SYMBOL INDEX (809 symbols across 34 files)

FILE: src/algorithms.hpp
  type LogInfo (line 60) | struct LogInfo {
    method LogInfo (line 64) | LogInfo(bool enabled = true, ostream& fout = cerr): fout(fout), enable...
    method LogInfo (line 66) | LogInfo& operator<< (const T& v) {
    method LogInfo (line 71) | LogInfo& operator<< (basic_ostream<char, std::char_traits<char> >& (*e...
  type Hasher (line 79) | struct Hasher{
  function string (line 85) | string formatBootstrap(double s){
  type AnnotatedTree (line 91) | struct AnnotatedTree{
    type Node (line 92) | struct Node{
      method CustomizedAnnotation (line 102) | const CustomizedAnnotation& annotation() const{
      method Node (line 107) | Node(){}
      method isLeaf (line 109) | bool isLeaf() const{
      method parent (line 113) | shared_ptr<Node> parent() const{
      method leftChild (line 117) | shared_ptr<Node> leftChild() const{
      method rightChild (line 121) | shared_ptr<Node> rightChild() const{
      method taxonID (line 125) | int taxonID() const{
      method string (line 129) | string taxonName() const{
      method support (line 133) | double support() const{
      method length (line 137) | double length() const{
    method root (line 144) | shared_ptr<Node> root(){
    method addRoot (line 148) | shared_ptr<Node> addRoot(){
    method addLeft (line 153) | shared_ptr<Node> addLeft(shared_ptr<Node> node){
    method addRight (line 160) | shared_ptr<Node> addRight(shared_ptr<Node> node){
  type PlacementAlgorithm (line 168) | struct PlacementAlgorithm{
    type Node (line 170) | struct Node{
      method Node (line 171) | Node(int leafId = -1): leafId(leafId){}
    method PlacementAlgorithm (line 191) | PlacementAlgorithm(const vector<hash_t> &taxonHash, TripartitionInitia...
    method score_t (line 214) | score_t& sYes(int v){
    method score_t (line 218) | score_t& sNo(int v){
    method makeNode (line 230) | int makeNode(int v, int u, bool modifyRoot = false){
    method addSibling (line 252) | void addSibling(int v, int i){
    method forceLeftHeavy (line 258) | void forceLeftHeavy(int v){
    method defaultInitializer (line 270) | void defaultInitializer(){
    method place (line 283) | void place(int i){
    method tripUpdateSet (line 287) | void tripUpdateSet(int tgt, int i){
    method tripUpdateGet (line 292) | void tripUpdateGet(int tgt, int i){
    method tripScoreSet (line 296) | void tripScoreSet(){
    method score_t (line 301) | score_t tripScoreGet(){
    method score_t (line 305) | score_t tripScore(){
    method switchSubtreeSet (line 310) | void switchSubtreeSet(int v, int src, int tgt){
    method switchSubtreeGet (line 320) | void switchSubtreeGet(int v, int src, int tgt){
    method switchSubtree (line 330) | void switchSubtree(int v, int src, int tgt){
    method scoringPlacementDPSet (line 335) | void scoringPlacementDPSet(int v, int i){
    method scoringPlacementDPGet (line 366) | void scoringPlacementDPGet(int v, int i){
    method locateBranchAddingSet (line 415) | void locateBranchAddingSet(int i){
    method locateBranchAddingGet (line 422) | int locateBranchAddingGet(int i){
    method locateBranchAdding (line 436) | int locateBranchAdding(int i){
    method locateBranch (line 441) | int locateBranch(int i){
    method score_t (line 449) | inline score_t nnPerform(int v, int best_case, score_t top_score){
    method score_t (line 489) | score_t nnLocal(int v, bool recurse, score_t e_ab_cd){
    method score_t (line 640) | score_t nnMove(int v){
    method nnLocal2 (line 774) | bool nnLocal2(int v, score_t& e_ab_cd) {
    method nnCheckLight (line 837) | bool nnCheckLight(int v, score_t& e_ab_cd, score_t& abe_c_d) {
    method score_t (line 941) | score_t nnPrecheckHeavy(int v) {
    method nnCheckHeavy (line 962) | bool nnCheckHeavy(int v, score_t& e_ab_cd, score_t& cde_a_b, bool prec...
    method score_t (line 1076) | score_t nnMove2(int v) {
    method nnMove (line 1107) | void nnMove(){
    method tripHashGeneratorSet (line 1118) | void tripHashGeneratorSet(int v){
    method tripHashGeneratorGet (line 1138) | pair<bool, hash_t> tripHashGeneratorGet(int v){
    method run (line 1163) | void run(){
    method string (line 1177) | string printSubtree(int v){
    method string (line 1182) | string printTree(){
    method string (line 1186) | string printSubtree(int v, const vector<string> &names){
    method string (line 1191) | string printTree(const vector<string> &names){
  type ConstrainedOptimizationAlgorithm (line 1196) | struct ConstrainedOptimizationAlgorithm{
    type Node (line 1197) | struct Node{
      method Node (line 1198) | Node(int leafId, hash_t hash): hash(hash), leafId(leafId) {}
    method ConstrainedOptimizationAlgorithm (line 1221) | ConstrainedOptimizationAlgorithm(const int ntaxa, TripartitionInitiali...
    method ConstrainedOptimizationAlgorithm (line 1233) | ConstrainedOptimizationAlgorithm(const ConstrainedOptimizationAlgorith...
    method subsampleSubtree (line 1236) | int subsampleSubtree(int v, PlacementAlgorithm &pAlg, const unordered_...
    method createPlacementAlgorithm (line 1280) | void createPlacementAlgorithm(PlacementAlgorithm &pAlg, const unordere...
    method subsampleSubtree (line 1299) | int subsampleSubtree(int v, PlacementAlgorithm &pAlg, double subsample...
    method createPlacementAlgorithm (line 1343) | void createPlacementAlgorithm(PlacementAlgorithm &pAlg, double subsamp...
    method guideSubtree (line 1363) | int guideSubtree(PlacementAlgorithm &pAlg, const string &tree, const u...
    method addGuideTree (line 1432) | void addGuideTree(const string &tree, const unordered_map<string, int>...
    method hash2node (line 1446) | int hash2node(hash_t h){
    method addTripartitions (line 1454) | void addTripartitions(const vector<tuple<hash_t, hash_t, score_t> > tr...
    method optimalTreeDP (line 1462) | void optimalTreeDP(int v){
    method score_t (line 1476) | score_t computeOptimalTree(){
    method string (line 1482) | string printOptimalSubtree(int v){
    method string (line 1488) | string printOptimalTree(){
    method string (line 1492) | string printOptimalSubtreeWithScore(int v){
    method string (line 1498) | string printOptimalTreeWithScore(){
    method run (line 1502) | pair<score_t, string> run(int nJobs = 1, double subsampleRate = 0, boo...
    method constrainedRun (line 1515) | pair<score_t, string> constrainedRun(int nJobs, const string tree, con...
    method placeNode (line 1522) | static bool placeNode(PlacementAlgorithm &pAlg, vector<PlacementAlgori...
    method twoStepWorkflow (line 1551) | void twoStepWorkflow(PlacementAlgorithm &pAlg){
    method twoStepRun (line 1631) | pair<score_t, string> twoStepRun(int nJobs){
    method gTest (line 1644) | inline static double gTest(double v1, double v2, double v3){
    method switchSubtree (line 1659) | void switchSubtree(Quadrupartition &quad, int v, int s, int t){
    method computeOptimalSubtreeWithSupport (line 1670) | void computeOptimalSubtreeWithSupport(SpeciesTree &tree, Quadrupartiti...
    method SpeciesTree (line 1789) | SpeciesTree optimalTreeWithSupport(double lambda, double weight) {
    method string (line 1838) | string subtreeLeaves(shared_ptr<SpeciesTree::Node> node){
    method printFreqQuadCSVRecursion (line 1843) | void printFreqQuadCSVRecursion(shared_ptr<SpeciesTree::Node> v, shared...
    method printFreqQuadCSV (line 1857) | void printFreqQuadCSV(SpeciesTree& tree){
  type MetaAlgorithm (line 1868) | struct MetaAlgorithm{
    method MetaAlgorithm (line 1883) | MetaAlgorithm(){
    method MetaAlgorithm (line 1887) | MetaAlgorithm(int argc, char** argv) {
    method staticInitialize (line 1892) | static void staticInitialize(int argc, char** argv) {
    method initialize (line 1933) | void initialize(int argc, char** argv, string dummy1 = "", string dumm...
    method initialize (line 1938) | void initialize(){
    method string (line 1966) | string mappedname(string name){
    method run (line 1971) | pair<score_t, string> run(){

