValIter>
    class compressed_row_matrix (line 185) | class compressed_row_matrix
      method compressed_row_matrix (line 224) | compressed_row_matrix(RowIter rstart, RowIter rend,
      method compressed_row_matrix (line 254) | compressed_row_matrix(RowIter rstart, RowIter rend,
      method nonzero_iterator (line 261) | nonzero_iterator begin_nonzeros() const
      method nonzero_iterator (line 266) | nonzero_iterator end_nonzeros() const
      method dimensions (line 271) | inline std::pair<size_type, size_type> dimensions() const
      method size_type (line 276) | inline size_type nnz() const
      method row_iterator (line 281) | row_iterator begin_rows() const
      method row_iterator (line 286) | row_iterator end_rows() const
      method row_nonzero_iterator (line 291) | row_nonzero_iterator begin_row(index_type r) const
      method row_nonzero_iterator (line 298) | row_nonzero_iterator end_row(index_type r) const
      method value_iterator (line 304) | value_iterator begin_values() const
      method value_iterator (line 309) | value_iterator end_values() const
    function pack_storage (line 324) | void pack_storage(compressed_row_matrix<RowIter, ColIter, ValIter>& m,...
    function pack_storage (line 401) | void pack_storage(compressed_row_matrix<RowIter, ColIter, ValIter>& m)
    function sort_storage (line 414) | void sort_storage(compressed_row_matrix<RowIter, ColIter, ValIter>& m,
    type impl (line 420) | namespace impl
      class compressed_row_nonzero_const_iterator (line 35) | class compressed_row_nonzero_const_iterator
        method compressed_row_nonzero_const_iterator (line 49) | compressed_row_nonzero_const_iterator() {}
        method compressed_row_nonzero_const_iterator (line 51) | compressed_row_nonzero_const_iterator(
        method compressed_row_nonzero_const_iterator (line 64) | compressed_row_nonzero_const_iterator(
        method increment (line 76) | inline void increment()
        method equal (line 96) | bool equal(compressed_row_nonzero_const_iterator const& other) const
        method dereference (line 101) | yasmic::simple_nonzero<
      class crm_row_nonzero_const_iterator (line 123) | class crm_row_nonzero_const_iterator
        method crm_row_nonzero_const_iterator (line 137) | crm_row_nonzero_const_iterator() {}
        method crm_row_nonzero_const_iterator (line 139) | crm_row_nonzero_const_iterator(
        method increment (line 153) | void increment()
        method equal (line 160) | bool equal(crm_row_nonzero_const_iterator const& other) const
        method dereference (line 165) | yasmic::simple_nonzero<
      type crm_row_nonzero_iter_help (line 176) | struct crm_row_nonzero_iter_help
      type crm_col_val_iter_helper_type (line 423) | struct crm_col_val_iter_helper_type
      class crm_col_val_iter (line 439) | class crm_col_val_iter
        method crm_col_val_iter (line 448) | crm_col_val_iter()
        method crm_col_val_iter (line 451) | crm_col_val_iter(ColIter ci, ValIter vi)
        method increment (line 465) | void increment()
        method decrement (line 470) | void decrement()
        method equal (line 475) | bool equal(crm_col_val_iter const& other) const
        method dereference (line 480) | typename crm_col_val_iter_helper_type<ColIter, ValIter>::ref_type ...
        method advance (line 487) | void advance(my_difference_type n)
        method my_difference_type (line 493) | my_difference_type distance_to(crm_col_val_iter const& other) const
      type crm_col_val_iter_tuple_compare (line 502) | struct crm_col_val_iter_tuple_compare
      function crm_make_col_val_iter (line 516) | crm_col_val_iter<ColIter, ValIter>
    function sort_storage (line 529) | void sort_storage(compressed_row_matrix<RowIter, ColIter, ValIter>& m)
    function mult (line 564) | void mult(const compressed_row_matrix<RowIter, ColIter, ValIter>& m, I...
    function trans_mult (line 596) | void trans_mult(const compressed_row_matrix<RowIter, ColIter, ValIter>...
    function value (line 636) | typename smatrix_traits< compressed_row_matrix<RowIter, ColIter, ValIt...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/compressed_row_matrix_graph.hpp
  type boost (line 21) | namespace boost
    type yasmic_compressed_row_matrix_traversal_category (line 23) | struct yasmic_compressed_row_matrix_traversal_category :
    type impl (line 32) | namespace impl
      class crm_graph_edge_iter (line 35) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 164) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 166) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 179) | crm_graph_edge_iter(
        method increment (line 189) | void increment()
        method equal (line 209) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 214) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_edge (line 36) | struct crm_graph_edge
      type crm_graph (line 39) | struct crm_graph
      type nonzero_to_adjacency_transform (line 61) | struct nonzero_to_adjacency_transform
        method result_type (line 68) | result_type operator() (argument_type arg) const
      class crm_graph_edge_type (line 132) | class crm_graph_edge_type :
        method crm_graph_edge_type (line 136) | crm_graph_edge_type() { }
        method crm_graph_edge_type (line 137) | crm_graph_edge_type(V s, V d, S id)
        method S (line 140) | S id() { return (_id); }
      type crm_graph_edge (line 147) | struct crm_graph_edge
      class crm_graph_edge_iter (line 156) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 164) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 166) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 179) | crm_graph_edge_iter(
        method increment (line 189) | void increment()
        method equal (line 209) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 214) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_ret (line 230) | struct crm_graph_ret
    type graph_traits< yasmic::compressed_row_matrix<RowIter, ColIter, ValIter> > (line 78) | struct graph_traits< yasmic::compressed_row_matrix<RowIter, ColIter, V...
      method vertex_descriptor (line 107) | static vertex_descriptor null_vertex()
    type graph_traits< const yasmic::compressed_row_matrix<RowIter, ColIter, ValIter> > (line 113) | struct graph_traits< const yasmic::compressed_row_matrix<RowIter, ColI...
    type edge_property_type< yasmic::compressed_row_matrix<RowIter, ColIter, ValIter> > (line 118) | struct edge_property_type< yasmic::compressed_row_matrix<RowIter, ColI...
    type vertex_property_type< yasmic::compressed_row_matrix<RowIter, ColIter, ValIter> > (line 123) | struct vertex_property_type< yasmic::compressed_row_matrix<RowIter, Co...
    type impl (line 127) | namespace impl
      class crm_graph_edge_iter (line 35) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 164) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 166) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 179) | crm_graph_edge_iter(
        method increment (line 189) | void increment()
        method equal (line 209) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 214) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_edge (line 36) | struct crm_graph_edge
      type crm_graph (line 39) | struct crm_graph
      type nonzero_to_adjacency_transform (line 61) | struct nonzero_to_adjacency_transform
        method result_type (line 68) | result_type operator() (argument_type arg) const
      class crm_graph_edge_type (line 132) | class crm_graph_edge_type :
        method crm_graph_edge_type (line 136) | crm_graph_edge_type() { }
        method crm_graph_edge_type (line 137) | crm_graph_edge_type(V s, V d, S id)
        method S (line 140) | S id() { return (_id); }
      type crm_graph_edge (line 147) | struct crm_graph_edge
      class crm_graph_edge_iter (line 156) | class crm_graph_edge_iter
        method crm_graph_edge_iter (line 164) | crm_graph_edge_iter() {}
        method crm_graph_edge_iter (line 166) | crm_graph_edge_iter(
        method crm_graph_edge_iter (line 179) | crm_graph_edge_iter(
        method increment (line 189) | void increment()
        method equal (line 209) | bool equal(crm_graph_edge_iter const& other) const
        method dereference (line 214) | typename crm_graph_edge<RowIter, ColIter, ValIter>::type
      type crm_graph_ret (line 230) | struct crm_graph_ret
    function num_vertices (line 252) | inline typename boost::graph_traits< yasmic::compressed_row_matrix<Row...
    function num_edges (line 259) | inline typename boost::graph_traits< yasmic::compressed_row_matrix<Row...
    function source (line 266) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::g_trai...
    function target (line 275) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::g_trai...
    function out_edges (line 285) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::out_ed...
    function out_degree (line 310) | typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::g_traits::deg...
    function adjacent_vertices (line 330) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::adjace...
    function vertices (line 347) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::vertic...
    function edges (line 357) | inline typename impl::crm_graph_ret<RowIter, ColIter, ValIter>::edges_ret
    class compressed_row_matrix_graph_id_map (line 369) | class compressed_row_matrix_graph_id_map
      method compressed_row_matrix_graph_id_map (line 384) | compressed_row_matrix_graph_id_map() { }
      method S (line 385) | S operator [] (T x) const { return x._nzi; }
    function identity_property_map (line 391) | inline identity_property_map get(vertex_index_t,
    function get (line 399) | inline compressed_row_matrix_graph_id_map<RowIter, ColIter, ValIter> g...
    type compressed_row_matrix_graph_property_map (line 410) | struct compressed_row_matrix_graph_property_map { }
    type compressed_row_matrix_graph_property_map<vertex_index_t> (line 413) | struct compressed_row_matrix_graph_property_map<vertex_index_t> {
      type bind_ (line 415) | struct bind_ {
    type compressed_row_matrix_graph_property_map<edge_index_t> (line 422) | struct compressed_row_matrix_graph_property_map<edge_index_t> {
      type bind_ (line 424) | struct bind_ {
    type compressed_row_matrix_graph_property_map<edge_weight_t> (line 431) | struct compressed_row_matrix_graph_property_map<edge_weight_t> {
      type bind_ (line 433) | struct bind_ {
    type property_map<yasmic::compressed_row_matrix<RowIter, ColIter, ValIter>, Tag> (line 440) | struct property_map<yasmic::compressed_row_matrix<RowIter, ColIter, Va...
    function get (line 448) | inline typename property_map<yasmic::compressed_row_matrix<RowIter, Co...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/generic_matrix_operations.hpp
  type yasmic (line 9) | namespace yasmic
    type simple_nonzero (line 16) | struct simple_nonzero
      method simple_nonzero (line 18) | simple_nonzero()
      method simple_nonzero (line 22) | simple_nonzero(Index row, Index col, Value val, NonzeroIndex nzi)
    function make_simple_nonzero (line 47) | simple_nonzero<Index, Value, NonzeroIndex>
    function nnz (line 65) | inline typename smatrix_traits<Matrix>::size_type
    function dimensions (line 82) | inline std::pair<typename smatrix_traits<Matrix>::size_type,
    function ncols (line 90) | inline typename smatrix_traits<Matrix>::size_type
    function nrows (line 101) | inline typename smatrix_traits<Matrix>::size_type
    function row (line 112) | inline typename smatrix_traits<Matrix>::index_type
    function row (line 122) | inline typename smatrix_traits<Matrix>::index_type
    function column (line 132) | inline typename smatrix_traits<Matrix>::index_type
    function column (line 142) | inline typename smatrix_traits<Matrix>::index_type
    function column (line 161) | inline typename smatrix_traits<Matrix>::index_type
    function value (line 170) | inline typename smatrix_traits<Matrix>::value_type
    function value (line 180) | inline typename smatrix_traits<Matrix>::value_type
    function value (line 212) | inline typename smatrix_traits<Matrix>::value_type
    function nonzeros (line 221) | inline std::pair<typename smatrix_traits<Matrix>::nonzero_iterator,
    function rows (line 229) | inline std::pair<typename smatrix_traits<Matrix>::row_iterator,
    function row_nonzeros (line 237) | inline std::pair<typename smatrix_traits<Matrix>::row_nonzero_iterator,
    function value (line 248) | typename smatrix_traits<Matrix>::value_type value(
    function mult (line 274) | void mult(Matrix& m, Iter1 x, Iter2 y)
    function trans_mult (line 300) | void trans_mult(Matrix& m, Iter1 x, Iter2 y)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/graph_ifstream_matrix.hpp
  type yasmic (line 15) | namespace yasmic
    type impl (line 17) | namespace impl
      class graph_ifstream_matrix_const_iterator (line 20) | class graph_ifstream_matrix_const_iterator
        method graph_ifstream_matrix_const_iterator (line 30) | graph_ifstream_matrix_const_iterator()
        method graph_ifstream_matrix_const_iterator (line 34) | graph_ifstream_matrix_const_iterator(std::ifstream &str, std::istr...
        method increment (line 51) | void increment()
        method equal (line 86) | bool equal(graph_ifstream_matrix_const_iterator const& other) const
        method dereference (line 91) | boost::tuple<
    type graph_ifstream_matrix (line 111) | struct graph_ifstream_matrix
      method graph_ifstream_matrix (line 116) | graph_ifstream_matrix(std::ifstream& f)
    type smatrix_traits<graph_ifstream_matrix<i_index_type, i_value_type, i_size_type> > (line 123) | struct smatrix_traits<graph_ifstream_matrix<i_index_type, i_value_type...
    function dimensions (line 144) | inline std::pair<typename smatrix_traits<graph_ifstream_matrix<i_index...
    function nnz (line 163) | typename smatrix_traits<graph_ifstream_matrix<i_index_type, i_value_ty...
    function nonzeros (line 181) | std::pair<typename smatrix_traits<graph_ifstream_matrix<i_index_type, ...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/ifstream_as_matrix.hpp
  type yasmic (line 12) | namespace yasmic
    type smatrix_traits<std::ifstream> (line 15) | struct smatrix_traits<std::ifstream>
    function dimensions (line 33) | inline std::pair<smatrix_traits<std::ifstream>::size_type,
    function nnz (line 47) | smatrix_traits<std::ifstream>::size_type nnz(std::ifstream& f)
    function nonzeros (line 60) | inline std::pair<smatrix_traits<std::ifstream>::nonzero_iterator,

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/ifstream_matrix.hpp
  type yasmic (line 13) | namespace yasmic
    type ifstream_matrix (line 17) | struct ifstream_matrix
      method ifstream_matrix (line 19) | ifstream_matrix(std::istream& f)
      method ifstream_matrix (line 26) | ifstream_matrix(std::istream& f, index_type nrows, index_type ncols,...
    type smatrix_traits<ifstream_matrix<i_index_type, i_value_type, i_size_type, header> > (line 39) | struct smatrix_traits<ifstream_matrix<i_index_type, i_value_type, i_si...
    type impl (line 61) | namespace impl
      type ifstream_matrix_help (line 64) | struct ifstream_matrix_help
    function dimensions (line 78) | inline typename
    function nnz (line 96) | inline typename
    function nonzeros (line 113) | inline typename

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/indexed_list.hpp
  type yasmic (line 13) | namespace yasmic
    type impl (line 18) | namespace impl
    type indexed_list (line 37) | struct indexed_list
      method indexed_list (line 52) | indexed_list(nonzero_iterator start, nonzero_iterator end)
      method indexed_list (line 76) | indexed_list(nonzero_iterator start, nonzero_iterator end,
    function nrows (line 91) | inline typename Collection::size_type nrows(const indexed_list<Val, Co...
    function ncols (line 97) | inline typename Collection::size_type ncols(const indexed_list<Val, Co...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/indexed_list.old.hpp
  type impl (line 18) | namespace impl
    type indexed_list_nonzero_iterator (line 21) | struct indexed_list_nonzero_iterator
    type indexed_list (line 41) | struct indexed_list
      method indexed_list (line 56) | indexed_list(nonzero_iterator start, nonzero_iterator end)
      method indexed_list (line 80) | indexed_list(nonzero_iterator start, nonzero_iterator end,
    function nrows (line 95) | inline typename Collection::size_type nrows(const indexed_list<Val, Co...
    function ncols (line 101) | inline typename Collection::size_type ncols(const indexed_list<Val, Co...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/istream_as_matrix.hpp
  type yasmic (line 9) | namespace yasmic
    type smatrix_traits<std::istream> (line 12) | struct smatrix_traits<std::istream>
    function dimensions (line 26) | inline std::pair<typename smatrix_traits<std::istream>::size_type,
    function ncols (line 38) | inline smatrix_traits<std::istream>::size_type ncols(std::istream& f)
    function nrows (line 47) | inline smatrix_traits<std::istream>::size_type nrows(std::istream& f)
    function nnz (line 56) | inline smatrix_traits<std::istream>::size_type nnz(std::istream& f)
    function nonzeros (line 66) | inline std::pair<smatrix_traits<std::istream>::nonzero_iterator,

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/iterator_utility.hpp
  type yasmic (line 7) | namespace yasmic
    type constant_iterator (line 85) | struct constant_iterator
      method constant_iterator (line 101) | constant_iterator()
      method constant_iterator (line 104) | constant_iterator(constant_iterator const& rhs) : super_t(rhs.base())
      method constant_iterator (line 107) | constant_iterator(Type* x)
      method increment (line 112) | inline void increment()
      method decrement (line 115) | inline void decrement()
      method advance (line 118) | inline void advance(typename super_t::difference_type n)
      method distance_to (line 121) | inline typename super_t::difference_type distance_to(constant_iterat...
      method equal (line 124) | inline bool equal(constant_iterator const& other) const

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/matrix_row_col_graph.hpp
  type yasmic (line 22) | namespace yasmic
    type impl (line 25) | namespace impl
      type matrix_row_col_graph_nz_iter_help (line 28) | struct matrix_row_col_graph_nz_iter_help
      class matrix_row_col_graph_nz_iterator (line 39) | class matrix_row_col_graph_nz_iterator
        method matrix_row_col_graph_nz_iterator (line 48) | matrix_row_col_graph_nz_iterator()
        method matrix_row_col_graph_nz_iterator (line 52) | matrix_row_col_graph_nz_iterator(Matrix& m)
        method matrix_row_col_graph_nz_iterator (line 58) | matrix_row_col_graph_nz_iterator(Matrix& m,bool)
        method increment (line 68) | void increment()
        method equal (line 81) | bool equal(matrix_row_col_graph_nz_iterator const& other) const
        method dereference (line 86) | typename matrix_row_col_graph_nz_iter_help<Matrix>::nz_type
      type matrix_row_col_graph_help (line 143) | struct matrix_row_col_graph_help
    class matrix_row_col_graph (line 114) | class matrix_row_col_graph
      method matrix_row_col_graph (line 119) | matrix_row_col_graph(Matrix& m)
    type impl (line 140) | namespace impl
      type matrix_row_col_graph_nz_iter_help (line 28) | struct matrix_row_col_graph_nz_iter_help
      class matrix_row_col_graph_nz_iterator (line 39) | class matrix_row_col_graph_nz_iterator
        method matrix_row_col_graph_nz_iterator (line 48) | matrix_row_col_graph_nz_iterator()
        method matrix_row_col_graph_nz_iterator (line 52) | matrix_row_col_graph_nz_iterator(Matrix& m)
        method matrix_row_col_graph_nz_iterator (line 58) | matrix_row_col_graph_nz_iterator(Matrix& m,bool)
        method increment (line 68) | void increment()
        method equal (line 81) | bool equal(matrix_row_col_graph_nz_iterator const& other) const
        method dereference (line 86) | typename matrix_row_col_graph_nz_iter_help<Matrix>::nz_type
      type matrix_row_col_graph_help (line 143) | struct matrix_row_col_graph_help
    function nnz (line 155) | inline typename impl::matrix_row_col_graph_help<Matrix>::nnz_ret_type
    function dimensions (line 162) | inline typename impl::matrix_row_col_graph_help<Matrix>::dims_ret_type
    function nonzeros (line 170) | inline typename impl::matrix_row_col_graph_help<Matrix>::nzs_ret_type

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/nonzero_union.hpp
  type yasmic (line 14) | namespace yasmic
    type impl (line 17) | namespace impl
      type nonzero_union_iter_help (line 20) | struct nonzero_union_iter_help
      class nonzero_union_iterator (line 33) | class nonzero_union_iterator
        method nonzero_union_iterator (line 41) | nonzero_union_iterator()
        method nonzero_union_iterator (line 45) | nonzero_union_iterator(Matrix1& m1, Matrix2& m2)
        method increment (line 56) | void increment()
        method equal (line 77) | bool equal(nonzero_union_iterator const& other) const
        method dereference (line 82) | typename nonzero_union_iter_help<Matrix1,Matrix2>::nz_type
      type nonzero_union_help (line 153) | struct nonzero_union_help
    class nonzero_union (line 120) | class nonzero_union
      method nonzero_union (line 126) | nonzero_union(Matrix1& m1, Matrix2& m2)
    type impl (line 150) | namespace impl
      type nonzero_union_iter_help (line 20) | struct nonzero_union_iter_help
      class nonzero_union_iterator (line 33) | class nonzero_union_iterator
        method nonzero_union_iterator (line 41) | nonzero_union_iterator()
        method nonzero_union_iterator (line 45) | nonzero_union_iterator(Matrix1& m1, Matrix2& m2)
        method increment (line 56) | void increment()
        method equal (line 77) | bool equal(nonzero_union_iterator const& other) const
        method dereference (line 82) | typename nonzero_union_iter_help<Matrix1,Matrix2>::nz_type
      type nonzero_union_help (line 153) | struct nonzero_union_help
    function nnz (line 165) | inline typename impl::nonzero_union_help<Matrix1, Matrix2>::nnz_ret_type
    function dimensions (line 172) | inline typename impl::nonzero_union_help<Matrix1, Matrix2>::dims_ret_type
    function nonzeros (line 185) | inline typename impl::nonzero_union_help<Matrix1, Matrix2>::nzs_ret_type

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/simple_csr_matrix.hpp
  type yasmic (line 30) | namespace yasmic
    type simple_csr_matrix (line 43) | struct simple_csr_matrix
      method simple_csr_matrix (line 57) | simple_csr_matrix()
      method simple_csr_matrix (line 60) | simple_csr_matrix(IndexType nrows, IndexType ncols, NzSizeType nnz,
    type smatrix_traits< simple_csr_matrix<IndexType, ValueType, NzSizeType> > (line 67) | struct smatrix_traits< simple_csr_matrix<IndexType, ValueType, NzSizeT...
      type properties (line 83) | struct properties
    function IndexType (line 89) | IndexType nrows(const simple_csr_matrix<IndexType, ValueType, NzSizeTy...
    function IndexType (line 93) | IndexType ncols(const simple_csr_matrix<IndexType, ValueType, NzSizeTy...
    function NzSizeType (line 97) | NzSizeType nnz(const simple_csr_matrix<IndexType, ValueType, NzSizeTyp...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/simple_csr_matrix_as_graph.hpp
  type yasmic (line 39) | namespace yasmic {
    type impl (line 40) | namespace impl {
      type remove_signedness (line 42) | struct remove_signedness {
      type remove_signedness<long> (line 46) | struct remove_signedness<long> { typedef unsigned long type; }
      type remove_signedness<int> (line 47) | struct remove_signedness<int> { typedef unsigned int type; }
      type remove_signedness<short> (line 48) | struct remove_signedness<short> { typedef unsigned short type; }
      type remove_signedness<char> (line 49) | struct remove_signedness<char> { typedef unsigned char type; }
      class simple_csr_edge (line 52) | class simple_csr_edge {
        method simple_csr_edge (line 56) | simple_csr_edge(Index row, EdgeIndex ind) : r(row), i(ind) {}
        method simple_csr_edge (line 57) | simple_csr_edge() : r(0), i(0) {}
      type simple_csr_graph_traversal (line 61) | struct simple_csr_graph_traversal :
      class simple_csr_edge_iterator (line 67) | class simple_csr_edge_iterator
      class simple_csr_out_edge_iterator (line 69) | class simple_csr_out_edge_iterator
  class yasmic::impl::simple_csr_edge_iterator (line 74) | class yasmic::impl::simple_csr_edge_iterator
    method simple_csr_edge_iterator (line 86) | simple_csr_edge_iterator() : ai(NULL), current_edge(), end_of_this_ver...
    method simple_csr_edge_iterator (line 88) | simple_csr_edge_iterator(
    method reference (line 96) | reference operator*() const { return current_edge; }
    method pointer (line 97) | pointer operator->() const { return &current_edge; }
    method simple_csr_edge_iterator (line 106) | simple_csr_edge_iterator& operator++() {
    method simple_csr_edge_iterator (line 115) | simple_csr_edge_iterator operator++(int) {
  class yasmic::impl::simple_csr_out_edge_iterator (line 127) | class yasmic::impl::simple_csr_out_edge_iterator
    method simple_csr_out_edge_iterator (line 142) | simple_csr_out_edge_iterator() {}
    method simple_csr_out_edge_iterator (line 145) | explicit simple_csr_out_edge_iterator(edge_descriptor e) : _e(e) { }
    method edge_descriptor (line 149) | const edge_descriptor& dereference() const { return _e; }
    method equal (line 151) | bool equal(const simple_csr_out_edge_iterator<Index,Value,EdgeIndex>& ...
    method increment (line 154) | void increment() { ++_e.i; }
    method decrement (line 155) | void decrement() { ++_e.i; }
    method advance (line 156) | void advance(difference_type n) { _e.i += n; }
    method difference_type (line 158) | difference_type distance_to(const yasmic::impl::simple_csr_out_edge_it...
  type boost (line 166) | namespace boost {
    type graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE> (line 172) | struct graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE> {
      method vertex_descriptor (line 179) | static vertex_descriptor null_vertex()
    type graph_traits<const YASMIC_SIMPLE_CSR_GRAPH_TYPE> (line 200) | struct graph_traits<const YASMIC_SIMPLE_CSR_GRAPH_TYPE>
    function num_vertices (line 206) | inline typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>::vertices_s...
    function vertices (line 211) | inline std::pair<counting_iterator<Index>,counting_iterator<Index> >
    function Index (line 220) | inline Index source(
    function Index (line 227) | inline Index target(
    function num_edges (line 234) | inline typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>::edges_size...
    function edges (line 240) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>:...
    function out_degree (line 259) | inline typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>::degree_siz...
    function out_edges (line 264) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>:...
    function adjacent_vertices (line 276) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>:...
    type detail (line 285) | namespace detail {
      type simple_csr_edge_index_map (line 288) | struct simple_csr_edge_index_map {
      function EdgeIndex (line 296) | inline EdgeIndex
    type property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, Tag> (line 303) | struct property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, Tag> {
    function identity_property_map (line 328) | inline identity_property_map
    function Index (line 335) | inline Index
    function get (line 343) | inline typename property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, edge_index_...
    function EdgeIndex (line 352) | inline EdgeIndex
    function get (line 360) | inline typename property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, edge_weight...
    function Value (line 367) | inline Value
    type edge_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE > (line 375) | struct edge_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE >  {
    type vertex_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE > (line 380) | struct vertex_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE >  {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/simple_row_and_column_matrix.hpp
  type yasmic (line 27) | namespace yasmic
    type simple_row_and_column_matrix (line 35) | struct simple_row_and_column_matrix
      method simple_row_and_column_matrix (line 43) | simple_row_and_column_matrix() {}
      method simple_row_and_column_matrix (line 45) | simple_row_and_column_matrix(IndexType nrows, IndexType ncols, NzSiz...
    type smatrix_traits< simple_row_and_column_matrix<IndexType, ValueType, NzSizeType> > (line 53) | struct smatrix_traits< simple_row_and_column_matrix<IndexType, ValueTy...
      type properties (line 69) | struct properties
    function IndexType (line 76) | IndexType nrows(const simple_row_and_column_matrix<IndexType, ValueTyp...
    function IndexType (line 80) | IndexType ncols(const simple_row_and_column_matrix<IndexType, ValueTyp...
    function NzSizeType (line 84) | NzSizeType nnz(const simple_row_and_column_matrix<IndexType, ValueType...
    function build_row_and_column_from_csr (line 101) | void build_row_and_column_from_csr(

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/simple_row_and_column_matrix_as_graph.hpp
  type yasmic (line 34) | namespace yasmic {
    type impl (line 35) | namespace impl {
      type simple_rac_graph_traversal (line 36) | struct simple_rac_graph_traversal :
      class simple_rac_in_edge_iterator (line 43) | class simple_rac_in_edge_iterator
  class yasmic::impl::simple_rac_in_edge_iterator (line 48) | class yasmic::impl::simple_rac_in_edge_iterator
    method simple_rac_in_edge_iterator (line 64) | explicit simple_rac_in_edge_iterator(Index *atj, EdgeIndex *atid)
    method simple_rac_in_edge_iterator (line 68) | simple_rac_in_edge_iterator() {}
    method edge_descriptor (line 72) | edge_descriptor dereference() const { return edge_descriptor(*atj,*ati...
    method equal (line 74) | bool equal(const simple_rac_in_edge_iterator<Index,Value,EdgeIndex>& o...
    method increment (line 77) | void increment() { ++atid; ++atj; }
    method decrement (line 78) | void decrement() { ++atid; ++atj; }
    method advance (line 79) | void advance(difference_type n) { atid+=n; atj+=n; }
    method difference_type (line 81) | difference_type distance_to(const simple_rac_in_edge_iterator<Index,Va...
  type boost (line 90) | namespace boost {
    type graph_traits<YASMIC_SIMPLE_RAC_GRAPH_TYPE> (line 95) | struct graph_traits<YASMIC_SIMPLE_RAC_GRAPH_TYPE>
    function in_degree (line 108) | inline typename graph_traits<YASMIC_SIMPLE_RAC_GRAPH_TYPE>::degree_siz...
    function degree (line 113) | inline typename graph_traits<YASMIC_SIMPLE_RAC_GRAPH_TYPE>::degree_siz...
    function in_edges (line 118) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_RAC_GRAPH_TYPE>:...
    type property_map<YASMIC_SIMPLE_RAC_GRAPH_TYPE, Tag> (line 131) | struct property_map<YASMIC_SIMPLE_RAC_GRAPH_TYPE, Tag>

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/smatrix_traits.hpp
  type yasmic (line 13) | namespace yasmic
    type no_property_tag (line 15) | struct no_property_tag {}
    type nonzero_index_tag (line 16) | struct nonzero_index_tag { }
    type row_access_tag (line 17) | struct row_access_tag { }
    type column_access_tag (line 18) | struct column_access_tag { }
    type op_traits (line 21) | struct op_traits
    type smatrix_traits (line 27) | struct smatrix_traits : public op_traits<Mat>

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/transpose_matrix.hpp
  type yasmic (line 16) | namespace yasmic
    class transpose_matrix (line 20) | class transpose_matrix
      method transpose_matrix (line 25) | transpose_matrix(Matrix& m)
    type impl (line 47) | namespace impl
      type transpose_matrix_help (line 50) | struct transpose_matrix_help
    function nnz (line 62) | inline typename impl::transpose_matrix_help<Matrix>::nnz_ret_type
    function dimensions (line 69) | inline typename impl::transpose_matrix_help<Matrix>::dims_ret_type
    function nonzeros (line 78) | inline typename impl::transpose_matrix_help<Matrix>::nzs_ret_type
    function row (line 85) | inline typename impl::transpose_matrix_help<Matrix>::traits::index_type
    function column (line 92) | inline typename impl::transpose_matrix_help<Matrix>::traits::index_type

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/tuple_utility.hpp
  type yasmic (line 6) | namespace yasmic
    function tuple_get_2 (line 9) | boost::tuple<
    type tuple_get_2_fn (line 19) | struct tuple_get_2_fn
      method result_type (line 26) | result_type operator() (argument_type arg) const
    type tuple_get_fn (line 33) | struct tuple_get_fn
      method result_type (line 39) | result_type operator() (argument_type arg) const

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/undir_simple_csr_matrix.hpp
  type yasmic (line 18) | namespace yasmic
    type undir_simple_csr_matrix (line 31) | struct undir_simple_csr_matrix
      method undir_simple_csr_matrix (line 45) | undir_simple_csr_matrix()
      method undir_simple_csr_matrix (line 48) | undir_simple_csr_matrix(IndexType nrows, IndexType ncols, NzSizeType...
    type smatrix_traits< undir_simple_csr_matrix<IndexType, ValueType, NzSizeType> > (line 55) | struct smatrix_traits< undir_simple_csr_matrix<IndexType, ValueType, N...
      type properties (line 71) | struct properties
    function IndexType (line 77) | IndexType nrows(const undir_simple_csr_matrix<IndexType, ValueType, Nz...
    function IndexType (line 81) | IndexType ncols(const undir_simple_csr_matrix<IndexType, ValueType, Nz...
    function NzSizeType (line 85) | NzSizeType nnz(const undir_simple_csr_matrix<IndexType, ValueType, NzS...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/undir_simple_csr_matrix_as_graph.hpp
  type yasmic (line 33) | namespace yasmic {
    type impl (line 34) | namespace impl {
      class undir_simple_csr_edge_iterator (line 36) | class undir_simple_csr_edge_iterator
      class undir_simple_csr_out_edge_iterator (line 38) | class undir_simple_csr_out_edge_iterator
  class yasmic::impl::undir_simple_csr_edge_iterator (line 43) | class yasmic::impl::undir_simple_csr_edge_iterator
    method undir_simple_csr_edge_iterator (line 55) | undir_simple_csr_edge_iterator() : ai(NULL), current_edge(), end_of_th...
    method undir_simple_csr_edge_iterator (line 57) | undir_simple_csr_edge_iterator(
    method reference (line 65) | reference operator*() const { return current_edge; }
    method pointer (line 66) | pointer operator->() const { return &current_edge; }
    method undir_simple_csr_edge_iterator (line 75) | undir_simple_csr_edge_iterator& operator++() {
    method undir_simple_csr_edge_iterator (line 84) | undir_simple_csr_edge_iterator operator++(int) {
  class yasmic::impl::undir_simple_csr_out_edge_iterator (line 96) | class yasmic::impl::undir_simple_csr_out_edge_iterator
    method undir_simple_csr_out_edge_iterator (line 111) | undir_simple_csr_out_edge_iterator() {}
    method undir_simple_csr_out_edge_iterator (line 114) | explicit undir_simple_csr_out_edge_iterator(edge_descriptor e) : _e(e)...
    method edge_descriptor (line 118) | const edge_descriptor& dereference() const { return _e; }
    method equal (line 120) | bool equal(const simple_csr_out_edge_iterator<Index,Value,EdgeIndex>& ...
    method increment (line 123) | void increment() { ++_e.i; }
    method decrement (line 124) | void decrement() { ++_e.i; }
    method advance (line 125) | void advance(difference_type n) { _e.i += n; }
    method difference_type (line 127) | difference_type distance_to(const yasmic::impl::undir_simple_csr_out_e...
  type boost (line 135) | namespace boost {
    type graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE> (line 140) | struct graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE> {
      method vertex_descriptor (line 147) | static vertex_descriptor null_vertex()
    type graph_traits<const YASMIC_SIMPLE_CSR_GRAPH_TYPE> (line 169) | struct graph_traits<const YASMIC_SIMPLE_CSR_GRAPH_TYPE>
    function num_vertices (line 176) | inline typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>::vertices_s...
    function vertices (line 181) | inline std::pair<counting_iterator<Index>,counting_iterator<Index> >
    function Index (line 190) | inline Index source(
    function Index (line 197) | inline Index target(
    function num_edges (line 204) | inline typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>::edges_size...
    function edges (line 210) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>:...
    function out_degree (line 229) | inline typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>::degree_siz...
    function out_edges (line 234) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>:...
    function adjacent_vertices (line 246) | inline std::pair< typename graph_traits<YASMIC_SIMPLE_CSR_GRAPH_TYPE>:...
    type property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, Tag> (line 253) | struct property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, Tag> {
    function identity_property_map (line 278) | inline identity_property_map
    function Index (line 285) | inline Index
    function get (line 293) | inline typename property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, edge_index_...
    function EdgeIndex (line 302) | inline EdgeIndex
    function get (line 310) | inline typename property_map<YASMIC_SIMPLE_CSR_GRAPH_TYPE, edge_weight...
    function Value (line 317) | inline Value
    type edge_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE > (line 325) | struct edge_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE >  {
    type vertex_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE > (line 330) | struct vertex_property_type< YASMIC_SIMPLE_CSR_GRAPH_TYPE >  {

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/util/crm_matrix.hpp
  function symmetrize_crm (line 35) | void symmetrize_crm(std::vector<index_type>& rows, std::vector<index_typ...
  type max_fo (line 75) | struct max_fo
    method Type (line 78) | Type operator()(const Type& _Left, const Type& _Right) const
  function pack_and_sort_storage_crm (line 97) | void pack_and_sort_storage_crm(std::vector<index_type>& rows, std::vecto...
  function transpose_crm (line 119) | void transpose_crm(std::vector<index_type>& rows, std::vector<index_type...
  function build_bipartite_crm (line 164) | void build_bipartite_crm(std::vector<index_type>& rows, std::vector<inde...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/util/filtered_matrix.hpp
  type yasmic (line 16) | namespace yasmic
    type impl (line 18) | namespace impl
      type filtered_matrix_nonzero_helper (line 21) | struct filtered_matrix_nonzero_helper
      class filtered_matrix_const_iterator (line 30) | class filtered_matrix_const_iterator
        method filtered_matrix_const_iterator (line 38) | filtered_matrix_const_iterator()
        method filtered_matrix_const_iterator (line 42) | filtered_matrix_const_iterator(const Matrix& m, FilterMap fm,
        method increment (line 55) | void increment()
        method equal (line 61) | bool equal(filtered_matrix_const_iterator const& other) const
        method dereference (line 66) | typename filtered_matrix_nonzero_helper<Matrix>::nz
        method skip_nnzs (line 82) | void skip_nnzs()
    class row_column_filtered_matrix (line 94) | class row_column_filtered_matrix
      method row_column_filtered_matrix (line 115) | row_column_filtered_matrix(const Matrix &m, RowColFilterMap fm)
      method row_column_filtered_matrix (line 138) | row_column_filtered_matrix(const Matrix &m, RowColFilterMap fm,
      method row_column_filtered_matrix (line 155) | row_column_filtered_matrix(const Matrix &m, RowColFilterMap fm,
      method dimensions (line 162) | std::pair<size_type, size_type> dimensions() const
      method size_type (line 167) | size_type nnz() const
      method nonzero_iterator (line 172) | nonzero_iterator begin_nonzeros() const
      method nonzero_iterator (line 177) | nonzero_iterator end_nonzeros() const
    function make_filter_map_from_indicator (line 264) | void make_filter_map_from_indicator(Iterator start, Iterator end)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/util/load_crm_graph.hpp
  function load_matrix_to_crm (line 43) | bool load_matrix_to_crm(InputMatrix& m,
  function load_crm_graph_type (line 142) | bool load_crm_graph_type(InputMatrix& m, std::string filename,
  function load_crm_graph (line 269) | bool load_crm_graph(std::string filename,

