SYMBOL INDEX (2758 symbols across 167 files)

FILE: doc/html/igenome/igenome_table.py
  function generate_table (line 26) | def generate_table():

FILE: src/GArgs.h
  type GArgsDef (line 21) | struct GArgsDef {
  function class (line 28) | class GArgs {

FILE: src/GBase.cpp
  function GAssert (line 54) | void GAssert(const char* expression, const char* filename, unsigned int ...
  function GError (line 66) | void GError(const char* format,...){
  function GMessage (line 91) | void GMessage(const char* format,...){
  function GMalloc (line 111) | bool GMalloc(pointer* ptr,unsigned long size){
  function GCalloc (line 118) | bool GCalloc(pointer* ptr,unsigned long size){
  function GRealloc (line 125) | bool GRealloc(pointer* ptr,unsigned long size){
  function GFree (line 149) | void GFree(pointer* ptr){
  function Gstrcmp (line 180) | int Gstrcmp(const char* a, const char* b, int n) {
  function G_mkdir (line 191) | int G_mkdir(const char* path, int perms=0775) {
  function Gmkdir (line 204) | int Gmkdir(const char *path, bool recursive, int perms) {
  function GstrEq (line 235) | bool GstrEq(const char* a, const char* b) {
  function GstriEq (line 245) | bool GstriEq(const char* a, const char* b) {
  function Gstricmp (line 254) | int Gstricmp(const char* a, const char* b, int n) {
  function strsplit (line 279) | int strsplit(char* str, char** fields, int maxfields, const char* delim) {
  function strsplit (line 303) | int strsplit(char* str, char** fields, int maxfields, const char delim) {
  function strsplit (line 327) | int strsplit(char* str, char** fields, int maxfields) {
  function chrInStr (line 523) | bool chrInStr(char c, const char* str) {
  function startsWith (line 571) | bool startsWith(const char* s, const char* prefix) {
  function startsiWith (line 578) | bool startsiWith(const char* s, const char* prefix) {
  function endsWith (line 587) | bool endsWith(const char* s, const char* suffix) {
  function strhash (line 629) | int strhash(const char* str){
  function delFileName (line 645) | void delFileName(char* filepath) {
  function fileExists (line 674) | int fileExists(const char* fname) {
  function int64 (line 701) | int64 fileSize(const char* fpath) {
  function parseNumber (line 712) | bool parseNumber(char* &p, double& v) {
  function parseDouble (line 735) | bool parseDouble(char* &p, double& v) {
  function parseInt (line 739) | bool parseInt(char* &p, int& i) {
  function parseUInt (line 757) | bool parseUInt(char* &p, uint& i) {
  function parseHex (line 775) | bool parseHex(char* &p, uint& i) {
  function writeFasta (line 795) | void writeFasta(FILE *fw, const char* seqid, const char* descr,

FILE: src/GBase.h
  type int32 (line 68) | typedef int32_t int32;
  type uint32 (line 69) | typedef uint32_t uint32;
  type int16 (line 70) | typedef int16_t int16;
  type uint16 (line 71) | typedef uint16_t uint16;
  type uchar (line 73) | typedef unsigned char uchar;
  type byte (line 74) | typedef unsigned char byte;
  type int64 (line 92) | typedef int64_t int64;
  type uint64 (line 93) | typedef uint64_t uint64;
  type uint (line 145) | typedef unsigned int uint;
  type pointer (line 149) | typedef pointer GFLoadProc(FILE* fstorage);
  function iround (line 170) | inline int iround(double x) {
  function Gintcmp (line 179) | inline int Gintcmp(int a, int b) {
  function class (line 286) | class GSeg {
  function operator (line 348) | bool operator==(GSeg& d){
  function operator (line 351) | bool operator<(GSeg& d){
  function class (line 362) | class GLineReader {

FILE: src/GFaSeqGet.h
  function class (line 8) | class GSubSeq {
  function class (line 41) | class GFaSeqGet {
  function load (line 121) | void load(uint cstart, uint cend) {
  function getsublen (line 127) | int getsublen() { return lastsub!=NULL ? lastsub->sqlen : 0 ; }
  function getseqlen (line 128) | int getseqlen() { return seq_len; }
  function off_t (line 129) | off_t getseqofs() { return fseqstart; }
  function getLineLen (line 130) | int getLineLen() { return line_len; }
  function getLineBLen (line 131) | int getLineBLen() { return line_blen; }