FILE: src/argparser.hpp
  class ArgParser (line 14) | class ArgParser{
    method addArg (line 27) | void addArg(char sName, string lName, string description, bool priorit...
    method addIntArg (line 35) | void addIntArg(char sName, string lName, int defaultValue, string desc...
    method addDoubleArg (line 41) | void addDoubleArg(char sName, string lName, double defaultValue, strin...
    method addStringArg (line 47) | void addStringArg(char sName, string lName, string defaultValue, strin...
    method addFlag (line 53) | void addFlag(char sName, string lName, string description, function<vo...
    method string (line 67) | string& getStringArg(string name){
    method setProgramName (line 71) | void setProgramName(string name, string fname = "Accurate Species Tree...
    method string (line 76) | string getFullName(){
    method printHelp (line 80) | void printHelp(string name){
    method ArgParser (line 88) | ArgParser(){
    method parse (line 109) | void parse(int argc, char** argv){

FILE: src/aster-gui.py
  class FileButton (line 14) | class FileButton(QtWidgets.QPushButton):
    method __init__ (line 15) | def __init__(self, arg):
    method setPath (line 20) | def setPath(self):
  class FolderButton (line 24) | class FolderButton(QtWidgets.QPushButton):
    method __init__ (line 25) | def __init__(self, arg):
    method setPath (line 30) | def setPath(self):
  class Ui_MainWindow (line 34) | class Ui_MainWindow(object):
    method setupUi (line 35) | def setupUi(self, MainWindow):
    method retranslateUi (line 132) | def retranslateUi(self, MainWindow):
    method run (line 167) | def run(self):

FILE: src/astral-hybrid.cpp
  function score_t (line 26) | score_t from_string(const string s){
  function ostream (line 30) | ostream& operator<<(ostream& cout, long double x){
  function score_t (line 36) | score_t from_string(const string s){
  function MAPPING (line 62) | int MAPPING(long long begin, long long end){
  function score_t (line 84) | score_t WEIGHT_S(long long begin, long long end){
  function score_t (line 92) | score_t DEFAULT_WEIGHT_S(){
  function score_t (line 96) | score_t WEIGHT_L(long long begin, long long end){
  function parse (line 104) | void parse(score_t treeweight, int parent = -1, bool isLeft = true){
  function readInputTrees (line 157) | void readInputTrees(string input, string mapping, string treeweights) {
  function DETECT (line 183) | void DETECT(long long begin, long long end){
  function detectSupport (line 192) | void detectSupport(){
  function detectSupportType (line 209) | void detectSupportType(string input) {
  function main (line 242) | int main(int argc, char** argv){

FILE: src/astral-pro.cpp
  function string (line 29) | string to_string(const __int128 x){
  function ostream (line 33) | ostream& operator<<(ostream& cout, __int128 x){
  function from_string (line 41) | double from_string(const string s){
  class DynamicBitset (line 67) | class DynamicBitset{
    method DynamicBitset (line 72) | DynamicBitset(){}
    method DynamicBitset (line 73) | DynamicBitset(int sz): size(sz), vec((sz + 63) / 64){}
    method set (line 75) | void set(int i){
    method DynamicBitset (line 85) | DynamicBitset operator|(const DynamicBitset &b) const{
    method DynamicBitset (line 97) | DynamicBitset operator&(const DynamicBitset &b) const{
    method DynamicBitset (line 106) | DynamicBitset operator^(const DynamicBitset &b) const{
    method DynamicBitset (line 118) | DynamicBitset operator-(const DynamicBitset &b) const{
    method isDisjointTo (line 142) | bool isDisjointTo(const DynamicBitset &b) const{
    method setBits (line 150) | vector<int> setBits() const{
  class GenetreeAnnotator (line 161) | class GenetreeAnnotator{
    type Node (line 163) | struct Node{
    method createSubtree (line 177) | tuple<int, int, int> createSubtree(const unordered_map<long long, stri...
    method scoreSubtree (line 237) | int scoreSubtree(int cur){
    method annotateTree (line 256) | int annotateTree(const unordered_map<long long, string> &leafname, con...
    method buildTree (line 292) | int buildTree(int cur, int p, int depth = 0) const{
    method string (line 328) | string printTree(int cur, int depth = 0) const{
  function string (line 343) | string MAPPING(long long begin, long long end){
  function string (line 352) | string GET_NAME(long long begin, long long end){
  function LENGTH (line 360) | double LENGTH(long long begin, long long end){
  function parse (line 367) | long long parse(unordered_map<long long, string> &leafname, unordered_ma...
  function string (line 410) | string convert2string(const unordered_map<long long, string> &leafname, ...
  function annotate (line 417) | void annotate(string input, string mapping){
  function examplePrintSubtreeWithSupport (line 459) | void examplePrintSubtreeWithSupport(shared_ptr<AnnotatedTree::Node> node){
  function string (line 478) | string sampleGenetree(int p, int inode, const unordered_set<int> &outgro...
  function outgroupLength (line 492) | pair<double, int> outgroupLength(const Tree& tr, string label = "outgrou...
  function computeOutgroupLength (line 504) | double computeOutgroupLength(){
  function main (line 521) | int main(int argc, char** argv){

FILE: src/astral.cpp
  function string (line 31) | string to_string(const __int128 x){
  function ostream (line 35) | ostream& operator<<(ostream& cout, __int128 x){
  function from_string (line 43) | double from_string(const string s){
  function MAPPING (line 64) | int MAPPING(long long begin, long long end){
  function LENGTH (line 80) | double LENGTH(long long begin, long long end){
  function parse (line 87) | void parse(int parent = -1, bool isLeft = true){
  function readInputTrees (line 136) | void readInputTrees(string input, string mapping) {
  function examplePrintSubtreeWithSupport (line 158) | void examplePrintSubtreeWithSupport(shared_ptr<AnnotatedTree::Node> node){
  function string (line 177) | string sampleGenetree(int p, int inode, const unordered_set<int> &outgro...
  function outgroupLength (line 187) | pair<double, int> outgroupLength(const Tree& tr, string label = "outgrou...
  function computeOutgroupLength (line 199) | double computeOutgroupLength(){
  function main (line 216) | int main(int argc, char** argv){

FILE: src/biallelic-cuda.hpp
  type TripartitionInitializer (line 15) | struct TripartitionInitializer{
  type Tripartition (line 23) | struct Tripartition{
    method Tripartition (line 35) | Tripartition(const TripartitionInitializer &TI): n(TI.h.size()), color...
    method Tripartition (line 103) | Tripartition (Tripartition && T): GI(T.GI), GF(T.GF), S(T.S), H(T.H), ...
    method Tripartition (line 108) | Tripartition& operator= ( Tripartition && ) = delete;
    method Tripartition (line 109) | Tripartition( const Tripartition & ) = delete;
    method Tripartition (line 110) | Tripartition& operator= ( const Tripartition & ) = delete;
    method update (line 112) | void update(int x, int i){
    method score_t (line 118) | score_t score(){
    method updatePart (line 127) | void updatePart(int part, int x, int i){
    method score_t (line 137) | score_t scorePart(int part){
    method gpuWork (line 149) | void gpuWork(queue<score_t>& Q){