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/util/load_crm_matrix.hpp
  function load_matrix_to_crm (line 62) | bool load_matrix_to_crm(InputMatrix& m,
  function load_crm_graph_type (line 171) | bool load_crm_graph_type(InputMatrix& m, std::string filename,
  function load_crm_matrix_graph_test (line 289) | bool load_crm_matrix_graph_test(InputStream& ifs)
  function load_crm_matrix (line 327) | bool load_crm_matrix(std::string filename,
  type yasmic (line 490) | namespace yasmic
    type impl (line 492) | namespace impl
      function lower_case (line 496) | int lower_case ( int c )
  function load_crm_matrix (line 504) | bool load_crm_matrix(std::string filetype_hint, std::string filename,

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/util/write_matrix.hpp
  type impl (line 6) | namespace impl
    type endian (line 8) | namespace endian
      function swap_int_4 (line 10) | void swap_int_4(int *tni4)                  /* 4 byte signed integer...
      function swap_double_8 (line 16) | void swap_double_8(double *tndd8)          /* 8 byte double numbers ...
    type write (line 39) | namespace write
      type custom_smat_writer (line 42) | struct custom_smat_writer
        method write_matrix (line 45) | bool write_matrix(std::ostream& f, Matrix& m)
      type custom_bsmat_writer (line 70) | struct custom_bsmat_writer
        method write_matrix (line 73) | bool write_matrix(std::ostream& f, Matrix& m)
      type smat_writer (line 105) | struct smat_writer
      type bsmat_writer (line 110) | struct bsmat_writer
      type cluto_writer (line 115) | struct cluto_writer
        method write_matrix (line 118) | bool write_matrix(std::ostream& f, RowAccessMatrix& m)
      type petsc_writer (line 141) | struct petsc_writer
        method write_petsc_matrix (line 149) | bool write_petsc_matrix(std::ostream& f,
        method write_matrix (line 219) | bool write_matrix(std::ostream& f, NonzeroAccessMatrix& m)
  type impl::write::smat_writer (line 247) | struct impl::write::smat_writer
  type impl::write::bsmat_writer (line 248) | struct impl::write::bsmat_writer
  type impl::write::petsc_writer (line 249) | struct impl::write::petsc_writer
  type impl::write::cluto_writer (line 250) | struct impl::write::cluto_writer
  type parametrized_writers (line 253) | struct parametrized_writers
    type impl::write::custom_bsmat_writer<index_type,nz_index_type,value_type,true> (line 255) | struct impl::write::custom_bsmat_writer<index_type,nz_index_type,value...
    type impl::write::custom_smat_writer<index_type,nz_index_type,value_type,true> (line 257) | struct impl::write::custom_smat_writer<index_type,nz_index_type,value_...
  function write_matrix (line 262) | void write_matrix(std::ostream& f, Matrix& m, Tag type)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/util/write_petsc_matrix.hpp
  type impl (line 4) | namespace impl
    type endian (line 6) | namespace endian
      function swap_int_4 (line 8) | void swap_int_4(int *tni4)                  /* 4 byte signed integer...
      function swap_double_8 (line 14) | void swap_double_8(double *tndd8)          /* 8 byte double numbers ...
  function write_petsc_matrix (line 44) | bool write_petsc_matrix(std::ostream& f,
  function write_petsc_matrix (line 120) | bool write_petsc_matrix(std::ostream& f, const Matrix& m)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/libmbgl/yasmic/verbose_util.hpp
  type yasmic (line 18) | namespace yasmic
  type yasmic (line 23) | namespace yasmic

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/astar_search_mex.c
  type mwIndex (line 39) | typedef int mwIndex;
  type mwSize (line 40) | typedef int mwSize;
  function mexFunction (line 70) | void mexFunction(int nlhs,mxArray *plhs[], int nrhs, const mxArray *prhs[])
  function astar_heuristic (line 293) | double astar_heuristic(void *pdata, mwIndex u)

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/betweenness_centrality_mex.c
  type mwIndex (line 18) | typedef int mwIndex;
  type mwSize (line 19) | typedef int mwSize;
  function mexFunction (line 30) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/bfs_dfs_vis_mex.c
  type mwIndex (line 20) | typedef int mwIndex;
  type mwSize (line 21) | typedef int mwSize;
  function bfs_vis (line 43) | void bfs_vis(mwIndex n, mwIndex *ja, mwIndex *ia, mwIndex u,
  function dfs_vis (line 69) | void dfs_vis(mwIndex n, mwIndex *ja, mwIndex *ia, mwIndex u,
  function mexFunction (line 96) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/bfs_mex.c
  type mwIndex (line 28) | typedef int mwIndex;
  type mwSize (line 29) | typedef int mwSize;
  function mexFunction (line 42) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/biconnected_components_mex.c
  type mwIndex (line 25) | typedef int mwIndex;
  type mwSize (line 26) | typedef int mwSize;
  function mexFunction (line 42) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/clustering_coefficients_mex.c
  type mwIndex (line 16) | typedef int mwIndex;
  type mwSize (line 17) | typedef int mwSize;
  function mexFunction (line 30) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/common_functions.h
  function intmin (line 16) | int intmin(int a, int b) { if (a<b) { return a; } else { return b; } }
  function isscalar (line 18) | int isscalar(const mxArray* a) {
  function isscalardouble (line 26) | int isscalardouble(const mxArray* a) {
  function load_scalar_arg (line 66) | double load_scalar_arg(const mxArray* a, int k)
  function load_scalar_double_arg (line 75) | double load_scalar_double_arg(int nrhs, const mxArray *prhs[], int arg) {
  function load_graph_arg (line 149) | void load_graph_arg(int nrhs, const mxArray *prhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/components_mex.c
  type mwIndex (line 22) | typedef int mwIndex;
  type mwSize (line 23) | typedef int mwSize;
  function mexFunction (line 36) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/core_numbers_mex.c
  type mwIndex (line 16) | typedef int mwIndex;
  type mwSize (line 17) | typedef int mwSize;
  function mexFunction (line 30) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/dfs_mex.c
  type mwIndex (line 28) | typedef int mwIndex;
  type mwSize (line 29) | typedef int mwSize;
  function mexFunction (line 42) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/dominator_tree_mex.c
  type mwIndex (line 20) | typedef int mwIndex;
  type mwSize (line 21) | typedef int mwSize;
  function mexFunction (line 35) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/expand_macros.h
  function expand_int_to_double (line 17) | void expand_int_to_double(int* src, double* dst, mwSize len, double offset)
  function expand_degree_to_double (line 25) | void expand_degree_to_double(mbglDegreeType* src, double* dst, mwSize len,
  function expand_index_to_double (line 34) | void expand_index_to_double(mwIndex* src, double* dst, mwSize len,
  function expand_index_to_double_zero_equality (line 48) | void expand_index_to_double_zero_equality(mwIndex* src, double* dst,
  function expand_index_to_double_zero_special (line 67) | void expand_index_to_double_zero_special(mwIndex* src, double* dst, mwSi...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/fruchterman_reingold_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function mexFunction (line 26) | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prh...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/gursoy_atun_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function parse_topology_arg (line 29) | void parse_topology_arg(const char* topology,
  function mexFunction (line 63) | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prh...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/kamada_kawai_spring_layout_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function mexFunction (line 26) | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prh...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/matching_mex.c
  type mwIndex (line 20) | typedef int mwIndex;
  type mwSize (line 21) | typedef int mwSize;
  function mexFunction (line 35) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/matlab_bgl_all_sp_mex.c
  type mwIndex (line 30) | typedef int mwIndex;
  type mwSize (line 31) | typedef int mwSize;
  function mexFunction (line 45) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/matlab_bgl_sp_mex.c
  type mwIndex (line 39) | typedef int mwIndex;
  type mwSize (line 40) | typedef int mwSize;

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/max_flow_mex.c
  type mwIndex (line 26) | typedef int mwIndex;
  type mwSize (line 27) | typedef int mwSize;
  function build_matrix (line 55) | void build_matrix(mbglIndex n, mbglIndex *ia, mbglIndex *pja, double *a,...
  function build_cut (line 152) | void build_cut(mbglIndex u, mbglIndex n, mbglIndex *pia, mbglIndex *ja, ...
  function test_cut (line 235) | void test_cut(int flow, int* pimincut,
  function mexFunction (line 262) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/mst_mex.c
  type mwIndex (line 23) | typedef int mwIndex;
  type mwSize (line 24) | typedef int mwSize;
  function mexFunction (line 38) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/path_from_pred_mex.c
  type mwIndex (line 22) | typedef int mwIndex;
  type mwSize (line 23) | typedef int mwSize;
  function mexFunction (line 31) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/planar_drawing_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function mexFunction (line 26) | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prh...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/planar_edges_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function mexFunction (line 26) | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prh...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/planar_test_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function mexFunction (line 26) | void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prh...

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/test_matching_mex.c
  type mwIndex (line 20) | typedef int mwIndex;
  type mwSize (line 21) | typedef int mwSize;
  function mexFunction (line 35) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/dependencies/matlab_bgl/private/topological_order_mex.c
  type mwIndex (line 14) | typedef int mwIndex;
  type mwSize (line 15) | typedef int mwSize;
  function mexFunction (line 28) | void mexFunction(int nlhs, mxArray *plhs[],

FILE: Algorithms/2013-Seed-Set-Expansion/src/cutcond_mex.cc
  function sparse_array_volume (line 24) | double sparse_array_volume(const mxArray* mat)
  function cluster_conductance (line 41) | void cluster_conductance(const mxArray* mat, const std::vector<size_t >&...
  function copy_array_to_index_vector (line 82) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 97) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2013-Seed-Set-Expansion/src/pprgrow_mex.cc
  class array_queue (line 31) | class array_queue {
    method array_queue (line 37) | array_queue(size_t _max_size)
    method empty (line 41) | void empty() {
    method size (line 47) | size_t size() {
    method push (line 51) | void push(int i) {
    method front (line 61) | int front() {
    method pop (line 66) | void pop() {
  type sparsevec (line 76) | struct sparsevec {
    method get (line 82) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 94) | double sum() {
    method mwIndex (line 104) | mwIndex max_index() {
  type sparserow (line 114) | struct sparserow {
  function mwIndex (line 121) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function compute_local_pagerank (line 126) | int compute_local_pagerank(sparserow *s, sparsevec& r, sparsevec& p,
  type greater2nd (line 165) | struct greater2nd {
  function cluster_from_sweep (line 171) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_pagerank_stats (line 249) | struct local_pagerank_stats {
  function hypercluster_pagerank_multiple (line 268) | int hypercluster_pagerank_multiple(sparserow* G,
  function pprgrow (line 326) | void pprgrow(sparserow* G, std::vector<mwIndex>& set, double alpha,
  function copy_array_to_index_vector (line 342) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 360) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2013-Seed-Set-Expansion/src/triangleclusters_mex.cc
  function triangle_clusters (line 11) | void triangle_clusters(const mxArray* mat, mxArray* cond, mxArray* cut,
  function mxFullAssert (line 78) | void mxFullAssert(int flag, const char* str) {
  function mexFunction (line 84) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2013-Seed-Set-Expansion/src/vpprgrow_mex.cc
  class array_queue (line 28) | class array_queue {
    method array_queue (line 34) | array_queue(size_t _max_size)
    method empty (line 38) | void empty() {
    method size (line 44) | size_t size() {
    method push (line 48) | void push(int i) {
    method front (line 58) | int front() {
    method pop (line 63) | void pop() {
  type sparsevec (line 73) | struct sparsevec {
    method get (line 79) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 91) | double sum() {
    method mwIndex (line 101) | mwIndex max_index() {
  type sparserow (line 111) | struct sparserow {
  function mwIndex (line 118) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function compute_local_pagerank (line 123) | int compute_local_pagerank(sparserow *s, sparsevec& r, sparsevec& p,
  type greater2nd (line 162) | struct greater2nd {
  function cluster_from_sweep (line 168) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_pagerank_stats (line 246) | struct local_pagerank_stats {
  function hypercluster_pagerank_multiple (line 265) | int hypercluster_pagerank_multiple(sparserow* G,
  function pprgrow (line 318) | void pprgrow(sparserow* G, std::vector<mwIndex>& set, double alpha,
  function copy_array_to_index_vector (line 334) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 352) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/authors_original_files/experiments/chirikov/pprgrow_mex.cc
  class array_queue (line 28) | class array_queue {
    method array_queue (line 34) | array_queue(size_t _max_size)
    method empty (line 38) | void empty() {
    method size (line 44) | size_t size() {
    method push (line 48) | void push(int i) {
    method front (line 58) | int front() {
    method pop (line 63) | void pop() {
  type sparsevec (line 73) | struct sparsevec {
    method get (line 79) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 91) | double sum() {
    method mwIndex (line 102) | mwIndex max_index() {
  type sparserow (line 112) | struct sparserow {
  function mwIndex (line 119) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function compute_local_pagerank (line 124) | int compute_local_pagerank(sparserow *s, sparsevec& r, sparsevec& p,
  type greater2nd (line 163) | struct greater2nd {
  function cluster_from_sweep (line 169) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_pagerank_stats (line 247) | struct local_pagerank_stats {
  function hypercluster_pagerank_multiple (line 266) | int hypercluster_pagerank_multiple(sparserow* G,
  function pprgrow (line 324) | void pprgrow(sparserow* G, std::vector<mwIndex>& set, double alpha,
  function copy_array_to_index_vector (line 340) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 358) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/authors_original_files/ppr_src/pprgrow_mex.cc
  class array_queue (line 27) | class array_queue {
    method array_queue (line 33) | array_queue(size_t _max_size)
    method empty (line 37) | void empty() {
    method size (line 43) | size_t size() {
    method push (line 47) | void push(int i) {
    method front (line 57) | int front() {
    method pop (line 62) | void pop() {
  type sparsevec (line 72) | struct sparsevec {
    method get (line 78) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 90) | double sum() {
    method mwIndex (line 101) | mwIndex max_index() {
  type sparserow (line 111) | struct sparserow {
  function mwIndex (line 118) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function compute_local_pagerank (line 123) | int compute_local_pagerank(sparserow *s, sparsevec& r, sparsevec& p,
  type greater2nd (line 162) | struct greater2nd {
  function cluster_from_sweep (line 168) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_pagerank_stats (line 246) | struct local_pagerank_stats {
  function hypercluster_pagerank_multiple (line 265) | int hypercluster_pagerank_multiple(sparserow* G,
  function pprgrow (line 323) | void pprgrow(sparserow* G, std::vector<mwIndex>& set, double alpha,
  function copy_array_to_index_vector (line 339) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 357) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/authors_original_files/src/hkgrow_mex.cpp
  type sparsevec (line 47) | struct sparsevec {
    method get (line 53) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 65) | double sum() {
    method mwIndex (line 76) | mwIndex max_index() {
  type sparserow (line 86) | struct sparserow {
  function mwIndex (line 97) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function taylordegree (line 108) | unsigned int taylordegree(const double t, const double eps) {
  function gsqexpmseed (line 149) | int gsqexpmseed(sparserow * G, sparsevec& set, sparsevec& y,
  type greater2nd (line 245) | struct greater2nd {
  function cluster_from_sweep (line 251) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_hkpr_stats (line 329) | struct local_hkpr_stats {
  function hypercluster_heatkernel_multiple (line 348) | int hypercluster_heatkernel_multiple(sparserow* G,
  function hkgrow (line 413) | void hkgrow(sparserow* G, std::vector<mwIndex>& seeds, double t,
  function copy_array_to_index_vector (line 432) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 450) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/authors_original_files/src/hkgrow_mex_kdd.cpp
  type sparsevec (line 47) | struct sparsevec {
    method get (line 53) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 65) | double sum() {
    method mwIndex (line 76) | mwIndex max_index() {
  type sparserow (line 86) | struct sparserow {
  function mwIndex (line 97) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function taylordegree (line 108) | unsigned int taylordegree(const double t, const double eps) {
  function gsqexpmseed (line 149) | int gsqexpmseed(sparserow * G, sparsevec& set, sparsevec& y,
  type greater2nd (line 246) | struct greater2nd {
  function cluster_from_sweep (line 252) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_hkpr_stats (line 330) | struct local_hkpr_stats {
  function hypercluster_heatkernel_multiple (line 349) | int hypercluster_heatkernel_multiple(sparserow* G,
  function hkgrow (line 414) | void hkgrow(sparserow* G, std::vector<mwIndex>& seeds, double t,
  function copy_array_to_index_vector (line 433) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 451) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/src_cpp_matlab/hkgrow_mex.cpp
  type sparsevec (line 47) | struct sparsevec {
    method get (line 53) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 65) | double sum() {
    method mwIndex (line 76) | mwIndex max_index() {
  type sparserow (line 86) | struct sparserow {
  function mwIndex (line 97) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function taylordegree (line 108) | unsigned int taylordegree(const double t, const double eps) {
  function gsqexpmseed (line 149) | int gsqexpmseed(sparserow * G, sparsevec& set, sparsevec& y,
  type greater2nd (line 245) | struct greater2nd {
  function cluster_from_sweep (line 251) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_hkpr_stats (line 329) | struct local_hkpr_stats {
  function hypercluster_heatkernel_multiple (line 348) | int hypercluster_heatkernel_multiple(sparserow* G,
  function hkgrow (line 413) | void hkgrow(sparserow* G, std::vector<mwIndex>& seeds, double t,
  function copy_array_to_index_vector (line 432) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 450) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/src_cpp_matlab/hkgrow_mex_kdd.cpp
  type sparsevec (line 47) | struct sparsevec {
    method get (line 53) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 65) | double sum() {
    method mwIndex (line 76) | mwIndex max_index() {
  type sparserow (line 86) | struct sparserow {
  function mwIndex (line 97) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function taylordegree (line 108) | unsigned int taylordegree(const double t, const double eps) {
  function gsqexpmseed (line 149) | int gsqexpmseed(sparserow * G, sparsevec& set, sparsevec& y,
  type greater2nd (line 246) | struct greater2nd {
  function cluster_from_sweep (line 252) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_hkpr_stats (line 330) | struct local_hkpr_stats {
  function hypercluster_heatkernel_multiple (line 349) | int hypercluster_heatkernel_multiple(sparserow* G,
  function hkgrow (line 414) | void hkgrow(sparserow* G, std::vector<mwIndex>& seeds, double t,
  function copy_array_to_index_vector (line 433) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 451) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/src_python/demo_files/yche_numerical_linear_algebra_exp.py
  function demo_gauss_sedel_method (line 5) | def demo_gauss_sedel_method():
  function demo_jacobi_method (line 44) | def demo_jacobi_method():

FILE: Algorithms/2014-Heat-Kernel/src_python/main_files/algo_hr_grow.py
  class HRGrow (line 12) | class HRGrow:
    method __init__ (line 13) | def __init__(self, N, t, eps, svg_graph):
    method generate_seed_list (line 21) | def generate_seed_list(self):
    method estimate_hkpr_vector (line 25) | def estimate_hkpr_vector(self, seed_list):
    method sweep_cut (line 63) | def sweep_cut(self, x_dict):
    method do_iterations (line 81) | def do_iterations(self):

FILE: Algorithms/2014-Heat-Kernel/src_python/main_files/algo_ppr.py
  class PPR (line 7) | class PPR:
    method __init__ (line 8) | def __init__(self, graph, alpha, tolerance):
    method generate_seed_list (line 14) | def generate_seed_list(self):
    method out_degree (line 18) | def out_degree(self, v):
    method estimate_ppr_vector (line 21) | def estimate_ppr_vector(self, seed_list):
    method sweep_cut (line 45) | def sweep_cut(self, x_dict):
    method do_iterations (line 62) | def do_iterations(self):

FILE: Algorithms/2014-Heat-Kernel/src_python/main_files/util_helper.py
  function get_sample_graph (line 6) | def get_sample_graph():
  function get_edge_num (line 12) | def get_edge_num(adj_list_dict):
  function compute_psis (line 19) | def compute_psis(N, t=1):
  function compute_thresholds (line 26) | def compute_thresholds(eps, N, psis):
  function load_twitter_graph (line 34) | def load_twitter_graph():
  function compute_conductance (line 51) | def compute_conductance(cut_num, vol_s, vol_g):

FILE: Algorithms/2014-Heat-Kernel/yche_refactor/hkgrow_mex_kdd.cpp
  type sparsevec (line 47) | struct sparsevec {
    method get (line 53) | double get(mwIndex index, double default_value=0.0) {
    method sum (line 65) | double sum() {
    method mwIndex (line 76) | mwIndex max_index() {
  type sparserow (line 86) | struct sparserow {
  function mwIndex (line 97) | mwIndex sr_degree(sparserow *s, mwIndex u) {
  function taylordegree (line 108) | unsigned int taylordegree(const double t, const double eps) {
  function gsqexpmseed (line 149) | int gsqexpmseed(sparserow * G, sparsevec& set, sparsevec& y,
  type greater2nd (line 245) | struct greater2nd {
  function cluster_from_sweep (line 251) | void cluster_from_sweep(sparserow* G, sparsevec& p,
  type local_hkpr_stats (line 329) | struct local_hkpr_stats {
  function hypercluster_heatkernel_multiple (line 348) | int hypercluster_heatkernel_multiple(sparserow* G,
  function hkgrow (line 413) | void hkgrow(sparserow* G, std::vector<mwIndex>& seeds, double t,
  function copy_array_to_index_vector (line 432) | void copy_array_to_index_vector(const mxArray* v, std::vector<mwIndex>& ...
  function mexFunction (line 450) | void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prh...

FILE: Algorithms/2014-Heat-Kernel/yche_refactor/main.cpp
  function main (line 5) | int main() {

FILE: Algorithms/2015-LEMON/python_yche_refactor/io_helper.py
  function sort_two_vertices (line 8) | def sort_two_vertices(a, b):
  function read_edge_list (line 14) | def read_edge_list(filename, delimiter=None, nodetype=int):
  function read_ground_truth (line 64) | def read_ground_truth(filename, delimiter=None, nodetype=int):

FILE: Algorithms/2015-LEMON/python_yche_refactor/lemon.py
  function set_initial_prob (line 14) | def set_initial_prob(n, starting_nodes):
  function set_initial_prob_proportional (line 20) | def set_initial_prob_proportional(n, degree_sequence, starting_nodes):
  function adj_to_laplacian (line 30) | def adj_to_laplacian(G):
  function cal_conductance (line 44) | def cal_conductance(G, cluster):
  function sample_graph (line 56) | def sample_graph(G_linklist, node_number, degree_sequence, starting_node...
  function map_from_ori_to_new (line 129) | def map_from_ori_to_new(nodelist, map_dict_reverse):
  function random_walk (line 134) | def random_walk(G, initial_prob, subspace_dim=3, walk_steps=3):
  function min_one_norm (line 153) | def min_one_norm(B, initial_seed, seed):
  function seed_expand_auto (line 183) | def seed_expand_auto(G, seedset, min_comm_size, max_comm_size, expand_st...
  function global_minimum (line 249) | def global_minimum(sequence, start_index):
  function cal_f_score (line 273) | def cal_f_score(detected_comm, ground_truth_comm, beta=1):
  class MyParser (line 286) | class MyParser(OptionParser):
    method format_epilog (line 287) | def format_epilog(self, formatter):

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/benchm.cpp
  function they_are_mate (line 41) | bool they_are_mate(int a, int b, const deque<deque<int> > & member_list) {
  function deque_int_sum (line 65) | int deque_int_sum(const deque<int> & a) {
  function integral (line 75) | double integral (double a, double b) {
  function average_degree (line 89) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 97) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function integer_average (line 151) | double integer_average (int n, int min, double tau) {
  function change_community_size (line 170) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 208) | int build_bipartite_network(deque<deque<int> >  & member_matrix, const d...
  function internal_degree_and_membership (line 382) | int internal_degree_and_membership (double mixing_parameter, int overlap...
  function compute_internal_degree_per_node (line 665) | int compute_internal_degree_per_node(int d, int m, deque<int> & a) {
  function build_subgraph (line 719) | int build_subgraph(deque<set<int> > & E, const deque<int> & nodes, const...
  function build_subgraphs (line 954) | int build_subgraphs(deque<set<int> > & E, const deque<deque<int> > & mem...
  function connect_all_the_parts (line 1144) | int connect_all_the_parts(deque<set<int> > & E, const deque<deque<int> >...
  function internal_kin (line 1415) | int internal_kin(deque<set<int> > & E, const deque<deque<int> > & member...
  function internal_kin_only_one (line 1428) | int internal_kin_only_one(set<int> & E, const deque<int> & member_matrix...
  function erase_links (line 1443) | int erase_links(deque<set<int> > & E, const deque<deque<int> > & member_...
  function print_network (line 1539) | int print_network(deque<set<int> > & E, const deque<deque<int> > & membe...
  function benchmark (line 1670) | int benchmark(bool excess, bool defect, int num_nodes, double  average_k...
  function erase_file_if_exists (line 1790) | void erase_file_if_exists(string s) {
  function main (line 1810) | int main(int argc, char * argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/cast.cpp
  function cast_int (line 77) | int cast_int(double u) {
  function cast_string_to_char (line 88) | int cast_string_to_char(string &file_name, char *b) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/cc.cpp
  function common_neighbors (line 2) | int common_neighbors(int a, int b, deque<set<int> > & en) {
  function compute_cc (line 23) | double compute_cc(deque<set<int> > & en, int i) {
  function compute_cc (line 41) | double compute_cc(deque<set<int> > & en) {
  function compute_tot_t (line 75) | double compute_tot_t(deque<set<int> > & en) {
  function choose_the_least (line 93) | int choose_the_least(deque<set<int> > & en, deque<int> & A, int a, int &...
  function cclu (line 123) | int cclu(deque<set<int> > & en, const deque<deque<int> > & member_list, ...

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 305) | int shuffle_s(deque<int> & sq) {
  function shuffle_s (line 334) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 362) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 377) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 408) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 477) | int random_from_set(set<int> & s) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/histograms.cpp
  function log_histogram (line 15) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function histogram (line 116) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 217) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 320) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 419) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 519) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function int_histogram (line 616) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 645) | int int_histogram (deque <int> &c, ostream & out) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/print.cpp
  function cherr (line 15) | int cherr(double a) {
  function prints (line 26) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 34) | void prints(pair <uno, due> &sq) {
  function prints (line 42) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 55) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 70) | void prints(Seq &sq, ostream &out) {
  function prints (line 82) | void prints(type_ *a, int b) {
  function printm (line 93) | void printm(C<T>& c, ostream &out) {
  function prints (line 108) | void prints(map <uno, due> &sq) {
  function prints (line 121) | void prints(multimap <uno, due> &sq) {
  function prints (line 136) | void prints(Seq &sq) {
  function prints (line 149) | void prints(const deque<type> & sq) {
  function printm (line 163) | void printm(C<T>& c) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/binary_networks/Sources/set_parameters.cpp
  class Parameters (line 7) | class Parameters {
  function statement (line 356) | void statement() {
  function set_from_file (line 409) | bool set_from_file(string & file_name, Parameters & par1) {
  function set_parameters (line 478) | bool set_parameters(int argc, char * argv[], Parameters & par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/benchm.cpp
  function deque_int_sum (line 80) | int deque_int_sum(const deque<int> & a) {
  function integral (line 90) | double integral (double a, double b) {
  function average_degree (line 104) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 112) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function integer_average (line 166) | double integer_average (int n, int min, double tau) {
  function change_community_size (line 185) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 227) | int build_bipartite_network(deque<deque<int> >  & member_matrix, const d...
  function internal_degree_and_membership (line 401) | int internal_degree_and_membership (double mixing_parameter, int overlap...
  function compute_internal_degree_per_node (line 650) | int compute_internal_degree_per_node(int d, int m, deque<int> & a) {
  function build_subgraph (line 704) | int build_subgraph(deque<set<int> > & Ein, deque<set<int> > & Eout, cons...
  function build_subgraphs (line 1069) | int build_subgraphs(deque<set<int> > & Ein, deque<set<int> > & Eout, con...
  function they_are_mate (line 1293) | bool they_are_mate(int a, int b, const deque<deque<int> > & member_list) {
  function compute_var_mate (line 1308) | int compute_var_mate(deque<set<int> > & en_in,  const deque<deque<int> >...
  function connect_all_the_parts (line 1322) | int connect_all_the_parts(deque<set<int> > & Ein, deque<set<int> > & Eou...
  function internal_kin (line 1710) | int internal_kin(deque<set<int> > & Ein, const deque<deque<int> > & memb...
  function internal_kin_only_one (line 1723) | int internal_kin_only_one(set<int> & Ein, const deque<int> & member_matr...
  function erase_links (line 1738) | int erase_links(deque<set<int> > & Ein, deque<set<int> > & Eout, const d...
  function print_network (line 1835) | int print_network(deque<set<int> > & Ein, deque<set<int> > & Eout, const...
  function benchmark (line 1987) | int benchmark(bool excess, bool defect, int num_nodes, double  average_k...
  function erase_file_if_exists (line 2103) | void erase_file_if_exists(string s) {
  function main (line 2125) | int main(int argc, char * argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/cast.cpp
  function cast_int (line 77) | int cast_int(double u) {
  function cast_string_to_char (line 88) | int cast_string_to_char(string &file_name, char *b) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, const int &dim) {		// it sets due as a ran...
  function shuffle_s (line 301) | int shuffle_s(deque<int> &sq) {
  function compute_r (line 335) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 350) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 381) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function compute_self_links (line 436) | double compute_self_links(int k, int n, int x) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/histograms.cpp
  function log_histogram (line 15) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function histogram (line 116) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 217) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 320) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 419) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 519) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function int_histogram (line 616) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 645) | int int_histogram (deque <int> &c, ostream & out) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/print.cpp
  function cherr (line 15) | int cherr(double a) {
  function prints (line 26) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 34) | void prints(pair <uno, due> &sq) {
  function prints (line 42) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 55) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 70) | void prints(Seq &sq, ostream &out) {
  function prints (line 82) | void prints(type_ *a, int b) {
  function printm (line 93) | void printm(C<T>& c, ostream &out) {
  function prints (line 108) | void prints(map <uno, due> &sq) {
  function prints (line 121) | void prints(multimap <uno, due> &sq) {
  function prints (line 136) | void prints(Seq &sq) {
  function prints (line 149) | void prints(const deque<type> & sq) {
  function printm (line 163) | void printm(C<T>& c) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/directed_networks/Sources/set_parameters.cpp
  class Parameters (line 7) | class Parameters {
  function statement (line 344) | void statement() {
  function set_from_file (line 395) | bool set_from_file(string & file_name, Parameters & par1) {
  function set_parameters (line 464) | bool set_parameters(int argc, char * argv[], Parameters & par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/benchm.cpp
  function print_network (line 38) | int print_network(deque<set<int> > & E, const deque<deque<int> > & membe...
  function benchmark (line 169) | int benchmark(bool excess, bool defect, int num_nodes, double  average_k...
  function erase_file_if_exists (line 317) | void erase_file_if_exists(string s) {
  function choose_macro_sizes (line 338) | int choose_macro_sizes(int N, deque<int> & msizes, int minC, int maxC, d...
  function main (line 374) | int main(int argc, char * argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/binary_benchm.cpp
  function they_are_mate (line 9) | bool they_are_mate(int a, int b, const deque<deque<int> > & member_list) {
  function deque_int_sum (line 33) | int deque_int_sum(const deque<int> & a) {
  function integral (line 43) | double integral (double a, double b) {
  function average_degree (line 57) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 65) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function integer_average (line 119) | double integer_average (int n, int min, double tau) {
  function change_community_size (line 138) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 176) | int build_bipartite_network(deque<deque<int> >  & member_matrix, const d...
  function internal_degree_and_membership (line 350) | int internal_degree_and_membership (double mixing_parameter, int overlap...
  function compute_internal_degree_per_node (line 633) | int compute_internal_degree_per_node(int d, int m, deque<int> & a) {
  function build_subgraph (line 687) | int build_subgraph(deque<set<int> > & E, const deque<int> & nodes, const...
  function build_subgraphs (line 922) | int build_subgraphs(deque<set<int> > & E, const deque<deque<int> > & mem...
  function connect_all_the_parts (line 1112) | int connect_all_the_parts(deque<set<int> > & E, const deque<deque<int> >...
  function internal_kin (line 1383) | int internal_kin(deque<set<int> > & E, const deque<deque<int> > & member...
  function internal_kin_only_one (line 1396) | int internal_kin_only_one(set<int> & E, const deque<int> & member_matrix...
  function erase_links (line 1411) | int erase_links(deque<set<int> > & E, const deque<deque<int> > & member_...

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/cc.cpp
  function common_neighbors (line 2) | int common_neighbors(int a, int b, deque<set<int> > & en) {
  function compute_cc (line 23) | double compute_cc(deque<set<int> > & en, int i) {
  function compute_cc (line 41) | double compute_cc(deque<set<int> > & en) {
  function compute_tot_t (line 75) | double compute_tot_t(deque<set<int> > & en) {
  function choose_the_least (line 93) | int choose_the_least(deque<set<int> > & en, deque<int> & A, int a, int &...
  function cclu (line 123) | int cclu(deque<set<int> > & en, const deque<deque<int> > & member_list, ...

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/set_parameters.cpp
  class Parameters (line 7) | class Parameters {
  function statement (line 440) | void statement() {
  function set_from_file (line 481) | bool set_from_file(string & file_name, Parameters & par1) {
  function set_parameters (line 550) | bool set_parameters(int argc, char * argv[], Parameters & par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/cast.cpp
  function cast_string_to_double (line 142) | double cast_string_to_double(string &b) {
  function cast_int (line 152) | inline int cast_int(double u) {
  function cast_string_to_char (line 159) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 171) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 218) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 235) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 281) | double approx(double a, int digits) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 302) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 330) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 358) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 373) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 404) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 473) | int random_from_set(set<int> & s) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 146) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 156) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function norm_one (line 167) | double norm_one(const deque<double> & a) {
  function normalize_one (line 182) | int normalize_one(deque<double> & a) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/histograms.cpp
  function intlog_binning (line 14) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function xybinning (line 141) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 267) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function compute_quantiles (line 277) | double compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 303) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 430) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function log_histogram (line 527) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 624) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 725) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 828) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 929) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1029) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1127) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1229) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1330) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1359) | int int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1388) | int int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1403) | int int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1418) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1444) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1470) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1497) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1527) | int int_histogram(string infile, string outfile) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 542) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/pajek.cpp
  function get_partition_from_file_list_pajek (line 4) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function pajek_format (line 62) | int pajek_format(string filename, bool directed) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/partition.cpp
  function get_partition_from_file_list (line 38) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 147) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 155) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 164) | void prints(Seq &sq) {
  function prints (line 177) | void prints(const deque<type> & sq) {
  function prints (line 187) | void prints(const vector<type> & sq) {
  function printm (line 200) | void printm(deque<type> & M) {
  function printm (line 210) | void printm(vector<type> & M) {
  function get_data_from_file (line 223) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 264) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 301) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/hierarchical_bench2_2/hier_ben_Sources/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/benchm.cpp
  function print_network (line 35) | int print_network(deque<set<int> > & Ein, deque<set<int> > & Eout, const...
  function check_weights (line 283) | int check_weights(deque<map <int, double > > & neigh_weigh_in, deque<map...
  function propagate_one (line 384) | int propagate_one(deque<map <int, double > > & neighbors_weights, const ...
  function propagate_two (line 458) | int propagate_two(deque<map <int, double > > & neighbors_weights, const ...
  function propagate (line 586) | int propagate(deque<map <int, double > > & neigh_weigh_in, deque<map <in...
  function weights (line 608) | int weights(deque<set<int> > & ein, deque<set<int> > & eout, const deque...
  function benchmark (line 750) | int benchmark(bool excess, bool defect, int num_nodes, double  average_k...
  function erase_file_if_exists (line 884) | void erase_file_if_exists(string s) {
  function main (line 909) | int main(int argc, char * argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/cast.cpp
  function cast_int (line 77) | int cast_int(double u) {
  function cast_string_to_char (line 88) | int cast_string_to_char(string &file_name, char *b) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, const int &dim) {		// it sets due as a ran...
  function shuffle_s (line 301) | int shuffle_s(deque<int> &sq) {
  function compute_r (line 335) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 350) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 381) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function compute_self_links (line 436) | double compute_self_links(int k, int n, int x) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/dir_benchm.cpp
  function deque_int_sum (line 47) | int deque_int_sum(const deque<int> & a) {
  function integral (line 57) | double integral (double a, double b) {
  function average_degree (line 71) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 79) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function integer_average (line 133) | double integer_average (int n, int min, double tau) {
  function change_community_size (line 152) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 194) | int build_bipartite_network(deque<deque<int> >  & member_matrix, const d...
  function internal_degree_and_membership (line 368) | int internal_degree_and_membership (double mixing_parameter, int overlap...
  function compute_internal_degree_per_node (line 617) | int compute_internal_degree_per_node(int d, int m, deque<int> & a) {
  function build_subgraph (line 671) | int build_subgraph(deque<set<int> > & Ein, deque<set<int> > & Eout, cons...
  function build_subgraphs (line 1036) | int build_subgraphs(deque<set<int> > & Ein, deque<set<int> > & Eout, con...
  function they_are_mate (line 1260) | bool they_are_mate(int a, int b, const deque<deque<int> > & member_list) {
  function compute_var_mate (line 1275) | int compute_var_mate(deque<set<int> > & en_in,  const deque<deque<int> >...
  function connect_all_the_parts (line 1289) | int connect_all_the_parts(deque<set<int> > & Ein, deque<set<int> > & Eou...
  function internal_kin (line 1677) | int internal_kin(deque<set<int> > & Ein, const deque<deque<int> > & memb...
  function internal_kin_only_one (line 1690) | int internal_kin_only_one(set<int> & Ein, const deque<int> & member_matr...
  function erase_links (line 1705) | int erase_links(deque<set<int> > & Ein, deque<set<int> > & Eout, const d...