FILE: src/caster-pair.cpp
  type Workflow (line 43) | struct Workflow {
    method addName (line 50) | void addName(const string& name) {
    method infoCount (line 57) | static int infoCount(const array<int, 4> &cnt){
    method add (line 65) | static array<int, 4> add(const array<int, 4> &a, const array<int, 4> &b){
    method sum (line 73) | static int sum(const array<int, 4> &cnt){
    method buildGeneSeq (line 81) | void buildGeneSeq(TripartitionInitializer::Gene::Initializer &gene, co...
    method formatGene (line 94) | void formatGene(const vector<int> &ind2species, size_t pos, size_t nSi...
    method read (line 102) | void read(const string &file, const string &fileFormat, const string &...
    method Workflow (line 207) | Workflow(int argc, char** argv){
    method init (line 213) | void init(){
  function main (line 226) | int main(int argc, char** argv){

FILE: src/caster-site.cpp
  type Workflow (line 48) | struct Workflow {
    method addName (line 55) | void addName(const string& name) {
    method infoCount (line 62) | static int infoCount(const array<int, 4> &cnt){
    method add (line 70) | static array<int, 4> add(const array<int, 4> &a, const array<int, 4> &b){
    method sum (line 78) | static int sum(const array<int, 4> &cnt){
    method buildGeneSeq (line 86) | void buildGeneSeq(TripartitionInitializer::Gene::Initializer &gene, co...
    method formatGene (line 98) | void formatGene(const vector<int> &ind2species, size_t pos, size_t nSi...
    method read (line 105) | void read(const string &file, const string &fileFormat, const string &...
    method Workflow (line 166) | Workflow(int argc, char** argv){
    method init (line 173) | void init(){
  function main (line 187) | int main(int argc, char** argv){

FILE: src/castles.hpp
  type CastlesNode (line 3) | struct CastlesNode{
    method length_t (line 4) | static length_t safe_div(length_t n, length_t d){
    method length_t (line 9) | static length_t lambertw(length_t x, length_t err = 1e-9){
    method CastlesNode (line 30) | CastlesNode(const CustomizedAnnotation &annot, length_t s = 1000, leng...

FILE: src/codonSplit.py
  function split_codon_positions (line 3) | def split_codon_positions(input_fasta):

FILE: src/debug.cpp
  function main (line 3) | int main(){

FILE: src/dstar-branch-merge-diag.cpp
  type Row (line 14) | struct Row{
  type Birow (line 18) | struct Birow{
  function main (line 40) | int main(int argc, char *argv[])

FILE: src/dstar-branch.cpp
  type Tree (line 15) | struct Tree{
    type Node (line 16) | struct Node{
      method Node (line 21) | Node(const string &nw, int &i){
      method print (line 36) | void print(ostream& fout){
      method addLabel (line 47) | void addLabel(int &cnt){
    type Instruction (line 62) | struct Instruction{
      type Unit (line 63) | struct Unit{
        method Unit (line 68) | Unit operator+ (const Unit &o) const{
      method print (line 84) | void print(ostream &fout, const string &prefix){
    method Tree (line 107) | Tree(const string &nw){
    method Instruction (line 123) | static Instruction createInstruction(Node *ingroup, Node *tgt1, Node *...
      type Unit (line 63) | struct Unit{
        method Unit (line 68) | Unit operator+ (const Unit &o) const{
      method print (line 84) | void print(ostream &fout, const string &prefix){
    method createJobTgt (line 134) | static void createJobTgt(vector<Instruction> &jobs, Node *ingroup, Nod...
    method createJobIngroup (line 141) | static void createJobIngroup(vector<Instruction> &jobs, Node *ingroup){
    method createJob (line 157) | vector<Instruction> createJob(){
    method print (line 163) | void print(ostream& fout){
  type DataType16 (line 173) | struct DataType16{
  type DataType8 (line 180) | struct DataType8{
  class DStarQuadrupartitionScorer (line 187) | class DStarQuadrupartitionScorer{
    type Block (line 194) | struct Block{
    method CounterType (line 201) | inline static CounterType quadXXYY(CounterType x0, CounterType x1, Cou...
    method ScoreType (line 205) | static ScoreType scoreSite(int pos, const array<vector<FreqType>, 4> &...
    method ScoreType (line 231) | static ScoreType scoreInterval(int start, int end, const array<vector<...
    method dstar (line 238) | static vector<ScoreType> dstar(int windowSize, const array<vector<Freq...
    method CounterType (line 248) | static CounterType quartetCnt(int start, int end, const array<vector<F...
    method dstarQuartetCnt (line 261) | static vector<CounterType> dstarQuartetCnt(int windowSize, const array...
    method Block (line 271) | static Block parseFreqs(const array<vector<FreqType>, 4> &f1, const ar...
    method string (line 295) | static string multiind(string input, string mapping = "", int interval...
  type Algorithm (line 390) | struct Algorithm{
    method string2seq (line 401) | static array<vector<unsigned short>, 4> string2seq(const string &s){
    method cntReset (line 410) | void cntReset(array<vector<DataType::FreqType>, 4> &res){
    method convert (line 417) | void convert(array<vector<DataType::FreqType>, 4> &res, const array<ve...
    method instructionCnt (line 422) | void instructionCnt(Tree::Node *node, array<vector<DataType::FreqType>...
    method instructionScore (line 431) | int instructionScore(Tree::Node *node, array<vector<DataType::FreqType...
    method runInstruction (line 454) | void runInstruction(Tree &tree, Tree::Instruction &ins){
    method threadJobs (line 474) | void threadJobs(Tree &tree, vector<Tree::Instruction> &jobs, int L, in...
    method Algorithm (line 478) | Algorithm(const string &faFile, const string &nwFile, const string &ts...
  function main (line 561) | int main(int argc, char *argv[])

FILE: src/dstar.cpp
  type DataType16 (line 14) | struct DataType16{
  class DStarQuadrupartitionScorer (line 21) | class DStarQuadrupartitionScorer{
    type Block (line 28) | struct Block{
    method CounterType (line 35) | inline static CounterType quadXXYY(CounterType x0, CounterType x1, Cou...
    method ScoreType (line 39) | static ScoreType scoreSite(int pos, const array<vector<FreqType>, 4> &...
    method ScoreType (line 65) | static ScoreType scoreInterval(int start, int end, const array<vector<...
    method dstar (line 72) | static vector<ScoreType> dstar(int windowSize, const array<vector<Freq...
    method CounterType (line 82) | static CounterType quartetCnt(int start, int end, const array<vector<F...
    method dstarQuartetCnt (line 95) | static vector<CounterType> dstarQuartetCnt(int windowSize, const array...
    method Block (line 105) | static Block parseFreqs(const array<vector<FreqType>, 4> &f1, const ar...
    method string (line 129) | static string multiind(string input, string mapping = "", int interval...
  function main (line 237) | int main(int argc, char *argv[])