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/histograms.cpp
  function log_histogram (line 15) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function histogram (line 116) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 217) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 320) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 419) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 519) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function int_histogram (line 616) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 645) | int int_histogram (deque <int> &c, ostream & out) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/print.cpp
  function cherr (line 15) | int cherr(double a) {
  function prints (line 26) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 34) | void prints(pair <uno, due> &sq) {
  function prints (line 42) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 55) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 70) | void prints(Seq &sq, ostream &out) {
  function prints (line 82) | void prints(type_ *a, int b) {
  function printm (line 93) | void printm(C<T>& c, ostream &out) {
  function prints (line 108) | void prints(map <uno, due> &sq) {
  function prints (line 121) | void prints(multimap <uno, due> &sq) {
  function prints (line 136) | void prints(Seq &sq) {
  function prints (line 149) | void prints(const deque<type> & sq) {
  function printm (line 163) | void printm(C<T>& c) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_directed_nets/Sources/set_parameters.cpp
  class Parameters (line 7) | class Parameters {
  function statement (line 368) | void statement() {
  function set_from_file (line 421) | bool set_from_file(string & file_name, Parameters & par1) {
  function set_parameters (line 490) | bool set_parameters(int argc, char * argv[], Parameters & par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/benchm.cpp
  function print_network (line 37) | int print_network(deque<set<int> > & E, const deque<deque<int> > & membe...
  function check_weights (line 256) | int check_weights(deque<map <int, double > > & neigh_weigh, const deque<...
  function propagate (line 342) | int propagate(deque<map <int, double > > & neigh_weigh, const deque<dequ...
  function weights (line 553) | int weights(deque<set<int> > & en, const deque<deque<int> > & member_lis...
  function benchmark (line 686) | int benchmark(bool excess, bool defect, int num_nodes, double  average_k...
  function erase_file_if_exists (line 818) | void erase_file_if_exists(string s) {
  function main (line 839) | int main(int argc, char * argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/binary_benchm.cpp
  function they_are_mate (line 9) | bool they_are_mate(int a, int b, const deque<deque<int> > & member_list) {
  function deque_int_sum (line 33) | int deque_int_sum(const deque<int> & a) {
  function integral (line 43) | double integral (double a, double b) {
  function average_degree (line 57) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 65) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function integer_average (line 119) | double integer_average (int n, int min, double tau) {
  function change_community_size (line 138) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 176) | int build_bipartite_network(deque<deque<int> >  & member_matrix, const d...
  function internal_degree_and_membership (line 350) | int internal_degree_and_membership (double mixing_parameter, int overlap...
  function compute_internal_degree_per_node (line 633) | int compute_internal_degree_per_node(int d, int m, deque<int> & a) {
  function build_subgraph (line 687) | int build_subgraph(deque<set<int> > & E, const deque<int> & nodes, const...
  function build_subgraphs (line 922) | int build_subgraphs(deque<set<int> > & E, const deque<deque<int> > & mem...
  function connect_all_the_parts (line 1112) | int connect_all_the_parts(deque<set<int> > & E, const deque<deque<int> >...
  function internal_kin (line 1383) | int internal_kin(deque<set<int> > & E, const deque<deque<int> > & member...
  function internal_kin_only_one (line 1396) | int internal_kin_only_one(set<int> & E, const deque<int> & member_matrix...
  function erase_links (line 1411) | int erase_links(deque<set<int> > & E, const deque<deque<int> > & member_...

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/cast.cpp
  function cast_int (line 77) | int cast_int(double u) {
  function cast_string_to_char (line 88) | int cast_string_to_char(string &file_name, char *b) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/cc.cpp
  function common_neighbors (line 2) | int common_neighbors(int a, int b, deque<set<int> > & en) {
  function compute_cc (line 23) | double compute_cc(deque<set<int> > & en, int i) {
  function compute_cc (line 41) | double compute_cc(deque<set<int> > & en) {
  function compute_tot_t (line 75) | double compute_tot_t(deque<set<int> > & en) {
  function choose_the_least (line 93) | int choose_the_least(deque<set<int> > & en, deque<int> & A, int a, int &...
  function cclu (line 123) | int cclu(deque<set<int> > & en, const deque<deque<int> > & member_list, ...

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 305) | int shuffle_s(deque<int> & sq) {
  function shuffle_s (line 334) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 362) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 377) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 408) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 477) | int random_from_set(set<int> & s) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/histograms.cpp
  function log_histogram (line 15) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function histogram (line 116) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 217) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 320) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 419) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 519) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function int_histogram (line 616) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 645) | int int_histogram (deque <int> &c, ostream & out) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/print.cpp
  function cherr (line 15) | int cherr(double a) {
  function prints (line 26) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 34) | void prints(pair <uno, due> &sq) {
  function prints (line 42) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 55) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 70) | void prints(Seq &sq, ostream &out) {
  function prints (line 82) | void prints(type_ *a, int b) {
  function printm (line 93) | void printm(C<T>& c, ostream &out) {
  function prints (line 108) | void prints(map <uno, due> &sq) {
  function prints (line 121) | void prints(multimap <uno, due> &sq) {
  function prints (line 136) | void prints(Seq &sq) {
  function prints (line 149) | void prints(const deque<type> & sq) {
  function printm (line 163) | void printm(C<T>& c) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Benchmark/2009-LFR-Benchmark/src_original_cpp/weighted_networks/Sources/set_parameters.cpp
  class Parameters (line 7) | class Parameters {
  function statement (line 379) | void statement() {
  function set_from_file (line 434) | bool set_from_file(string & file_name, Parameters & par1) {
  function set_parameters (line 503) | bool set_parameters(int argc, char * argv[], Parameters & par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/benchmark_gen.py
  function generate_different_avg (line 4) | def generate_different_avg(vertex_num):
  function generate_different_coefficient (line 19) | def generate_different_coefficient(vertex_num):

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/directed_graph/benchm.cpp
  function deque_int_sum (line 53) | int deque_int_sum(const deque<int> &a) {
  function integral (line 61) | double integral(double a, double b) {
  function average_degree (line 69) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 75) | double solve_dmin(const double &dmax, const double &dmed, const double &...
  function integer_average (line 106) | double integer_average(int n, int min, double tau) {
  function change_community_size (line 117) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 138) | int build_bipartite_network(deque<deque<int> > &member_matrix, const deq...
  function internal_degree_and_membership (line 233) | int internal_degree_and_membership(double mixing_parameter, int overlapp...
  function compute_internal_degree_per_node (line 379) | int compute_internal_degree_per_node(int d, int m, deque<int> &a) {
  function build_subgraph (line 414) | int build_subgraph(deque<set<int> > &Ein, deque<set<int> > &Eout, const ...
  function build_subgraphs (line 616) | int build_subgraphs(deque<set<int> > &Ein, deque<set<int> > &Eout, const...
  function compute_var_mate (line 739) | int compute_var_mate(deque<set<int> > &en_in, const deque<deque<int> > &...
  function connect_all_the_parts (line 749) | int connect_all_the_parts(deque<set<int> > &Ein, deque<set<int> > &Eout,...
  function internal_kin (line 954) | int internal_kin(deque<set<int> > &Ein, const deque<deque<int> > &member...
  function internal_kin_only_one (line 962) | int internal_kin_only_one(set<int> &Ein,
  function erase_links (line 972) | int erase_links(deque<set<int> > &Ein, deque<set<int> > &Eout, const deq...
  function print_network (line 1026) | int print_network(deque<set<int> > &Ein, deque<set<int> > &Eout, const d...
  function benchmark (line 1116) | int benchmark(bool excess, bool defect, int num_nodes, double average_k,...
  function erase_file_if_exists (line 1177) | void erase_file_if_exists(string s) {
  function main (line 1188) | int main(int argc, char *argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/directed_graph/set_parameters.cpp
  function statement (line 4) | void statement() {
  function set_from_file (line 45) | bool set_from_file(string &file_name, Parameters &par1) {
  function set_parameters (line 83) | bool set_parameters(int argc, char *argv[], Parameters &par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/hierarchical_comm_graph/benchm.cpp
  function print_network (line 46) | int print_network(deque<set<int> > &E, const deque<deque<int> > &member_...
  function benchmark (line 128) | int benchmark(bool excess, bool defect, int num_nodes, double average_k,...
  function erase_file_if_exists (line 196) | void erase_file_if_exists(string s) {
  function choose_macro_sizes (line 207) | int choose_macro_sizes(int N, deque<int> &msizes, int minC, int maxC, do...
  function main (line 223) | int main(int argc, char *argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/hierarchical_comm_graph/binary_benchm.cpp
  function deque_int_sum (line 12) | int deque_int_sum(const deque<int> &a) {
  function integral (line 20) | double integral(double a, double b) {
  function average_degree (line 28) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 34) | double solve_dmin(const double &dmax, const double &dmed, const double &...
  function integer_average (line 65) | double integer_average(int n, int min, double tau) {
  function change_community_size (line 76) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 97) | int build_bipartite_network(deque<deque<int>> &member_matrix, const dequ...
  function internal_degree_and_membership (line 194) | int internal_degree_and_membership(double mixing_parameter, int overlapp...
  function compute_internal_degree_per_node (line 381) | int compute_internal_degree_per_node(int d, int m, deque<int> &a) {
  function build_subgraph (line 422) | int build_subgraph(deque<set<int>> &E, const deque<int> &nodes, const de...
  function build_subgraphs (line 555) | int build_subgraphs(deque<set<int>> &E, const deque<deque<int>> &member_...
  function connect_all_the_parts (line 645) | int
  function internal_kin (line 788) | int internal_kin(deque<set<int>> &E, const deque<deque<int>> &member_lis...
  function internal_kin_only_one (line 796) | int internal_kin_only_one(set<int> &E,
  function erase_links (line 806) | int erase_links(deque<set<int>> &E, const deque<deque<int>> &member_list...

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/hierarchical_comm_graph/set_parameters.cpp
  function statement (line 220) | void statement() {
  function set_from_file (line 250) | bool set_from_file(string &file_name, Parameters &par1) {
  function set_parameters (line 288) | bool set_parameters(int argc, char *argv[], Parameters &par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/playground/nmi_usage_demo.cpp
  function main (line 7) | int main() {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/playground/tabdeg_demo.cpp
  function main (line 3) | int main() {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/undirected_graph/benchm.cpp
  function deque_int_sum (line 55) | int deque_int_sum(const deque<int> &a) {
  function integral (line 63) | double integral(double a, double b) {
  function average_degree (line 71) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 77) | double solve_dmin(const double &dmax, const double &dmed, const double &...
  function integer_average (line 108) | double integer_average(int n, int min, double tau) {
  function change_community_size (line 119) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 140) | int build_bipartite_network(deque<deque<int> > &member_matrix, const deq...
  function internal_degree_and_membership (line 235) | int internal_degree_and_membership(double mixing_parameter, int overlapp...
  function compute_internal_degree_per_node (line 355) | int compute_internal_degree_per_node(int d, int m, deque<int> &a) {
  function build_subgraph (line 368) | int build_subgraph(deque<set<int> > &E, const deque<int> &nodes, const d...
  function build_subgraphs (line 494) | int build_subgraphs(deque<set<int> > &E, const deque<deque<int> > &membe...
  function connect_all_the_parts (line 585) | int
  function internal_kin (line 728) | int internal_kin(deque<set<int> > &E, const deque<deque<int> > &member_l...
  function internal_kin_only_one (line 736) | int internal_kin_only_one(set<int> &E,
  function erase_links (line 746) | int erase_links(deque<set<int> > &E, const deque<deque<int> > &member_li...
  function print_network (line 799) | int print_network(deque<set<int> > &E, const deque<deque<int> > &member_...
  function benchmark (line 869) | int benchmark(bool excess, bool defect, int num_nodes, double average_k,...
  function erase_file_if_exists (line 927) | void erase_file_if_exists(string s) {
  function main (line 938) | int main(int argc, char *argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/undirected_graph/set_parameters.cpp
  function statement (line 171) | void statement() {
  function set_from_file (line 216) | bool set_from_file(string &file_name, Parameters &par1) {
  function set_parameters (line 254) | bool set_parameters(int argc, char *argv[], Parameters &par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/cast.cpp
  function cast_string_to_double (line 9) | bool cast_string_to_double(string &b, double &h) {
  function cast_int (line 46) | int cast_int(double u) {
  function cast_string_to_char (line 53) | int cast_string_to_char(string &file_name, char *b) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/cc.cpp
  function they_are_mate (line 9) | bool they_are_mate(int a, int b, const deque<deque<int>> &member_list) {
  function common_neighbors (line 17) | int common_neighbors(int a, int b, deque<set<int>> &en) {
  function compute_cc (line 27) | double compute_cc(deque<set<int>> &en, int i) {
  function compute_cc (line 35) | double compute_cc(deque<set<int>> &en) {
  function compute_tot_t (line 48) | double compute_tot_t(deque<set<int>> &en) {
  function choose_the_least (line 56) | int choose_the_least(deque<set<int>> &en, deque<int> &A, int a, int &cn_...
  function cclu (line 72) | int cclu(deque<set<int>> &en, const deque<deque<int>> &member_list,

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/combinatorics.cpp
  function log_factorial (line 12) | double log_factorial(int num) {
  function log_combination (line 19) | double log_combination(int n, int k) {
  function binomial (line 35) | double binomial(int n, int x, double p) {
  function binomial_cumulative (line 56) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 69) | int powerlaw(int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 83) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 94) | int cumulative_from_distribution(deque<double> &cum, const deque<double>...
  function poisson (line 104) | double poisson(int x, double mu) {
  function shuffle_and_set (line 108) | int shuffle_and_set(int *due, int dim) {        // it sets due as a rand...
  function shuffle_s (line 119) | int shuffle_s(deque<int> &sq) {
  function compute_r (line 133) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 140) | int add_factors(deque<double> &num, deque<double> &den, int n, int k) {
  function compute_hypergeometric (line 154) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 197) | int random_from_set(set<int> &s) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/histograms.cpp
  function int_histogram (line 9) | int int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 18) | int int_histogram(vector<int> &c, ostream &out) {
  function int_histogram (line 33) | int int_histogram(deque<int> &c, ostream &out) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/input_output/tab_degree.h
  type multiset (line 20) | typedef multiset<pair<double, int>> muspi;
  function class (line 22) | class TabDegree {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/metric/mutual.cpp
  function H (line 9) | double H(double a) {
  function H (line 13) | double H(deque<double> &p) {
  function overlap_grouping (line 20) | int overlap_grouping(deque<deque<int>> ten, int unique) {        //hrepi...
  function mutual (line 33) | double mutual(deque<deque<int>> en, deque<deque<int>> ten) {
  function H_x_given_y (line 94) | double H_x_given_y(deque<deque<int>> &en, deque<deque<int>> &ten, int di...
  function mutual2 (line 148) | double mutual2(deque<deque<int>> en, deque<deque<int>> ten) {
  function H_x_given_y3 (line 181) | double H_x_given_y3(deque<deque<int>> &en, deque<deque<int>> &ten, int d...
  function mutual3 (line 244) | double mutual3(deque<deque<int>> en, deque<deque<int>> ten) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/pretty_print.h
  function namespace (line 25) | namespace pretty_print {
  type custom_delims_base (line 360) | struct custom_delims_base {
  type T (line 404) | typedef const T *const_iterator;
  type T (line 405) | typedef T value_type;
  type typename (line 424) | typedef typename T::const_local_iterator const_iterator;
  type typename (line 425) | typedef typename T::size_type size_type;
  function namespace (line 462) | namespace std {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/random.cpp
  function ran2 (line 12) | double ran2(long *idum) {
  function ran4 (line 45) | double ran4(bool t, long s) {
  function ran4 (line 55) | double ran4() {
  function srand4 (line 59) | void srand4(void) {
  function srand5 (line 64) | void srand5(int rank) {
  function irand (line 69) | int irand(int n) {
  function srand_file (line 73) | void srand_file(void) {
  function configuration_model (line 87) | int configuration_model(deque<set<int>> &en, deque<int> &degrees) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/unused/deque_numeric.cpp
  function compare (line 4) | bool compare(deque<double> &one, deque<double> &two) {
  function Euclidean_norm (line 14) | double Euclidean_norm(const deque<double> &a) {
  function Euclidean_normalize (line 22) | int Euclidean_normalize(deque<double> &a) {
  function scalar_product (line 30) | double scalar_product(deque<double> &a, deque<double> &b) {
  function orthogonalize (line 38) | int orthogonalize(deque<double> &a, deque <deque<double>> &M) {
  function matrix_time_vector (line 49) | int matrix_time_vector(deque <deque<double>> &Q, deque<double> &v, deque...
  function set_to_deque (line 60) | void set_to_deque(const set<int> &s, deque<int> &a) {
  function set_to_deque (line 66) | void set_to_deque(const set<double> &s, deque<double> &a) {
  function deque_to_set (line 72) | void deque_to_set(const deque<double> &a, set<double> &s) {
  function deque_to_set (line 78) | void deque_to_set(const deque<int> &a, set<int> &s) {
  function norm_one (line 84) | double norm_one(const deque<double> &a) {
  function normalize_one (line 92) | int normalize_one(deque<double> &a) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/unused/input_output/pajek.cpp
  function get_partition_from_file_list_pajek (line 1) | int get_partition_from_file_list_pajek(string s, deque <deque<int>> &ten...
  function pajek_format (line 28) | int pajek_format(string filename, bool directed) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/util/unused/input_output/partition.cpp
  function get_partition_from_file (line 4) | int get_partition_from_file(string s, deque <deque<int>> &M) {
  function get_partition_from_file_list (line 20) | int get_partition_from_file_list(string s, deque <deque<int>> &ten) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/weighted_directed_graph/benchm.cpp
  function print_network (line 44) | int print_network(deque<set<int> > &Ein, deque<set<int> > &Eout, const d...
  function check_weights (line 189) | int check_weights(deque<map<int, double> > &neigh_weigh_in, deque<map<in...
  function propagate_one (line 249) | int
  function propagate_two (line 288) | int
  function propagate (line 350) | int propagate(deque<map<int, double> > &neigh_weigh_in, deque<map<int, d...
  function weights (line 366) | int weights(deque<set<int> > &ein, deque<set<int> > &eout, const deque<d...
  function benchmark (line 438) | int benchmark(bool excess, bool defect, int num_nodes, double average_k,...
  function erase_file_if_exists (line 508) | void erase_file_if_exists(string s) {
  function main (line 519) | int main(int argc, char *argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/weighted_directed_graph/dir_benchm.cpp
  function deque_int_sum (line 4) | int deque_int_sum(const deque<int> &a) {
  function integral (line 12) | double integral(double a, double b) {
  function average_degree (line 20) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 26) | double solve_dmin(const double &dmax, const double &dmed, const double &...
  function integer_average (line 57) | double integer_average(int n, int min, double tau) {
  function change_community_size (line 68) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 89) | int build_bipartite_network(deque<deque<int> > &member_matrix, const deq...
  function internal_degree_and_membership (line 184) | int internal_degree_and_membership(double mixing_parameter, int overlapp...
  function compute_internal_degree_per_node (line 330) | int compute_internal_degree_per_node(int d, int m, deque<int> &a) {
  function build_subgraph (line 371) | int build_subgraph(deque<set<int> > &Ein, deque<set<int> > &Eout, const ...
  function build_subgraphs (line 573) | int build_subgraphs(deque<set<int> > &Ein, deque<set<int> > &Eout, const...
  function compute_var_mate (line 696) | int compute_var_mate(deque<set<int> > &en_in, const deque<deque<int> > &...
  function connect_all_the_parts (line 706) | int connect_all_the_parts(deque<set<int> > &Ein, deque<set<int> > &Eout,...
  function internal_kin (line 911) | int internal_kin(deque<set<int> > &Ein, const deque<deque<int> > &member...
  function internal_kin_only_one (line 919) | int internal_kin_only_one(set<int> &Ein,
  function erase_links (line 929) | int erase_links(deque<set<int> > &Ein, deque<set<int> > &Eout, const deq...

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/weighted_directed_graph/set_parameters.cpp
  function statement (line 178) | void statement() {
  function set_from_file (line 223) | bool set_from_file(string &file_name, Parameters &par1) {
  function set_parameters (line 261) | bool set_parameters(int argc, char *argv[], Parameters &par1) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/weighted_graph/benchm.cpp
  function print_network (line 46) | int print_network(deque<set<int>> &E, const deque<deque<int>> &member_li...
  function check_weights (line 173) | int check_weights(deque<map<int, double>> &neigh_weigh, const deque<dequ...
  function propagate (line 220) | int propagate(deque<map<int, double>> &neigh_weigh, const deque<deque<in...
  function weights (line 316) | int weights(deque<set<int>> &en, const deque<deque<int>> &member_list, c...
  function benchmark (line 379) | int benchmark(bool excess, bool defect, int num_nodes, double average_k,...
  function erase_file_if_exists (line 439) | void erase_file_if_exists(string s) {
  function main (line 450) | int main(int argc, char *argv[]) {

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/weighted_graph/binary_benchm.cpp
  function deque_int_sum (line 11) | int deque_int_sum(const deque<int> &a) {
  function integral (line 19) | double integral(double a, double b) {
  function average_degree (line 27) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 33) | double solve_dmin(const double &dmax, const double &dmed, const double &...
  function integer_average (line 64) | double integer_average(int n, int min, double tau) {
  function change_community_size (line 75) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 96) | int build_bipartite_network(deque<deque<int>> &member_matrix, const dequ...
  function internal_degree_and_membership (line 193) | int internal_degree_and_membership(double mixing_parameter, int overlapp...
  function compute_internal_degree_per_node (line 380) | int compute_internal_degree_per_node(int d, int m, deque<int> &a) {
  function build_subgraph (line 421) | int build_subgraph(deque<set<int>> &E, const deque<int> &nodes, const de...
  function build_subgraphs (line 554) | int build_subgraphs(deque<set<int>> &E, const deque<deque<int>> &member_...
  function connect_all_the_parts (line 644) | int
  function internal_kin (line 787) | int internal_kin(deque<set<int>> &E, const deque<deque<int>> &member_lis...
  function internal_kin_only_one (line 795) | int internal_kin_only_one(set<int> &E,
  function erase_links (line 805) | int erase_links(deque<set<int>> &E, const deque<deque<int>> &member_list...

FILE: Benchmark/2009-LFR-Benchmark/src_refactor_cpp/weighted_graph/set_parameters.cpp
  function statement (line 184) | void statement() {
  function set_from_file (line 233) | bool set_from_file(string &file_name, Parameters &par1) {
  function set_parameters (line 271) | bool set_parameters(int argc, char *argv[], Parameters &par1) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/benchm.cpp
  function sample_graph (line 7) | void sample_graph(ostream & pout, deque<pair<int, int> > & all_edges_deq...
  function create_layers (line 19) | int create_layers(int & layer_index, int num_of_layers, int ori, ostream...
  function main (line 75) | int main(int argc, char * argv[]) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/cast.cpp
  function cast_int (line 77) | int cast_int(double u) {
  function cast_string_to_char (line 88) | int cast_string_to_char(string &file_name, char *b) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/cc.cpp
  function common_neighbors (line 2) | int common_neighbors(int a, int b, deque<set<int> > & en) {
  function compute_cc (line 23) | double compute_cc(deque<set<int> > & en, int i) {
  function compute_cc (line 41) | double compute_cc(deque<set<int> > & en) {
  function compute_tot_t (line 75) | double compute_tot_t(deque<set<int> > & en) {
  function choose_the_least (line 93) | int choose_the_least(deque<set<int> > & en, deque<int> & A, int a, int &...
  function cclu (line 123) | int cclu(deque<set<int> > & en, const deque<deque<int> > & member_list, ...

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 193) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 217) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 240) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 257) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 273) | double poisson (int x, double mu) {
  function shuffle_and_set (line 283) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 307) | int shuffle_s(deque<int> & sq) {
  function shuffle_s (line 336) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 364) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 379) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 410) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function random_from_set (line 479) | int random_from_set(set<int> & s) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/histograms.cpp
  function log_histogram (line 15) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function histogram (line 116) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 217) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 320) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 419) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 519) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function int_histogram (line 616) | void int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 645) | void int_histogram (deque <int> &c, ostream & out) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function prints (line 26) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 34) | void prints(pair <uno, due> &sq) {
  function prints (line 42) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 55) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 70) | void prints(Seq &sq, ostream &out) {
  function prints (line 82) | void prints(type_ *a, int b) {
  function printm (line 93) | void printm(C<T>& c, ostream &out) {
  function prints (line 108) | void prints(map <uno, due> &sq) {
  function prints (line 121) | void prints(multimap <uno, due> &sq) {
  function prints (line 136) | void prints(Seq &sq) {
  function prints (line 149) | void prints(const deque<type> & sq) {
  function printm (line 163) | void printm(C<T>& c) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/set_parameters.cpp
  class Parameters (line 7) | class Parameters {
  function statement (line 372) | void statement() {
  function set_from_file (line 427) | bool set_from_file(string & file_name, Parameters & par1) {
  function set_parameters (line 496) | bool set_parameters(int argc, char * argv[], Parameters & par1) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexBenchmark/Sources/standard_bench.cpp
  function they_are_mate (line 41) | bool they_are_mate(int a, int b, const deque<deque<int> > & member_list) {
  function deque_int_sum (line 65) | int deque_int_sum(const deque<int> & a) {
  function integral (line 75) | double integral (double a, double b) {
  function average_degree (line 89) | double average_degree(const double &dmax, const double &dmin, const doub...
  function solve_dmin (line 97) | double solve_dmin(const double& dmax, const double &dmed, const double &...
  function integer_average (line 151) | double integer_average (int n, int min, double tau) {
  function change_community_size (line 170) | int change_community_size(deque<int> &seq) {
  function build_bipartite_network (line 208) | int build_bipartite_network(deque<deque<int> >  & member_matrix, const d...
  function internal_degree_and_membership (line 382) | int internal_degree_and_membership (double mixing_parameter, int overlap...
  function compute_internal_degree_per_node (line 665) | int compute_internal_degree_per_node(int d, int m, deque<int> & a) {
  function build_subgraph (line 719) | int build_subgraph(deque<set<int> > & E, const deque<int> & nodes, const...
  function build_subgraphs (line 954) | int build_subgraphs(deque<set<int> > & E, const deque<deque<int> > & mem...
  function connect_all_the_parts (line 1144) | int connect_all_the_parts(deque<set<int> > & E, const deque<deque<int> >...
  function internal_kin (line 1415) | int internal_kin(deque<set<int> > & E, const deque<deque<int> > & member...
  function internal_kin_only_one (line 1428) | int internal_kin_only_one(set<int> & E, const deque<int> & member_matrix...
  function erase_links (line 1443) | int erase_links(deque<set<int> > & E, const deque<deque<int> > & member_...
  function print_network (line 1539) | int print_network(deque<set<int> > & E, const deque<deque<int> > & membe...
  function benchmark (line 1671) | int benchmark(bool excess, bool defect, int num_nodes, double  average_k...
  function erase_file_if_exists (line 1791) | void erase_file_if_exists(string s) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/nmi_multiplex.cpp
  function set_partition_from_list (line 5) | int set_partition_from_list(mapii & node_cluster, deque<deque<int> > & o...
  function read_level_node_cluster (line 35) | void read_level_node_cluster(   string infile, \
  function main (line 85) | int main(int argc, char * argv[]) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/assert.cpp
  function assert_floats (line 3) | inline void assert_floats(double a, double b, \
  function assert_ints (line 12) | inline void assert_ints(int a, int b, string error_message=" no message") {
  function general_assert (line 21) | inline void general_assert(bool to_be_checked, string error_message=" no...

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/cast.cpp
  function string (line 13) | string str_cast(int number) {
  function cast_string_to_double (line 21) | bool cast_string_to_double (string b, double &h) {
  function cast_string_to_double (line 154) | double cast_string_to_double(string b) {
  function cast_int (line 163) | inline int cast_int(double u) {
  function cast_string_to_char (line 172) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 184) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 231) | bool cast_string_to_doubles(string &b, deque<int> & v) {
  function separate_strings (line 248) | bool separate_strings(string &b, deque<string> & v) {
  function approx (line 294) | double approx(double a, int digits) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 193) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 217) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 239) | int distribution_from_cumulative(const DD & cum, DD & distr) {
  function cumulative_from_distribution (line 252) | int cumulative_from_distribution(DD & cum, const DD & distr) {
  function poisson (line 267) | double poisson (int x, double mu) {
  function shuffle_and_set (line 277) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 298) | int shuffle_s(deque<T> &sq) {
  function shuffle_s (line 326) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 354) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 369) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 400) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function T (line 471) | T random_from_deque(deque<T> &sq)  {
  function random_from_set (line 477) | int random_from_set(set<int> & s) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/deque_numeric.cpp
  function argmax (line 25) | int argmax(DD & a) {
  function Euclidean_norm (line 43) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 58) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 73) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 97) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 123) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 146) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 156) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function deque_to_set (line 166) | void deque_to_set(const deque<double> & a, set<double> & s) {
  function deque_to_set (line 176) | void deque_to_set(const deque<int> & a, set<int> & s) {
  function deque_to_set_app (line 188) | void deque_to_set_app(const deque<int> & a, set<int> & s) {
  function norm_one (line 200) | double norm_one(const deque<double> & a) {
  function normalize_one (line 215) | int normalize_one(deque<double> & a) {
  function jaccard (line 235) | double jaccard(set<int> & a1,  set<int> & a2) {
  function norm_two (line 256) | double norm_two(const deque<double> & a) {
  function normalize_two (line 267) | int normalize_two(deque<double> & a) {
  function diff_norm_two (line 279) | double diff_norm_two(DD & a, DD & b) {
  function diff_norm_one (line 289) | double diff_norm_one(DD & a, DD & b) {
  function diff_norm_one (line 298) | double diff_norm_one(deque<DD> & a, deque<DD> & b) {
  function dot_product (line 305) | double dot_product(DD & a, DD & b) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/histograms.cpp
  function intlog_binning (line 10) | int intlog_binning(deque<int> c, int number_of_bins, deque<double> & Xs,...
  function intlog_binning (line 126) | void intlog_binning(deque<int> c, int number_of_bins, string file) {
  function xybinning (line 148) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning (line 256) | int xybinning(deque<type> &c, deque<type> &d, int number_of_bins, deque<...
  function xybinning_and_plot (line 267) | int xybinning_and_plot(deque<type> &c, deque<type> &d, int number_of_bin...
  function compute_quantiles (line 282) | void compute_quantiles(double q, deque<double> & y, deque<double> & qs) {
  function xybinning_quantiles (line 308) | int xybinning_quantiles(deque<type> &c, deque<type> &d, int number_of_bi...
  function log_histogram (line 435) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function print_quantiles (line 532) | void print_quantiles(ostream & pout, DD & css, DD & pvalues) {
  function log_histogram_quantiles (line 553) | int log_histogram_quantiles(deque<double> &c, deque<double> &c2, ostream...
  function log_histogram (line 657) | int log_histogram(deque<double> &c, deque<double> &c2, ostream & out, in...
  function histogram (line 740) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 841) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 944) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 1045) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 1145) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function histogram (line 1236) | int histogram (deque<double> &c, deque<double> &c2, ostream & out, int n...
  function not_norm_histogram (line 1338) | int not_norm_histogram (deque<double> &c, deque<double> &c2, ostream & o...
  function int_histogram (line 1439) | void int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 1468) | void int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 1497) | void int_histogram(int c, map<int, int> & hist) {
  function int_histogram (line 1512) | void int_histogram(int c, map<int, double> & hist, double w) {
  function print_cumulative (line 1527) | int print_cumulative (deque<double> & kws, string file, int number_of_st...
  function print_cumulative (line 1544) | int print_cumulative (deque<int> & kws, string file, int number_of_step) {
  function print_cumulative (line 1570) | int print_cumulative (vector<double> & kws, string file, int number_of_s...
  function print_cumulative (line 1597) | int print_cumulative (vector<int> & kws, string file, int number_of_step) {
  function int_histogram (line 1627) | void int_histogram(string infile, string outfile) {
  function int_histogram (line 1654) | void int_histogram(int c, map<int, int> & hist, int w) {
  function int_histogram (line 1669) | void int_histogram(const int & c, map<int, pair<int, double> >  & hist, ...
  function int_histogram (line 1688) | void int_histogram(int c, map<int, pair<double, double> > & hist, double...
  function int_histogram (line 1709) | void int_histogram(int c, map<int, pair<int, int> > & hist, int w1, int ...
  function int_histogram (line 1727) | void int_histogram(int c, double w, map<int, DD> & hist) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/map_utilities.cpp
  function argmax (line 3) | int argmax(mapid & topic_distr) {
  function compute_biggest_key (line 19) | int compute_biggest_key(mapid & m) {
  function get_best_of (line 29) | int get_best_of(mapid & a) {
  function update_mapid (line 46) | inline void update_mapid(mapid & m, const int & key, double value) {
  function get_from_mapid (line 59) | inline double get_from_mapid(const mapid & m, int key) {
  function check_mapid (line 74) | void check_mapid(mapid & a, mapid & b, string error_message) {
  function normalize_mapid (line 89) | double normalize_mapid(mapid & a) {
  function sum_mapid (line 104) | double sum_mapid(mapid & a) {
  function check_distr_equal (line 113) | void check_distr_equal(mapid & distr1, mapii & distr2) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y (line 212) | double H_x_given_y(deque<deque<int> > &en, deque<deque<int> > &ten, int ...
  function mutual2 (line 322) | double mutual2(deque<deque<int> > en, deque<deque<int> > ten) {
  function H_x_given_y3 (line 413) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 543) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {
  function c_nodes_jacc (line 612) | double c_nodes_jacc(int_matrix & ten, int_matrix & en, int dim) {
  function c_nodes (line 666) | int c_nodes(int_matrix & ten, int_matrix & en, int dim) {
  function correctly_classified_nodes (line 704) | double correctly_classified_nodes(deque<deque<int> > en, deque<deque<int...
  function new_labels (line 965) | int new_labels(deque<deque<int> > & a, map<int, int> & Alabels) {
  function old_labels (line 984) | int old_labels(deque<deque<int> > & a, map<int, int> & Alabels) {
  function set_membership (line 1001) | int set_membership(deque<deque<int> > & a, deque<vector<int> > & mem, in...
  function compute_relations (line 1030) | int compute_relations(deque<deque<int> >  a, deque<deque<int> >  b) {
  function best_match (line 1104) | double best_match(deque<deque<int> >  a, deque<deque<int> >  b, string o...
  function mutual_fast (line 1178) | pair<double, double> mutual_fast(int_matrix a, int_matrix b) {
  function H_entropy_partition (line 1235) | double H_entropy_partition(int_matrix A) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/pajek.cpp
  function number_together (line 4) | int number_together(deque<int> & a) {
  function get_partition_from_file_list_pajek (line 36) | int get_partition_from_file_list_pajek(string s, deque<deque<int> > & te...
  function set_partition_from_list (line 90) | void set_partition_from_list(deque<int> & mems, deque<deque<int> > & ten) {
  function get_partition_from_file_list_pajek_tree (line 129) | int get_partition_from_file_list_pajek_tree(string s, deque<deque<deque<...
  function pajek_format (line 228) | int pajek_format(string filename, bool directed) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/partition.cpp
  function get_partition_from_file_tp_format_with_homeless (line 52) | int get_partition_from_file_tp_format_with_homeless(string S, deque<dequ...
  function get_partition_from_file_tp_format (line 99) | int get_partition_from_file_tp_format(string S, map<int, deque<int> > & ...
  function get_partition_from_file_tp_format (line 141) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 202) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M, ...
  function get_partition_from_file_tp_format (line 240) | int get_partition_from_file_tp_format(string S, deque<deque<int> > & M) {
  function get_partition_from_file (line 246) | int get_partition_from_file(string s, deque<deque<int> > & M, int min) {
  function get_partition_from_file (line 277) | void get_partition_from_file(string s, deque<deque<double> > & M) {
  function get_partition_from_file (line 293) | int get_partition_from_file(string s, deque<deque<int> > & M) {
  function get_partition_from_file_list (line 299) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {
  function set_partition_from_memberships (line 354) | void set_partition_from_memberships(DI & node_community, int_matrix & B) {
  function print_tree_format (line 381) | int print_tree_format(deque<int_matrix> & ten, ostream & po) {
  function take_common_elements (line 431) | void take_common_elements(int_matrix & en, int_matrix & ten, int & dim, ...

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function prints (line 109) | void prints(map <uno, due> &sq) {
  function prints (line 122) | void prints(multimap <uno, due> &sq) {
  function prints (line 136) | void prints(deque<uno> & a, deque<due> &b) {
  function prints (line 144) | void prints(deque<uno> & a, deque<due> &b, ostream &out) {
  function prints (line 153) | void prints(Seq &sq) {
  function prints (line 166) | void prints(const deque<type> & sq) {
  function prints (line 176) | void prints(const vector<type> & sq) {
  function printm (line 189) | void printm(deque<type> & M, ostream & pout) {
  function printm (line 195) | void printm(deque<type> & M) {
  function printm (line 201) | void printm(vector<type> & M) {
  function get_data_from_file (line 214) | void get_data_from_file(string s, deque<type> & a1, int col) {
  function get_data_from_file (line 246) | void get_data_from_file(string s, deque<type> & a1) {
  function get_data_from_file (line 255) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2, in...
  function get_data_from_file (line 292) | void get_data_from_file(string s, deque<type> & a1, deque<type> & a2) {
  function get_data_from_file_string (line 302) | void get_data_from_file_string(string s, deque<string> & a1, int col) {
  function check_if_file_exists (line 335) | bool check_if_file_exists(string netfile) {			/* check if file_name exis...

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: Metrics/MultiplexNMI-Benchmark/MultiplexNMI/standard_package/tabdeg.cpp
  class tabdeg (line 23) | class tabdeg {
    method tabdeg (line 28) | tabdeg(){}
    method size (line 35) | int size() {return nodes_indeg.size();}
  function main (line 155) | int main() {

FILE: Metrics/analyze_algo_quality.py
  function get_graph_info (line 6) | def get_graph_info(file_path):
  function get_community_result (line 18) | def get_community_result(file_path):
  function print_comm (line 35) | def print_comm(comm_list):

FILE: Metrics/metrics/link_belong_modularity.py
  class FuncTag (line 7) | class FuncTag:
    method __init__ (line 8) | def __init__(self):
  function get_coefficient_func (line 17) | def get_coefficient_func(tag):
  function cal_modularity (line 28) | def cal_modularity(input_graph, comm_result):
  class LinkBelongModularity (line 33) | class LinkBelongModularity:
    method __init__ (line 36) | def __init__(self, input_graph, comm_result, coefficient_func):
    method calculate_modularity (line 67) | def calculate_modularity(self):

FILE: Metrics/metrics/omega_idx.py
  function calc_omega_idx (line 1) | def calc_omega_idx(num_vertices, result_comm_list, ground_truth_comm_list):
  class OmegaIdx (line 5) | class OmegaIdx:
    method __init__ (line 6) | def __init__(self, num_vertices, result_comm_list, ground_truth_comm_l...
    method calculate_omega_idx (line 11) | def calculate_omega_idx(self):

FILE: Metrics/metrics/overlap_nmi.py
  function calc_overlap_nmi (line 5) | def calc_overlap_nmi(num_vertices, result_comm_list, ground_truth_comm_l...
  class OverlapNMI (line 9) | class OverlapNMI:
    method entropy (line 11) | def entropy(num):
    method __init__ (line 14) | def __init__(self, num_vertices, result_comm_list, ground_truth_comm_l...
    method calculate_overlap_nmi (line 19) | def calculate_overlap_nmi(self):

FILE: Metrics/metrics/util.py
  function get_graph_info (line 5) | def get_graph_info(file_path):

FILE: Metrics/mutual3/mutual3.cpp
  function main (line 8) | int main(int argc, char * argv[]) {

FILE: Metrics/mutual3/standard_package/cast.cpp
  function cast_string_to_double (line 136) | double cast_string_to_double(string &b) {
  function cast_int (line 146) | int cast_int(double u) {
  function cast_string_to_char (line 157) | int cast_string_to_char(string file_name, char *b) {
  function cast_string_to_doubles (line 169) | bool cast_string_to_doubles(string &b, deque<double> & v) {
  function cast_string_to_doubles (line 217) | bool cast_string_to_doubles(string &b, deque<int> & v) {

FILE: Metrics/mutual3/standard_package/combinatorics.cpp
  function average_func (line 8) | double average_func(Seq &sq) {
  function variance_func (line 27) | double variance_func(Seq &sq) {
  function average_pf (line 61) | double average_pf(Seq &sq) {
  function variance_pf (line 83) | double variance_pf(Seq &sq) {
  function log_factorial (line 116) | double log_factorial (int num) {
  function log_combination (line 130) | double log_combination (int n, int k) {
  function binomial (line 153) | double binomial(int n, int x, double p) {		//	returns the binomial distr...
  function binomial_cumulative (line 191) | int binomial_cumulative(int n, double p, deque<double> &cum) {
  function powerlaw (line 215) | int powerlaw (int n, int min, double tau, deque<double> &cumulative) {
  function distribution_from_cumulative (line 238) | int distribution_from_cumulative(const deque<double> &cum, deque<double>...
  function cumulative_from_distribution (line 255) | int cumulative_from_distribution (deque<double> &cum, const deque<double...
  function poisson (line 271) | double poisson (int x, double mu) {
  function shuffle_and_set (line 281) | int shuffle_and_set(int *due, int dim) {		// it sets due as a random seq...
  function shuffle_s (line 302) | int shuffle_s(C<T> &sq) {
  function shuffle_s (line 331) | int shuffle_s(type_ *a, int b) {
  function compute_r (line 359) | double compute_r(int x, int k, int kout, int m) {
  function add_factors (line 374) | int add_factors (deque<double> & num, deque<double> &den, int  n, int k) {
  function compute_hypergeometric (line 405) | double compute_hypergeometric(int i, int k, int kout, int m) {
  function compute_self_links (line 460) | double compute_self_links(int k, int n, int x) {

FILE: Metrics/mutual3/standard_package/deque_numeric.cpp
  function Euclidean_norm (line 23) | double Euclidean_norm(const deque<double> & a) {
  function Euclidean_normalize (line 38) | int Euclidean_normalize(deque<double> & a) {
  function scalar_product (line 53) | double scalar_product(deque<double> & a, deque<double> & b) {
  function orthogonalize (line 77) | int orthogonalize(deque<double> & a, deque<deque<double> > & M) {
  function matrix_time_vector (line 103) | int matrix_time_vector(deque<deque<double> > & Q, deque<double> & v, deq...
  function set_to_deque (line 126) | void set_to_deque(const set<int> & s, deque<int> & a) {
  function set_to_deque (line 136) | void set_to_deque(const set<double> & s, deque<double> & a) {
  function norm_one (line 146) | double norm_one(const deque<double> & a) {
  function normalize_one (line 161) | int normalize_one(deque<double> & a) {

FILE: Metrics/mutual3/standard_package/histograms.cpp
  function log_histogram (line 15) | int log_histogram(deque<type> &c, ostream & out, int number_of_bins) {		...
  function histogram (line 116) | int histogram (vector <type> &c, ostream & out, int number_of_bins, doub...
  function not_norm_histogram_correlated (line 217) | int not_norm_histogram_correlated (deque<type> &c, deque<type> &d, ostre...
  function histogram (line 320) | int histogram (deque <type> &c, ostream & out, int number_of_bins, doubl...
  function not_norm_histogram (line 419) | int not_norm_histogram (vector<type> &c, ostream & out, int number_of_bi...
  function not_norm_histogram (line 519) | int not_norm_histogram (deque<type> &c, ostream & out, int number_of_bin...
  function int_histogram (line 616) | int int_histogram (vector <int> &c, ostream & out) {
  function int_histogram (line 645) | int int_histogram (deque <int> &c, ostream & out) {
  function int_histogram (line 674) | int int_histogram(int c, map<int, int> & hist) {

FILE: Metrics/mutual3/standard_package/mutual.cpp
  function mutual (line 40) | double mutual (deque<deque<int> > en, deque<deque<int> > ten) {
  function H (line 189) | double H(double a) {
  function H (line 200) | double H(deque <double> &p) {
  function H_x_given_y3 (line 213) | double H_x_given_y3(deque<deque<int> > &en, deque<deque<int> > &ten, int...
  function mutual3 (line 342) | double mutual3(deque<deque<int> > en, deque<deque<int> > ten) {

FILE: Metrics/mutual3/standard_package/partition.cpp
  function get_partition_from_file_list (line 38) | int get_partition_from_file_list(string s, deque<deque<int> > & ten) {

FILE: Metrics/mutual3/standard_package/print.cpp
  function cherr (line 15) | void cherr(double a) {
  function cherr (line 24) | void cherr(double a, double ee) {
  function prints (line 38) | void prints(pair <uno, due> &sq,  ostream &out) {
  function prints (line 46) | void prints(pair <uno, due> &sq) {
  function prints (line 54) | void prints(map <uno, due> &sq,  ostream &out) {
  function prints (line 67) | void prints(multimap <uno, due> &sq,  ostream &out) {
  function prints (line 82) | void prints(Seq &sq, ostream &out) {
  function prints (line 94) | void prints(type_ *a, int b) {
  function printm (line 105) | void printm(C<T>& c, ostream &out) {
  function prints (line 120) | void prints(map <uno, due> &sq) {
  function prints (line 133) | void prints(multimap <uno, due> &sq) {
  function prints (line 148) | void prints(Seq &sq) {
  function prints (line 161) | void prints(const deque<type> & sq) {
  function prints (line 171) | void prints(const vector<type> & sq) {
  function printm (line 184) | void printm(deque<type> & M) {
  function printm (line 194) | void printm(vector<type> & M) {

FILE: Metrics/mutual3/standard_package/random.cpp
  function ran2 (line 24) | double ran2(long *idum) {
  function ran4 (line 60) | double ran4(bool t, long s) {
  function ran4 (line 77) | double ran4() {
  function srand4 (line 83) | void srand4(void) {
  function srand5 (line 92) | void srand5(int rank) {
  function irand (line 101) | int irand(int n) {
  function srand_file (line 108) | void srand_file(void) {
  function configuration_model (line 132) | int configuration_model(deque<set<int> > & en, deque<int> & degrees) {

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/cat.c
  function mcxstatus (line 34) | mcxstatus mclxCatPush
  function mcxstatus (line 94) | mcxstatus mclxCatTransposeAll
  function mclxCatInit (line 108) | void mclxCatInit
  function mcxstatus (line 118) | mcxstatus mclxCatConify
  function mcxstatus (line 144) | mcxstatus mclxCatUnconify
  function mcxstatus (line 174) | mcxstatus mclxCBdomTree
  function mcxstatus (line 186) | mcxstatus mclxCBdomStack
  function mcxstatus (line 198) | mcxstatus mclxCatUnaryCheck
  function mclxCatReverse (line 239) | void mclxCatReverse
  function mcxstatus (line 251) | mcxstatus mclxCatWrite
  type newicky (line 271) | struct newicky
  type newicky (line 280) | struct newicky
  function compute_branch_length (line 293) | static void compute_branch_length
  function compute_trivial_count (line 318) | static void compute_trivial_count
  function compute_branch_factors (line 336) | void compute_branch_factors
  function mcxTing (line 429) | mcxTing* mclxCatNewick
  function mcxstatus (line 597) | mcxstatus mclxCatRead
  function mclx (line 783) | mclx*  clmContingency
  function dim (line 795) | dim clmStats
  function clm_cut_overlap (line 829) | static void clm_cut_overlap
  function clm_split_overlap (line 851) | static void clm_split_overlap
  function dim (line 941) | dim clmEnstrict
  function cmp_annot_ssq (line 1006) | static int cmp_annot_ssq
  function cmp_annot_ssq_rev (line 1021) | static int cmp_annot_ssq_rev
  function mclxCatSortCoarseFirst (line 1029) | void mclxCatSortCoarseFirst
  function mclxCatSortCoarseLast (line 1036) | void mclxCatSortCoarseLast

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/cat.h
  type mclxAnnot (line 31) | typedef struct
  type mclxCat (line 44) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/claw.c
  function clm_dump_line (line 29) | static void clm_dump_line
  function clmDumpNodeScores (line 82) | void clmDumpNodeScores
  function set_cl_to_projection (line 158) | static void set_cl_to_projection
  function prune_el_on_cl (line 180) | static void prune_el_on_cl
  function clmCastActors (line 212) | void clmCastActors
  function dim (line 239) | static dim clm_clm_adjust
  function dim (line 480) | dim clmAdjust
  function dim (line 609) | static dim clm_clm_prune
  function dim (line 737) | dim clmAssimilate

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/clm.c
  function mclx (line 47) | mclx* clmProject
  function clmLogVariance (line 69) | double clmLogVariance
  function clmVIDistance (line 87) | void clmVIDistance
  function dim (line 154) | dim clmSJDistance
  function mclx (line 218) | mclx* clmMeet
  function clmMKDistance (line 269) | void clmMKDistance
  function mcxstatus (line 308) | mcxstatus clmGranularity
  function clmGranularityPrint (line 356) | void clmGranularityPrint
  function clmPerformancePrint (line 382) | void clmPerformancePrint
  function mcxstatus (line 398) | mcxstatus clmXPerformance
  function mcxstatus (line 601) | mcxstatus clmPerformance
  function mclx (line 633) | mclx* clmComponents
  function mclx (line 646) | mclx* clmUGraphComponents

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/clm.h
  type clmPerformanceTable (line 25) | typedef struct
  type clmGranularityTable (line 120) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/scan.c
  function clmVScan (line 25) | void clmVScan
  function clmVScoreCoverage (line 134) | void clmVScoreCoverage
  function clmXScanInit (line 167) | void clmXScanInit
  function clmXScanDomain (line 190) | void clmXScanDomain
  function clmXScanDomainSet (line 249) | void clmXScanDomainSet
  function clmXScoreCoverage (line 267) | void clmXScoreCoverage
  function clmCoverage (line 285) | double clmCoverage

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/clew/scan.h
  type clmVScore (line 65) | typedef struct
  type clmXScore (line 84) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/gryphon/path.c
  function mclgSSPxyFree (line 31) | void mclgSSPxyFree
  function SSPxy (line 42) | SSPxy* mclgSSPxyNew
  function mclgSSPxyReset (line 75) | void mclgSSPxyReset
  function sspxy_dump_aow_unused (line 92) | static void sspxy_dump_aow_unused
  function sspxy_flood (line 112) | static void sspxy_flood
  function sspx_make_vector (line 204) | static void sspx_make_vector
  function sspxy_rm_dead_ends (line 223) | static void sspxy_rm_dead_ends
  function mcxstatus (line 304) | static mcxstatus sspxy_make_pathmx
  function mcxstatus (line 377) | mcxstatus mclgSSPxyQuery
  function mclv (line 424) | mclv* mclgSSPd
  function mclnCLCF (line 465) | double mclnCLCF
  function clcf_dispatch (line 505) | static void clcf_dispatch
  function mclv (line 516) | mclv* mclgCLCFdispatch
  function dim (line 532) | dim mclgEcc
  function dim (line 540) | dim mclgEcc2

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/gryphon/path.h
  type SSPxy (line 25) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/app.c
  function app_report_version (line 21) | void app_report_version
  function mclxSetBinaryIO (line 37) | void mclxSetBinaryIO
  function mclxSetInterchangeIO (line 46) | void mclxSetInterchangeIO
  function mclx_app_init (line 55) | void mclx_app_init
  function dim (line 66) | dim mclx_set_threads_or_die

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/compose.c
  type mclIOV (line 23) | struct mclIOV
  type mclxComposeHelper (line 42) | struct mclxComposeHelper
  function mclxComposeSetThreadCount (line 61) | int mclxComposeSetThreadCount
  function mclxComposeHelper (line 74) | mclxComposeHelper* mclxComposePrepare
  function mclxComposeRelease (line 101) | void mclxComposeRelease
  function mclVector (line 116) | mclVector* mclxVectorCompose
  type compose_data (line 205) | struct compose_data
  function compose_thread (line 216) | void compose_thread
  function mclMatrix (line 230) | mclMatrix* mclxCompose

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/compose.h
  type mclxComposeHelper (line 16) | typedef struct mclxComposeHelper mclxComposeHelper;
  type mclIOV (line 17) | typedef struct mclIOV mclIOV;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/edge.c
  function mclv (line 17) | mclv* mclgUnionv
  function mclv (line 28) | mclv* mclgUnionv2
  function mcxstatus (line 115) | mcxstatus mclgEdgeInc
  function mcxstatus (line 137) | mcxstatus mclgEdgeIterInit
  function select_highest_dispatch (line 148) | static void select_highest_dispatch
  function mclgKNNdispatch (line 158) | void mclgKNNdispatch
  function mclgKNN (line 191) | void mclgKNN
  function mclgKNNmerge (line 200) | void mclgKNNmerge

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/edge.h
  type mclgEdgeIter (line 110) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/io.c
  type mclxIOinfo (line 161) | typedef struct
  function loop_adjust_discard (line 174) | static double loop_adjust_discard
  function loop_adjust_force (line 183) | static double loop_adjust_force
  function mclxIOinfoFree (line 194) | void mclxIOinfoFree
  function mcxstatus (line 203) | mcxstatus mclxIOinfoReset
  function mclxIOformat (line 217) | int mclxIOformat
  function mclxIOinfo (line 228) | mclxIOinfo* mclxIOinfofy
  function tell_read_native (line 250) | static void tell_read_native
  function tell_wrote_native (line 266) | static void tell_wrote_native
  function get_env_flags (line 284) | unsigned long get_env_flags
  function get_quad_mode (line 295) | unsigned long get_quad_mode
  function mcxbool (line 338) | mcxbool mclxIOgetQMode
  function get_interchange_digits (line 350) | int get_interchange_digits
  function mcxstatus (line 377) | mcxstatus mclxReadDimensions
  function mcxstatus (line 436) | mcxstatus mclxReadDomains
  function mclx (line 472) | static mclx* mclxReadBody
  function mclx (line 489) | mclx* mclxReadSkeleton
  function mclx (line 521) | mclx* mclxSubRead
  function mclx (line 531) | mclx* mclxSubReadx
  function mcxstatus (line 594) | mcxstatus mclIOvcheck
  function mclx (line 650) | static mclx* mclxb_read_body_all
  function mcxstatus (line 891) | static mcxstatus mclxb_read_dompart
  function mcxstatus (line 1048) | static mcxstatus mclxa_read_dimpart
  function mcxstatus (line 1116) | static mcxstatus mclxa_parse_dompart
  function mcxstatus (line 1186) | static mcxstatus mclxa_read_dompart
  function mclx (line 1244) | static mclx* mclxa_read_body
  function mcxstatus (line 1323) | mcxstatus mclxTaggedWrite
  function mclva_dump (line 1391) | static void mclva_dump
  function mclxa_write_header (line 1461) | static void mclxa_write_header
  function mcxstatus (line 1518) | mcxstatus mclvWrite
  function mcxstatus (line 1538) | mcxstatus mclxWrite
  function mcxstatus (line 1552) | mcxstatus mclxaWrite
  function mcxPrettyPrint (line 1611) | void mcxPrettyPrint
  function mclxBoolPrint (line 1653) | void mclxBoolPrint
  function report_vector_size (line 1690) | static void report_vector_size
  function mcxstatus (line 1708) | mcxstatus mclvEmbedRead
  function mclpAR (line 1761) | mclpAR* mclpReaDaList
  function mcxstatus (line 1848) | static mcxstatus mclxa_readavec
  function mcxstatus (line 1878) | mcxstatus mclvEmbedWrite
  function mcxstatus (line 1905) | mcxstatus mclvbWrite
  function mcxstatus (line 1927) | static mcxstatus mclxa_parse_domain
  function mcxstatus (line 1961) | static mcxstatus mclxa_parse_dimpart
  function mclx (line 1996) | mclx* mclxReadx
  function mclx (line 2005) | mclx* mclxRead
  function mclFlowPrettyPrint (line 2013) | void mclFlowPrettyPrint
  function mclvaWrite (line 2029) | void mclvaWrite
  function mclpAR (line 2045) | mclpAR *mclpaReadRaw
  function mclv (line 2060) | mclv* mclvaReadRaw
  function mcxstatus (line 2093) | mcxstatus mclxaSubReadRaw
  function mclvaDump (line 2251) | void mclvaDump
  function mclxIOdumpSet (line 2306) | void mclxIOdumpSet
  function dump_label (line 2330) | static void dump_label
  function mcxstatus (line 2347) | mcxstatus mclxIOdump
  function mclxDebug (line 2551) | void mclxDebug

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/io.h
  type mclxIOdumper (line 358) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/ivp.c
  function mclIvp (line 27) | mclIvp* mclpInstantiate
  function mclpAR (line 42) | mclpAR* mclpARinit
  function mclpARreset (line 60) | void mclpARreset
  function mclpAR (line 75) | mclpAR* mclpARensure
  function mclpAR (line 101) | mclpAR* mclpARfromIvps
  function mclpARfree (line 116) | void mclpARfree
  function mcxbool (line 127) | mcxbool mclpARbatchCheck
  function mcxstatus (line 154) | mcxstatus mclpARextend
  function mcxbool (line 192) | mcxbool mclpGivenValGQ
  function mcxbool (line 203) | mcxbool mclpGivenValLQ
  function mclpIdxGeq (line 214) | int mclpIdxGeq
  function mclpIdxCmp (line 222) | int mclpIdxCmp
  function mclpIdxRevCmp (line 231) | int mclpIdxRevCmp
  function mclpValCmp (line 240) | int mclpValCmp
  function mclpValRevCmp (line 249) | int mclpValRevCmp
  function mclpMergeLeft (line 259) | void mclpMergeLeft
  function mclpMergeRight (line 267) | void mclpMergeRight
  function mclpMergeAdd (line 275) | void mclpMergeAdd
  function mclpMergeMin (line 283) | void mclpMergeMin
  function mclpMergeMax (line 291) | void mclpMergeMax
  function mclpMergeMul (line 299) | void mclpMergeMul
  function mclIvp (line 307) | mclIvp* mclpInit
  function mclIvp (line 321) | mclIvp* mclpCreate
  function mclpGetDouble (line 329) | double mclpGetDouble
  function mclpFree (line 336) | void mclpFree
  function mclpUnary (line 393) | double mclpUnary
  function mcxbool (line 423) | mcxbool mclpSelectIdcs
  function mcxbool (line 451) | mcxbool mclpSelectValues
  function mcleCmp (line 478) | int mcleCmp(const void* a, const void* b)
  function mcleSrcCmp (line 484) | int mcleSrcCmp(const void* a, const void* b)
  function mcleDstCmp (line 489) | int mcleDstCmp(const void* a, const void* b)

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/ivp.h
  type mclIvp (line 22) | typedef struct
  type mclpAR (line 152) | typedef struct
  type mclpVRange (line 214) | typedef struct
  type mclpIRange (line 228) | typedef struct
  type mclEdge (line 241) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/ivptypes.h
  type pval (line 18) | typedef  double pval;
  type pval (line 24) | typedef float pval;
  type pnum (line 36) | typedef  long  pnum;
  type pnum (line 41) | typedef  int  pnum;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/matrix.c
  function mcxbool (line 135) | static mcxbool is_identity_map
  function mclv (line 149) | mclv* mclxMapVectorPermute
  function mcxstatus (line 203) | mcxstatus mclxMapCols
  function mcxstatus (line 239) | mcxstatus  mclxMapRows
  function mcxbool (line 296) | mcxbool mclxMapTest
  function mclxInflate (line 313) | void mclxInflate
  function mclx (line 327) | mclx* mclxAllocClone
  function mclx (line 347) | mclx* mclxAllocZero
  function mclx (line 380) | mclx* mclxCartesian
  function mcxstatus (line 400) | static mcxstatus meet_the_joneses
  function mclx (line 441) | mclx*  mclxExtSub
  function mclxReduce (line 483) | void mclxReduce
  function mclx (line 500) | mclx*  mclxSub
  function dim (line 528) | dim mclxSelectLower
  function dim (line 540) | dim mclxSelectUpper
  function mclxSelectValues (line 552) | double mclxSelectValues
  function mclx (line 566) | mclx* mclxConstDiag
  function mclxScaleDiag (line 576) | void mclxScaleDiag
  function mclx (line 590) | mclx* mclxDiag
  function mclx (line 606) | mclx* mclxCopy
  function mclx_release (line 614) | static void mclx_release
  function mclxTransplant (line 630) | void mclxTransplant
  function mclxFree (line 643) | void mclxFree
  function mclxMakeStochastic (line 655) | void mclxMakeStochastic
  function mclv (line 668) | mclv* mclxColSelect
  type sparse_sel (line 686) | struct sparse_sel
  function sparse_sel_cb (line 693) | double sparse_sel_cb
  function mclv (line 706) | mclv* mclgUnlinkNodes
  function mclv (line 731) | mclv* mclgCeilNB
  function mclxUnary (line 790) | void mclxUnary
  function mclxAccommodate (line 804) | void mclxAccommodate
  function mclxChangeDomains (line 817) | void mclxChangeDomains
  function mclxChangeRDomain (line 829) | void mclxChangeRDomain
  function mclxChangeCDomain (line 844) | void mclxChangeCDomain
  function mclx (line 895) | mclx*  mclxBlocksC
  function mclx (line 931) | mclx*  mclxBlockUnion
  function mclx (line 957) | mclx*  mclxBlockPartition
  function mclx (line 1009) | mclx*  mclxBlockUnion2
  function mclxMerge (line 1035) | void mclxMerge
  function mclx (line 1100) | mclx* mclxCollectVectors
  function mclxAppendVectors (line 1114) | void mclxAppendVectors
  function mclxAugment (line 1131) | void mclxAugment
  function mclx (line 1170) | mclx* mclxBinary
  function ofs (line 1219) | ofs mclxGetVectorOffset
  function mclv (line 1235) | mclv* mclxGetNextVector
  function mclp (line 1271) | inline mclp* mclxInsertIvp
  function mclp (line 1284) | inline mclp* mclgArcAddto
  function mclp (line 1297) | inline mclp* mclgArcAdd
  function ofs (line 1310) | inline ofs mclgEdgeAddto
  function ofs (line 1324) | inline ofs mclgEdgeAdd
  function mclv (line 1339) | mclv* mclxGetVector
  function mclx (line 1396) | mclx* mclxMakeMap
  function mclx (line 1415) | mclx* mclxTranspose2
  function mclx (line 1484) | mclx* mclxTranspose
  function mclv (line 1491) | mclv* mclxRowSizes
  function mclv (line 1518) | mclv* mclxColNums
  function mclv (line 1539) | mclv* mclxDiagValues
  function mclv (line 1546) | mclv* mclxColSums
  function mclv (line 1553) | mclv* mclxPowColSums
  function mclxMass (line 1573) | double mclxMass
  function dim (line 1584) | dim mclxNrofEntries
  function mclxColumnsRealign (line 1595) | void  mclxColumnsRealign
  function mclxMaxValue (line 1606) | double mclxMaxValue
  function mclx (line 1615) | mclx* mclxIdentity
  function mclxZeroValues (line 1622) | void mclxZeroValues
  function mclxMakeCharacteristic (line 1631) | void mclxMakeCharacteristic
  function mclx (line 1639) | mclx* mclxMax
  function mclx (line 1647) | mclx* mclxMinus
  function mclx (line 1655) | mclx* mclxAdd
  function mclxMergeColumn (line 1663) | void mclxMergeColumn
  function mclxMergeTranspose (line 1694) | void mclxMergeTranspose
  function mclxMergeTranspose3 (line 1727) | void mclxMergeTranspose3
  function mclxAddTranspose (line 1761) | void mclxAddTranspose
  function mclx (line 1770) | mclx* mclxHadamard
  function mclxLoopCBset (line 1778) | double mclxLoopCBset
  function mclxLoopCBifEmpty (line 1787) | double mclxLoopCBifEmpty
  function mclxLoopCBremove (line 1796) | double mclxLoopCBremove
  function mclxLoopCBsum (line 1805) | double mclxLoopCBsum
  function mclxLoopCBmax (line 1817) | double mclxLoopCBmax
  function dim (line 1829) | dim mclxAdjustLoops
  function mclxScrub (line 1860) | void mclxScrub
  function dim (line 1882) | dim mclxUnaryList
  function sym_reduce_dispatch (line 1897) | static void sym_reduce_dispatch
  function mclxSymReduceDispatch (line 1914) | void mclxSymReduceDispatch
  function mclxSymReduce (line 1931) | void mclxSymReduce
  function mclxILS (line 1939) | void mclxILS
  type generic_arg (line 1968) | struct generic_arg
  type generic_arg (line 1984) | struct generic_arg
  function mcxstatus (line 2051) | mcxstatus mclxVectorDispatch
  function mcxstatus (line 2062) | mcxstatus mclxVectorDispatchGroup
  function mclv_sosq (line 2136) | static double mclv_sosq
  function mclxPerturb (line 2143) | void  mclxPerturb
  function dim (line 2185) | dim mclxQuantiles
  function mclxNormSelf (line 2201) | void mclxNormSelf
  function mclxFold (line 2216) | void mclxFold
  function ofs (line 2254) | ofs mclxGetClusterID

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/matrix.h
  type mclMatrix (line 54) | typedef struct
  type mclx_thread_map (line 674) | struct mclx_thread_map
  type mclx_thread_map (line 688) | struct mclx_thread_map
  type mclx_thread_map (line 699) | struct mclx_thread_map

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/pval.c
  function fltxConst (line 20) | double fltxConst
  function fltxGQ (line 28) | double fltxGQ
  function fltxGT (line 36) | double fltxGT
  function fltxLT (line 44) | double fltxLT
  function fltxPositive (line 52) | double fltxPositive
  function fltxLQ (line 60) | double fltxLQ
  function fltxCopy (line 68) | double fltxCopy
  function fltxScale (line 76) | double fltxScale
  function fltxMul (line 85) | double fltxMul
  function fltxRand (line 93) | double fltxRand
  function fltxAdd (line 102) | double fltxAdd
  function fltxPower (line 110) | double fltxPower
  function fltxLog (line 118) | double fltxLog
  function fltxAbs (line 134) | double fltxAbs
  function fltxNeglog (line 142) | double fltxNeglog
  function fltxExp (line 150) | double fltxExp
  function fltxCeil (line 162) | double fltxCeil
  function fltxFloor (line 170) | double fltxFloor
  function fltxAcos (line 178) | double fltxAcos
  function fltxPropagateMax (line 186) | double fltxPropagateMax
  function fltLeft (line 196) | double fltLeft
  function fltRight (line 204) | double fltRight
  function fltAdd (line 212) | double fltAdd
  function flt0p0 (line 220) | double flt0p0
  function flt0p5 (line 228) | double flt0p5
  function flt1p0 (line 236) | double flt1p0
  function flt1p5 (line 244) | double flt1p5
  function fltSubtract (line 252) | double fltSubtract
  function fltMultiply (line 260) | double fltMultiply
  function fltCross (line 268) | double fltCross
  function fltMin (line 276) | double fltMin
  function fltMax (line 284) | double fltMax
  function fltMinNZ (line 292) | double fltMinNZ
  function fltMaxNZ (line 300) | double fltMaxNZ
  function fltLoR (line 308) | double fltLoR
  function fltLaNR (line 316) | double fltLaNR
  function fltLaR (line 324) | double fltLaR
  function fltArcMaxGQ (line 333) | double fltArcMaxGQ(pval lft, pval rgt, pval arg) {  return lft >= arg ||...
  function fltArcMaxGT (line 334) | double fltArcMaxGT(pval lft, pval rgt, pval arg) {  return lft >  arg ||...
  function fltArcMaxLQ (line 335) | double fltArcMaxLQ(pval lft, pval rgt, pval arg) {  return lft <= arg ||...
  function fltArcMaxLT (line 336) | double fltArcMaxLT(pval lft, pval rgt, pval arg) {  return lft <  arg ||...
  function fltArcMinGQ (line 338) | double fltArcMinGQ(pval lft, pval rgt, pval arg) {  return lft >= arg &&...
  function fltArcMinGT (line 339) | double fltArcMinGT(pval lft, pval rgt, pval arg) {  return lft >  arg &&...
  function fltArcMinLQ (line 340) | double fltArcMinLQ(pval lft, pval rgt, pval arg) {  return lft <= arg &&...
  function fltArcMinLT (line 341) | double fltArcMinLT(pval lft, pval rgt, pval arg) {  return lft <  arg &&...
  function fltArcDiffGQ (line 343) | double fltArcDiffGQ(pval lft, pval rgt, pval arg) {  return lft - rgt >=...
  function fltArcDiffGT (line 344) | double fltArcDiffGT(pval lft, pval rgt, pval arg) {  return lft - rgt > ...
  function fltArcDiffLQ (line 345) | double fltArcDiffLQ(pval lft, pval rgt, pval arg) {  return lft - rgt <=...
  function fltArcDiffLT (line 346) | double fltArcDiffLT(pval lft, pval rgt, pval arg) {  return lft - rgt < ...
  function fltArcMax (line 349) | double fltArcMax

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/stream.c
  function mcxstatus (line 81) | static mcxstatus write_u32_be
  function mcxstatus (line 98) | static mcxstatus read_u32_be
  type etc_state (line 128) | typedef struct
  type map_state (line 138) | typedef struct
  type stream_state (line 147) | typedef struct
  function mcxstatus (line 177) | static mcxstatus handle_label
  function mcxstatus (line 239) | static mcxstatus read_etc
  function mcxstatus (line 479) | static mcxstatus read_abc
  function mcxstatus (line 612) | static mcxstatus read_123
  function mcxstatus (line 703) | static mcxstatus pars_realloc
  function stream_state_set_map (line 746) | static void stream_state_set_map
  function mclx (line 803) | static mclx* make_mx_from_pars
  function mclTab (line 875) | static mclTab* make_tab
  function free_pars (line 887) | static void free_pars
  function mclx (line 902) | mclx* mclxIOstreamIn

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/stream.h
  type mclxIOstreamer (line 74) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/tab.c
  function mclTabFree (line 30) | void mclTabFree
  function mclTab (line 53) | mclTab*   mclTabRead
  function mclTabHashSet (line 174) | void mclTabHashSet
  function mclx (line 187) | mclx* mclTabDuplicated
  function mcxHash (line 232) | mcxHash* mclTabHash
  function mclTab (line 273) | mclTab* mclTabFromMap
  function mcxstatus (line 344) | mcxstatus mclTabWriteDomain
  function mcxstatus (line 369) | mcxstatus mclTabWrite
  function mclTab (line 438) | mclTab* mclTabMap
  function mclTab (line 499) | static mclTab* mclTabAlloc
  function mclTab (line 513) | mclTab* mclTabSelect

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/tab.h
  type mclTab (line 25) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/vector.c
  function mclp (line 36) | static inline mclp* mclpBsearchCeil
  function mclp (line 70) | static inline mclp* mclpBsearchFloor
  function mclVector (line 115) | mclVector* mclvInit
  function mclVector (line 126) | mclVector* mclvInstantiate
  function mclVector (line 180) | mclVector* mclvNew
  function mclVector (line 188) | mclVector* mclvClone
  function mclVector (line 195) | mclVector* mclvCopy
  function mclvRelease (line 207) | void mclvRelease
  function mclvRelease_v (line 218) | void mclvRelease_v
  function mclvFree (line 225) | void mclvFree
  function mclvFree_v (line 236) | void mclvFree_v
  function mclVector (line 243) | mclVector* mclvRenew
  function mclVector (line 252) | mclVector*  mclvResize
  function mclvRuntime (line 260) | void mclvRuntime
  function mcxstatus (line 270) | mcxstatus mclvCheck
  function mclvIn (line 337) | double mclvIn
  function mclvSortUniq (line 360) | void mclvSortUniq
  function mclvSortDescVal (line 368) | void mclvSortDescVal
  function mclvSortAscVal (line 375) | void mclvSortAscVal
  function mclvSort (line 382) | void mclvSort
  function dim (line 394) | dim mclvUniqIdx
  function mclvKBar (line 414) | double mclvKBar
  function mclvSelectGqBar (line 520) | double mclvSelectGqBar
  function dim (line 545) | dim mclvCountGiven
  function dim (line 565) | dim mclvSelectIdcs
  function mclvSelectGtBar (line 582) | double mclvSelectGtBar
  function mclvSelectValues (line 590) | double mclvSelectValues
  function mclVector (line 607) | mclVector* mclvCopyGiven
  function mclvUnary (line 645) | void mclvUnary
  function dim (line 674) | static dim update_meet_small_large
  function dim (line 747) | static dim update_meet_zip
  function dim (line 772) | static dim update_meet_canonical
  function dim (line 795) | dim mclvUpdateMeet
  function dim (line 815) | static dim update_diff_zip
  function dim (line 850) | static dim update_diff_canonical
  function dim (line 881) | static dim update_diff_small_large
  function dim (line 927) | dim mclvUpdateDiff
  function mclVector (line 948) | mclVector* mclvBinaryx
  function mclVector (line 1029) | mclVector* mclvBinary
  function mclVector (line 1108) | mclVector* mclvMap
  function mclVector (line 1135) | mclVector* mclvCanonicalExtend
  function dim (line 1166) | dim mclvEmbed
  function mclVector (line 1195) | mclVector* mclvCanonicalEmbed
  function mclVector (line 1235) | mclVector* mclvRange
  function mclVector (line 1249) | mclVector* mclvCanonical
  function mclvScale (line 1268) | void mclvScale
  function mclvNormalize (line 1283) | double mclvNormalize
  function mclvInflate (line 1310) | double mclvInflate
  function mclvVal (line 1350) | double mclvVal
  function mclvSize (line 1357) | double mclvSize
  function mclvSelf (line 1364) | double mclvSelf
  function mclvSum (line 1371) | double mclvSum
  function mclvPowSum (line 1386) | double mclvPowSum
  function mclvNorm (line 1400) | double mclvNorm
  function ofs (line 1412) | ofs mclvGetIvpOffset
  function mclIvp (line 1428) | mclIvp* mclvGetIvpCeil
  function mclIvp (line 1444) | mclIvp* mclvGetIvpFloor
  function mclIvp (line 1459) | mclIvp* mclvGetIvp
  function mclvIdxVal (line 1477) | double mclvIdxVal
  function mcxstatus (line 1495) | mcxstatus mclvReplaceIdx
  function mclVector (line 1554) | mclVector* mclvInsertIvp
  function mclVector (line 1584) | inline mclVector* mclvInsertIdx
  function mclVector (line 1596) | inline mclVector* mclvAddtoIdx
  function mclvRemoveIdx (line 1608) | void mclvRemoveIdx
  function mclvVidCmp (line 1625) | int mclvVidCmp
  function mclvValCmp (line 1634) | int mclvValCmp
  function mclvValRevCmp (line 1643) | int mclvValRevCmp
  function mclvSizeRevCmp (line 1652) | int mclvSizeRevCmp
  function mclvSizeCmp (line 1664) | int mclvSizeCmp
  function mclvLexCmp (line 1672) | int mclvLexCmp
  function mclvSumCmp (line 1695) | int mclvSumCmp
  function mclvSumRevCmp (line 1704) | int mclvSumRevCmp
  function mclvSelectHighest (line 1712) | void mclvSelectHighest
  function mclvSelectHighestGQ (line 1732) | void mclvSelectHighestGQ
  function mclvSelectHighestGT (line 1750) | void mclvSelectHighestGT
  function mclvZeroValues (line 1768) | void mclvZeroValues
  function mclvMakeConstant (line 1779) | void mclvMakeConstant
  function mclvMakeCharacteristic (line 1790) | void mclvMakeCharacteristic
  function mclvHdp (line 1799) | void mclvHdp
  function mclVector (line 1807) | mclVector* mclvAdd
  function mclVector (line 1816) | mclVector* mcldMerge
  function mclVector (line 1829) | mclVector* mcldMinus
  function mclVector (line 1855) | mclVector* mcldMeet
  function mclVector (line 1866) | mclVector* mcldMeet2
  function mcxbool (line 1905) | mcxbool mcldEquate
  function dim (line 1954) | dim mcldCountSet
  function dim (line 1971) | dim mcldCountParts
  function mclv (line 2015) | mclv* mclvFromIvps
  function mclv (line 2030) | mclv* mclvFromPAR
  function mcxbool (line 2108) | mcxbool mcldIsCanonical
  function mclvHighestIdx (line 2120) | long mclvHighestIdx
  function mclvHasLoop (line 2130) | double mclvHasLoop
  function mclvMinValue (line 2138) | double mclvMinValue
  function mclvMaxValue (line 2153) | double mclvMaxValue
  function mclvUnaryList (line 2168) | long mclvUnaryList
  function mclvMean (line 2196) | void mclvMean
  function mclvAffine (line 2229) | void mclvAffine
  function mclvSprintf (line 2245) | void mclvSprintf