FILE: src/genetreewithbinaryweight.hpp
  type CustomizedAnnotation (line 20) | struct CustomizedAnnotation{
    type Quadrupartition (line 21) | struct Quadrupartition{
      method numericalBalancing (line 29) | void numericalBalancing(){
      method Quadrupartition (line 39) | Quadrupartition operator+ (const Quadrupartition& o) const{
      method Quadrupartition (line 50) | Quadrupartition& operator+= (const Quadrupartition& o){
      method Quadrupartition (line 60) | Quadrupartition operator- (const Quadrupartition& o) const{
    method CustomizedAnnotation (line 73) | CustomizedAnnotation operator+ (const CustomizedAnnotation& o) const{
    method CustomizedAnnotation (line 81) | CustomizedAnnotation& operator+= (const CustomizedAnnotation& o){
    method CustomizedAnnotation (line 88) | CustomizedAnnotation operator- (const CustomizedAnnotation& o) const{
  type TripartitionInitializer (line 97) | struct TripartitionInitializer{
    type Node (line 98) | struct Node{
  type Tripartition (line 108) | struct Tripartition{
    type Partition (line 109) | struct Partition{
      type Node (line 110) | struct Node{
      method score_t (line 119) | score_t normal(Node& w){
      method Partition (line 157) | Partition(TripartitionInitializer init, int p): leafParent(init.leaf...
      method update (line 166) | void update(int x, int i){
      method score_t (line 182) | score_t score(){
    method Tripartition (line 189) | Tripartition(const TripartitionInitializer &init){
    method updatePart (line 193) | void updatePart(int part, int x, int i){
    method update (line 197) | void update(int x, int i){
    method score_t (line 204) | score_t scorePart(int part){
    method score_t (line 208) | score_t score(){
  type Quadrupartition (line 215) | struct Quadrupartition{
    type Partition (line 216) | struct Partition{
      type Node (line 217) | struct Node{
        type Topology (line 218) | struct Topology{
      method extended (line 242) | void extended(Node& w, Node& u, Node& v){
      method CustomizedAnnotation (line 352) | CustomizedAnnotation extended(Node& w){
      method Partition (line 382) | Partition(TripartitionInitializer init, int p): leafParent(init.leaf...
      method update (line 393) | void update(int x, int i){
      method score (line 431) | array<double, 3> score(){
      method CustomizedAnnotation (line 435) | CustomizedAnnotation annotate(){
    method Quadrupartition (line 445) | Quadrupartition(const TripartitionInitializer &init){
    method update (line 449) | void update(int x, int i){
    method score (line 456) | array<double, 3> score(){
    method CustomizedAnnotation (line 470) | CustomizedAnnotation annotate(){

FILE: src/genetreewithhybridweight.hpp
  type TripartitionInitializer (line 17) | struct TripartitionInitializer{
    type Node (line 18) | struct Node{
  type Tripartition (line 28) | struct Tripartition{
    type Partition (line 29) | struct Partition{
      type Node (line 30) | struct Node{
      method score_t (line 39) | score_t normal(Node& w){
      method Partition (line 78) | Partition(const TripartitionInitializer &init, int p): leafParent(in...
      method update (line 89) | void update(int x, int i){
      method score_t (line 105) | score_t score(){
    method Tripartition (line 112) | Tripartition(const TripartitionInitializer &init){
    method updatePart (line 116) | void updatePart(int part, int x, int i){
    method update (line 120) | void update(int x, int i){
    method score_t (line 127) | score_t scorePart(int part){
    method score_t (line 131) | score_t score(){
  type Quadrupartition (line 138) | struct Quadrupartition{
    type Partition (line 139) | struct Partition{
      type Node (line 140) | struct Node{
      method normal (line 155) | array<score_t, 3> normal(Node& w){
      method Partition (line 217) | Partition(TripartitionInitializer init, int p): leafParent(init.leaf...
      method update (line 227) | void update(int x, int i){
      method score (line 255) | array<score_t, 5> score(){
    method Quadrupartition (line 262) | Quadrupartition(const TripartitionInitializer &init){
    method update (line 266) | void update(int x, int i){
    method score (line 273) | array<double, 3> score(){

FILE: src/incbeta.c
  function incbeta (line 32) | double incbeta(double a, double b, double x) {

FILE: src/landmark.hpp
  type Vector (line 9) | struct Vector{
    method Vector (line 12) | Vector operator+(const Vector& b) const{
    method Vector (line 16) | Vector operator-(const Vector& b) const{
    method Vector (line 20) | Vector& operator+=(const Vector& b){
    method Vector (line 25) | Vector& operator-=(const Vector& b){
    method Vector (line 30) | Vector operator*(double c) const{
    method Vector (line 35) | Vector operator/(double c) const{
    method Vector (line 40) | Vector& operator*=(double c){
    method Vector (line 45) | Vector& operator/=(double c){
    method norm (line 55) | double norm() const{
    method normalize (line 59) | void normalize(){
    method Vector (line 63) | Vector(double x, double y, double z = 0, bool normalized = false): x(x...
    method Vector (line 67) | Vector(): x(0), y(0), z(0){}
  type TripartitionInitializer (line 70) | struct TripartitionInitializer{
  type Tripartition (line 74) | struct Tripartition{
    method Tripartition (line 83) | Tripartition(TripartitionInitializer &init): M(init.M), n(init.M.size(...
    method updatePart (line 90) | void updatePart(int part, int x, int i){
    method score_t (line 108) | score_t scorePart(int part){

FILE: src/merge-pairend.cpp
  function string (line 34) | const string STRING_REVERSE_COMPLEMENT(const string &seq){
  function string (line 42) | const string STRING_REVERSE(const string &seq){
  function string (line 50) | const string STRING_UPPER(const string &seq){
  function MATCH_LENGTH (line 58) | int MATCH_LENGTH(const string &seqL, const string &seqR, int offset, int...
  function BEST_MATCH (line 70) | int BEST_MATCH(const string &seqL, const string &seqR, int minmatch = 20...
  function MERGE (line 82) | void MERGE(string &seq, string &qc, const string &seqL, const string &se...
  function main (line 110) | int main(int argc, char** argv){

FILE: src/monster.cpp
  function addName (line 28) | void addName(const string& name) {
  function main (line 35) | int main(int argc, char** argv){

FILE: src/multitree.hpp
  type CustomizedAnnotation (line 20) | struct CustomizedAnnotation{
    type Quadrupartition (line 21) | struct Quadrupartition{
      method numericalBalancing (line 29) | void numericalBalancing(){
      method Quadrupartition (line 40) | Quadrupartition operator+ (const Quadrupartition& o) const{
      method Quadrupartition (line 51) | Quadrupartition& operator+= (const Quadrupartition& o){
      method Quadrupartition (line 61) | Quadrupartition operator- (const Quadrupartition& o) const{
    method CustomizedAnnotation (line 74) | CustomizedAnnotation operator+ (const CustomizedAnnotation& o) const{
    method CustomizedAnnotation (line 82) | CustomizedAnnotation& operator+= (const CustomizedAnnotation& o){
    method CustomizedAnnotation (line 89) | CustomizedAnnotation operator- (const CustomizedAnnotation& o) const{
  type TripartitionInitializer (line 98) | struct TripartitionInitializer{
    type Node (line 99) | struct Node{
  type Tripartition (line 109) | struct Tripartition{
    type Partition (line 110) | struct Partition{
      type Node (line 111) | struct Node{
      method score_t (line 117) | score_t normal(Node& w){
      method special (line 132) | void special(Node& w){
      method Partition (line 145) | Partition(const TripartitionInitializer &init, int p): leafParent(in...
      method update (line 154) | void update(int x, int i){
      method score_t (line 175) | score_t score(){
    type Node (line 182) | struct Node{
    method Tripartition (line 188) | Tripartition(const TripartitionInitializer &init){
    method updatePart (line 222) | void updatePart(int part, int x, int i){
    method update (line 226) | void update(int x, int i){
    method score_t (line 233) | score_t scorePart(int part){
    method score_t (line 237) | score_t score(){
  type Quadrupartition (line 244) | struct Quadrupartition{
    type Partition (line 245) | struct Partition{
      type Node (line 246) | struct Node{
        type Topology (line 247) | struct Topology{
      method extended (line 277) | void extended(Node& w, Node& u, Node& v){
      method CustomizedAnnotation (line 423) | CustomizedAnnotation extended(Node& w){
      method normal (line 459) | array<score_t, 3> normal(Node& w){
      method special (line 497) | void special(Node& w){
      method Partition (line 523) | Partition(const TripartitionInitializer &init, int p): leafParent(in...
      method update (line 533) | void update(int x, int i){
      method score (line 575) | array<double, 3> score(){
      method CustomizedAnnotation (line 581) | CustomizedAnnotation annotate(){
    method Quadrupartition (line 591) | Quadrupartition(const TripartitionInitializer &init){
    method update (line 595) | void update(int x, int i){
    method score (line 602) | array<double, 3> score(){
    method CustomizedAnnotation (line 616) | CustomizedAnnotation annotate(){