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/impala/vector.h
  type mclVector (line 43) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/alg.c
  type grade (line 138) | typedef struct grade
  function postprocess (line 644) | void postprocess
  function mcl_unshadow_matrix (line 791) | static void mcl_unshadow_matrix
  function mcl_unshadow (line 806) | static void mcl_unshadow
  function mcxstatus (line 833) | mcxstatus mclAlgorithm
  function mcxbool (line 958) | mcxbool set_bit
  function make_output_name (line 995) | void make_output_name
  function mcxstatus (line 1080) | mcxstatus mclAlgorithmInit
  function showSettings (line 1511) | void showSettings
  function mclAlgParam (line 1518) | static mclAlgParam* mclAlgParamNew
  function mclAlgParamFree (line 1611) | void mclAlgParamFree
  function mclAlgPrintInfo (line 1648) | void mclAlgPrintInfo
  function juryCharter (line 1684) | void juryCharter
  function mclWriteLog (line 1699) | void mclWriteLog
  function howMuchRam (line 1712) | void  howMuchRam
  function mclAlgOptionsInit (line 1734) | void mclAlgOptionsInit
  function mclx (line 1745) | static mclx* test_tab
  function mcl_add_nullsink (line 1774) | static void mcl_add_nullsink
  function mclx (line 1804) | static mclx* mclAlgorithmStreamIn
  function mclAlgorithmTransform (line 1856) | static int mclAlgorithmTransform
  function mcxstatus (line 1979) | static mcxstatus mclAlgorithmWriteGraph
  function mcxstatus (line 2006) | mcxstatus mclAlgorithmStart
  function mcxstatus (line 2148) | mcxstatus mclAlgInterface

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/alg.h
  type mclAlgParam (line 40) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/dpsd.c
  function mclMatrix (line 24) | mclMatrix* mclDiagOrdering

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/expand.c
  type vecbuffer (line 42) | typedef struct
  function vecbuffer (line 49) | static vecbuffer* vecbuffer_init
  function vecbuffer_free (line 64) | static void vecbuffer_free
  function matrix_vector_array (line 73) | static void matrix_vector_array
  function get_homg (line 143) | static double get_homg
  type mclExpandVectorLine_arg (line 156) | typedef struct
  function mclExpandParam (line 179) | mclExpandParam* mclExpandParamNew
  function mclExpandParamFree (line 216) | void mclExpandParamFree
  function compose_dispatch (line 227) | static void compose_dispatch
  function warn_pruning (line 273) | static void warn_pruning
  function mclExpandVector1 (line 297) | static double mclExpandVector1
  function mclMatrix (line 514) | mclMatrix* mclExpand
  function mclExpandStats (line 633) | mclExpandStats* mclExpandStatsNew
  function mclExpandStatsReset (line 652) | void mclExpandStatsReset
  function mclExpandStatsFree (line 668) | void mclExpandStatsFree
  function vecMeasure (line 684) | static void vecMeasure
  function mclExpandParamDim (line 708) | void mclExpandParamDim
  function cmp_pval (line 718) | static int cmp_pval
  function pval (line 802) | pval selectk
  function mclExpandVector2 (line 840) | static double mclExpandVector2
  function mclExpandVector (line 1058) | static double mclExpandVector

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/expand.h
  type mclExpandStats (line 32) | typedef struct
  type mclExpandParam (line 51) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/inflate.c
  type mclvInflateLine_arg (line 27) | typedef struct
  function mclxInflateBoss (line 37) | void mclxInflateBoss
  function mclvInflateLine (line 84) | void  mclvInflateLine

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/interpret.c
  function mclMatrix (line 42) | mclMatrix* mclDag
  function calc_depth (line 91) | static int calc_depth
  function mclDagTest (line 129) | int mclDagTest
  function mclv (line 160) | static mclv* get_closure
  function mclMatrix (line 179) | mclMatrix* mclInterpret
  function clusterMeasure (line 227) | void  clusterMeasure
  function mcxDiagnosticsAttractor (line 255) | void mcxDiagnosticsAttractor
  function mcxDiagnosticsPeriphery (line 291) | void mcxDiagnosticsPeriphery
  function mclVector (line 300) | mclVector*  mcxAttractivityScale
  function mclInterpretParamFree (line 326) | void mclInterpretParamFree
  function mclInterpretParam (line 336) | mclInterpretParam* mclInterpretParamNew

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/interpret.h
  type mclInterpretParam (line 15) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/proc.c
  function mclSigCatch (line 62) | void mclSigCatch
  function mclProcParam (line 70) | mclProcParam* mclProcParamNew
  function mclProcParamFree (line 116) | void mclProcParamFree
  function mclMatrix (line 128) | mclMatrix*  mclProcess
  function mclInflate (line 254) | void mclInflate
  function mclDumpMatrix (line 458) | void mclDumpMatrix
  function mclDumpVector (line 529) | void  mclDumpVector
  function mclProcPrintInfo (line 567) | void mclProcPrintInfo

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/proc.h
  type mclProcParam (line 25) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/procinit.c
  function mclSetProgress (line 309) | void  mclSetProgress
  function mcxstatus (line 325) | mcxstatus mclProcessInit
  function mclShowSchemes (line 637) | void mclShowSchemes
  function makeSettings (line 663) | void makeSettings
  function mclShowSettings (line 682) | void mclShowSettings
  function mclProcOptionsInit (line 794) | void mclProcOptionsInit

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/shadow.c
  function mclvMedian (line 25) | double mclvMedian
  function mclvAvg (line 42) | double mclvAvg
  function mclv (line 51) | mclv* mcl_shadow_matrix
  function mclv (line 110) | mclv* mcl_get_shadow_turtle_factors
  function mclv (line 275) | mclv* mcl_density_adjust

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/transform.c
  type mclg_transform (line 30) | struct mclg_transform
  function mclgTF (line 79) | mclgTF* mclgTFparse
  function mclg_tf_step (line 311) | static void mclg_tf_step
  function tf_ssq (line 328) | static void tf_ssq
  function tf_do_mcl (line 344) | static void tf_do_mcl
  function mclgTFgraph (line 388) | void mclgTFgraph
  function dim (line 440) | dim mclgTFexecx
  function dim (line 475) | dim mclgTFexec
  function mclgTFfree (line 483) | void mclgTFfree
  function mclpAR (line 494) | mclpAR* mclgTFgetEdgePar

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/mcl/transform.h
  type mclgTF (line 19) | typedef struct mclg_transform mclgTF;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clm.c
  function mcxstatus (line 183) | mcxstatus sharedArgHandle
  function main (line 269) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmadjust.c
  function mcxstatus (line 96) | static mcxstatus adjustInit
  function mcxstatus (line 109) | static mcxstatus adjustArgHandle
  function mcxstatus (line 153) | static mcxstatus adjustMain
  function mcxDispHook (line 252) | mcxDispHook* mcxDispHookAdjust

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmclose.c
  function mcxstatus (line 205) | static mcxstatus closeInit
  function mcxstatus (line 226) | static mcxstatus closeArgHandle
  function mclv_check_ccbound (line 328) | static double mclv_check_ccbound
  function mcxstatus (line 337) | static mcxstatus closeMain
  function mcxDispHook (line 546) | mcxDispHook* mcxDispHookClose

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmdag.c
  function main (line 42) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmdist.c
  function mclv_choose_sum (line 55) | static double mclv_choose_sum
  function mclx_choose_sum (line 72) | static double mclx_choose_sum
  function mcxstatus (line 213) | static mcxstatus distInit
  function mcxstatus (line 229) | static mcxstatus volInit
  function mcxstatus (line 243) | static mcxstatus volArgHandle
  function mcxstatus (line 266) | static mcxstatus distArgHandle
  function mcxstatus (line 335) | static mcxstatus distMain
  function mcxDispHook (line 567) | mcxDispHook* mcxDispHookDist
  function mcxDispHook (line 586) | mcxDispHook* mcxDispHookVol

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmformat.c
  function print_el_scores (line 288) | void print_el_scores
  function freenames (line 319) | void freenames
  function dodump (line 338) | void dodump
  function mclMatrix (line 455) | mclMatrix* mkclvals
  function clmVScore (line 487) | clmVScore* mkelvals
  function getclusid (line 503) | long getclusid
  function mkanindex (line 512) | void mkanindex
  function mkindex (line 616) | void mkindex
  function main (line 685) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmframe.c
  type treenode (line 201) | typedef struct treenode
  type cnode (line 215) | typedef struct
  type map_start (line 223) | typedef struct
  function treenode (line 264) | treenode* treenode_new
  function treenode_release (line 330) | void treenode_release
  function dim (line 342) | dim get_projection
  function mclv (line 368) | mclv* get_leaves_from_node
  function mclx (line 383) | mclx* frame_matrix
  function report_treenode (line 421) | void report_treenode
  function dim (line 464) | dim report_target_incidence
  function report_distance (line 490) | void report_distance
  function dim (line 506) | dim dump_dist
  function dump_state (line 527) | void dump_state
  function clean_up_most_globals (line 572) | void clean_up_most_globals
  function mcxLink (line 598) | mcxLink* fun_descend_tree_predict
  function report_target_list (line 635) | void report_target_list
  function report_treenode_list (line 647) | void report_treenode_list
  function init_map_target (line 659) | void init_map_target
  function fun_ascend_frame_update (line 693) | void fun_ascend_frame_update
  function fun_ascend_treenode_cmp (line 729) | int fun_ascend_treenode_cmp
  function init_whittle_frame (line 743) | void init_whittle_frame
  function mcxLink (line 794) | mcxLink* init_frame
  function mcxbool (line 845) | mcxbool not_in_skiplist
  function fun_ascend_target_predict (line 860) | void fun_ascend_target_predict     /* target onto tree */
  function fun_descend_target_predict (line 914) | void fun_descend_target_predict     /* target onto tree */
  function fun_ascend_state_update (line 983) | void fun_ascend_state_update
  function mcxLink (line 1090) | mcxLink* fun_descend_state_update
  function mcxLink (line 1208) | mcxLink* fun_ascend_tree_predict
  function fun_ascend_the_tree (line 1312) | void fun_ascend_the_tree
  function fun_descend_the_tree (line 1460) | void fun_descend_the_tree
  function main (line 1567) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmimac.c
  function mcxstatus (line 104) | static mcxstatus imacInit
  function mcxstatus (line 116) | static mcxstatus imacArgHandle
  function mcxstatus (line 170) | static mcxstatus imacMain
  function mcxDispHook (line 252) | mcxDispHook* mcxDispHookImac

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clminfo.c
  function mcxstatus (line 138) | static mcxstatus infoInit
  function mcxstatus (line 157) | static mcxstatus infoArgHandle
  function do_stack (line 220) | void do_stack
  function mcxstatus (line 255) | static mcxstatus infoMain
  function mcxDispHook (line 373) | mcxDispHook* mcxDispHookInfo

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clminfo2.c
  function mcxstatus (line 148) | static mcxstatus info2Init
  function mcxstatus (line 167) | static mcxstatus info2ArgHandle
  type info_bundle (line 232) | struct info_bundle
  function info_do (line 241) | double info_do
  function info_dispatch (line 257) | static void info_dispatch
  function mcxstatus (line 272) | static mcxstatus info2Main
  function mcxDispHook (line 382) | mcxDispHook* mcxDispHookInfo2

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmmate.c
  function mcxstatus (line 74) | static mcxstatus mateInit
  function mcxstatus (line 84) | static mcxstatus mateArgHandle
  function mcxstatus (line 112) | static mcxstatus mateMain
  function mcxDispHook (line 197) | mcxDispHook* mcxDispHookMate

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmmeet.c
  function mcxstatus (line 55) | static mcxstatus meetInit
  function mcxstatus (line 63) | static mcxstatus meetArgHandle
  function mcxstatus (line 81) | static mcxstatus meetMain
  function mcxDispHook (line 160) | mcxDispHook* mcxDispHookMeet

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmoptics.c
  function mcxstatus (line 144) | static mcxstatus opticsInit
  function mcxstatus (line 161) | static mcxstatus opticsArgHandle
  function reverse_range (line 231) | static double reverse_range
  function cmp_double (line 238) | static int cmp_double(const void* d, const void* e)
  function mclv (line 262) | mclv* init_reachability
  function mclv (line 285) | mclv* get_coredistance
  function test_heap (line 346) | void test_heap
  function heap_update_node (line 360) | void heap_update_node
  function heap_refresh_root (line 387) | void heap_refresh_root
  function do_optics (line 430) | void do_optics
  function mcxstatus (line 658) | static mcxstatus opticsMain
  function mcxDispHook (line 706) | mcxDispHook* mcxDispHookOptics

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmorder.c
  function mcxstatus (line 95) | static mcxstatus orderInit
  function mcxstatus (line 105) | static mcxstatus stableInit
  function mcxstatus (line 115) | static mcxstatus orderArgHandle
  function mcxstatus (line 139) | static mcxstatus stableArgHandle
  function report_sizes (line 169) | static void report_sizes
  function stable_dump_clustering (line 178) | static void stable_dump_clustering
  function extend_result (line 200) | static void extend_result
  function mcxstatus (line 217) | static mcxstatus orderMain
  function mcxstatus (line 400) | static mcxstatus rerank
  function mcxDispHook (line 462) | mcxDispHook* mcxDispHookOrder
  function mcxDispHook (line 481) | mcxDispHook* mcxDispHookStable

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmps.c
  function kvcmp (line 218) | int kvcmp
  function write_defs (line 295) | void write_defs
  function write_params (line 307) | void write_params
  function list_params (line 336) | void list_params
  function mcxstatus (line 347) | static mcxstatus set_param
  function mcxstatus (line 381) | static mcxstatus PSInit
  function mcxstatus (line 411) | static mcxstatus PSArgHandle
  function mcxstatus (line 540) | static mcxstatus PSMain
  function mcxDispHook (line 762) | mcxDispHook* mcxDispHookPS

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/clmresidue.c
  function mcxstatus (line 93) | static mcxstatus residueInit
  function mcxstatus (line 104) | static mcxstatus residueArgHandle
  function mcxstatus (line 137) | static mcxstatus residueMain
  function mcxDispHook (line 246) | mcxDispHook* mcxDispHookResidue
  function mcxstatus (line 282) | static mcxstatus enstrictArgHandle
  function mcxstatus (line 303) | static mcxstatus enstrictInit
  function mcxstatus (line 312) | static mcxstatus enstrictMain
  function mcxDispHook (line 328) | mcxDispHook* mcxDispHookEnstrict
  function mcxstatus (line 376) | static mcxstatus foldArgHandle
  function mcxstatus (line 405) | static mcxstatus foldInit
  function mcxstatus (line 416) | static mcxstatus foldMain
  function mcxDispHook (line 446) | mcxDispHook* mcxDispHookFold

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shcl/report.c
  function report_partition (line 19) | void report_partition
  function report_exit (line 38) | void report_exit
  function report_domain (line 53) | void report_domain
  function report_fixit (line 69) | void report_fixit

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcl/mcl.c
  function helpful_reminder (line 87) | static void helpful_reminder
  function main (line 110) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcl/mclcm.c
  function helpful_reminder (line 81) | static void helpful_reminder
  function mclx (line 335) | static mclx* control_test
  function write_clustering (line 374) | void write_clustering
  function help (line 416) | void help
  function annot_cmp_coarse_first (line 437) | static int annot_cmp_coarse_first
  function mcxstatus (line 452) | static mcxstatus get_interface
  function mclx (line 499) | static mclx* get_coarse
  function write_coarse (line 547) | static void write_coarse
  function integrate_results (line 560) | static void integrate_results
  function mclx (line 574) | static mclx* get_base
  function main (line 629) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/glob.c
  type zgglob_t (line 56) | typedef struct zgglob_t
  function globInitialize (line 185) | void globInitialize
  function globExit (line 192) | void globExit (void)
  function zgUser (line 197) | int zgUser
  function zgglob_p (line 289) | zgglob_p zgNewHandle
  function zgglob_p (line 304) | zgglob_p zgNew
  function zgglob_p (line 351) | zgglob_p zgCopyObject
  function zgglob_p (line 381) | zgglob_p zgDupObject
  function zgMDup (line 427) | int zgMDup
  function zgglob_p (line 447) | zgglob_p zgPow
  function zgglob_p (line 497) | zgglob_p zgMul
  function zgglob_p (line 564) | static zgglob_p zgBinary
  function zgglob_p (line 641) | zgglob_p zgAdd
  function zgglob_p (line 649) | zgglob_p zgMin
  function zgglob_p (line 657) | zgglob_p zgMax
  function zgglob_p (line 665) | zgglob_p zgLt
  function zgglob_p (line 687) | zgglob_p zgEq
  function zgglob_p (line 715) | zgglob_p zgLq
  function zgPushHandle (line 736) | int zgPushHandle
  function zgPush (line 750) | int zgPush
  function zgFree (line 764) | void zgFree
  function zgglob_p (line 785) | zgglob_p zgRip
  function zsGetType (line 807) | int zsGetType
  function zgt (line 933) | int zgt
  function zgGetType (line 953) | int zgGetType
  function zgGetGlype (line 960) | int zgGetGlype
  function zgSupportError (line 967) | void zgSupportError
  function zgAccessError (line 979) | void zgAccessError
  function zgglob_p (line 991) | zgglob_p zgGetGlobByHandle
  function zgUnlink (line 999) | int zgUnlink
  function zgVars (line 1034) | int zgVars
  function zgDef (line 1081) | int zgDef
  function zgInfo (line 1126) | void zgInfo

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/glob.h
  type zgglob_t (line 30) | struct zgglob_t

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/mcxi.c
  function main (line 24) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/ops.c
  type opHook (line 112) | typedef struct
  type opAlias (line 126) | typedef struct
  function opHookHelp (line 599) | void opHookHelp
  function opInitialize (line 613) | void opInitialize
  function opExit (line 663) | void opExit (void)
  function opHookCmp (line 668) | int opHookCmp
  function opAliasCmp (line 676) | int opAliasCmp
  function opTranspose (line 684) | int opTranspose
  function opImac (line 694) | int opImac
  function opMakeStochastic (line 708) | int opMakeStochastic
  function opTransform (line 718) | int opTransform
  function opWriteMatrix (line 736) | int opWriteMatrix
  function opDigits (line 754) | int opDigits
  function opMakeCharacteristic (line 764) | int opMakeCharacteristic
  function opLoadFile (line 773) | int opLoadFile
  function opLoadMatrix (line 803) | int opLoadMatrix
  function opViewMatrix (line 828) | int opViewMatrix
  function opCopy (line 868) | int opCopy
  function opDup (line 886) | int opDup
  function opDong (line 903) | int opDong
  function opThreads (line 933) | int opThreads
  function opSearch (line 951) | int opSearch
  function opHelp (line 972) | int opHelp
  function opOpList (line 996) | int opOpList
  function opStackRoll (line 1033) | int opStackRoll
  function opFree (line 1049) | int opFree
  function opSize (line 1063) | int opSize
  function opMul (line 1088) | int opMul
  function opBlock (line 1121) | int opBlock
  function opSelect (line 1148) | int opSelect
  function opSelectc (line 1170) | int opSelectc
  function opAddto (line 1192) | int opAddto
  function opAddtp (line 1215) | int opAddtp
  function opAdd (line 1230) | int opAdd
  function opMax (line 1253) | int opMax
  function opMin (line 1276) | int opMin
  function opDiv (line 1299) | int opDiv
  function opMod (line 1337) | int opMod
  function opPow (line 1355) | int opPow
  function opExpand (line 1379) | int opExpand
  function opInflate (line 1399) | int opInflate
  function opSet (line 1413) | int opSet
  function opNew (line 1462) | int opNew
  function opHadamard (line 1492) | int opHadamard
  function opColsums (line 1508) | int opColsums
  function opWhile (line 1527) | int opWhile
  function opIfelse (line 1580) | int opIfelse
  function opDo (line 1612) | int opDo
  function opRepeat (line 1638) | int opRepeat
  function opEq (line 1669) | int opEq
  function opLq (line 1692) | int opLq
  function opLt (line 1715) | int opLt
  function opGq (line 1738) | int opGq
  function opGt (line 1748) | int opGt
  function opRowDimension (line 1758) | int opRowDimension
  function opColDimension (line 1770) | int opColDimension
  function opHadamardPower (line 1782) | int opHadamardPower
  function opDimension (line 1793) | int opDimension
  function opAllOne (line 1815) | int opAllOne
  function opIdentity (line 1841) | int opIdentity
  function opFunc (line 1866) | opFunc opGetOpByToken
  function opTell (line 1879) | int opTell
  function opInfo (line 1891) | int opInfo
  function opStackMDup (line 1898) | int opStackMDup
  function opStackClear (line 1909) | int opStackClear
  function opStackExch (line 1916) | int opStackExch
  function opStackList (line 1923) | int opStackList
  function opQuit (line 1930) | int opQuit
  function opTut (line 1939) | int opTut
  function opVars (line 1947) | int opVars
  function opStackPop (line 1954) | int opStackPop
  function opUnlink (line 1961) | int opUnlink
  function opDef (line 1968) | int opDef

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/stack.c
  type zscard_t (line 23) | typedef struct zscard_t
  function zscard_p (line 30) | zscard_p zsNew
  function zgglob_p (line 41) | zgglob_p zsGetGlob
  function zsHaveNargs (line 49) | int zsHaveNargs
  function zsDoSequence (line 56) | int zsDoSequence
  function zsEmpty (line 92) | int zsEmpty
  function zsList (line 99) | int zsList
  function zsShift (line 116) | int zsShift
  function zsRoll (line 145) | int zsRoll
  function zsPop (line 161) | int zsPop
  function zsClear (line 177) | int zsClear
  function zsExch (line 191) | int zsExch
  function zscard_p (line 210) | zscard_p zsGetCard
  function zsPush (line 227) | int zsPush
  function zsFree (line 235) | void zsFree

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/stack.h
  type zscard_t (line 18) | struct zscard_t

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcx/util.c
  function zmTell (line 25) | void zmTell
  function zmNotSupported1 (line 57) | void zmNotSupported1
  function zmNotSupported2 (line 65) | void zmNotSupported2

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmcxquery/mcxquery.c
  function main (line 34) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcx.c
  function mcxstatus (line 161) | mcxstatus sharedArgHandle
  function main (line 251) | int main
  function mclx (line 277) | mclx* mcx_get_graph
  function mcxstatus (line 327) | mcxstatus mcx_dump_node

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxalter.c
  function mcxstatus (line 139) | static mcxstatus alterInit
  function mcxstatus (line 156) | static mcxstatus alterArgHandle
  function mcxstatus (line 220) | static mcxstatus alterMain
  function mcxDispHook (line 317) | mcxDispHook* mcxDispHookAlter

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxarray.c
  type jobinfo (line 236) | struct jobinfo
  function ji_init (line 255) | static void ji_init
  function ji_step (line 296) | static int ji_step
  function mclvChebyshev (line 336) | double mclvChebyshev
  function mclvMinkowski (line 372) | double mclvMinkowski
  function mclv_inner_minkowski (line 401) | static double mclv_inner_minkowski
  function mclv_inner_dot (line 431) | static double mclv_inner_dot
  function pearson (line 448) | double pearson
  type rank_unit (line 464) | typedef struct rank_unit
  function rank_unit_cmp_index (line 483) | int rank_unit_cmp_index
  function rank_unit_cmp_value (line 493) | int rank_unit_cmp_value
  function mclx (line 928) | static mclx* read_data
  function mydiv (line 1125) | double mydiv
  function ivp_get_double (line 1139) | static double ivp_get_double
  function get_array_content_score (line 1146) | static double get_array_content_score
  function dim (line 1332) | static dim get_correlation
  function dim (line 1484) | dim do_range_do
  function dim (line 1568) | dim do_range
  type array_data (line 1631) | typedef struct
  function mclx (line 1680) | mclx* normalise
  function write_the_table (line 1702) | void write_the_table
  function main (line 1729) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxassemble.c
  function main (line 315) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxclcf.c
  function mcxstatus (line 128) | static mcxstatus clcfInit
  function mcxstatus (line 146) | static mcxstatus clcfArgHandle
  function clcf_dispatch (line 206) | static void clcf_dispatch
  function mcxstatus (line 217) | static mcxstatus clcfMain
  function mcxDispHook (line 287) | mcxDispHook* mcxDispHookClcf

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxcollect.c
  function mcxstatus (line 130) | static mcxstatus collectInit
  function mcxstatus (line 145) | static mcxstatus collectArgHandle
  type aggr (line 204) | typedef struct
  function aggr_cmp_val (line 212) | int aggr_cmp_val(const void* a1, const void* a2)
  function dim (line 218) | static dim do_a_file
  function mcxstatus (line 308) | static mcxstatus collectMain
  function mcxDispHook (line 440) | mcxDispHook* mcxDispHookCollect

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxconvert.c
  function mcxstatus (line 96) | static mcxstatus convertInit
  function mcxstatus (line 110) | static mcxstatus convertArgHandle
  function mcxstatus (line 154) | static mcxstatus convertMain
  function mcxDispHook (line 203) | mcxDispHook* mcxDispHookConvert

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxdiameter.c
  function dim (line 65) | static dim diameter_rough
  function dim (line 130) | dim diamFlood2
  type SSPnode (line 177) | typedef struct
  function mcxstatus (line 385) | static mcxstatus allInit
  function mcxstatus (line 408) | static mcxstatus cttyArgHandle
  function mcxstatus (line 485) | static mcxstatus diameterArgHandle
  function rough_it (line 548) | static void rough_it
  function ecc_compute (line 591) | static void ecc_compute
  type diam_data (line 607) | typedef struct
  function diam_dispatch (line 614) | static void diam_dispatch
  function mcxstatus (line 626) | static mcxstatus diameterMain
  function mcxDispHook (line 735) | mcxDispHook* mcxDispHookDiameter
  function cttyUpdateDS (line 756) | void cttyUpdateDS
  function dim (line 798) | dim cttyFlood2
  function compute_scores_up_ec (line 855) | void compute_scores_up_ec              /* edge centrality */
  function compute_scores_up_vc (line 911) | void compute_scores_up_vc              /* vertex centrality */
  function ctty_compute2 (line 939) | static void ctty_compute2
  type ctty_data (line 986) | typedef struct
  function ctty_dispatch (line 996) | static void ctty_dispatch
  function mcxstatus (line 1008) | static mcxstatus cttyMain
  function mcxDispHook (line 1136) | mcxDispHook* mcxDispHookCtty

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxdump.c
  function main (line 437) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxerdos.c
  function mcxstatus (line 146) | static mcxstatus allInit
  function mcxstatus (line 164) | static mcxstatus erdosArgHandle
  function label_not_found (line 222) | void label_not_found
  function mcxstatus (line 229) | mcxstatus check_bounds
  function erdos_link_together (line 242) | static void erdos_link_together
  function handle_tf (line 278) | void handle_tf
  function handle_clcf (line 291) | void handle_clcf
  function handle_list (line 317) | void handle_list
  function handle_top (line 349) | void handle_top
  function mclx (line 396) | mclx* handle_query
  function mclx (line 445) | static mclx* process_queries
  function mcxstatus (line 608) | static mcxstatus erdosMain
  function mcxDispHook (line 710) | mcxDispHook* mcxDispHookErdos

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxfp.c
  function mcxstatus (line 463) | static mcxstatus fpInit
  function mcxstatus (line 479) | static mcxstatus fpArgHandle
  type chem (line 558) | struct chem
  type chem (line 567) | struct chem
  function chem_set_bit (line 575) | void chem_set_bit
  function bucket_print (line 588) | void bucket_print
  function chem_count_bits (line 599) | unsigned chem_count_bits
  function chem_tanimoto (line 615) | float chem_tanimoto
  function dim (line 637) | dim chem_n_buckets
  function chem_print (line 657) | void chem_print
  function chem_sim (line 671) | void chem_sim
  function chem_printall (line 705) | void chem_printall
  function write_hist (line 716) | void write_hist
  function mcxstatus (line 736) | static mcxstatus fpMain
  function mcxDispHook (line 943) | mcxDispHook* mcxDispHookFp

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxload.c
  function mclx (line 443) | mclx* read_packed
  function main (line 488) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxmap.c
  function main (line 189) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxmetric.c
  function mclv (line 70) | mclv* reduce_v
  function dim (line 84) | static dim update_meet_zip
  function dim (line 108) | static dim update_todo
  function mclv_inner (line 124) | static double mclv_inner
  function pearson (line 141) | double pearson
  function add_edge (line 160) | void add_edge
  function fltxCos (line 176) | double fltxCos
  function main (line 184) | int main
  function over (line 414) | over todo[todo != 0] {

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxminusmeet.c
  function mclv (line 78) | mclv* mcldMinus1
  function pairwise_setops (line 87) | void pairwise_setops
  function main (line 212) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxmm.c
  function mcxstatus (line 170) | mcxstatus fire_node_next
  function ofs (line 198) | ofs fire_node
  function test_cross_ratio (line 223) | void test_cross_ratio
  function test_for_cycles (line 254) | void test_for_cycles
  function get_attr (line 285) | void get_attr
  function dump_label (line 349) | void dump_label
  function walk_dag (line 366) | void walk_dag
  function dump_dag (line 384) | void dump_dag
  function dag_diff_select (line 401) | void dag_diff_select
  function main (line 449) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxquery.c
  function valcmpdesc (line 50) | int valcmpdesc
  function valcmpasc (line 58) | int valcmpasc
  function pearson (line 66) | double pearson
  type vary_threshold (line 323) | struct vary_threshold
  type vary_step (line 333) | struct vary_step
  type vary_threshold (line 342) | struct vary_threshold
  type vary_step (line 343) | struct vary_step
  type level (line 379) | struct level
  function mclv (line 382) | static mclv* matrix_vector
  function mclv (line 399) | static mclv* run_through
  function test_cycle (line 421) | static int test_cycle
  function mcxstatus (line 456) | static mcxstatus qInit
  function mcxstatus (line 483) | mcxstatus parse_steps
  function mcxstatus (line 505) | mcxstatus parse_threshold
  function mcxstatus (line 532) | static mcxstatus qArgHandle
  type level (line 739) | struct level
  function pval_get_double (line 763) | static double pval_get_double
  function ivp_get_double (line 769) | static double ivp_get_double
  function dim (line 776) | dim get_n_sort_allvals
  function do_vary_threshold (line 806) | static void do_vary_threshold
  function ofs (line 1176) | static ofs get_cls_id
  function do_attr (line 1194) | int do_attr
  function do_attr_clsonly (line 1247) | int do_attr_clsonly
  function do_testmetric (line 1263) | int do_testmetric
  function do_values (line 1328) | int do_values
  function do_degrees_hist (line 1373) | int do_degrees_hist
  function do_size (line 1394) | int do_size
  function do_dimension (line 1435) | int do_dimension
  function mcxstatus (line 1459) | static mcxstatus qMain
  function mcxDispHook (line 1545) | mcxDispHook* mcxDispHookquery

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxrand.c
  function dimCmp (line 260) | int dimCmp
  function mx_readd_diagonal (line 268) | static void mx_readd_diagonal
  function mclx (line 287) | mclx* mcleAddtoCanonical
  function mclx (line 323) | static mclx* pref_attach3
  function mclx (line 384) | static mclx* pref_attach2
  function mclx (line 455) | static mclx* pref_attach
  function do_the_shuffle (line 508) | void static do_the_shuffle
  function dim (line 646) | static dim do_remove
  function dim (line 697) | static dim do_add2
  function dim (line 741) | static dim do_add
  function main (line 819) | int main

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxsubs.c
  type subspec_mt (line 277) | typedef struct
  type context_mt (line 302) | typedef struct
  function thin_out (line 341) | void thin_out
  function prune_edges (line 356) | void prune_edges
  function spec_init (line 388) | void spec_init
  function main (line 423) | int main
  function mcxstatus (line 756) | mcxstatus parse_fin
  function mcxstatus (line 814) | mcxstatus parse_out
  function mcxstatus (line 855) | mcxstatus add_vec
  function mclv (line 954) | mclv* vec_from_ilist
  function mcxstatus (line 990) | mcxstatus parse_dom
  function mcxstatus (line 1117) | mcxstatus parse_path
  function mcxstatus (line 1147) | mcxstatus parse_ext
  function mcxstatus (line 1202) | mcxstatus parse_size
  function mcxstatus (line 1259) | mcxstatus dispatch
  function mcxstatus (line 1345) | mcxstatus extend_path
  function mcxstatus (line 1363) | mcxstatus extend_disc
  function mcxstatus (line 1391) | mcxstatus spec_parse
  function spec_exec (line 1410) | void spec_exec

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxtab.c
  function cmp_keys (line 37) | static int cmp_keys
  function mcxstatus (line 88) | static mcxstatus tabInit
  function mcxstatus (line 96) | static mcxstatus tabArgHandle
  function mcxstatus (line 130) | static mcxstatus tabMain
  function mcxDispHook (line 221) | mcxDispHook* mcxDispHookTab

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxtest.c
  function mclv (line 62) | mclv* reduce_v
  function dim (line 76) | static dim update_meet_zip
  function dim (line 100) | static dim update_todo
  function mclv_inner (line 116) | static double mclv_inner
  function pearson (line 133) | double pearson
  function add_edge (line 152) | void add_edge
  function fltxCos (line 168) | double fltxCos
  function main (line 176) | int main
  function over (line 422) | over todo[todo != 0] {

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/src/shmx/mcxtest2.c
  function mclv (line 63) | mclv* reduce_v
  function dim (line 77) | static dim update_meet_zip
  function dim (line 101) | static dim update_todo
  function mclv_inner (line 117) | static double mclv_inner
  function pearson (line 134) | double pearson
  function add_edge (line 153) | void add_edge
  function fltxCos (line 169) | double fltxCos
  function main (line 177) | int main
  function over (line 313) | over todo[todo != 0] {

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/alloc.c
  function mcxAllocLimits (line 42) | void mcxAllocLimits
  function mcxNFree (line 106) | void mcxNFree
  function mcxMemDenied (line 158) | void mcxMemDenied
  function mcxFree (line 174) | void mcxFree

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/array.c
  function mcxstatus (line 22) | mcxstatus mcxSplice
  function dim (line 133) | dim mcxDedup
  function mcxstatus (line 164) | mcxstatus mcxResize
  function mcxstatus (line 184) | mcxstatus mcxBufInit
  function dim (line 252) | dim mcxBufFinalize
  function mcxBufReset (line 282) | void mcxBufReset
  function mcxMedian (line 405) | double mcxMedian
  function mcxShuffle (line 452) | void mcxShuffle

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/array.h
  type mcxBuf (line 107) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/ding.c
  function dim (line 41) | dim mcxStrCountChar
  function mcxTing (line 367) | mcxTing* mcxMemPrint
  function mcxEditDistance (line 391) | int mcxEditDistance
  function mcxSetenv (line 474) | int mcxSetenv
  function mcxstatus (line 485) | mcxstatus mcxStrTol
  function mcxstatus (line 507) | mcxstatus mcxStrToul

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/equate.c
  function dblCmp (line 15) | int dblCmp
  function dblRevCmp (line 29) | int dblRevCmp
  function fltCmp (line 43) | int fltCmp
  function fltRevCmp (line 57) | int fltRevCmp
  function intCmp (line 71) | int intCmp
  function intRevCmp (line 79) | int intRevCmp
  function intnCmp (line 87) | int intnCmp
  function intLt (line 103) | int intLt
  function intLq (line 111) | int intLq
  function intGt (line 119) | int intGt
  function intGq (line 127) | int intGq
  function fltLt (line 135) | int fltLt
  function fltLq (line 143) | int fltLq
  function fltGt (line 151) | int fltGt
  function fltGq (line 159) | int fltGq