FILE: src/numerical.hpp
  type CustomizedAnnotation (line 13) | struct CustomizedAnnotation{
    method CustomizedAnnotation (line 16) | CustomizedAnnotation(){}
    method CustomizedAnnotation (line 17) | CustomizedAnnotation(int len): bs(len){}
    method bootstrap (line 19) | array<int, 3> bootstrap(){
    method CustomizedAnnotation (line 29) | CustomizedAnnotation operator+ (const CustomizedAnnotation& o) const{
    method CustomizedAnnotation (line 39) | CustomizedAnnotation& operator+= (const CustomizedAnnotation& o){
  type TripartitionInitializer (line 49) | struct TripartitionInitializer{
  type Tripartition (line 54) | struct Tripartition{
    method Tripartition (line 60) | Tripartition(TripartitionInitializer &init): M(init.M), cnt(init.cnt),...
    method updatePart (line 68) | void updatePart(int part, int x, int i){
    method score_t (line 85) | score_t scorePart(int part){
  type Quadrupartition (line 96) | struct Quadrupartition{
    method Quadrupartition (line 104) | Quadrupartition(TripartitionInitializer &init): M(init.M), cnt(init.cn...
    method update (line 116) | void update(int x, int i){
    method score (line 131) | array<double, 3> score(){
    method CustomizedAnnotation (line 142) | CustomizedAnnotation annotate(){

FILE: src/sequence-pair.hpp
  type CustomizedAnnotation (line 16) | struct CustomizedAnnotation{
    method CustomizedAnnotation (line 19) | CustomizedAnnotation(){}
    method CustomizedAnnotation (line 20) | CustomizedAnnotation(int len): bs(len){}
    method bootstrap (line 22) | array<int, 3> bootstrap(){
    method CustomizedAnnotation (line 32) | CustomizedAnnotation operator+ (const CustomizedAnnotation& o) const{
    method CustomizedAnnotation (line 42) | CustomizedAnnotation& operator+= (const CustomizedAnnotation& o){
  function score_t (line 52) | inline score_t scorePos(const array<array<unsigned short, 4>, 3> &cnt, s...
  type TripartitionInitializer (line 67) | struct TripartitionInitializer{
    type Sequence (line 68) | struct Sequence{
      method Sequence (line 72) | Sequence(){
      method append (line 76) | void append(char c1, char c2) {
      method len (line 100) | size_t len() const {
      method get (line 104) | bool get(size_t id, size_t pos) const {
      method add (line 110) | void add(size_t id, array<size_t, 4>& cnt) const {
      method add (line 119) | inline void add(size_t id, array<unsigned short, 4>& cnt) const {
      method rmv (line 128) | inline void rmv(size_t id, array<unsigned short, 4>& cnt) const {
    type Array (line 138) | struct Array {
      method Array (line 142) | Array() : seq(1) {}
      method append (line 144) | void append(const T& t) {
      method T (line 153) | const T& get(size_t id) const {
    type Gene (line 159) | struct Gene{
      type Initializer (line 160) | struct Initializer {
        method Initializer (line 168) | Initializer(int nInd, int nSpecies, int nSite, int nKernal, int nR...
        method setIndSiteRep2kernal (line 172) | void setIndSiteRep2kernal(int iInd, int iSite, int iRep, int iKern...
      type Kernal (line 201) | struct Kernal {
        method reset (line 204) | void reset(){
        method update (line 210) | void update(int y, int x, const Sequence &seq, size_t pSeq){
        method score_t (line 215) | score_t score(const score_t pq){
      method Gene (line 231) | Gene(): nInd(0), nSpecies(0), nSite(0), nKernal(0), nRep(0),
      method Gene (line 235) | Gene(const Initializer& init): nInd(init.nInd), nSpecies(init.nSpeci...
      method updateCnt (line 239) | void updateCnt(int i, int y, int x, const Sequence &seq) {
      method score_t (line 263) | score_t scoreCnt() {
      method clearCntScore (line 274) | void clearCntScore(){
  type Tripartition (line 288) | struct Tripartition{
    method Tripartition (line 292) | Tripartition(TripartitionInitializer &init): TI(init), color(init.nThr...
    method updatePart (line 298) | void updatePart(int part, int x, int i){
    method score_t (line 307) | score_t scorePart(int part){
  function score_t (line 317) | inline score_t quadPos(const array<unsigned short, 4> &cnt0, const array...
  function quadPos (line 328) | inline array<score_t, 3> quadPos(const array<array<unsigned short, 4>, 4...
  type Quadrupartition (line 334) | struct Quadrupartition{
    type Gene (line 335) | struct Gene{
      type Kernal (line 336) | struct Kernal {
        method reset (line 339) | void reset(){
        method update (line 345) | void update(int y, int x, const TripartitionInitializer::Sequence ...
        method score (line 350) | array<score_t, 3> score(score_t pq){
      method Gene (line 368) | Gene(TripartitionInitializer::Gene& init, int ufb_size, int ufb_fold...
      method updateCnt (line 376) | void updateCnt(int i, int y, int x, const TripartitionInitializer::S...
      method scoreCnt (line 400) | array<score_t, 3> scoreCnt() {
      method annotate (line 412) | void annotate(CustomizedAnnotation &annot){
      method clearCntScore (line 439) | void clearCntScore(){
    method Quadrupartition (line 451) | Quadrupartition(TripartitionInitializer &init): TI(init), color(init.n...
    method updatePart (line 458) | void updatePart(int part, int x, int i){
    method scorePart (line 467) | void scorePart(int part, array<score_t, 3> &result){
    method annotatePart (line 477) | void annotatePart(int part, CustomizedAnnotation &result){
    method update (line 486) | void update(int x, int i){
    method score (line 493) | array<double, 3> score(){
    method CustomizedAnnotation (line 511) | CustomizedAnnotation annotate(){

FILE: src/sequence.hpp
  type CustomizedAnnotation (line 21) | struct CustomizedAnnotation{
    method CustomizedAnnotation (line 25) | CustomizedAnnotation(){}
    method CustomizedAnnotation (line 26) | CustomizedAnnotation(int len): bs(len){}
    method bootstrap (line 28) | array<int, 3> bootstrap(){
    method lengths (line 38) | array<score_t, 5> lengths(){
    method CustomizedAnnotation (line 53) | CustomizedAnnotation operator+ (const CustomizedAnnotation& o) const{
    method CustomizedAnnotation (line 68) | CustomizedAnnotation& operator+= (const CustomizedAnnotation& o){
  function XXYY (line 83) | inline long long XXYY(long long x0, long long x1, long long x2, long lon...
  function score_t (line 88) | inline score_t scorePos(const array<array<unsigned short, 4>, 3> &cnt, c...
  type TripartitionInitializer (line 121) | struct TripartitionInitializer{
    type Sequence (line 122) | struct Sequence{
      method Sequence (line 126) | Sequence(){
      method append (line 130) | void append(char c) {
      method len (line 146) | size_t len() const {
      method get (line 150) | bool get(size_t id, size_t pos) const {
      method get (line 156) | char get(size_t id) const {
      method add (line 164) | void add(size_t id, array<size_t, 4>& cnt) const {
      method add (line 173) | inline void add(size_t id, array<unsigned short, 4>& cnt) const {
      method rmv (line 182) | inline void rmv(size_t id, array<unsigned short, 4>& cnt) const {
    type Array (line 192) | struct Array {
      method Array (line 196) | Array() : seq(1) {}
      method append (line 198) | void append(const T& t) {
      method T (line 207) | const T& get(size_t id) const {
    type Gene (line 213) | struct Gene{
      type Initializer (line 214) | struct Initializer {
        method Initializer (line 222) | Initializer(int nInd, int nSpecies, int nSite, int nKernal, int nR...
        method setIndSiteRep2kernal (line 226) | void setIndSiteRep2kernal(int iInd, int iSite, int iRep, int iKern...
      type Kernal (line 255) | struct Kernal {
        method reset (line 258) | void reset(){
        method update (line 264) | void update(int y, int x, const Sequence &seq, size_t pSeq){
        method score_t (line 269) | score_t score(const array<float, 4> &pi){
      method Gene (line 285) | Gene(): nInd(0), nSpecies(0), nSite(0), nKernal(0), nRep(0),
      method Gene (line 289) | Gene(const Initializer& init): nInd(init.nInd), nSpecies(init.nSpeci...
      method updateCnt (line 293) | void updateCnt(int i, int y, int x, const Sequence &seq) {
      method score_t (line 317) | score_t scoreCnt() {
      method clearCntScore (line 328) | void clearCntScore(){
  type Tripartition (line 342) | struct Tripartition{
    method Tripartition (line 346) | Tripartition(TripartitionInitializer &init): TI(init), color(init.nThr...
    method updatePart (line 352) | void updatePart(int part, int x, int i){
    method score_t (line 361) | score_t scorePart(int part){
  function quadXXYY (line 371) | inline long long quadXXYY(long long x0, long long x1, long long x2, long...
  function score_t (line 375) | inline score_t quadPos(const array<unsigned short, 4> &cnt0, const array...
  function quadPos (line 408) | inline array<score_t, 3> quadPos(const array<array<unsigned short, 4>, 4...
  function roughBlCntPos (line 414) | inline array<int, 2> roughBlCntPos(const array<unsigned short, 4> &a, co...
  function blCntPos (line 425) | inline array<double, 2> blCntPos(const array<unsigned short, 4> &a, cons...
  type Quadrupartition (line 432) | struct Quadrupartition{
    type Gene (line 433) | struct Gene{
      type Kernal (line 434) | struct Kernal {
        method reset (line 437) | void reset(){
        method update (line 443) | void update(int y, int x, const TripartitionInitializer::Sequence ...
        method score (line 448) | array<score_t, 3> score(const array<float, 4> &pi){
      method Gene (line 466) | Gene(TripartitionInitializer::Gene& init, int ufb_size, int ufb_fold...
      method updateCnt (line 474) | void updateCnt(int i, int y, int x, const TripartitionInitializer::S...
      method scoreCnt (line 498) | array<score_t, 3> scoreCnt() {
      method blCnt (line 510) | void blCnt(array<score_t, 2> &res, int i, int j){
      method annotate (line 537) | void annotate(CustomizedAnnotation &annot){
      method clearCntScore (line 570) | void clearCntScore(){
    method Quadrupartition (line 582) | Quadrupartition(TripartitionInitializer &init): TI(init), color(init.n...
    method updatePart (line 589) | void updatePart(int part, int x, int i){
    method scorePart (line 598) | void scorePart(int part, array<score_t, 3> &result){
    method annotatePart (line 608) | void annotatePart(int part, CustomizedAnnotation &result){
    method update (line 617) | void update(int x, int i){
    method score (line 624) | array<double, 3> score(){
    method CustomizedAnnotation (line 642) | CustomizedAnnotation annotate(){

FILE: src/sequencenontrivialpi.hpp
  function score_t (line 7) | inline score_t scorePos(const array<array<int, 4>, 3> cnt, const score_t...
  type TripartitionInitializer (line 24) | struct TripartitionInitializer{
  type Tripartition (line 32) | struct Tripartition{
    method Tripartition (line 43) | Tripartition(const TripartitionInitializer &init): nThreads(init.nThre...
    method resetWork (line 45) | void resetWork(int start, int end){
    method addTotalWork (line 55) | void addTotalWork(int i, int start, int end){
    method rmvTotalWork (line 62) | void rmvTotalWork(int i, int start, int end){
    method addWork (line 69) | void addWork(int x, int i, int start, int end){
    method rmvWork (line 76) | void rmvWork(int x, int i, int start, int end){
    method scoreWork (line 83) | void scoreWork(score_t &res, int start, int end){
    method reset (line 94) | void reset(){
    method addTotal (line 101) | void addTotal(int i){
    method rmvTotal (line 109) | void rmvTotal(int i){
    method add (line 117) | void add(int x, int i){
    method rmv (line 124) | void rmv(int x, int i){
    method score_t (line 131) | score_t score(){

FILE: src/sequtils.hpp
  type SeqUtils (line 17) | namespace SeqUtils{
    function string (line 20) | string fastaFormatName(const string &name){
    function string (line 28) | string fastaFormatRead(const string &name){
  type SeqParser (line 37) | struct SeqParser{
    method SeqParser (line 45) | SeqParser(string fileName, string fileFormat = "auto"){
    method nextSeq (line 64) | bool nextSeq(){
    method string (line 69) | string getSeq(size_t threshold = 0){
    method string (line 80) | static string STRING_REVERSE_COMPLEMENT(const string &seq){
    method string (line 94) | static string formatSeq(const string raw){
    method seemsFastq (line 110) | static bool seemsFastq(const string &line){
    method seemsFasta (line 114) | static bool seemsFasta(const string &line){
    method initFastq (line 118) | void initFastq(const string &fileName){
    method initFasta (line 123) | void initFasta(const string &fileName){
    method nextFastaSeq (line 133) | bool nextFastaSeq(){
    method nextFastqSeq (line 164) | bool nextFastqSeq(){
  type AlignmentParser (line 183) | struct AlignmentParser{
    method AlignmentParser (line 196) | AlignmentParser(string fileName, string fileFormat = "auto", string se...
    method nextAlignment (line 216) | bool nextAlignment(){
    method getLength (line 223) | size_t getLength(){
    method nextSeq (line 227) | bool nextSeq(){
    method string (line 238) | string getName(){
    method string (line 242) | string getSeq(){
    method string (line 254) | static string getFastaName(const string &fasta){
    method string (line 275) | static string removeSpace(const string &seq){
    method seemsPhylip (line 283) | static bool seemsPhylip(const string &line){
    method seemsFasta (line 296) | static bool seemsFasta(const string &line){
    method initPhylip (line 300) | void initPhylip(const string &fileName){
    method initFasta (line 305) | void initFasta(const string &fileName){
    method initFastaList (line 310) | void initFastaList(const string &fileName){
    method parseSeqFasta (line 319) | bool parseSeqFasta(){
    method nextAlignmentFasta (line 340) | bool nextAlignmentFasta(){
    method nextSeqFasta (line 356) | bool nextSeqFasta(){
    method nextAlignmentPhylip (line 364) | bool nextAlignmentPhylip(){
    method nextSeqPhylip (line 371) | bool nextSeqPhylip(){
    method string (line 379) | string toFormatNA(const string &seq){
    method string (line 393) | string toAmbiguity(const string &seq){
    method string (line 420) | string toFormatAA2NA(const string &seq){
  type SeqHot (line 435) | struct SeqHot{
    method SeqHot (line 438) | SeqHot(){}
    method SeqHot (line 439) | SeqHot(int n): b(n){}
    method SeqHot (line 440) | SeqHot(const vector<bool> b): b(b){}
    method nSites (line 446) | int nSites() const{
    method SeqHot (line 450) | SeqHot operator|(const SeqHot x) const{
    method SeqHot (line 459) | SeqHot operator&(const SeqHot x) const{
    method SeqHot (line 468) | SeqHot operator^(const SeqHot x) const{
    method SeqHot (line 484) | SeqHot sample(const vector<int> &cols) const{
    method sum (line 492) | int sum() const{
  type AlignmentHot (line 499) | struct AlignmentHot
    method AlignmentHot (line 504) | AlignmentHot(){}
    method AlignmentHot (line 505) | AlignmentHot(int n): s(n){}
    method AlignmentHot (line 506) | AlignmentHot(const vector<SeqHot> s, double p): s(s), p(p){}
    method SeqHot (line 508) | SeqHot& operator[](int i){
    method SeqHot (line 512) | const SeqHot& operator[](int i) const{
    method nTaxa (line 516) | int nTaxa() const{
    method nSites (line 520) | int nSites() const{
    method AlignmentHot (line 524) | AlignmentHot operator+(const AlignmentHot &x) const{
    method AlignmentHot (line 533) | AlignmentHot operator-(const AlignmentHot &x) const{
    method SeqHot (line 549) | SeqHot seqOr() const{
    method seqSum (line 556) | vector<int> seqSum() const{
    method AlignmentHot (line 564) | AlignmentHot sample(const vector<int> &cols) const{
  type MSA (line 574) | struct MSA
    method AlignmentHot (line 578) | AlignmentHot& A(){ return a[0]; }
    method AlignmentHot (line 579) | AlignmentHot& C(){ return a[1]; }
    method AlignmentHot (line 580) | AlignmentHot& G(){ return a[2]; }
    method AlignmentHot (line 581) | AlignmentHot& T(){ return a[3]; }
    method AlignmentHot (line 582) | const AlignmentHot& A() const{ return a[0]; }
    method AlignmentHot (line 583) | const AlignmentHot& C() const{ return a[1]; }
    method AlignmentHot (line 584) | const AlignmentHot& G() const{ return a[2]; }
    method AlignmentHot (line 585) | const AlignmentHot& T() const{ return a[3]; }
    method AlignmentHot (line 586) | AlignmentHot& operator[](int i){ return a[i]; }
    method AlignmentHot (line 587) | const AlignmentHot& operator[](int i) const{ return a[i]; }
    method MSA (line 589) | MSA(){}
    method MSA (line 591) | MSA(const vector<string> seqs){
    method nTaxa (line 613) | int nTaxa() const{
    method nSites (line 617) | int nSites() const{
    method alleleCnt (line 633) | vector<int> alleleCnt() const{
    method minorAlleleSum (line 642) | vector<int> minorAlleleSum() const{
    method MSA (line 657) | MSA sample(const vector<int> &cols) const{
  type DistanceMatrix (line 666) | struct DistanceMatrix{
    method nTaxa (line 677) | int nTaxa() const{
    method DistanceMatrix (line 681) | DistanceMatrix(){}
    method DistanceMatrix (line 683) | DistanceMatrix(int n): d(n, vector<double>(n)), w(n, vector<double>(n)){}
    method DistanceMatrix (line 685) | DistanceMatrix(const AlignmentHot &a, const AlignmentHot &b, bool floy...
    method cluster (line 709) | vector<vector<int> > cluster(mt19937 &eng, double threshold = 3, bool ...
    method partition (line 773) | vector<DistanceMatrix> partition(const vector<vector<int> > &groups){