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/err.c
  function mcx_err_f (line 33) | void  mcx_err_f
  function mcxFail (line 51) | void mcxFail
  function mcxDie (line 58) | void mcxDie
  function mcxExit (line 72) | void mcxExit
  function mcxErrorFile (line 79) | void mcxErrorFile
  function mcxTellFile (line 85) | void mcxTellFile
  function mcxLogSetFILE (line 91) | void mcxLogSetFILE
  function FILE (line 101) | FILE* mcxLogGetFILE
  function mcxWarnFile (line 108) | void mcxWarnFile
  function mcxErrf (line 115) | void  mcxErrf
  function mcxErr (line 128) | void  mcxErr
  function mcxWarn (line 141) | void  mcxWarn
  function mcx_write_f (line 160) | static void  mcx_write_f
  function mcxTellf (line 177) | void  mcxTellf
  function mcxTell (line 190) | void  mcxTell
  type mcx_log_class_annotated (line 203) | struct mcx_log_class_annotated
  type mcx_log_class_annotated (line 210) | struct mcx_log_class_annotated
  function mcxbool (line 225) | mcxbool mcxLogGet
  function mcxLog2 (line 261) | void mcxLog2
  function mcxLog (line 274) | void mcxLog
  function mcx_level_parsenum (line 299) | static int mcx_level_parsenum
  function mcx_level_setnum (line 321) | static int mcx_level_setnum
  function mcxLogSig (line 343) | void mcxLogSig
  function mcxLogLevelSetByString (line 350) | void mcxLogLevelSetByString

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/gralloc.c
  type memnext (line 23) | typedef struct memnext
  type grim_buf (line 34) | typedef struct grim_buf
  type mcxGrim (line 43) | struct mcxGrim
  function grim_buf (line 53) | grim_buf* grim_buf_new
  function mcxGrim (line 91) | mcxGrim* mcxGrimNew
  function dim (line 115) | dim mcxGrimMemSize
  function mcxbool (line 128) | mcxbool mcx_grim_extend
  function mcxGrimFree (line 150) | void  mcxGrimFree
  function mcxGrimLet (line 165) | void mcxGrimLet
  function dim (line 189) | dim mcxGrimCount

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/gralloc.h
  type mcxGrim (line 18) | typedef struct mcxGrim mcxGrim;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/hash.c
  type hash_link (line 55) | typedef struct hash_link
  type mcx_bucket (line 65) | typedef struct bucket
  type mcxHash (line 82) | struct mcxHash
  type mcxHashWalk (line 99) | struct mcxHashWalk
  function mcxHash (line 124) | mcxHash* mcxHashNew
  function dim (line 185) | dim mcxHashMemSize
  function mcxHashGetSettings (line 194) | void mcxHashGetSettings
  function dim (line 205) | static dim hash_link_size
  function mcxHashStats (line 216) | void mcxHashStats
  function mcxHashSetOpts (line 300) | void mcxHashSetOpts
  function mcxHashFreeScalar (line 312) | void mcxHashFreeScalar
  function mcxHashFree (line 319) | void mcxHashFree
  function hash_link (line 361) | static hash_link* mcx_bucket_search
  function hash_link (line 418) | static hash_link* mcx_bucket_search
  function mcxKV (line 481) | mcxKV* mcxHashSearchx
  function mcxHashApply (line 512) | void mcxHashApply
  function mcxKV (line 590) | mcxKV* mcxHashWalkStep
  function mcxHashWalk (line 609) | mcxHashWalk* mcxHashWalkInit
  function mcxHashWalkFree (line 629) | void mcxHashWalkFree
  function mcxHash (line 637) | mcxHash* mcxHashMerge
  function mcxstatus (line 698) | static mcxstatus mcx_hash_double
  function u32 (line 799) | u32 mcxBJhash
  function u32 (line 887) | u32   mcxSvDhash
  function u32 (line 912) | u32   mcxSvD2hash
  function u32 (line 933) | u32   mcxSvD1hash
  function u32 (line 952) | u32   mcxDPhash
  function u32 (line 971) | u32 mcxGEhash
  function u32 (line 988) | u32   mcxFNVhash
  function u32 (line 1010) | u32 mcxBDBhash
  function u32 (line 1025) | u32 mcxOAThash
  function u32 (line 1046) | u32 mcxDJBhash
  function u32 (line 1060) | u32 mcxELFhash
  function u32 (line 1080) | u32 mcxStrHash
  function mcxStrCmp (line 1088) | int mcxStrCmp
  function bitprint (line 1097) | void bitprint
  function bitcount (line 1108) | int bitcount
  function __u32 (line 1124) | static __u32 dx_hack_hash (const char *name, int len)

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/hash.h
  type mcxHash (line 82) | typedef struct mcxHash mcxHash;
  type mcxKV (line 85) | typedef struct
  type mcxHashSettings (line 115) | typedef struct mcxHashSettings
  type mcxHashWalk (line 286) | typedef struct mcxHashWalk mcxHashWalk;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/heap.c
  function mcxHeap (line 20) | mcxHeap* mcxHeapInit
  function mcxHeap (line 37) | mcxHeap* mcxHeapNew
  function mcxHeapClean (line 69) | void mcxHeapClean
  function mcxHeapRelease (line 76) | void mcxHeapRelease
  function mcxHeapFree (line 88) | void mcxHeapFree
  function mcxHeapInsert (line 102) | void mcxHeapInsert

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/heap.h
  type mcxHeap (line 20) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/inttypes.h
  type MCX_UINT32 (line 26) | typedef  MCX_UINT32     u32 ;
  type MCX_INT32 (line 27) | typedef  MCX_INT32      i32 ;
  type u8 (line 28) | typedef  unsigned char  u8  ;
  type dim (line 47) | typedef  size_t         dim;
  type ofs (line 48) | typedef  ssize_t        ofs;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/io.c
  function buffer_empty (line 54) | static void buffer_empty
  function buffer_spout (line 62) | static void buffer_spout
  function begets_stdio (line 78) | int begets_stdio
  function mcxIOwarnOpenfp (line 95) | static int mcxIOwarnOpenfp
  function mcxstatus (line 107) | mcxstatus mcxIOclose
  function mcxstatus (line 138) | mcxstatus mcxIOreset
  function mcxIOerr (line 157) | void mcxIOerr
  function mcxIO (line 175) | mcxIO* mcxIOnew
  function mcxIO (line 193) | mcxIO* mcxIOrenew
  function mcxstatus (line 269) | mcxstatus  mcxIOopen
  function mcxstatus (line 308) | mcxstatus mcxIOtestOpen
  function mcxIOrelease (line 322) | void mcxIOrelease
  function mcxstatus (line 336) | mcxstatus mcxIOappendName
  function mcxstatus (line 356) | mcxstatus mcxIOnewName
  function mcxstatus (line 365) | mcxstatus mcxIOnewName
  function mcxIOstepback (line 374) | int mcxIOstepback
  function mcxIOstep (line 406) | int mcxIOstep
  function mcxstatus (line 460) | mcxstatus  mcxIOreadFile
  function dim (line 501) | static dim  mcxIO__rl_fillbuf__
  function dim (line 548) | dim mcxIOdiscardLine
  function ofs (line 570) | ofs mcxIOappendChunk
  function mcxstatus (line 620) | mcxstatus  mcxIOreadLine
  function mcxIOlistParmodes (line 723) | void mcxIOlistParmodes
  function mcxIOpos (line 743) | void mcxIOpos
  function mcxIOfree_v (line 759) | void mcxIOfree_v
  function mcxIOfree (line 766) | void mcxIOfree
  function mcxstatus (line 782) | mcxstatus mcxIOexpectReal
  function mcxstatus (line 812) | mcxstatus mcxIOexpectNum
  function mcxIOskipSpace (line 850) | int mcxIOskipSpace
  function mcxbool (line 861) | mcxbool mcxIOtryCookie
  function mcxbool (line 896) | mcxbool mcxIOwriteCookie
  function mcxIOexpect (line 913) | int mcxIOexpect
  type mcxIOpat (line 951) | typedef struct
  function mcxio_newpat (line 961) | static void mcxio_newpat
  function mcxIOcleanpat (line 994) | static void mcxIOcleanpat
  function fillpatbuf (line 1002) | static int fillpatbuf
  function dim (line 1099) | dim mcxIOdiscard

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/io.h
  type mcxIO (line 136) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/let.c
  type real (line 170) | typedef double real;
  type num (line 174) | typedef long long num;
  type num (line 178) | typedef long num;
  type tn (line 190) | typedef struct tn          /* the lex/parse/interpret one stop-shop    */
  type telRaam (line 207) | struct telRaam
  type tokentype (line 225) | typedef enum
  type opHook (line 285) | typedef struct opHook
  function sign (line 293) | double sign
  function letround (line 300) | double letround
  function letlog2 (line 307) | double letlog2
  type fun1Hook (line 311) | typedef struct fun1Hook
  function show_bits (line 322) | double show_bits(double a) {
  function max (line 350) | double max ( double a, double b ) { return a > b ? a  : b ; }
  function min (line 351) | double min ( double a, double b ) { return a < b ? a  : b ; }
  function num (line 352) | num maxl  ( num a, num b ) { return a > b ? a  : b ; }
  function num (line 353) | num minl  ( num a, num b ) { return a < b ? a  : b ; }
  type fun2Hook (line 356) | typedef struct fun2Hook
  function mcxbool (line 424) | mcxbool trmIsNan
  function mcxbool (line 430) | mcxbool trmError
  function mcxbool (line 436) | mcxbool trmIsInf
  function mcxbool (line 442) | mcxbool trmIsNum
  function mcxbool (line 448) | mcxbool trmIsReal
  function trmDump (line 471) | void trmDump
  function tn (line 479) | tn* tnNewToken
  function tn (line 513) | tn* tnDup
  function mcxstatus (line 536) | mcxstatus tnFree
  function tnLink2 (line 566) | void tnLink2
  function tnLink3 (line 577) | void tnLink3
  function mcxstatus (line 592) | mcxstatus tnPushToken
  function mcxstatus (line 636) | mcxstatus tnPushThis
  function trmDebug (line 652) | void trmDebug
  function telRaam (line 659) | telRaam* trmInit
  function mcxstatus (line 688) | mcxstatus trmExit
  function untoken (line 700) | void untoken
  function dump (line 707) | void dump
  function getatoken (line 747) | int getatoken
  function i32 (line 839) | i32  gettoken
  function tn (line 852) | tn* findop
  function tn (line 874) | tn* finduser
  function mcxstatus (line 888) | mcxstatus tnUser
  function mcxstatus (line 916) | mcxstatus flatten
  function fun1Hook (line 1206) | fun1Hook* getfun1id
  function fun2Hook (line 1216) | fun2Hook* getfun2id
  function tn (line 1226) | tn* funcx
  function tn (line 1343) | tn* match
  function mcxstatus (line 1372) | mcxstatus compute
  function mcxstatus (line 1534) | mcxstatus getatom
  function mcxstatus (line 1618) | mcxstatus getexpression
  function mcxstatus (line 1715) | mcxstatus trmParse
  function trmRegister (line 1736) | void trmRegister
  function trmEval (line 1748) | int trmEval
  function trmStack (line 1768) | int trmStack

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/let.h
  type telRaam (line 22) | typedef struct telRaam telRaam;

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/list.c
  type mcx_list (line 51) | typedef struct
  type lsptr (line 57) | typedef struct lsptr
  function mcx_link_init (line 66) | void mcx_link_init
  function mcxLink (line 76) | mcxLink* mcx_list_shift
  function mcxLink (line 94) | mcxLink*  mcxListSource
  function mcxLink (line 119) | mcxLink*  mcxLinkSpawn
  function mcxLinkClose (line 128) | void mcxLinkClose
  function mcxLink (line 139) | mcxLink*  mcxLinkBefore
  function mcxLink (line 161) | mcxLink*  mcxLinkAfter
  function mcxLinkRemove (line 187) | void mcxLinkRemove
  function mcxLink (line 195) | mcxLink* mcxLinkDelete
  function mcxGrim (line 210) | mcxGrim* mcxLinkGrim
  function mcxListFree (line 218) | void  mcxListFree

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/list.h
  type mcxLink (line 54) | typedef struct mcxLink

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/opt.c
  function strcmp_void (line 30) | static int strcmp_void
  function mcxHash (line 38) | mcxHash* mcxOptHash
  function mcxOptHashFree (line 75) | void mcxOptHashFree
  function mcxOptAnchor (line 92) | mcxOptAnchor* mcxOptFind
  function mcxOption (line 101) | mcxOption* mcxOptParse__
  function mcxOption (line 197) | mcxOption* mcxOptExhaust
  function mcxOption (line 213) | mcxOption* mcxOptParse
  function mcxOption (line 228) | mcxOption* mcxHOptExhaust
  function mcxOption (line 241) | mcxOption* mcxHOptParse
  function mcxOptFree (line 253) | void mcxOptFree
  function mcxUsage (line 262) | void mcxUsage
  function checkBoundsUsage (line 297) | static int checkBoundsUsage
  function mcxstatus (line 350) | static mcxstatus checkBounds
  function mcxTing (line 370) | static mcxTing* checkBoundsRange
  function mcxbool (line 441) | mcxbool mcxOptCheckBounds
  function mcxOptAnchorCmpId (line 486) | int mcxOptAnchorCmpId
  function mcxOptAnchorCmpTag (line 497) | int mcxOptAnchorCmpTag
  function mcxOptAnchorSortByTag (line 511) | void mcxOptAnchorSortByTag
  function mcxOptAnchorSortById (line 520) | void mcxOptAnchorSortById
  function parse_descr (line 529) | void parse_descr
  function mcxOptApropos (line 550) | void mcxOptApropos
  function mcxbool (line 674) | mcxbool mcxOptIsInfo
  function mcxTing (line 686) | mcxTing* mcxOptArgLine
  function mcxDispatch (line 717) | int mcxDispatch

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/opt.h
  type mcxOptAnchor (line 84) | typedef struct mcxOptAnchor
  type mcxOption (line 111) | typedef struct mcxOption
  type mcxDispHook (line 286) | typedef struct
  type mcxDispEntry (line 301) | typedef struct
  type mcxDispBundle (line 309) | typedef struct mcx_disp_bundle

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/rand.c
  function mcxSeed (line 20) | unsigned long mcxSeed
  function mcxNormalBoxMuller (line 44) | double mcxNormalBoxMuller
  function mcxNormal (line 53) | double mcxNormal
  function mcxNormalCut (line 60) | double mcxNormalCut
  function mcxNormalSample (line 76) | double mcxNormalSample
  function mcxNormalZiggurat (line 222) | double mcxNormalZiggurat

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/ting.c
  function mcxTingRelease (line 28) | void mcxTingRelease
  function mcxTingFree (line 36) | void mcxTingFree
  function mcxTingFree_v (line 50) | void mcxTingFree_v
  function mcxTingAbandon (line 58) | void mcxTingAbandon
  function mcxTing (line 67) | mcxTing* mcxTingShrink
  function mcxTing (line 91) | mcxTing* mcxTingEnsure
  function mcxTing (line 193) | mcxTing*  mcxTingPrintSplice
  function mcxTing (line 226) | mcxTing*  mcxTingPrint
  function mcxTing (line 240) | mcxTing*  mcxTingPrintAfter
  function mcxTing (line 276) | mcxTing*  mcxTingRoman
  function mcxTing (line 311) | mcxTing*  mcxTingDouble
  function mcxTing (line 343) | mcxTing*  mcxTingInteger
  function mcxTing (line 380) | mcxTing* mcxTingInstantiate
  function mcxTingRevCmp (line 402) | int mcxTingRevCmp
  function mcxTingCmp (line 410) | int mcxTingCmp
  function mcxTingPCmp (line 418) | int mcxTingPCmp
  function mcxTingPRevCmp (line 426) | int mcxTingPRevCmp
  function mcxPKeyTingCmp (line 434) | int mcxPKeyTingCmp
  function mcxPKeyTingRevCmp (line 446) | int mcxPKeyTingRevCmp
  function mcxstatus (line 458) | mcxstatus mcxTingSplice
  function mcxTing (line 547) | mcxTing* mcxTingNew
  function mcxTing (line 554) | mcxTing* mcxTingNNew
  function mcxTing (line 571) | mcxTing* mcxTingEmpty
  function mcxTing (line 584) | mcxTing* mcxTingWrite
  function mcxTing (line 592) | mcxTing* mcxTingNWrite
  function mcxTing (line 633) | mcxTing* mcxTingify
  function mcxTing (line 662) | mcxTing* mcxTingAppend
  function mcxTing (line 685) | mcxTing* mcxTingKAppend
  function mcxTing (line 706) | mcxTing* mcxTingNAppend
  function mcxTing (line 730) | mcxTing* mcxTingInsert
  function mcxTing (line 755) | mcxTing* mcxTingNInsert
  function mcxTing (line 780) | mcxTing* mcxTingDelete
  function u32 (line 805) | u32 mcxTingDJBhash
  function u32 (line 812) | u32 mcxTingBDBhash
  function u32 (line 819) | u32 mcxTingBJhash
  function u32 (line 826) | u32 mcxTingCThash
  function u32 (line 833) | u32 mcxTingDPhash
  function u32 (line 840) | u32 mcxTingGEhash
  function u32 (line 847) | u32 mcxTingOAThash
  function u32 (line 854) | u32 mcxTingELFhash
  function u32 (line 861) | u32 mcxTingFNVhash
  function u32 (line 868) | u32 (*mcxTingHFieByName(const char* id))(const void* ting)
  function u32 (line 898) | u32 mcxTingSvDhash
  function u32 (line 905) | u32 mcxTingSvD2hash
  function u32 (line 912) | u32 mcxTingSvD1hash
  function u32 (line 919) | u32 mcxTingHash
  function mcxstatus (line 929) | mcxstatus mcxTingTackc
  function mcxstatus (line 944) | mcxstatus mcxTingTickc

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/ting.h
  type mcxTing (line 15) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/tok.c
  function mcxstatus (line 48) | mcxstatus mcxTokMatch
  function mcxstatus (line 125) | mcxstatus mcxTokFind
  function mcxTokFuncFree (line 172) | void mcxTokFuncFree
  function mcxstatus (line 180) | mcxstatus mcxTokExpectFunc
  function mcxLink (line 278) | mcxLink* mcxTokArgs

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/tok.h
  type mcxTokFunc (line 94) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/tr.c
  function mcxTing (line 156) | mcxTing* mcxTRsplash
  function ofs (line 183) | ofs mcxTRtranslate
  function ofs (line 213) | ofs mcxTingTranslate
  function ofs (line 226) | ofs mcxTingTr
  function mcx_tr_enc_dump (line 496) | static void mcx_tr_enc_dump
  function mcxstatus (line 515) | static mcxstatus xtr_get_spec
  function mcxstatus (line 601) | static mcxstatus mcx_tr_encode_boolean
  function mcxstatus (line 622) | static mcxstatus mcx_tr_translate_encode
  function mcx_tr_complement (line 770) | static void mcx_tr_complement
  function mcxstatus (line 819) | static mcxstatus mcx_tr_encode
  function mcxstatus (line 894) | mcxstatus mcxTRloadTable

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/tr.h
  type mcxTR (line 63) | typedef struct

FILE: NonOverlappingCodes/2005-Markov-Clustering/mcl-14-137/util/types.h
  type mcxbits (line 15) | typedef unsigned long mcxbits  ;
  type mcxmode (line 16) | typedef unsigned long mcxmode  ;
  type mcxenum (line 17) | typedef unsigned long mcxenum  ;
  type mcxstatus (line 53) | typedef enum
  type mcxbool (line 73) | typedef enum
  type mcxbool (line 78) | typedef int mcxbool ;
  type mcxOnFail (line 81) | typedef enum

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/community.cpp
  function Graph (line 206) | Graph

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/community.h
  function class (line 32) | class Community {
  function remove (line 102) | inline void
  function insert (line 111) | inline void
  function modularity_gain (line 120) | inline double

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/graph.h
  function class (line 35) | class Graph {

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/graph_binary.h
  function class (line 36) | class Graph {
  function nb_neighbors (line 79) | inline unsigned int
  function nb_selfloops (line 89) | inline double
  function weighted_degree (line 105) | inline double

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/main_community.cpp
  function usage (line 42) | void
  function parse_args (line 58) | void
  function display_time (line 102) | void
  function main (line 110) | int

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/main_convert.cpp
  function usage (line 27) | void
  function parse_args (line 38) | void
  function main (line 74) | int

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/main_hierarchy.cpp
  function usage (line 32) | void
  function parse_args (line 46) | void
  function main (line 74) | int

FILE: NonOverlappingCodes/2008-Louvain-MultiLevel-Aggregation-Opt-Modularity/main_random.cpp
  function main (line 5) | int

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/cliqueHash.h
  function class (line 27) | class cliqueHash

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/communityTracker.h
  function class (line 33) | class CommunityTracker

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/dendrogram.h
  function class (line 30) | class Dendrogram
  function compareNodes (line 67) | static bool compareNodes(DendrogramNode * first, DendrogramNode * second...

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/k_clique.cpp
  type Link (line 50) | struct Link{
    method Link (line 54) | Link(size_t source=0,size_t dest=0, float weight=0.0) : source(source)...
  function determineHashSize (line 60) | size_t determineHashSize(const size_t numElements, const size_t k)
  function getNetSizeAndLinkNumbers (line 78) | bool getNetSizeAndLinkNumbers(char * fileName, size_t & netSize, size_t ...
  function readLine (line 120) | bool readLine(std::ifstream & myfile, size_t & source,  size_t & dest, f...
  function kCliquesFind (line 144) | void kCliquesFind(std::vector<weighedClique> & cliqueVector, NetType & n...
  function kCommunitiesFind (line 248) | void kCommunitiesFind(std::vector<weighedClique> & cliqueVector, Kruskal...
  function outputCommunityStructure (line 294) | void outputCommunityStructure(KruskalTree & communities, cliqueHash & k1...
  function unweightedSCP (line 323) | void unweightedSCP(NetType & net, std::list<Link> & linkList, const size...
  function weighedCliqueCmp (line 374) | bool weighedCliqueCmp(const weighedClique lhs, const weighedClique rhs)
  function kCommunitiesFindWeighted (line 379) | void kCommunitiesFindWeighted(std::vector<weighedClique> & cliqueVector,...
  function weightedSCP (line 403) | void weightedSCP(NetType & net, std::ifstream & file, const size_t numbe...
  function validateLinkList (line 434) | bool validateLinkList(std::list<Link> &linkList,size_t netSize,bool verb...
  function percolation (line 453) | int percolation(char * fileName, const size_t k, const size_t weighted, ...
  function main (line 481) | int main(int argc, char* argv[])

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/k_clique.h
  type Set (line 51) | typedef Set<size_t> nodeSet;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/kruskal.h
  function class (line 28) | class KruskalTree

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/Containers.H
  type DefaultContainerParams (line 41) | struct DefaultContainerParams {
  type Index (line 121) | typedef Index<KeyType, void, Policy, Params, Table> super;
  function super (line 124) | Set(size_t capacity): super(capacity) {}
  function put (line 131) | bool put(const KeyType & key) {
  function const (line 141) | bool operator[](const KeyType & key) const {
  function remove (line 145) | bool remove(const KeyType & key) {
  function setValue (line 157) | void setValue(const KeyType & key, bool value) {
  function WeightType (line 217) | static WeightType getWeight(const Set<KeyType, Index, Table, Policy, Par...
  type Index (line 266) | typedef Index<KeyType, ValueType, Policy, Params, Table> super;
  function super (line 297) | Map(size_t capacity): super(capacity) {
  type typename (line 307) | typedef typename super::value_reference reference;
  type typename (line 308) | typedef typename super::const_value_reference const_reference;
  function reference (line 317) | reference operator[](const KeyType & key) {
  function const_reference (line 328) | const_reference operator[](const KeyType & key) const {
  function setValue (line 332) | void setValue(const KeyType & key, const ValueType & value) {
  function _lce_finalize (line 352) | void _lce_finalize() {super::value_stub::_lce_finalize();}
  type stub (line 360) | typedef stub value_stub;
  function class (line 366) | class iterator: public super::iterator {
  function class (line 386) | class const_iterator: public super::const_iterator {
  function iterator (line 408) | iterator begin() {return iterator(this);}
  type Map (line 583) | typedef Map<KeyType, ValueType, Index, Table, Policy, Params> super;
  function super (line 590) | AutoMap(size_t capacity): super(capacity) {}
  type typename (line 600) | typedef typename super::stub SuperStub;
  function _lce_update (line 611) | void _lce_update() {
  function _lce_finalize (line 619) | void _lce_finalize() {
  function _lce_upToDate (line 632) | bool _lce_upToDate() {
  type stub (line 650) | typedef stub<true> reference;
  type stub (line 651) | typedef stub<false> value_stub;
  function reference (line 657) | reference operator[](const KeyType & key) {
  function ValueType (line 665) | ValueType operator[](const KeyType & key) const {
  function setValue (line 676) | void setValue(const KeyType & key, const ValueType & value) {
  function class (line 685) | class iterator:public super::iterator {
  type typename (line 728) | typedef typename super::const_iterator const_iterator;
  function keyLegal (line 730) | bool keyLegal(const KeyType & key) const {
  type Set (line 819) | typedef Set<KeyType, Index, Table, Policy, Params> super;
  function super (line 824) | AutoMap(size_t capacity): super(capacity) {}
  type value (line 826) | typedef bool value;
  type const_reference (line 827) | typedef bool const_reference;
  function class (line 831) | class stub {
  function WeightType (line 959) | static WeightType getWeight(const AutoMap<KeyType, bool, Index, Table,

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/Nets.H
  function DefaultContainerParams (line 43) | struct NetEdgeParams: public DefaultContainerParams {
  type Map (line 71) | typedef Map<size_t, EdgeMap, NodeIndex, NodeTable>  NodeMap;
  type SymmNet (line 72) | typedef SymmNet<_EdgeData, EdgeTable, NodeTable,
  type NodeMap (line 74) | typedef NodeMap super;
  type _EdgeData (line 75) | typedef _EdgeData EdgeData;
  function edgesLegal (line 98) | bool edgesLegal(const size_t source, const size_t dest) const {
  function localLegal (line 116) | bool localLegal(const size_t source, const size_t dest) const {
  function resize (line 142) | void resize(const size_t newSize) {
  function increase_size (line 162) | size_t increase_size(const size_t i) {
  function EdgeData (line 181) | const EdgeData & operator()(const size_t i, const size_t j) const {
  function class (line 236) | class EdgeIter:public EdgeMap::iterator {
  type typename (line 271) | typedef typename NodeMap::value_stub SuperStub;
  function MyType (line 278) | const MyType & getConstNet() {return getNet().c();}
  function EdgeIter (line 302) | EdgeIter begin() {
  function class (line 325) | class NodeIter:public NodeMap::iterator {
  type NodeIter (line 338) | typedef NodeIter iterator;
  type typename (line 339) | typedef typename super::const_iterator const_iterator;
  type EdgeIter (line 340) | typedef EdgeIter edge_iterator;
  function iterator (line 342) | iterator begin() {return NodeIter(this);}
  type typename (line 344) | typedef typename EdgeMap::const_iterator const_edge_iterator;
  function Node (line 346) | Node operator[](const size_t i) {
  function typename (line 356) | typename NodeMap::const_reference operator[](const size_t i) const {
  function operator (line 447) | bool operator==(const MyType & other) const {
  function operator (line 451) | bool operator!=(const MyType & other) const {
  type WeightPair (line 588) | typedef WeightPair<EdgeData> EdgePair;
  type AutoMap (line 589) | typedef AutoMap<size_t, EdgePair, EdgeIndex, EdgeTable,
  type Map (line 591) | typedef Map<size_t, EdgeMap, NodeIndex, NodeTable>  NodeMap;
  type DirNet (line 592) | typedef DirNet<EdgeData, EdgeTable, NodeTable,
  type NodeMap (line 594) | typedef NodeMap super;
  function edgesLegal (line 617) | bool edgesLegal(const size_t source, const size_t dest) const {
  function localLegal (line 637) | bool localLegal(const size_t source, const size_t dest) const {
  function resize (line 663) | void resize(const size_t newSize) {
  function increase_size (line 683) | size_t increase_size(const size_t i) {
  function EdgePair (line 702) | const EdgePair & operator()(const size_t i, const size_t j) const {
  function operator (line 759) | operator EdgeData() {
  function class (line 772) | class EdgeIter:public EdgeMap::iterator {
  type typename (line 807) | typedef typename NodeMap::value_stub SuperStub;
  function MyType (line 814) | const MyType & getConstNet() {return getNet().c();}
  function EdgeIter (line 838) | EdgeIter begin() {
  function class (line 855) | class NodeIter:public NodeMap::iterator {
  type NodeIter (line 868) | typedef NodeIter iterator;
  type typename (line 869) | typedef typename super::const_iterator const_iterator;
  type EdgeIter (line 870) | typedef EdgeIter edge_iterator;
  function iterator (line 872) | iterator begin() {return NodeIter(this);}
  type typename (line 874) | typedef typename EdgeMap::const_iterator const_edge_iterator;
  function Node (line 876) | Node operator[](const size_t i) {
  function typename (line 886) | typename NodeMap::const_reference operator[](const size_t i) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/Neural/NNet.H
  function key (line 56) | unsigned key() {return target;}
  function DelayType (line 58) | DelayType delay() {return xmitDelay;}
  function TimeType (line 72) | TimeType getDelay() {return delay;}
  function virtual (line 97) | virtual SynBase & operator[](size_t i) {
  function virtual (line 101) | virtual const SynBase & operator[](size_t i) const {
  function virtual (line 105) | virtual void setSynAt(size_t i, SynBase & src) {
  function virtual (line 109) | virtual EventBase * zap(TimeType time) {
  function virtual (line 113) | virtual void postSynZap(SynBase * target) {
  function class (line 130) | class NeuronBase<bool isVirtual> {
  function class (line 155) | class ActPot::public NetworkType::EventBase {
  function ActPot (line 185) | ActPot * zap() {
  function postSynZap (line 189) | void postSynZap(TimeType time, Synapse::Base * loc) {
  type EventQueue (line 203) | typedef EventQueue::
  function update (line 210) | void update(TimeType when) {
  function TimeType (line 214) | TimeType zap(const float strength, const TimeType time) {
  type Soma (line 235) | typedef Soma<TimeType> Soma;
  type SynBaseTemplate (line 236) | typedef SynBaseTemplate<_TimeType> SynBase;
  type EvQueueTemplate (line 237) | typedef EvQueueTemplate<_TimeType> EventQueue;
  type SpikeNet (line 238) | typedef SpikeNet<SomaTemplate, SynBaseTemplate, IsVirtual,
  type Axon (line 240) | typedef Axon<SynBase, IsVirtual> AxonType;
  type AutoMap (line 241) | typedef AutoMap<size_t, SynBase *> Dendritic;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/PrefetchPolicy.H
  function lce_prefetch (line 30) | void lce_prefetch(const void * const loc) {
  function prefetch (line 41) | void prefetch(const T & tgt) {}
  function safe_prefetch (line 42) | void safe_prefetch(const T & tgt) {}

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/Randgens.H
  type SeedType (line 37) | typedef int SeedType;
  function FloatType (line 73) | FloatType nextNormed() {return next();}
  function FloatType (line 76) | FloatType next() {
  type typename (line 119) | typedef typename Generator::SeedType SeedType;
  function Generator (line 121) | RandNumGen(SeedType seed):

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/bits/EmbBoolSelector.H
  type type (line 26) | typedef bool type;
  type SelectHelper (line 30) | struct SelectHelper
  type type (line 31) | typedef char type;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/bits/FiboHeapCore.H
  function precedes (line 39) | static bool precedes(KeyType first, KeyType second) {return (first<secon...
  function removeDeep (line 57) | void removeDeep(NodeType * subject) {
  function addToRootList (line 74) | void addToRootList(NodeType * subject) {
  function promoteChain (line 85) | void promoteChain(NodeType * subject) {
  function promoteNode (line 114) | void promoteNode(NodeType * subject) {
  function compress (line 128) | void compress() {
  function popNode (line 236) | void popNode(NodeType * node) {
  function deleteNode (line 292) | void deleteNode(NodeType * subject) {
  function push (line 308) | unsigned push(NodeType * node) {
  function justDecreased (line 335) | void justDecreased(NodeType * subject) {
  function justIncreased (line 348) | void justIncreased(NodeType * subject) {
  function getNumElems (line 354) | unsigned getNumElems() {
  function isEmpty (line 359) | bool isEmpty() {
  function NodeType (line 365) | NodeType * getRoot() const {return root;}
  function NodeType (line 376) | NodeType * pop() {
  function containsNode (line 391) | bool containsNode(const NodeType * const subject) const {
  type ValueType (line 472) | typedef ValueType & ValueRefType;
  function ValueRefType (line 473) | ValueRefType value() {return val;}
  type FiboHeapNode (line 488) | typedef FiboHeapNode<KeyType, ValueType> MyType;
  type HeapKeyTraits (line 490) | typedef HeapKeyTraits<KeyType> MyKeyTraits;
  function delNode (line 510) | void delNode() {
  function init (line 527) | void init() {
  function rightOperand (line 555) | bool operator<(const MyType & rightOperand) const {
  function decreaseKey (line 570) | void decreaseKey(const KeyType newKey, FiboHeapCore<MyType> & heap) {
  function setKey (line 578) | void setKey(const KeyType newKey, FiboHeapCore<MyType> & heap) {
  function subtreeValid (line 613) | bool subtreeValid() {
  function siblingTo (line 649) | bool siblingTo(const MyType * const subject) const {
  function countNodes (line 661) | unsigned countNodes() const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/bits/hashcore.H
  type IndexType (line 51) | typedef unsigned int IndexType;
  function IndexType (line 63) | static IndexType getKeyValue(KeyType key) {return key;}
  function IndexType (line 72) | static IndexType getKeyValue(KeyType * key) {
  type ValueType (line 85) | typedef ValueType& ref_type;
  type ValueType (line 86) | typedef const ValueType& const_ref_type;
  type ValueType (line 87) | typedef ValueType* pointer_type;
  function void (line 91) | struct HashValueTraits<void> {
  type ArrayDataContainer (line 107) | typedef ArrayDataContainer<DataType> MyType;
  function typename (line 131) | typename HashValueTraits<DataType>::ref_type operator[](const IndexType ...
  function typename (line 135) | typename HashValueTraits<DataType>::const_ref_type
  function moveElemTo (line 141) | void moveElemTo(const IndexType from,
  function prefetchAt (line 147) | void prefetchAt(const IndexType loc) const {
  function moveElemTo (line 172) | void moveElemTo(const IndexType from,
  function prefetchAt (line 176) | void prefetchAt(const IndexType loc) const {}
  function class (line 186) | class HashTableSize {
  type HashKeyTraits (line 205) | typedef HashKeyTraits<KeyType> myTraits;
  function IndexType (line 218) | IndexType getPrevPlace(const IndexType place) const {
  function IndexType (line 221) | IndexType getInitPlace(const KeyType key) const {
  function class (line 232) | class HashCounter: public HashTableSize {
  function markedVirgin (line 250) | void markedVirgin() {numVirgs++;}
  function wroteOn (line 258) | void wroteOn(const unsigned char status) {
  function removedKey (line 264) | void removedKey() {numKeys--;}
  function virginsLegal (line 272) | bool virginsLegal(IndexType compVal) const {
  function usedLegal (line 275) | bool usedLegal(IndexType compVal) const {return (compVal==getNumKeys());}
  function removedLegal (line 276) | bool removedLegal(IndexType compVal) const {
  function justRemoved (line 315) | unsigned char justRemoved(IndexType & newSize) {
  function aboutToPut (line 324) | bool aboutToPut(IndexType & newSize) {
  function rehash (line 376) | void rehash(const IndexType size) {
  function fillSlot (line 422) | bool fillSlot(IndexType & emptyPlace) {
  function rehashLocally (line 502) | void rehashLocally() {
  function keyFoundAt (line 739) | bool keyFoundAt(const IndexType place) const {
  function isLegal (line 767) | bool isLegal() const {
  function class (line 787) | class iterator {
  function isAtEnd (line 845) | bool isAtEnd() {
  function KeyType (line 851) | KeyType operator*() {
  function typename (line 859) | typename HashValueTraits<ValueType>::const_ref_type getValue() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/ArrayBase.H
  type ArrayBase (line 45) | typedef ArrayBase<DataType> MyType;
  type DataType (line 52) | typedef const DataType & const_reference;
  function resize (line 57) | void resize(const size_t newSize) {
  function resize (line 70) | void resize(const size_t newSize, const size_t oldSize,
  function resize (line 88) | void resize(const size_t newSize, const size_t oldSize) {
  function pushAt (line 105) | void pushAt(const size_t loc, const size_t oldSize) {
  function pullFrom (line 110) | void pullFrom(const size_t loc, const size_t oldSize) {
  function reference (line 114) | reference refTo(const size_t i) {return data[i];}
  function const_reference (line 116) | const_reference constRefTo(const size_t i) const {return data[i];}
  function elemSize (line 118) | static size_t elemSize() {return sizeof(DataType);}
  function initSet (line 136) | void initSet(const DataType & src, size_t loc) {
  function assemble (line 140) | void assemble() {}
  function copyElemTo (line 142) | void copyElemTo(MyType & dest, const size_t loc, const size_t i) {
  function copy (line 146) | void copy(const size_t to, const size_t from) {
  function isUsed (line 232) | bool isUsed(const size_t loc) const {return true;}
  type Log2BitsDown (line 272) | struct Log2BitsDown
  type ArrayBase (line 303) | typedef ArrayBase<size_t> super;
  function reprLen (line 311) | static size_t reprLen(const size_t len) {
  function filledSlot (line 317) | static size_t filledSlot(bool val) {
  function reprSlot (line 322) | size_t & reprSlot(const size_t loc) {
  function reprSlot (line 326) | const size_t & reprSlot(const size_t loc) const {
  function reprBit (line 330) | static size_t reprBit(const size_t loc) {
  function assemble (line 345) | void assemble() {}
  function resize (line 364) | void resize(const size_t newSize, const size_t oldSize,
  function resize (line 391) | void resize(const size_t newSize, const size_t oldSize) {
  function class (line 406) | class stub {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/ContainerPolicies.H
  type typename (line 38) | typedef typename TableType::WeightType WeightType;
  function WeightType (line 39) | static WeightType getWeight(const TableType & subj) {
  type WeightType (line 54) | typedef size_t WeightType;
  function WeightType (line 56) | static WeightType getWeight(const TableType & subj) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/DefaultIndexParams.H
  type typename (line 37) | typedef typename EmbStatusPolicy

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/KeyPolicy.H
  function getHashValue (line 32) | static size_t getHashValue(const KeyType & subj) {
  function getHashValue (line 54) | static size_t getHashValue(const KeyType * & key) {
  function getHashValue (line 61) | static size_t getHashValue(const IntegralType & key) {return key;}
  function firstSmaller (line 62) | static bool firstSmaller(const IntegralType & first,
  type KeyPolicy (line 71) | struct KeyPolicy
  type KeyPolicy (line 74) | struct KeyPolicy
  type KeyPolicy (line 77) | struct KeyPolicy
  type KeyPolicy (line 80) | struct KeyPolicy
  type KeyPolicy (line 83) | struct KeyPolicy
  type KeyPolicy (line 86) | struct KeyPolicy

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/Pair.H
  type SecondType (line 42) | typedef SecondType & second_reference;
  type FirstType (line 43) | typedef const FirstType & const_first_reference;
  type SecondType (line 44) | typedef const SecondType & const_second_reference;
  function removeSecond (line 50) | void removeSecond() {_second.~SecondType();}
  function clearSecond (line 51) | void clearSecond() {
  type FirstType (line 65) | typedef const FirstType & second_reference;
  type FirstType (line 66) | typedef const FirstType & const_first_reference;
  type FirstType (line 67) | typedef const FirstType & const_second_reference;
  function removeSecond (line 72) | void removeSecond() {}
  type SecondType (line 81) | typedef SecondType & second_reference;
  type SecondType (line 82) | typedef const SecondType & const_first_reference;
  type SecondType (line 83) | typedef const SecondType & const_second_reference;
  function removeSecond (line 88) | void removeSecond() {_second.~SecondType();}
  function clearSecond (line 90) | void clearSecond() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/WeightPolicy.H
  type DataType (line 37) | typedef DataType WeightType;
  type DataType (line 39) | typedef DataType & weight_reference;
  function WeightType (line 41) | static WeightType getWeight(const DataType & subj) {return subj;}
  function weight_reference (line 43) | static weight_reference refToWeight(DataType & subj) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/Array.H
  type Table (line 40) | typedef Table<KeyType, ValueType, Policy, Params, MyType> super;
  function findFirst (line 59) | bool findFirst(const KeyType & key, size_t & loc) const {
  function findNext (line 68) | bool findNext(const KeyType & key, size_t & loc) const {
  function forcedFind (line 72) | bool forcedFind(const KeyType & key, size_t & loc) {
  function placeToPut (line 83) | void placeToPut(const KeyType & key, size_t & loc) {
  function removeFrom (line 89) | void removeFrom(size_t loc) {
  function remove (line 96) | bool remove(const KeyType & key) {
  function trim (line 107) | void trim() {}
  function contains (line 122) | bool contains(const KeyType & key) const {
  function class (line 127) | class iterator {
  function class (line 150) | class const_iterator {
  function iterator (line 174) | iterator begin() {return iterator(this);}
  function keyLegal (line 177) | bool keyLegal(const KeyType & key) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/AutoVec.H
  type SizeHelper (line 23) | struct SizeHelper {
  type Table (line 49) | typedef Table<KeyType, ValueType, Policy, Params, MyType> super;
  function freePtr (line 73) | size_t & freePtr(size_t i) {
  function upsize (line 82) | size_t upsize() {
  function downsize (line 96) | void downsize() {
  function isUsed (line 137) | bool isUsed(size_t i) {
  function removeAt (line 146) | void removeAt(const size_t i) {
  function newElem (line 162) | size_t newElem() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/HashControllers.H
  type FiboHashMult (line 33) | struct FiboHashMult
  type FiboHashMult (line 38) | struct FiboHashMult
  function class (line 47) | class Pow2HashController {
  function Pow2HashController (line 79) | Pow2DivHashController(size_t logSize): Pow2HashController(logSize) {}
  function getInitPlace (line 80) | size_t getInitPlace(const size_t hashValue) const {
  function Pow2HashController (line 93) | Pow2MultHashController(size_t logSize): Pow2HashController(logSize) {}
  function getInitPlace (line 94) | size_t getInitPlace(const size_t hashValue) const {
  function aboutToPut (line 120) | bool aboutToPut(size_t & nativeSize) const {
  function trim (line 140) | bool trim(size_t & nativeSize) const {
  function removed (line 158) | void removed() {numKeys--;}
  function added (line 159) | void added() {numKeys++;}
  function isLegal (line 161) | bool isLegal(const size_t keyCount) const {
  function nativeSizeForCapacity (line 170) | static size_t nativeSizeForCapacity(const size_t capacity,
  function sizeForCapacity (line 177) | static size_t sizeForCapacity(const size_t capacity,

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/LinearHash.H
  type TableWithStatus (line 131) | typedef TableWithStatus<KeyType, ValueType, Policy, Params, Table,
  type typename (line 133) | typedef typename Params::HashController HashController;
  function rehash (line 148) | void rehash(const size_t nativeSize) {
  function rehash_put (line 195) | void rehash_put(const size_t i, MyType & dest) {
  function initPlaceAt (line 228) | size_t initPlaceAt(const size_t loc) const {
  function initPlaceBefore (line 246) | size_t initPlaceBefore(const size_t initProbe, const size_t currLoc) con...
  function pushProbeAt (line 260) | void pushProbeAt(const size_t loc) {
  function removeFrom (line 299) | void removeFrom(size_t toBeFilled) {
  function findFirst (line 371) | bool findFirst(const KeyType & key, size_t & location) const {
  function findFrom (line 380) | bool findFrom(const KeyType & key, size_t & location) const {
  function forcedFind (line 458) | bool forcedFind(const KeyType & key, size_t & location) {
  function clear (line 500) | void clear() {
  function contains (line 530) | bool contains(const KeyType & key) const {
  function remove (line 543) | bool remove(const KeyType & key) {
  function trim (line 556) | void trim() {
  function prefetch (line 563) | void prefetch(const KeyType & key) const {
  function preload (line 567) | bool preload(const KeyType & key) const {
  function iterator (line 577) | iterator begin() {return iterator(this);}
  function keyFoundAt (line 594) | bool keyFoundAt(const size_t place) const {
  function keyLegal (line 645) | bool keyLegal(const KeyType & key) const {
  function class (line 665) | class const_iterator {
  function class (line 770) | class iterator {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/OrderedArray.H
  type Table (line 40) | typedef Table<KeyType, ValueType, Policy, Params, MyType> super;
  function findFirstSlot (line 50) | size_t findFirstSlot(const KeyType & key) const {
  function findFirst (line 88) | bool findFirst(const KeyType & key, size_t & loc) const {
  function findNext (line 95) | bool findNext(const KeyType & key, size_t & loc) const {
  function forcedFind (line 99) | bool forcedFind(const KeyType & key, size_t & loc) {
  function placeToPut (line 128) | size_t placeToPut(const KeyType & key, size_t & loc) {
  function removeFrom (line 141) | void removeFrom(size_t loc) {
  function remove (line 148) | bool remove(const KeyType & key) {
  function trim (line 159) | void trim() {}
  function contains (line 174) | bool contains(const KeyType & key) const {
  function class (line 179) | class iterator {
  function class (line 202) | class const_iterator {
  function iterator (line 226) | iterator begin() {return iterator(this);}
  function keyLegal (line 229) | bool keyLegal(const KeyType & key) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/TableWithStatus.H
  type EmbStatusPolicy (line 31) | struct EmbStatusPolicy {}
  type ExtStatusPolicy (line 32) | struct ExtStatusPolicy {}
  type Table (line 48) | typedef Table<KeyType, ValueType, Policy, Params, Index> super;
  function KeyType (line 61) | const KeyType & constRefToKey(const size_t i) const {
  function setAsEmpty (line 73) | void setAsEmpty(const size_t i) {
  type Table (line 92) | typedef Table<KeyType, ValueType, Policy, Params, Index> super;
  function resize (line 112) | void resize(size_t newSize, size_t oldSize) {
  function copyElemTo (line 120) | void copyElemTo(MyType & dest, const size_t loc, const size_t i) {
  function setAsEmpty (line 134) | void setAsEmpty(const size_t i) {status[i]=false;}
  type Table (line 152) | typedef Table<Pair<KeyType,bool>, ValueType, Policy, Params, Index> super;
  function KeyType (line 163) | const KeyType & constRefToKey(size_t i) const {
  function setAsEmpty (line 179) | void setAsEmpty(size_t i) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/indices/Vector.H
  type Table (line 44) | typedef Table<KeyType, ValueType, Policy, Params, MyType> super;
  function forcedFind (line 70) | size_t forcedFind(const KeyType & key, size_t & loc) {
  function remove (line 75) | bool remove(const KeyType & key) {
  function contains (line 83) | bool contains(const KeyType & key) const {
  function trim (line 87) | void trim() {}
  function resize (line 97) | void resize(const size_t newSize) {
  function const_value_reference (line 108) | const_value_reference operator[](const KeyType & key) const {
  function class (line 117) | class iterator {
  function class (line 143) | class const_iterator {
  function iterator (line 169) | iterator begin() {return iterator(this);}
  function keyLegal (line 172) | bool keyLegal(const KeyType & key) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/tables/ExplSumTreeTable.H
  type ImplTreeHelper (line 50) | typedef ImplTreeHelper<Params::treeLogBase> help;
  type typename (line 51) | typedef typename Policy::WeightType WeightType;
  type ValueTable (line 52) | typedef ValueTable<Pair<KeyType, WeightType>, ValueType,
  type typename (line 55) | typedef typename Pair<KeyType, WeightType>::second_reference
  type typename (line 57) | typedef typename Pair<KeyType, WeightType>::const_second_reference
  type typename (line 59) | typedef typename Pair<KeyType, WeightType>::first_reference key_reference;
  type typename (line 60) | typedef typename Pair<KeyType, WeightType>::const_first_reference
  function updateAt (line 81) | void updateAt(size_t i, WeightType diff) {
  function WeightType (line 101) | WeightType sumAt(const size_t i) const {
  function const_key_reference (line 113) | const_key_reference constRefToKey(const size_t loc) const {
  function disassemble (line 118) | void disassemble() {
  function assemble (line 135) | void assemble() {
  function moveOrSwap (line 152) | void moveOrSwap(size_t to, size_t from) {
  function swap (line 181) | void swap(const size_t to, const size_t from) {
  function remove_stage_1 (line 189) | void remove_stage_1(const size_t i) {}
  function remove_stage_2 (line 196) | void remove_stage_2(const size_t i) {
  function setValue (line 210) | void setValue(const size_t loc, const ValueType & value) {
  type typename (line 226) | typedef typename super::value_stub super_stub;
  function _int_lce_update (line 231) | void _int_lce_update() {
  function _lce_update (line 252) | void _lce_update() {
  function _lce_finalize (line 258) | void _lce_finalize() {
  function _lce_upToDate (line 263) | bool _lce_upToDate() {
  type stub (line 299) | typedef stub<false> value_stub;
  function localLegal (line 316) | bool localLegal(const size_t loc) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/tables/ImplSumTreeTable.H
  type help (line 50) | typedef help ImplTreeHelper<Params::logBase>;
  type ValueTable (line 51) | typedef ValueTable<KeyType, ValueType, Policy, Params, Index> super;
  type stub (line 58) | typedef stub<false> value_stub;
  type ValueType (line 62) | typedef ValueType const_value_reference;
  function update (line 72) | void update(size_t i, const WeightType diff) const {
  function WeightType (line 80) | const WeightType & sumAt(const size_t i) const {
  function WeightType (line 88) | WeightType childSum(const size_t loc) const {
  function remove_stage_1 (line 106) | void remove_stage_1(const size_t i) {}
  function remove_stage_2 (line 113) | void remove_stage_2(const size_t i) {
  function moveOrSwap (line 127) | void moveOrSwap(const size_t to, const size_t from) {
  function swap (line 150) | void swap(const size_t to, const size_t from) {moveOrSwap(to, from);}
  function _lce_finalize (line 170) | void _lce_finalize() {
  function assemble (line 203) | void assemble(const size_t len) {
  function ValueType (line 215) | ValueType constRefToVal(const size_t i) const {
  function stub (line 223) | stub refToVal(const size_t i) const {
  function KeyType (line 230) | const KeyType & constRefToKey(const size_t loc) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/tables/ImplTreeHelper.H
  function isRoot (line 27) | static bool isRoot(const size_t i) {return i==0;}
  function father (line 33) | static size_t father(const size_t i) {return (i-1) >> logBase;}
  function child (line 39) | static size_t child(const size_t i) {
  function childLimit (line 52) | static size_t childLimit(const size_t i, const size_t len) {
  type ImplTreeHelper (line 63) | struct ImplTreeHelper
  function isRoot (line 65) | static bool isRoot(const size_t i) {return i==0;}
  function father (line 71) | static size_t father(const size_t i) {return ((i+1) >> 1)-1;}
  function child (line 77) | static size_t child(const size_t i) {
  function childLimit (line 92) | static size_t childLimit(const size_t i, const size_t len) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/tables/StubBase.H
  type typename (line 38) | typedef typename super::reference reference;
  type typename (line 39) | typedef typename super::ValueType ValueType;
  type typename (line 40) | typedef typename super::pointer pointer;
  type ArrayStub (line 41) | typedef ArrayStub<ArrayType, SuperStub> MyType;
  type ValueType (line 151) | typedef ValueType & reference;
  type ValueType (line 152) | typedef ValueType * pointer;
  function reference (line 160) | reference ref() {return target.directRefToValue(loc);}
  function pointer (line 161) | pointer pnt() {return &ref();}
  function _lce_finalize (line 163) | void _lce_finalize() {}
  function _lce_update (line 164) | void _lce_update() {}
  function _lce_upToDate (line 165) | bool _lce_upToDate() {return true;}
  type ValueType (line 186) | typedef ValueType & reference;
  type ValueType (line 187) | typedef ValueType * pointer;
  function reference (line 197) | reference ref() {return value;}
  function pointer (line 198) | pointer pnt() {return &ref();}
  function _lce_finalize (line 200) | void _lce_finalize() { /* Write back. */
  function _lce_update (line 206) | void _lce_update() {_lce_finalize();}
  function _lce_upToDate (line 207) | bool _lce_upToDate() {return value==target.directRefTo(loc);}

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/tables/ValueTable.H
  type ArrayBase (line 42) | typedef ArrayBase<Pair<KeyType, _ValueType> > super;
  type typename (line 48) | typedef typename Pair<KeyType, ValueType>::second_reference  value_refer...
  type typename (line 49) | typedef typename Pair<KeyType, ValueType>::const_second_reference
  type typename (line 51) | typedef typename Pair<KeyType, ValueType>::first_reference key_reference;
  type typename (line 52) | typedef typename Pair<KeyType, ValueType>::const_first_reference
  type ArrayStub (line 56) | typedef ArrayStub<MyType, ArrayRefStub>  value_stub;
  type typename (line 61) | typedef typename Policy::WeightType WeightType;
  type CountWeightPolicy (line 63) | typedef CountWeightPolicy<MyType> DefaultWeightPolicy;
  function usedByCRTP (line 87) | size_t usedByCRTP(const size_t i) const {
  function value_reference (line 109) | value_reference refToVal(const size_t loc) {
  function const_value_reference (line 114) | const_value_reference constRefToVal(const size_t loc) const {
  function key_reference (line 119) | key_reference refToKey(const size_t loc) {
  function const_key_reference (line 124) | const_key_reference constRefToKey(const size_t loc) const {
  function WeightType (line 131) | WeightType weightAt(const size_t i) const {
  function moveOrSwap (line 141) | void moveOrSwap(const size_t to, const size_t from) {
  function swapValues (line 147) | void swapValues(const size_t to, const size_t from) {
  function removeVal (line 157) | void removeVal(const size_t loc) {
  function clearVal (line 163) | void clearVal(const size_t loc) {
  function remove_stage_1 (line 173) | void remove_stage_1(const size_t loc) {
  function remove_stage_2 (line 178) | void remove_stage_2(const size_t loc) {}
  function final_remove (line 184) | void final_remove(const size_t loc) {
  function swapVals (line 193) | void swapVals(const size_t to, const size_t from) {
  function weighedSlotSelect (line 203) | size_t weighedSlotSelect(WeightType val) const {
  function assemble (line 216) | void assemble() {}
  function disassemble (line 218) | void disassemble() {}
  function localLegal (line 220) | bool localLegal(const size_t i) const {return true;}
  function setValue (line 222) | void setValue(const size_t loc, const_value_reference value) {
  function pushAt (line 228) | void pushAt(const size_t loc) {
  function pushToTail (line 234) | void pushToTail() {
  function pullFrom (line 238) | void pullFrom(const size_t loc) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/containers/tables/WeightSumTable.H
  type ValueTable (line 48) | typedef ValueTable<KeyType, ValueType, Policy, Params, Index> super;
  type WeightWeightPolicy (line 52) | typedef WeightWeightPolicy<MyType> DefaultWeightPolicy;
  function remove_stage_2 (line 69) | void remove_stage_2(const size_t loc) {
  function setValue (line 78) | void setValue(const size_t loc, const ValueType & value) {
  function pushAt (line 87) | void pushAt(const size_t loc) {
  function pushToTail (line 93) | void pushToTail() {
  function pullFrom (line 98) | void pullFrom(const size_t loc) {
  function _lce_finalize (line 121) | void _lce_finalize() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/hashes.H
  function myKey (line 61) | HashKeyBase(KeyType key): myKey(key) {}
  function keyEquals (line 64) | bool keyEquals(const HashKeyBase<KeyType> & cmp) const {
  function IndexType (line 81) | static IndexType getHashValue(const KeyType & src) {return src;}
  function setAsVirgin (line 87) | void setAsVirgin() {myKey=std::numeric_limits<KeyType>::max();}
  function IndexType (line 104) | static IndexType & getHashValue(const KeyType & src) {
  function setAsVirgin (line 111) | void setAsVirgin() {myKey=0;}
  function setAsVirgin (line 131) | void setAsVirgin() {count=0;}
  function IndexType (line 136) | IndexType getCount() {return count;}
  function IndexType (line 137) | IndexType incrCount() {return count++;}
  function IndexType (line 138) | IndexType decrCount() {return count--;}
  function super (line 149) | HashPair(const KeyType & key): super(key) {}
  type PackedHash (line 173) | typedef PackedHash<HashKey<KeyType>, HashController, false,StatusType> s...
  function put (line 184) | bool put(const KeyType & key) {
  function remove (line 216) | bool remove(const KeyType & key) {
  function IndexType (line 238) | IndexType size() {return controller.getNumKeys();}
  function class (line 240) | class iterator: public super::iterator {
  function iterator (line 253) | iterator begin() {return iterator(*this);}
  function iterator (line 254) | iterator end() {return iterator(*this, true);}
  type HashMultiKeySet (line 267) | typedef HashMultiKeySet<KeyType, HashController, StatusType> MyType;
  function put (line 278) | unsigned put(const KeyType & key) {
  function remove (line 301) | unsigned remove(const KeyType & key) {
  function contains (line 321) | unsigned contains(const KeyType & key) const {
  function class (line 331) | class iterator: public super::iterator {
  function iterator (line 344) | iterator begin() {return iterator(*this);}
  function iterator (line 345) | iterator end() {return iterator(*this, true);}
  function class (line 347) | class const_iterator: public super::const_iterator {
  type HashMap (line 370) | typedef HashMap<KeyType, ValueType, HashController, StatusType> MyType;
  function put (line 398) | bool put(const KeyType & key, const ValueType & value) {
  function remove (line 402) | bool remove(const KeyType key) {
  type HashKeyBase (line 418) | typedef HashKeyBase<IndexType> super;
  function IndexType (line 425) | static IndexType getHashValue(const KeyType & src) {return src;}
  function setValue (line 428) | void setValue(const ValueType & newValue) {value=newValue;}
  function setAsUsed (line 430) | void setAsUsed() {}
  function setAsVirgin (line 431) | void setAsVirgin() {val=ValueType();}
  function isVirgin (line 433) | bool isVirgin() {return val==ValueType();}
  function isInUse (line 434) | bool isInUse() {return val!=VAlueType();}
  function value (line 451) | bool value() {
  function setValue (line 455) | void setValue(bool val) {
  function substractFromSum (line 477) | void substractFromSum(const ValueType & value) {mySum-=value;}
  function substractFromSum (line 492) | void substractFromSum(const ValueType & value) {}
  function Stub (line 524) | Stub operator[](const IndexType key) {return Stub(*this, key)}
  function ValueType (line 534) | ValueType operator[](const IndexType key) const {
  function ValueType (line 629) | ValueType operator+=(const ValueType & value) {
  function ValueType (line 633) | ValueType operator-=(const ValueType & value) {
  function ValueType (line 637) | ValueType operator*=(const ValueType & value) {
  function ValueType (line 641) | ValueType operator/=(const ValueType & value) {
  function operator (line 645) | operator ValueType() {
  type KeyPacker (line 667) | typedef KeyPacker<InputType, OutputType, StatusType> MyType;
  function OutputType (line 671) | OutputType getPacked(InputType input) {
  function OutputType (line 682) | OutputType getKeyCount() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/k_clique/cliqueHash.H
  function class (line 27) | class cliqueHash {
  function contains (line 115) | bool contains(const clique & key) {
  function getValue (line 129) | int getValue(const clique & key) {
  function put (line 143) | void put(const clique & key, const size_t value) {
  function finished (line 202) | bool finished() {
  function getKeyCount (line 211) | size_t getKeyCount() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/k_clique/multiIter.H
  type std (line 28) | typedef std::list<size_t> nodeList;
  type Set (line 29) | typedef Set<size_t> nodeSet;
  function class (line 31) | class multiIter {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/k_clique/numSet.H
  function class (line 26) | class numSet {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/k_clique/numSet2.H
  function class (line 28) | class numSet2 {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/k_clique/weighedClique.H
  function class (line 26) | class clique {
  type SymmNet (line 153) | typedef  SymmNet<float> NetType;
  function class (line 157) | class weighedClique: public clique {
  function copyClique (line 252) | void copyClique(const weighedClique & old_clique) {
  function replaceNodes (line 259) | void replaceNodes(  const std::vector<size_t> & unsorted_nodes, const Ne...
  function class (line 280) | class Link: public clique {
  function getWeight (line 303) | float getWeight() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/Bindata.H
  function countElements (line 311) | int countElements(char * filename){
  function writeData (line 347) | void writeData(char * filename, double * data, int number_of_elements){

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/BinomialSampler.H
  function class (line 69) | class BinomialGenerator
  function get (line 104) | size_t get(double rand_num)
  function init_high_list (line 161) | void init_high_list()
  function expand_low_list (line 182) | size_t expand_low_list(double rand)
  function expand_high_list (line 214) | size_t expand_high_list(double rand)
  function binomial (line 274) | size_t binomial(size_t N, float p, double rand_normed)

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/CalQueue.H
  function SubclassType (line 71) | SubclassType * getNext() const {return next;}
  function setNext (line 72) | void setNext(SubclassType * ptrTarget) {next=ptrTarget;}
  type TimeType (line 79) | typedef unsigned long int TimeType;
  type EventType (line 80) | typedef EventType * EventPtr;
  type EventType (line 81) | typedef EventType * const ConstEventPtr;
  function TimeType (line 82) | static TimeType getEventTime(const ConstEventPtr subject) {
  function EventPtr (line 85) | static EventPtr getNext(const ConstEventPtr subject) {
  function setNext (line 88) | static void setNext(const EventPtr subject, const ConstEventPtr next) {
  function prefetch (line 91) | static void prefetch(const ConstEventPtr subject) {}
  type EventTypeTraits (line 96) | typedef EventTypeTraits<EventType> MyTraits;
  type MyTraits (line 97) | typedef MyTraits::EventPtr EventPtr;
  type MyTraits (line 98) | typedef MyTraits::ConstEventPtr ConstEventPtr;
  type MyTraits (line 99) | typedef MyTraits::TimeType TimeType;
  function push (line 151) | void push(const EventPtr subject) {
  function EventPtr (line 176) | EventPtr pop() {
  function TimeType (line 186) | TimeType getMinTime() {
  function isEmpty (line 191) | bool isEmpty() {return (root==0);}
  function remove (line 199) | bool remove(EventPtr subject) {
  function prefetch (line 219) | void prefetch() {__builtin_prefetch(root);}
  type MyTraits (line 232) | typedef MyTraits::EventPtr EventPtr;
  type MyTraits (line 233) | typedef MyTraits::TimeType TimeType;
  function getSlot (line 255) | unsigned int getSlot(const TimeType time) const {
  function push (line 307) | void push(const EventPtr subject) {
  function EventPtr (line 317) | EventPtr pop(unsigned int & probeLenAcc, unsigned int & numFutEvsAcc) {
  function remove (line 348) | bool remove(const EventPtr subject) { /* Const might seem strange :) */
  function consume (line 357) | void consume(CalQCore<EventType> & source) {
  type EventTypeTraits (line 405) | typedef EventTypeTraits<EventType>::TimeType TimeType;
  type EventTypeTraits (line 406) | typedef EventTypeTraits<EventType>::EventPtr EventPtr;
  function EventPtr (line 423) | EventPtr pop() {
  function remove (line 481) | bool remove(EventPtr subject) {return queue.remove(subject);}
  function getNumEvents (line 483) | unsigned getNumEvents() {return queue.getNumEvents();}

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/EventQueue.H
  function EventBase (line 92) | EventBase pop() {
  function push (line 99) | unsigned push(EventBase event) {
  function del (line 112) | void del() {
  function getSlot (line 147) | unsigned getSlot(const TimeType time) const {
  function resize (line 180) | void resize(unsigned logBinSize, unsigned logNumBins) {
  function prefetch (line 224) | void prefetch(const TimeType time) const {
  function push (line 235) | unsigned push(EventType subject) {
  function EventType (line 247) | EventType pop(unsigned int & probeLenAcc, unsigned int & numFutEvsAcc) {
  function remove (line 279) | void remove(const EventType subject) { /* Const might seem strange :) */
  type Event (line 331) | typedef Event * EventPtr;
  function EventPtr (line 349) | EventPtr pop(TimeType & time) {
  function remove (line 414) | bool remove(EventPtr subject, TimeType time) {
  function getNumEvents (line 418) | unsigned getNumEvents() {return queue.getNumEvents();}

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/FiboHeap.H
  type EmptyType (line 27) | struct EmptyType {}
  type T (line 31) | typedef T Type;
  function void (line 35) | struct VoidMask<void> {
  type FiboHeapNode (line 44) | typedef FiboHeapNode<KeyType, ValueType> NodeType;
  type typename (line 45) | typedef typename VoidMask<ValueType>::Type ValType;
  type ValType (line 46) | typedef ValType & ValRefType;
  type ValType (line 47) | typedef const ValType & constValRefType;
  function NodeType (line 61) | NodeType * push(const KeyType key, constValRefType value) {
  function KeyType (line 74) | KeyType operator*() const {
  function ValRefType (line 79) | ValRefType value() {
  function finished (line 84) | bool finished() {return heap.isEmpty();}
  function decreaseKey (line 86) | void decreaseKey(NodeType * subject, KeyType newKey) {
  function setKey (line 90) | void setKey(NodeType * subject, KeyType newKey) {
  function deleteNode (line 94) | void deleteNode(NodeType * subject) {
  function size (line 98) | unsigned size() {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/KruskalTree.H
  function IndexType (line 76) | IndexType getClusterID(const IndexType nodeIndex) const {
  function addEdge (line 105) | bool addEdge(const IndexType from, const IndexType to) {
  function IndexType (line 149) | IndexType getClusterSize(const IndexType nodeIndex) const {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/misc/KruskalTree2.H
  function getClusterID (line 76) | size_t getClusterID(const size_t nodeIndex) const {
  function addEdge (line 105) | bool addEdge(const size_t from, const size_t to) {
  function getClusterSize (line 147) | size_t getClusterSize(const size_t nodeIndex) const {
  type BiDirKruskalTree (line 157) | typedef BiDirKruskalTree<packTree> MyType;
  function addEdge (line 166) | bool addEdge(const size_t from, const size_t to) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/Dijkstrator.H
  type Dijkstrator (line 82) | typedef Dijkstrator<NetworkType, Policy, HeapType> MyType;
  type RouteEnds (line 84) | struct RouteEnds {
  type HeapType (line 89) | typedef HeapType<WeightType, RouteEnds> MyHeapType;
  type typename (line 90) | typedef typename MyHeapType::NodeType HeapNodeType;
  type HeapNodeType (line 91) | typedef HeapNodeType * HeapNodePtr;
  type typename (line 92) | typedef typename NetworkType::const_edge_iterator EdgeIter;
  function getSource (line 105) | struct RouteType {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/DirNetExtras.H
  type typename (line 83) | typedef typename NetType::EdgeData EdgeDataType;
  type typename (line 183) | typedef typename NetType::EdgeData EdgeDataType;
  type typename (line 208) | typedef typename NetType::EdgeData EdgeDataType;
  type typename (line 244) | typedef typename NetType::EdgeData EdgeDataType;
  function i (line 297) | size_t i) {
  function i (line 319) | size_t i) {
  function i (line 350) | size_t i) {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/NetExtras.H
  type SymmNet (line 123) | typedef SymmNet<EdgeDataType> MyNetType;
  type typename (line 219) | typedef typename NetType::EdgeData EdgeDataType;
  type typename (line 440) | typedef typename NetType::EdgeData EdgeDataType;
  type typename (line 529) | typedef typename NetType::EdgeData EdgeDataType;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/NetExtras2.H
  type typename (line 91) | typedef typename NetType::EdgeData EdgeDataType;
  type typename (line 172) | typedef typename NetType::EdgeData EdgeDataType;
  type std (line 217) | typedef std::set<size_t> setType;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/OldModels.H
  type SeedType (line 94) | enum SeedType {RANDOM, CLIQUE, CHAIN, RING}
  type Map (line 221) | typedef Map<size_t, Set<size_t> > ConnMap;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/Randomizer.H
  type Map (line 209) | typedef Map<size_t, float > WeighedNodes;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/UnweightedDijk.H
  type UnweighedDijk (line 58) | typedef UnweighedDijk<NetworkType> MyType;
  type typename (line 59) | typedef typename NetworkType::const_edge_iterator EdgeIter;
  type RouteType (line 74) | struct RouteType
  type RouteType (line 167) | struct RouteType {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/BA.H
  type Set (line 45) | typedef Set<size_t> nodeSet;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/Boguna.H
  type BogunaArgs (line 47) | struct BogunaArgs
  function readBogunaArgs (line 62) | void readBogunaArgs(struct BogunaArgs & args, int argc, char** argv)
  function outputBogunaArgs (line 95) | void outputBogunaArgs(struct BogunaArgs & args)
  function class (line 118) | class IDpoint
  function IDpoint_sort_function (line 127) | bool IDpoint_sort_function(IDpoint* p1, IDpoint* p2) { return (p1->x < p...

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/CommunityNet.H
  type CommNetArgs (line 158) | struct CommNetArgs {
  function commNetArgumentError (line 191) | void commNetArgumentError(void) {
  function readCommNetArgs (line 221) | void readCommNetArgs(struct CommNetArgs & args, int argc, char** argv) {
  function outputCommNetArgs (line 451) | void outputCommNetArgs(struct CommNetArgs & args) {
  function outputCommNetArguments2 (line 507) | void outputCommNetArguments2(int argc, char** argv) {
  type Map (line 564) | typedef Map<size_t, Set<size_t> > ConnMap;
  type SeedArgs (line 569) | struct SeedArgs
  type Map (line 796) | typedef Map<size_t, Set<size_t> > ConnMap;

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/Davidsen.H
  type DavidsenArgs (line 87) | struct DavidsenArgs
  function readDavidsenArgs (line 97) | void readDavidsenArgs(struct DavidsenArgs & args, int argc, char** argv)
  function outputDavidsenArgs (line 118) | void outputDavidsenArgs(struct DavidsenArgs & args)

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/HolmeKim.H
  type HolmeKimArgs (line 105) | struct HolmeKimArgs {
  function readHolmeKimArgs (line 122) | void readHolmeKimArgs(struct HolmeKimArgs & args, int argc, char** argv) {
  function outputHolmeKimArgs (line 198) | void outputHolmeKimArgs(struct HolmeKimArgs & args) {
  type SeedArgs (line 273) | struct SeedArgs

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/Marsili.H
  type Set (line 53) | typedef Set<size_t> nodeSet;
  type MarsiliArgs (line 57) | struct MarsiliArgs
  function readMarsiliArgs (line 69) | void readMarsiliArgs(struct MarsiliArgs & args, int argc, char** argv)
  function outputMarsiliArgs (line 92) | void outputMarsiliArgs(struct MarsiliArgs & args)

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/SeedNet.H
  type SeedType (line 92) | enum SeedType {RANDOM, CLIQUE, CHAIN, RING}
  type SeedArgs (line 102) | struct SeedArgs {

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/nets/models/Wong.H
  type WongArgs (line 49) | struct WongArgs
  function readWongArgs (line 71) | void readWongArgs(struct WongArgs & args, int argc, char** argv)
  function outputWongArgs (line 128) | void outputWongArgs(struct WongArgs & args)
  function class (line 165) | class IDpoint

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/lcelib/packedqueue.H
  type TimeType (line 62) | typedef unsigned long int TimeType;
  function TimeType (line 63) | static TimeType getEventTime(const PackedEventType & subject) {
  function eventUsed (line 66) | static bool eventUsed(const PackedEventType & subject) {
  function markUsageStatus (line 69) | static void markUsageStatus(PackedEventType & subject, bool whetherUsed) {
  function advance (line 74) | struct TestEvent {
  function push (line 175) | void push(PackedEventType & subject) { /* By ref. No copy. */
  function PackedEventType (line 204) | PackedEventType pop(unsigned int & probeLenAcc,
  function consume (line 261) | void consume(PackedCalQCore<PackedEventType> & source) {
  function eventAtPlace (line 298) | bool eventAtPlace(unsigned place) {
  function isLegal (line 311) | bool isLegal() {
  type PackedEventTypeTraits (line 348) | typedef PackedEventTypeTraits<PackedEventType>::TimeType TimeType;
  function requeue (line 356) | void requeue(const int binSizeLogChange,
  function PackedEventType (line 389) | PackedEventType pop() {
  function getNumEvents (line 440) | unsigned getNumEvents() {return queue.getNumEvents();}

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/nodeCommunities.h
  type Set (line 30) | typedef Set<size_t> nodeSet;
  function class (line 32) | class nodeCommunities

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/testScp.py
  function listComp (line 6) | def listComp(l1,l2):
  function compareCommunities (line 14) | def compareCommunities(scpComms,cfComms):

FILE: NonOverlappingCodes/2008-Sequential-Clique-Percolation/weighedClique.h
  function class (line 29) | class clique
  type SymmNet (line 82) | typedef  SymmNet<float> NetType;
  function class (line 86) | class weighedClique: public clique

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/cpp/Infomap-igraph-interface-library/src/Infomap-igraph-interface.cpp
  type infomap (line 3) | namespace infomap
    function igraphToInfomapNetwork (line 5) | void igraphToInfomapNetwork(infomap::Network& network, const igraph_t*...