FILE: src/sister.cpp
  function addName (line 26) | void addName(const string& name) {
  function main (line 33) | int main(int argc, char** argv){

FILE: src/speciestree.hpp
  type SpeciesTree (line 6) | struct SpeciesTree {
    type Node (line 7) | struct Node {
      method Node (line 15) | Node() {}
      method isLeaf (line 21) | bool isLeaf() const {
      method parent (line 25) | shared_ptr<Node> parent() const {
      method leftChild (line 29) | shared_ptr<Node> leftChild() const {
      method rightChild (line 33) | shared_ptr<Node> rightChild() const {
      method taxonID (line 37) | int taxonID() const {
      method string (line 41) | string taxonName() const {
    method string (line 46) | static string to_string(double v) {
    method root (line 55) | shared_ptr<Node> root() {
    method addRoot (line 59) | shared_ptr<Node> addRoot() {
    method addLeft (line 64) | shared_ptr<Node> addLeft(shared_ptr<Node> node) {
    method addRight (line 71) | shared_ptr<Node> addRight(shared_ptr<Node> node) {
    method string (line 78) | string simpleTree(const string &LEN, const string& SUP) {
    method string (line 91) | string simpleSubtree(shared_ptr<Node> node, const string& LEN, const s...
    method string (line 106) | string annotatedTree(const string& LEN) {
    method string (line 119) | string annotatedSubtree(shared_ptr<Node> node, const string& LEN, bool...
    method string (line 134) | string annotations(shared_ptr<Node> node) {

FILE: src/threadpool.hpp
  class ThreadPool (line 13) | class ThreadPool{
    type TaskBlock (line 14) | struct TaskBlock{
      method TaskBlock (line 15) | TaskBlock(){}
      method TaskBlock (line 17) | TaskBlock(const shared_ptr<const vector<function<score_t(const int)>...
    method worker (line 30) | static void worker(future<shared_ptr<TaskBlock> > next, const int id){
    method work (line 43) | void work(){
    method ThreadPool (line 70) | ThreadPool(){}
    method ThreadPool (line 72) | ThreadPool(int n){
    method initialize (line 76) | void initialize(int n){
    method push (line 90) | void push(function<score_t(const int)> f){
    method score_t (line 94) | score_t pop(){

FILE: src/treeutils.hpp
  type TreeUtils (line 17) | namespace TreeUtils{
    function string (line 18) | string PARSE_LEAFNAME(const string& TEXT){
    function from_string (line 26) | double from_string(const string s){
    function string (line 30) | string fastaFormatName(const string &name){
    function string (line 38) | string fastaFormatRead(const string &name){
  type TreeTokenizer (line 47) | struct TreeTokenizer{
    method TreeTokenizer (line 53) | TreeTokenizer(const string& TEXT): TEXT(TEXT){}
    method string (line 55) | string operator()(){
    method string (line 61) | string preview(){
  type Tree (line 84) | struct Tree{
    type Node (line 85) | struct Node
    method Tree (line 96) | Tree(){}
    method Tree (line 98) | Tree(TreeTokenizer &tk){
    method Tree (line 107) | Tree(TreeTokenizer &tk, const unordered_map<string, int>& name2id): Tr...
    method Tree (line 113) | Tree(const string& TEXT): Tree(){
    method Tree (line 123) | Tree(const string& TEXT, const unordered_map<string, int>& name2id): T...
    method text2trees (line 129) | static vector<Tree> text2trees(const string& TEXT){
    method text2trees (line 138) | static vector<Tree> text2trees(const string& TEXT, const unordered_map...
    method readSubtree (line 147) | int readSubtree(TreeTokenizer& tk){
    method string (line 184) | string subtree2string(int v, const vector<vector<int> > &children, boo...
    method string (line 204) | string newick(bool keepLength = true, bool keepInternalLabel = true, b...
    method string (line 213) | string subtree2string(int v, const vector<vector<int> > &children, con...
    method string (line 232) | string newick(const vector<string> &names, bool keepLength = true, boo...
  type BinaryTree (line 242) | struct BinaryTree{
    type Node (line 243) | struct Node{
    method string (line 269) | string& label(int i){
    method BinaryTree (line 281) | BinaryTree(){}
    method BinaryTree (line 283) | BinaryTree(const Tree& tree, bool resolveNonbinary = true){
    method build (line 292) | int build(const Tree& tree, const vector<vector<int> > &children, int ...
    method text2trees (line 320) | static vector<BinaryTree> text2trees(const string& TEXT){
    method text2trees (line 327) | static vector<BinaryTree> text2trees(const string& TEXT, const unorder...
    method string (line 338) | string newick(bool keepLength = true, bool keepInternalLabel = true, b...
    method string (line 342) | string newick(const vector<string> &names, bool keepLength = true, boo...
    method string (line 347) | string subtree2string(int v, bool keepLength, bool keepInternalLabel, ...
    method string (line 365) | string subtree2string(int v, const vector<string> &names, bool keepLen...

FILE: src/tutorial.hpp
  class MDGenerator (line 7) | class MDGenerator{
    method string (line 703) | string replace(string txt, string from, string to){
    method string (line 707) | string uniqueIntro(){
    method string (line 717) | string sharedIntro(){
    method string (line 726) | string inputOutput(){
    method string (line 735) | string sharedExe(){
    method string (line 744) | string uniqueExe(){
    method string (line 752) | string sharedAdv(){
    method string (line 761) | string uniqueAdv(){
    method MDGenerator (line 774) | MDGenerator(string programName): programName(programName){

FILE: src/waster-old.cpp
  function CHAR2BITS (line 45) | static unsigned char CHAR2BITS(char c){
  function CHAR2MASK (line 53) | static unsigned char CHAR2MASK(char c){
  class KmerTable (line 58) | class KmerTable{
    method shift (line 68) | static void shift(size_t &bits, size_t &mask, const unsigned char c){
    method rshift (line 73) | static void rshift(size_t &bits, size_t &mask, const unsigned char c){
    method REVERSE_COMPLEMENT (line 78) | static size_t REVERSE_COMPLEMENT(size_t bits){
    method KmerTable (line 87) | KmerTable(): table(new uint8_t[LEN]{}){}
    method add (line 93) | void add(const string &seqs, const string &seqn, bool bothStrands = tr...
    method postprocess (line 118) | void postprocess(){
    method fillProportion (line 130) | double fillProportion() const{
    method frequentPatterns (line 134) | vector<size_t> frequentPatterns(size_t n, bool optimize4noDownsample =...
  class SNP (line 160) | class SNP{
    method staticInit (line 169) | static void staticInit(){
    method staticFilter (line 181) | static void staticFilter(){
    method staticClear (line 197) | static void staticClear(){
    method locate (line 204) | static size_t locate(size_t pattern){
    method SNP (line 212) | SNP(): snps(sortedPattern.size(), (char) 0){}
    method add (line 214) | void add(size_t pattern, char c){
    method add (line 221) | void add(const string &seqs, const string &seqn, bool bothStrands = tr...
    method postprocess (line 237) | void postprocess(){
    method string (line 245) | const string& get(){
  type Workflow (line 257) | struct Workflow {
    method addName (line 271) | void addName(const string& name) {
    method buildGeneSeq (line 278) | void buildGeneSeq(TripartitionInitializer::Gene::Initializer &gene, si...
    method formatGene (line 295) | void formatGene(size_t pos, size_t nSite, size_t offset) {
    method countAT (line 302) | static int countAT(const string seq){
    method countCG (line 310) | static int countCG(const string seq){
    method readAlignment (line 318) | void readAlignment(){
    method Workflow (line 368) | Workflow(int argc, char** argv){
    method init (line 408) | void init(){
  function main (line 524) | int main(int argc, char** argv){

FILE: src/waster.cpp
  function CHAR2BITS (line 48) | unsigned char CHAR2BITS(char c){
  function CHAR2MASK (line 56) | unsigned char CHAR2MASK(char c){
  function REVERSE_COMPLEMENT (line 61) | char REVERSE_COMPLEMENT(char c){
  function REVERSE_COMPLEMENT (line 69) | size_t REVERSE_COMPLEMENT(size_t b){
  function string (line 79) | string print(size_t b){
  function string (line 87) | string print(size_t b1, size_t b2){
  function string (line 91) | string print(size_t b1, char c, size_t b2){
  class KmerTable (line 95) | class KmerTable{
    method shift (line 108) | static void shift(size_t &bits, size_t &mask, const unsigned char c){
    method rshift (line 113) | static void rshift(size_t &bits, size_t &mask, const unsigned char c){
    method REVERSE_COMPLEMENT (line 118) | static size_t REVERSE_COMPLEMENT(size_t bits){
    method KmerTable (line 127) | KmerTable(size_t nThreads = 1): table(new uint8_t[LEN]{}), cache(nThre...
    method addChar (line 142) | void addChar(size_t p, uint8_t c) {
    method performAddChar (line 149) | void performAddChar(){
    method performAddCharThread (line 171) | void performAddCharThread(size_t threadID){
    method add (line 182) | void add(const string &seqs, const string &seqn, bool bothStrands = tr...
    method postprocess (line 199) | void postprocess(){
    method performPostprocess (line 218) | void performPostprocess(size_t threadID, size_t &realcnt) {
    method fillProportion (line 237) | double fillProportion() const{
    method frequentPatterns (line 241) | vector<size_t> frequentPatterns(size_t n) const{
  class KmerConsensus (line 290) | class KmerConsensus {
    type Profile (line 298) | struct Profile {
      method add (line 303) | void add(size_t b1, size_t b2) {
      method output (line 318) | pair<size_t, double> output(size_t p) {
    method KmerConsensus (line 361) | KmerConsensus(const vector<size_t> &sortedPattern, size_t nThreads = 1):
    method profileAdd (line 371) | void profileAdd(size_t pattern, size_t b1, size_t b2){
    method performProfileAdd (line 378) | void performProfileAdd(){
    method performProfileAddThread (line 391) | void performProfileAddThread(size_t threadID){
    method add (line 411) | void add(const string& seqs, const string& seqn, bool bothStrands = tr...
    method postprocess (line 430) | void postprocess() {
    method generateConsensus (line 437) | vector<pair<size_t, double> > generateConsensus(size_t n) {
  class SNP (line 459) | class SNP {
    type SEQ (line 461) | struct SEQ{
      method debuginfo (line 468) | void debuginfo(){
      method SEQ (line 477) | SEQ(){}
      method SEQ (line 479) | SEQ(int n){
      method set (line 489) | void set(int i, char c){
      method string (line 496) | string get(){
      method uniqueCount (line 503) | size_t uniqueCount(){
      method countAT (line 507) | size_t countAT(){
      method countCG (line 515) | size_t countCG(){
    method dist (line 536) | static size_t dist(size_t a, size_t b) {
    method ufroot (line 546) | int ufroot(int node) {
    method ufrootConst (line 551) | int ufrootConst(int node) const{
    method pairup (line 556) | static size_t pairup(size_t b1, size_t b2) {
    method SNP (line 563) | SNP(const vector<pair<size_t, double> > &consensus) {
    method SNP (line 612) | SNP(const string &file){
    method save (line 651) | void save(const string &file){
    method SEQ (line 668) | SEQ initSeq(){
      method debuginfo (line 468) | void debuginfo(){
      method SEQ (line 477) | SEQ(){}
      method SEQ (line 479) | SEQ(int n){
      method set (line 489) | void set(int i, char c){
      method string (line 496) | string get(){
      method uniqueCount (line 503) | size_t uniqueCount(){
      method countAT (line 507) | size_t countAT(){
      method countCG (line 515) | size_t countCG(){
    method add (line 673) | void add(SEQ& seq, const string &seqs, const string &seqn) const{
  type Workflow (line 709) | struct Workflow {
    method addName (line 723) | void addName(const string& name) {
    method buildGeneSeq (line 730) | void buildGeneSeq(TripartitionInitializer::Gene::Initializer &gene, si...
    method formatGene (line 747) | void formatGene(size_t pos, size_t nSite, size_t offset) {
    method countAT (line 754) | static int countAT(const string seq){
    method countCG (line 762) | static int countCG(const string seq){
    method readAlignment (line 770) | void readAlignment(){
    method Workflow (line 820) | Workflow(int argc, char** argv){
    method processingFile (line 859) | static void processingFile(const SNP& snp, SNP::SEQ& snpseq, string fi...
    method init (line 881) | void init(){
  function main (line 1049) | int main(int argc, char** argv){