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/cpp/Infomap-igraph-interface-library/src/Infomap-igraph-interface.h
  function namespace (line 4) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/cpp/igraph/example-igraph.cpp
  function printClusters (line 7) | void printClusters(infomap::HierarchicalNetwork& tree)
  function partitionNetwork (line 15) | void partitionNetwork(igraph_t* graph)
  function main (line 30) | int main() {

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/cpp/minimal/example.cpp
  function printTreeHelper (line 37) | void printTreeHelper(std::ostream& out, infomap::SNode& node, std::strin...
  function printTree (line 53) | void printTree(infomap::HierarchicalNetwork& tree)
  function printClusters (line 59) | void printClusters(infomap::HierarchicalNetwork& tree)
  function main (line 67) | int main(int argc, char** argv)

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/cpp/minimal/mem-example.cpp
  function parseM2ClusterInfo (line 38) | void parseM2ClusterInfo(std::string line, int &n1, int &n2){
  function printClusters (line 48) | void printClusters(infomap::HierarchicalNetwork & tree) {
  function main (line 57) | int main(int argc, char** argv)

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/cpp/minimal/multi-example.cpp
  function parseM2ClusterInfo (line 38) | void parseM2ClusterInfo(std::string line, int &n1, int &n2){
  function printClusters (line 48) | void printClusters(infomap::HierarchicalNetwork & tree) {
  function main (line 57) | int main(int argc, char** argv)

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/examples/python/example-networkx.py
  function findCommunities (line 14) | def findCommunities(G):
  function drawNetwork (line 45) | def drawNetwork(G):

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/interfaces/js/pre-worker-module.js
  function readFile (line 35) | function readFile(filename) {

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/Infomap.cpp
  type infomap (line 44) | namespace infomap
    function runInfomap (line 48) | void runInfomap(Config const& config)
    function runInfomap (line 54) | void runInfomap(Config const& config, Network& input, HierarchicalNetw...
    function getConfig (line 60) | std::vector<ParsedOption> getConfig(Config& conf, const std::string& f...
    function initBenchmark (line 296) | void initBenchmark(const Config& conf, const std::string& flags)
    function Config (line 310) | Config init(const std::string& flags)
    function run (line 343) | int run(Network& input, HierarchicalNetwork& output)
    function run (line 357) | int run(const std::string& flags)
    function main (line 411) | int main(int argc, char* argv[])

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/Infomap.h
  function namespace (line 36) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/Informatter.cpp
  type infomap (line 46) | namespace infomap
    function getConfig (line 50) | std::vector<ParsedOption> getConfig(Config& conf, const std::string& a...
    function runInformatter (line 196) | void runInformatter(Config const& config)
    function run (line 209) | int run(const std::string& args)
    function main (line 249) | int main(int argc, char* argv[])

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/Edge.h
  function namespace (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/FlowNetwork.cpp
  type infomap (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/FlowNetwork.h
  function namespace (line 39) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapBase.cpp
  function DepthStat (line 2119) | DepthStat InfomapBase::calcMaxAndAverageDepth()

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapBase.h
  function namespace (line 41) | namespace infomap
  type TwoLevelCodelength (line 375) | struct TwoLevelCodelength
  type DepthStat (line 384) | struct DepthStat

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapContext.cpp
  type infomap (line 33) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapContext.h
  function namespace (line 35) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapGreedy.h
  function namespace (line 55) | namespace infomap
  function numActiveModules (line 358) | unsigned int InfomapGreedy<InfomapImplementation>::numActiveModules()
  function numDynamicModules (line 365) | unsigned int InfomapGreedy<InfomapImplementation>::numDynamicModules()

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapGreedyCommon.h
  function namespace (line 38) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapGreedySpecialized.h
  function namespace (line 35) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/InfomapGreedyTypeSpecialized.h
  function namespace (line 35) | namespace infomap
  type MemNodeSet (line 99) | struct MemNodeSet
  type InfomapGreedyCommon (line 110) | typedef InfomapGreedyCommon<InfomapGreedyTypeSpecialized<FlowType, WithM...
  type typename (line 111) | typedef typename flowData_traits<FlowType>::detailed_balance_type 						...
  type typename (line 112) | typedef typename flowData_traits<FlowType>::directed_with_recorded_telep...
  type typename (line 113) | typedef typename flowData_traits<FlowType>::teleportation_type 							Te...
  type MemNode (line 114) | typedef MemNode<FlowType>																NodeType;
  type Edge (line 115) | typedef Edge<NodeBase>																	EdgeType;
  type MemDeltaFlow (line 116) | typedef MemDeltaFlow																	DeltaFlowType;
  type std (line 117) | typedef std::map<unsigned int, MemNodeSet>												ModuleToMemNodes;
  type IndexedFlow (line 119) | struct IndexedFlow {
  function NodeType (line 192) | const NodeType& getNode(const NodeBase& node) const { return static_cast...
  type typename (line 816) | typedef typename std::map<unsigned int, IndexedFlow>::iterator Condensed...

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MemFlowNetwork.cpp
  type infomap (line 42) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MemFlowNetwork.h
  function namespace (line 35) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MemNetwork.cpp
  type infomap (line 40) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MemNetwork.h
  function namespace (line 43) | namespace infomap
  function addStateLink (line 276) | inline
  function addStateNode (line 282) | inline
  function addStateNode (line 292) | inline

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MemoryNetworkAdapter.cpp
  type infomap (line 32) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MemoryNetworkAdapter.h
  function namespace (line 16) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MultiplexNetwork.cpp
  type infomap (line 41) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/MultiplexNetwork.h
  function namespace (line 38) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/Network.cpp
  type infomap (line 42) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/Network.h
  function namespace (line 39) | namespace infomap
  type Bigram (line 288) | struct Bigram
  type BipartiteLink (line 299) | struct BipartiteLink
  type Weight (line 313) | struct Weight
  type std (line 330) | typedef std::map<key_t, submap_t> map_t;
  function virtual (line 336) | virtual ~MapMap() {}
  function insert (line 338) | bool insert(key_t key1, subkey_t key2, value_t value)
  function size (line 364) | unsigned int size() { return m_size; }
  function numAggregations (line 365) | unsigned int numAggregations() { return m_numAggregations; }
  function value_t (line 366) | value_t sumValue() { return m_sumValue; }
  type LinkMapMap (line 376) | typedef MapMap<unsigned int, unsigned int, double> LinkMapMap;

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/NetworkAdapter.cpp
  type infomap (line 47) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/NetworkAdapter.h
  function namespace (line 36) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/Node.cpp
  type infomap (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/Node.h
  function namespace (line 41) | namespace infomap
  type StateNode (line 56) | struct StateNode
  function subtractIndexOffset (line 83) | void subtractIndexOffset(unsigned int indexOffset)
  function StateNode (line 89) | bool operator<(StateNode other) const
  function StateNode (line 94) | bool operator==(StateNode other) const
  function StateNode (line 99) | bool operator!=(StateNode other) const
  function class (line 124) | class NodeBase
  function childIndex (line 393) | inline
  function addChild (line 414) | inline
  function releaseChildren (line 436) | inline
  function remove (line 444) | inline
  function replaceChildrenWithGrandChildren (line 451) | inline
  function replaceWithChildren (line 469) | inline
  function replaceChildrenWithGrandChildrenDebug (line 509) | inline
  function replaceWithChildrenDebug (line 526) | inline
  function setChildDegree (line 584) | inline
  function setNumLeafNodes (line 591) | inline
  type Edge (line 603) | typedef Edge<node_type>	edge_type;
  function virtual (line 625) | virtual void printData(std::ostream& out)
  type PhysData (line 633) | struct PhysData
  type Node (line 649) | typedef Node<T>				node_base_type;
  function virtual (line 670) | virtual StateNode getStateNode()

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/NodeFactory.h
  function namespace (line 35) | namespace infomap
  type MemNode (line 69) | typedef const MemNode<FlowType>		const_node_type;
  function NodeBase (line 75) | NodeBase* createNode(const NodeBase& node) const

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/TreeData.cpp
  type infomap (line 31) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/TreeData.h
  function namespace (line 38) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/flowData.h
  function namespace (line 33) | namespace infomap
  type FlowDirected (line 80) | struct FlowDirected
  type FlowDirectedWithTeleportation (line 123) | struct FlowDirectedWithTeleportation
  type FlowDirectedNonDetailedBalance (line 190) | struct FlowDirectedNonDetailedBalance
  type FlowDirectedNonDetailedBalanceWithTeleportation (line 236) | struct FlowDirectedNonDetailedBalanceWithTeleportation
  function DeltaFlow (line 447) | struct MemDeltaFlow : DeltaFlow
  function addMemFlowTerms (line 470) | void addMemFlowTerms(double _sumDeltaPlogpPhysFlow, double _sumPlogpPhys...

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/flowData_traits.h
  function namespace (line 34) | namespace infomap
  type FlowType (line 126) | typedef FlowType flow_type;
  type MemNode (line 127) | typedef MemNode<FlowType> node_type;
  type MemDeltaFlow (line 128) | typedef MemDeltaFlow deltaflow_type;
  type FlowType (line 137) | typedef FlowType flow_type;

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/infomap/treeIterators.h
  function namespace (line 35) | namespace infomap
  function explicit (line 161) | explicit
  function Base (line 164) | DepthFirstIterator(const DepthFirstIterator& other) : Base(other) {}
  function DepthFirstIterator (line 208) | DepthFirstIterator
  function explicit (line 230) | explicit
  function Base (line 233) | DepthFirstIterator(const DepthFirstIterator& other) : Base(other) { init...
  function init (line 242) | void init()
  function DepthFirstIterator (line 293) | DepthFirstIterator
  function explicit (line 313) | explicit
  function Base (line 316) | LeafNodeIterator(const LeafNodeIterator& other) : Base(other) { init(); }
  function init (line 325) | void init()
  function LeafNodeIterator (line 370) | LeafNodeIterator
  function explicit (line 390) | explicit
  function Base (line 393) | LeafModuleIterator(const LeafModuleIterator& other) : Base(other) { init...
  function init (line 402) | void init()
  function LeafModuleIterator (line 461) | LeafModuleIterator
  function explicit (line 484) | explicit
  function Base (line 487) | SiblingIterator(const SiblingIterator& other) : Base(other) {}

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/BipartiteClusterReader.cpp
  type infomap (line 13) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/BipartiteClusterReader.h
  function namespace (line 14) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/ClusterReader.cpp
  type infomap (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/ClusterReader.h
  function namespace (line 35) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/HierarchicalNetwork.cpp
  type infomap (line 35) | namespace infomap
    function SNode (line 65) | SNode& HierarchicalNetwork::addNode(SNode& parent, double flow, double...
    function SNode (line 74) | SNode& HierarchicalNetwork::addLeafNode(SNode& parent, double flow, do...
    function SNode (line 79) | SNode& HierarchicalNetwork::addLeafNode(SNode& parent, double flow, do...
    function SNode (line 102) | SNode& HierarchicalNetwork::addLeafNode(SNode& parent, double flow, do...

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/HierarchicalNetwork.h
  function namespace (line 48) | namespace infomap
  function class (line 389) | class LeafIterator
  function SNode (line 437) | SNode* base() const
  function isEnd (line 442) | bool isEnd()
  function class (line 535) | class TreeIterator
  function SNode (line 579) | SNode* base() const
  function isEnd (line 584) | bool isEnd()
  function class (line 693) | class ChildIterator
  function SNode (line 730) | SNode* base() const
  function isEnd (line 735) | bool isEnd()
  function class (line 801) | class HierarchicalNetwork
  function numLeafNodes (line 914) | unsigned int numLeafNodes() { return m_numLeafNodes; }
  function numLeafEdges (line 915) | unsigned int numLeafEdges() { return m_numLeafEdges; }
  function numNodesInTree (line 916) | unsigned int numNodesInTree() { return m_numNodesInTree; }
  function maxDepth (line 917) | unsigned int maxDepth() { return m_maxDepth; }
  function codelength (line 918) | double codelength() { return m_codelength; }
  function onelevelCodelength (line 919) | double onelevelCodelength() { return m_oneLevelCodelength; }
  function compareLeafNodePredicate (line 928) | static bool compareLeafNodePredicate(const SNode* lhs, const SNode* rhs)...
  function sortLeafNodes (line 930) | void sortLeafNodes()

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/ProgramInterface.cpp
  type infomap (line 37) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/ProgramInterface.h
  function namespace (line 41) | namespace infomap
  function Option (line 90) | struct IncrementalOption : Option
  function virtual (line 95) | virtual bool parse(std::string const&  value) {	Option::parse(value); re...
  function virtual (line 96) | virtual void set(bool value) { Option::set(value); if (value) { ++target...
  function virtual (line 97) | virtual std::ostream& printValue(std::ostream& out) const { return out <...
  function virtual (line 110) | virtual bool parse(std::string const&  value) {	Option::parse(value); re...
  function virtual (line 111) | virtual std::string printValue() const { return io::Str() << target; }
  function Option (line 119) | struct ArgumentOption<bool> : Option
  type ParsedOption (line 133) | struct ParsedOption
  type TargetBase (line 168) | struct TargetBase
  function virtual (line 188) | virtual ~Target() {}
  function virtual (line 190) | virtual bool parse(std::string const&  value)
  function virtual (line 204) | virtual ~OptionalTargets() {}
  function virtual (line 206) | virtual bool parse(std::string const&  value)
  function class (line 217) | class ProgramInterface
  function numRequiredArguments (line 288) | unsigned int numRequiredArguments() { return m_nonOptionArguments.size()...

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/SafeFile.h
  function namespace (line 38) | namespace infomap
  function class (line 84) | class SafeOutFile : public ofstream
  function write (line 105) | static size_t write(T value, std::FILE* file)
  function read (line 110) | static size_t read(T& value, ifstream& ifstream)
  function string (line 119) | struct BinaryHelper<std::string> {
  function class (line 145) | class ofstream_binary : public ofstream
  function size (line 160) | size_t size()
  function class (line 170) | class ifstream_binary : public ifstream
  function class (line 198) | class SafeBinaryOutFile {
  function size (line 224) | size_t size()

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/TreeDataWriter.cpp
  type infomap (line 32) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/TreeDataWriter.h
  function namespace (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/convert.h
  function namespace (line 37) | namespace infomap
  function std (line 262) | inline std::string toPlural(std::string object, unsigned int num)

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/version.cpp
  type infomap (line 31) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/io/version.h
  function namespace (line 32) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/Date.h
  function namespace (line 36) | namespace infomap
  function class (line 88) | class Date
  function virtual (line 98) | virtual ~Date() {}
  type std (line 102) | struct std

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/FileURI.cpp
  type infomap (line 33) | namespace infomap
    function FileURI (line 71) | FileURI& FileURI::operator =(const FileURI& other)
    function string (line 113) | string FileURI::getErrorMessage()

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/FileURI.h
  function namespace (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/Logger.cpp
  type infomap (line 31) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/Logger.h
  function namespace (line 39) | namespace infomap
  function class (line 167) | class Logger

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/MersenneTwister.h
  function class (line 54) | class MTRand {
  function MTRand (line 115) | inline MTRand::MTRand( const uint32& oneSeed )
  function MTRand (line 118) | inline MTRand::MTRand( uint32 *const bigSeed )
  function MTRand (line 121) | inline MTRand::MTRand()
  function rand (line 124) | inline double MTRand::rand()
  function rand (line 127) | inline double MTRand::rand( const double& n )
  function randExc (line 130) | inline double MTRand::randExc()
  function randExc (line 133) | inline double MTRand::randExc( const double& n )
  function randDblExc (line 136) | inline double MTRand::randDblExc()
  function randDblExc (line 139) | inline double MTRand::randDblExc( const double& n )
  function seed (line 172) | inline void MTRand::seed( uint32 oneSeed )
  function seed (line 186) | inline void MTRand::seed( uint32 *const bigSeed )
  function seed (line 202) | inline void MTRand::seed()
  function reload (line 235) | inline void MTRand::reload()
  function save (line 277) | inline void MTRand::save( uint32* saveArray ) const
  function load (line 287) | inline void MTRand::load( uint32 *const loadArray )

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/Stopwatch.h
  function namespace (line 33) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/gap_iterator.h
  function namespace (line 34) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/infomath.h
  function namespace (line 36) | namespace infomap

FILE: NonOverlappingCodes/2009-Community-Infomap-MapEquation/src/utils/types.h
  function namespace (line 32) | namespace infomap

FILE: NonOverlappingCodes/2014-Grappolo/RngStream.cpp
  function MultModM (line 88) | double MultModM (double a, double s, double c, double m)
  function MatVecModM (line 112) | void MatVecModM (const double A[3][3], const double s[3], double v[3],
  function MatMatModM (line 132) | void MatMatModM (const double A[3][3], const double B[3][3],
  function MatTwoPowModM (line 154) | void MatTwoPowModM (const double A[3][3], double B[3][3], double m, long e)
  function MatPowModM (line 173) | void MatPowModM (const double A[3][3], double B[3][3], double m, long n)
  function CheckSeed (line 200) | int CheckSeed (const unsigned long seed[6])

FILE: NonOverlappingCodes/2014-Grappolo/RngStream.h
  function class (line 8) | class RngStream

FILE: NonOverlappingCodes/2014-Grappolo/buildNextPhase.cpp
  function renumberClustersContiguously (line 48) | long renumberClustersContiguously(long *C, long size) {
  function buildNextLevelGraphOpt (line 83) | double buildNextLevelGraphOpt(graph *Gin, graph *Gout, long *C, long num...
  function buildNextLevelGraph (line 252) | void buildNextLevelGraph(graph *Gin, graph *Gout, long *C, long numUniqu...
  function buildCommunityBasedOnVoltages (line 389) | long buildCommunityBasedOnVoltages(graph *G, long *Volts, long *C, long ...
  function Visit (line 424) | inline void Visit(long v, long myCommunity, short *Visited, long *Volts,
  function segregateEdgesBasedOnVoltages (line 442) | void segregateEdgesBasedOnVoltages(graph *G, long *Volts) {

FILE: NonOverlappingCodes/2014-Grappolo/coloringDistanceOne.cpp
  function algoDistanceOneVertexColoringOpt (line 50) | int algoDistanceOneVertexColoringOpt(graph *G, int *vtxColor, int nThrea...
  function algoDistanceOneVertexColoring (line 250) | int algoDistanceOneVertexColoring(graph *G, int *vtxColor, int nThreads,...

FILE: NonOverlappingCodes/2014-Grappolo/convertFileToBinary.cpp
  function main (line 46) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/convertFileToEdgeList.cpp
  function main (line 44) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/convertSnapFileToBinary.cpp
  function main (line 46) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/defs.h
  type Comm (line 65) | typedef struct comm
  type edge (line 71) | typedef struct /* the edge data structure */
  type graph (line 79) | typedef struct /* the graph data structure */
  type clustering_parameters (line 88) | struct clustering_parameters

FILE: NonOverlappingCodes/2014-Grappolo/driverForColoringExperiments.cpp
  function main (line 44) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/driverForGraphClustering.cpp
  function main (line 46) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/driverForGraphClusteringBigMem.cpp
  function main (line 46) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/driverForPartitioningWithMetis.cpp
  function main (line 47) | int main(int argc, char** argv) {

FILE: NonOverlappingCodes/2014-Grappolo/driverProcessPowerGridNetworks.cpp
  function main (line 45) | int main(int argc, char** argv)

FILE: NonOverlappingCodes/2014-Grappolo/generateRGG.cpp
  function graph (line 53) | graph * generateRGG(long N, double r) {

FILE: NonOverlappingCodes/2014-Grappolo/generateRMAT.cpp
  function graph (line 51) | graph * generateRMAT(int SCALE, int SCALE_WT, double a, double b, double...

FILE: NonOverlappingCodes/2014-Grappolo/louvainMultiPhaseRun.cpp
  function runMultiPhaseLouvainAlgorithm (line 50) | void runMultiPhaseLouvainAlgorithm(graph *G, long *C_orig, int coloring,...

FILE: NonOverlappingCodes/2014-Grappolo/parallelLouvainMethod.cpp
  function parallelLouvianMethod (line 47) | double parallelLouvianMethod(graph *G, long *C, int nThreads, double Lower,

FILE: NonOverlappingCodes/2014-Grappolo/parallelLouvainMethodEager.cpp
  function parallelLouvianMethodEager (line 49) | double parallelLouvianMethodEager(graph *G, long *C, int nThreads, doubl...

FILE: NonOverlappingCodes/2014-Grappolo/parallelLouvainWithColoring.cpp
  function algoLouvainWithDistOneColoring (line 47) | double algoLouvainWithDistOneColoring(graph* G, long *C, int nThreads, i...

FILE: NonOverlappingCodes/2014-Grappolo/parseInputFiles.cpp
  function removeEdges (line 47) | long removeEdges(long NV, long NE, edge *edgeList) {
  function SortEdgesUndirected (line 98) | void SortEdgesUndirected(long NV, long NE, edge *list1, edge *list2, lon...
  function SortNodeEdgesByIndex (line 132) | void SortNodeEdgesByIndex(long NV, edge *list1, edge *list2, long *ptrs) {
  function loadMetisFileFormat (line 167) | void loadMetisFileFormat(graph *G, const char* filename) {
  function parse_MatrixMarket (line 350) | void parse_MatrixMarket(graph * G, char *fileName) {
  function parse_MatrixMarket_Sym_AsGraph (line 576) | void parse_MatrixMarket_Sym_AsGraph(graph * G, char *fileName) {
  function parse_Dimacs1Format (line 789) | void parse_Dimacs1Format(graph * G, char *fileName) {
  function parse_Dimacs9FormatDirectedNewD (line 896) | void parse_Dimacs9FormatDirectedNewD(graph * G, char *fileName) {
  function parse_PajekFormat (line 1034) | void parse_PajekFormat(graph * G, char *fileName) {
  function parse_PajekFormatUndirected (line 1199) | void parse_PajekFormatUndirected(graph * G, char *fileName) {
  function parse_DoulbedEdgeList (line 1505) | void parse_DoulbedEdgeList(graph * G, char *fileName) {
  function parse_EdgeListBinary (line 1617) | void parse_EdgeListBinary(graph * G, char *fileName) {
  function parse_SNAP (line 1757) | void parse_SNAP(graph * G, char *fileName) {

FILE: NonOverlappingCodes/2014-Grappolo/utilityClusteringFunctions.cpp
  function sumVertexDegree (line 46) | void sumVertexDegree(edge* vtxInd, long* vtxPtr, long* vDegree, long NV,...
  function calConstantForSecondTerm (line 61) | double calConstantForSecondTerm(long* vDegree, long NV) {
  function initCommAss (line 79) | void initCommAss(long* pastCommAss, long* currCommAss, long NV) {
  function buildLocalMapCounter (line 87) | long buildLocalMapCounter(long adj1, long adj2, map<long, long> &cluster...
  function max (line 111) | long max(map<long, long> &clusterLocalMap, vector<double> &Counter,

FILE: NonOverlappingCodes/2014-Grappolo/utilityFunctions.cpp
  function generateRandomNumbers (line 47) | void generateRandomNumbers(double *RandVec, long size) {
  function displayGraph (line 77) | void displayGraph(graph *G) {
  function duplicateGivenGraph (line 96) | void duplicateGivenGraph(graph *Gin, graph *Gout) {
  function displayGraphEdgeList (line 137) | void displayGraphEdgeList(graph *G) {
  function displayGraphEdgeList (line 155) | void displayGraphEdgeList(graph *G, FILE* out) {
  function writeEdgeListToFile (line 174) | void writeEdgeListToFile(graph *G, FILE* out) {
  function displayGraphCharacteristics (line 189) | void displayGraphCharacteristics(graph *G) {
  function graph (line 313) | graph * convertDirected2Undirected(graph *G) {

FILE: NonOverlappingCodes/2014-Grappolo/utilityGraphPartitioner.cpp
  function computeEdgeCut (line 6) | void computeEdgeCut( MilanGraphCompressedTwice &inputGraph,
  function MetisGraphPartitioner (line 112) | void MetisGraphPartitioner( MilanGraphCompressedTwice &inputGraph,

FILE: NonOverlappingCodes/2014-Grappolo/utilityGraphPartitioner.h
  function MetisGraphPartitioner (line 125) | void MetisGraphPartitioner( graph *G, long *VertexPartitioning, int numP...

FILE: NonOverlappingCodes/2014-Grappolo/utilityParseInputParameters.hpp
  type input_parameters (line 50) | struct input_parameters {

FILE: NonOverlappingCodes/2014-Grappolo/utilityStringTokenizer.hpp
  class StringTokenizer (line 55) | class StringTokenizer
  function string (line 165) | string StringTokenizer::GetDelimiterString() const
  function string (line 172) | string StringTokenizer::GetFirstToken()
  function string (line 198) | string StringTokenizer::GetInputString() const
  function string (line 205) | string StringTokenizer::GetLastToken()
  function string (line 222) | string StringTokenizer::GetNextToken()
  function string (line 297) | string StringTokenizer::GetNextToken(char * DelimiterChar)
  function string (line 306) | string StringTokenizer::GetToken(long TokenPosition)

FILE: NonOverlappingCodes/2014-Grappolo/vertexFollowing.cpp
  function vertexFollowing (line 46) | long vertexFollowing(graph *G, long *C)
  function buildNewGraphVF (line 91) | double buildNewGraphVF(graph *Gin, graph *Gout, long *C, long numUniqueC...

FILE: NonOverlappingCodes/2014-Grappolo/writeGraphDimacsFormat.cpp
  function writeGraphBinaryFormat (line 49) | void writeGraphBinaryFormat(graph* G, char *filename) {
  function writeGraphPajekFormat (line 85) | void writeGraphPajekFormat(graph* G, char *filename) {
  function writeGraphMetisSimpleFormat (line 129) | void writeGraphMetisSimpleFormat(graph* G, char *filename) {
  function writeGraphPajekFormatWithNodeVolts (line 162) | void writeGraphPajekFormatWithNodeVolts(graph* G, long *Cvolts, char * f...

FILE: Prensentation/algorithms/clique_percolation/community_result_visualization.py
  function get_comm_dict_and_partition (line 6) | def get_comm_dict_and_partition():
  function draw_comm_detection_res (line 18) | def draw_comm_detection_res(graph):

FILE: Prensentation/algorithms/clique_percolation/conradlee_clique_percolation.py
  function get_percolated_cliques (line 7) | def get_percolated_cliques(G, k):

FILE: Prensentation/algorithms/clique_percolation/problem_vis.py
  function vis_input (line 6) | def vis_input(graph):
  function vis_post_output (line 17) | def vis_post_output(graph, comm, color):

FILE: Prensentation/algorithms/dynamics/label_propagation.py
  function propagate_label_sync (line 5) | def propagate_label_sync(graph, max_iteration=100):

FILE: Prensentation/algorithms/dynamics/label_propagation_yche.py
  function get_rand_element (line 8) | def get_rand_element(l):
  function reverse_dict (line 15) | def reverse_dict(original_dict):
  function print_result (line 24) | def print_result(graph, label_name):
  function sync_label_propagation (line 30) | def sync_label_propagation():
  function async_label_propagation (line 57) | def async_label_propagation():

FILE: Prensentation/algorithms/dynamics/others/aync_vs_sync.py
  function lpa (line 14) | def lpa(graph):

FILE: Prensentation/algorithms/dynamics/others/copra_lpa.py
  function read_graph_from_file (line 9) | def read_graph_from_file(path):
  function read_game_info_from_file (line 21) | def read_game_info_from_file(path):
  function lpa (line 41) | def lpa(graph, v):
  function print_graph_info (line 140) | def print_graph_info(graph):

FILE: Prensentation/algorithms/dynamics/others/lpa.py
  function read_graph_from_file (line 9) | def read_graph_from_file(path):
  function read_game_info_from_file (line 20) | def read_game_info_from_file(path):
  function lpa (line 34) | def lpa(graph):
  function print_graph_info (line 85) | def print_graph_info(graph):

FILE: Prensentation/algorithms/dynamics/prev/disjoint_visualization.py
  function draw_label_propagation_graph (line 6) | def draw_label_propagation_graph(graph, comm_dict, number):
  function draw_graph (line 23) | def draw_graph(graph):
  function reverse_dict (line 45) | def reverse_dict(original_dict):

FILE: Prensentation/algorithms/dynamics/problem_vis.py
  function vis_post_output (line 8) | def vis_post_output(graph, node_dict, name):

FILE: Prensentation/algorithms/link_partition/graph_io_helper.py
  function get_sorted_edge (line 10) | def get_sorted_edge(a, b):
  function read_edge_list_unweighted (line 14) | def read_edge_list_unweighted(filename, node_type=str):
  function read_edge_list_weighted (line 31) | def read_edge_list_weighted(filename, node_type=str, weight_type=float):
  function write_edge2cid (line 47) | def write_edge2cid(e2c, filename, delimiter="\t"):
  function write_dendro (line 77) | def write_dendro(filename, orig_cid2edge, linkage):

FILE: Prensentation/algorithms/link_partition/link_clustering.py
  class MyParser (line 10) | class MyParser(OptionParser):
    method format_epilog (line 11) | def format_epilog(self, formatter):

FILE: Prensentation/algorithms/link_partition/link_clustering_algo.py
  class HLC (line 10) | class HLC:
    method get_sorted_pair (line 12) | def get_sorted_pair(a, b):
    method sort_edge_pairs_by_similarity (line 16) | def sort_edge_pairs_by_similarity(adj_list_dict):
    method sort_edge_pairs_by_similarity_weighted (line 31) | def sort_edge_pairs_by_similarity_weighted(adj_list_dict, edge_weight_...
    method __init__ (line 57) | def __init__(self, adj_list_dict, edges):
    method single_linkage (line 85) | def single_linkage(self, threshold=None, w=None, dendro_flag=False):

FILE: Prensentation/algorithms/link_partition/visualization/dendrogram/radial_demo.py
  function _s (line 8) | def _s(sp, t, o):
  function demo1 (line 13) | def demo1(n):

FILE: Prensentation/algorithms/link_partition/visualization/dendrogram/radial_grouper.py
  function _groub_by (line 12) | def _groub_by(p, tol, r):
  function _leafs (line 23) | def _leafs(p):
  function _create_leaf_nodes (line 26) | def _create_leaf_nodes(ndx):
  function _link_and_create_nodes (line 32) | def _link_and_create_nodes(_n, n_, cn, groups):
  function _process_level (line 39) | def _process_level(nodes, polar, p, tol, scale, _n, n_):
  function _create_tree (line 45) | def _create_tree(p, r0, scale, tols):
  function _simplify (line 63) | def _simplify(self):
  function _call (line 67) | def _call(self, node0, node1, f, level):
  function pre_order (line 70) | def pre_order(self, node0, f, level= 0):
  function post_order (line 75) | def post_order(self, node0, f, level= 0):
  class tree (line 80) | class tree(object):
    method __init__ (line 81) | def __init__(self, p, r0= pi, scale= .9, tols= None):
    method traverse (line 85) | def traverse(self, f, order= pre_order, cs= 'Cartesian'):
    method simplify (line 92) | def simplify(self):
    method is_root (line 96) | def is_root(self, ndx):
    method is_leaf (line 99) | def is_leaf(self, ndx):
  function _l (line 108) | def _l(t, n, l):

FILE: Prensentation/algorithms/link_partition/visualization/dendrogram/radial_support.py
  function _a (line 6) | def _a(a0, a1):
  function from_polar (line 9) | def from_polar(p):
  function to_polar (line 13) | def to_polar(c):
  function d_to_polar (line 17) | def d_to_polar(D):

FILE: Prensentation/algorithms/link_partition/visualization/dendrogram/radial_visualizer.py
  function simple_link (line 5) | def simple_link(t, ndx, level):

FILE: Prensentation/algorithms/link_partition/visualization/link_clustering_visualization.py
  function get_sorted_pair (line 6) | def get_sorted_pair(a, b):
  function get_link_graph (line 10) | def get_link_graph():
  function draw_link_graph (line 27) | def draw_link_graph(graph):
  function draw_link_graph_nodes (line 44) | def draw_link_graph_nodes(graph):
  function draw_partitioned_link_graph (line 62) | def draw_partitioned_link_graph(graph, comm_list):
  function get_link_partition_res (line 86) | def get_link_partition_res():
  function get_overlapping_community_detection_res (line 100) | def get_overlapping_community_detection_res(link_partition):

FILE: Prensentation/algorithms/local_expansion/cis_algo.py
  function fitness (line 16) | def fitness(new_members, is_print=False):
  function expand (line 31) | def expand(seed_set):

FILE: Prensentation/algorithms/local_expansion/cis_algo_visualization.py
  function get_cis_info (line 11) | def get_cis_info():
  function draw_local_expansion_graph (line 37) | def draw_local_expansion_graph(graph, iter_info, color_str):
  function draw_global_result_graph (line 53) | def draw_global_result_graph(graph, first_node_list, newly_added_node_li...

FILE: Prensentation/algorithms/local_expansion/problem_vis.py
  function vis_input (line 8) | def vis_input(graph):
  function vis_post_output (line 19) | def vis_post_output(graph, intra_comm, all_local_structure, color, nodes):

FILE: Prensentation/algorithms/local_expansion/src/cis_sequential_algorithm.cpp
  type yche (line 7) | namespace yche {
    function Community (line 173) | Community Cis::FindConnectedComponent(EntityIdxSet &member_set, Entity...
    function Community (line 207) | Community Cis::SplitAndChoose(EntityIdxSet &member_set) const {
    function EntityIdxVec (line 232) | EntityIdxVec Cis::ExpandSeed(EntityIdxSet &entity_idx_set) const {
    function EntityIdxVec (line 275) | EntityIdxVec Cis::GetUnion(const EntityIdxVec &left_community, const E...

FILE: Prensentation/algorithms/local_expansion/src/cis_sequential_algorithm.h
  function namespace (line 19) | namespace yche {
  function class (line 74) | class Cis {

FILE: Prensentation/algorithms/local_expansion/src/demo_cis.cpp
  function ConstructGraph (line 18) | unique_ptr<Graph> ConstructGraph(map<int, Vertex> &vertex_dict, map<int,...
  function main (line 44) | int main(int argc, char *argv[]) {

FILE: Prensentation/algorithms/local_expansion/src/util/basic_io_helper.h
  function namespace (line 10) | namespace yche {

FILE: Prensentation/algorithms/local_expansion/src/util/graph_io_helper.cpp
  type std (line 6) | namespace std {
    function ostream (line 7) | ostream &operator<<(ostream &my_output_stream, yche::Edge &edge) {
  type yche (line 13) | namespace yche {
    function ReadWeightedEdgeList (line 14) | vector<Edge> ReadWeightedEdgeList(string file_name_str) {
    function ReadEdgeList (line 40) | vector<pair<int, int>> ReadEdgeList(string file_name_str) {

FILE: Prensentation/algorithms/local_expansion/src/util/graph_io_helper.h
  function namespace (line 19) | struct Edge {

FILE: Prensentation/algorithms/local_expansion/src/util/pretty_print.h
  function namespace (line 25) | namespace pretty_print {
  type custom_delims_base (line 360) | struct custom_delims_base {
  type T (line 404) | typedef const T *const_iterator;
  type T (line 405) | typedef T value_type;
  type typename (line 424) | typedef typename T::const_local_iterator const_iterator;
  type typename (line 425) | typedef typename T::size_type size_type;
  function namespace (line 462) | namespace std {

FILE: Prensentation/algorithms/statistical_inference/block_model_demo.py
  function visualize_a_graph (line 6) | def visualize_a_graph(graph):

FILE: Prensentation/graph_tool_usage/intro_graph_tool/begining.py
  function first_example (line 6) | def first_example():
  function draw_football (line 14) | def draw_football():
  function draw_lesmis (line 33) | def draw_lesmis():

FILE: Prensentation/graph_tool_usage/intro_graph_tool/draw_pie_graph.py
  function get_comm_dict_and_partition (line 7) | def get_comm_dict_and_partition():

FILE: Prensentation/graph_tool_usage/intro_graph_tool/graph_creation_basics.py
  function create_graph (line 15) | def create_graph():
  function iterate_graph (line 36) | def iterate_graph():
  function build_price_network (line 54) | def build_price_network():

FILE: Prensentation/graph_tool_usage/intro_graph_tool/nx2gt.py
  function get_prop_type (line 5) | def get_prop_type(value, key=None):
  function nx2gt (line 40) | def nx2gt(nxG):

FILE: Prensentation/metrics/link_belong_modularity.py
  class FuncTag (line 7) | class FuncTag:
    method __init__ (line 8) | def __init__(self):
  function get_coefficient_func (line 17) | def get_coefficient_func(tag):
  function cal_modularity (line 28) | def cal_modularity(input_graph, comm_result):
  class LinkBelongModularity (line 33) | class LinkBelongModularity:
    method __init__ (line 36) | def __init__(self, input_graph, comm_result, coefficient_func):
    method calculate_modularity (line 67) | def calculate_modularity(self):

FILE: Prensentation/metrics/omega_idx.py
  function calc_omega_idx (line 1) | def calc_omega_idx(num_vertices, result_comm_list, ground_truth_comm_list):
  class OmegaIdx (line 5) | class OmegaIdx:
    method __init__ (line 6) | def __init__(self, num_vertices, result_comm_list, ground_truth_comm_l...
    method calculate_omega_idx (line 11) | def calculate_omega_idx(self):

FILE: Prensentation/metrics/overlap_nmi.py
  function calc_overlap_nmi (line 5) | def calc_overlap_nmi(num_vertices, result_comm_list, ground_truth_comm_l...
  class OverlapNMI (line 9) | class OverlapNMI:
    method entropy (line 11) | def entropy(num):
    method __init__ (line 14) | def __init__(self, num_vertices, result_comm_list, ground_truth_comm_l...
    method calculate_overlap_nmi (line 19) | def calculate_overlap_nmi(self):

FILE: Prensentation/metrics/util.py
  function get_graph_info (line 5) | def get_graph_info(file_path):

FILE: Prensentation/problem_definition/problem_vis.py
  function vis_input (line 6) | def vis_input(graph):
  function vis_output (line 21) | def vis_output(graph, comm, comm_color, idx):
  function vis_post_output (line 39) | def vis_post_output(graph, comm_list, color_list):

FILE: Prensentation/social_network/disjoint_community_detection.py
  function get_comm_dict_and_partition (line 7) | def get_comm_dict_and_partition(g):

FILE: Prensentation/social_network/visualization_karate.py
  function traverse_degree (line 8) | def traverse_degree(graph):
  function try_different_layouts (line 14) | def try_different_layouts(graph):
  function draw_comm_detection_res (line 55) | def draw_comm_detection_res(graph):

FILE: Prensentation/social_network/zachary_karate_club/gml_formatter.py
  function gml_formatter (line 4) | def gml_formatter(in_file, out_file):

FILE: Scripts/dataset_aggragation.py
  function get_edge_list (line 5) | def get_edge_list(file_name):
  function get_undirected_graph_info (line 12) | def get_undirected_graph_info(file_name):
  function get_dir_info (line 22) | def get_dir_info(dir_name):