FILE: src/GFastaIndex.h
  function class (line 14) | class GFastaRec {
  function d (line 28) | bool operator==(GFastaRec& d){
  function d (line 31) | bool operator>(GFastaRec& d){
  function d (line 34) | bool operator<(GFastaRec& d){
  function class (line 40) | class GFastaIndex {

FILE: src/GHash.hh
  class GHash (line 15) | class GHash {
    type GHashEntry (line 17) | struct GHashEntry {
    method OBJ (line 33) | OBJ* Data(uint pos) const { return (OBJ*) hash[pos].data; }
    method Mark (line 35) | bool Mark(uint pos) const { return hash[pos].mark; }
    method DefaultFreeProc (line 54) | static void DefaultFreeProc(pointer item) {
    method setFreeItem (line 60) | void setFreeItem(GFreeProc *freeProc) { fFreeProc=freeProc; }
    method setFreeItem (line 61) | void setFreeItem(bool doFree) { fFreeProc=(doFree)? &DefaultFreeProc :...
    method Capacity (line 62) | int Capacity() const { return fCapacity; }
    method Count (line 64) | int Count() const { return fCount; }
    method OBJ (line 82) | OBJ* operator[](const char* ky) { return Find(ky); }
    method GHashEntry (line 89) | GHashEntry* NextEntry() { //returns a pointer to a GHashEntry
  function OBJ (line 200) | const OBJ* GHash<OBJ>::Add(const char* ky,
  function OBJ (line 241) | const OBJ* GHash<OBJ>::shkAdd(const char* ky,
  function OBJ (line 284) | OBJ* GHash<OBJ>::Replace(const char* ky,const OBJ* pdata, bool mrk){
  function OBJ (line 326) | OBJ* GHash<OBJ>::Remove(const char* ky){
  function OBJ (line 386) | OBJ* GHash<OBJ>::Find(const char* ky, char** keyptr){
  function OBJ (line 428) | OBJ* GHash<OBJ>::NextData() {
  function OBJ (line 442) | OBJ* GHash<OBJ>::NextData(char* &nextkey) {

FILE: src/GList.hh
  class GArray (line 21) | class GArray:public GVec<OBJ> {
    method DefaultCompareProc (line 24) | static int DefaultCompareProc(const pointer item1, const pointer item2) {
    method setSorted (line 40) | void setSorted(bool sorted) {
    method Add (line 51) | int Add(OBJ& item) { return Add(&item); }
    method cAdd (line 53) | int cAdd(OBJ item) { return Add(&item); }
    method cPush (line 54) | int cPush(OBJ item) { return Add(&item); }
    method Push (line 55) | int Push(OBJ& item) { return Add(&item); }
    method setUnique (line 59) | void setUnique(bool beUnique) { fUnique = beUnique; }
    method Sorted (line 61) | bool Sorted() { return fCompareProc!=NULL; }
    method Unique (line 63) | int  Unique() { return fUnique; }
    method Insert (line 73) | void Insert(int idx, OBJ item) { Insert(idx,&item); }
  class GList (line 77) | class GList:public GPVec<OBJ> {
    method DefaultCompareProc (line 82) | static int DefaultCompareProc(const pointer item1, const pointer item2) {
    method Sorted (line 104) | bool Sorted() { return fCompareProc!=NULL; }
    method setSorted (line 105) | void setSorted(bool sorted) {
    method Unique (line 127) | int Unique() { return fUnique; }
    method setUnique (line 129) | void setUnique(bool beUnique) { fUnique = beUnique; }
    method GCompareProc (line 131) | GCompareProc* GetCompareProc() {return fCompareProc;}
  function OBJ (line 487) | OBJ* GList<OBJ>::AddIfNew(OBJ* item,

FILE: src/GStr.cpp
  function GStr (line 191) | GStr& GStr::operator=(const GStr& s) {
  function GStr (line 197) | GStr& GStr::operator=(const char *s) {
  function GStr (line 208) | GStr& GStr::operator=(const double f) {
  function GStr (line 218) | GStr& GStr::operator=(const int i) {
  function GStr (line 290) | GStr& GStr::append(char c) {
  function GStr (line 296) | GStr& GStr::append(int i) {
  function GStr (line 302) | GStr& GStr::append(uint i) {
  function GStr (line 308) | GStr& GStr::append(long l) {
  function GStr (line 314) | GStr& GStr::append(unsigned long l) {
  function GStr (line 320) | GStr& GStr::append(double f) {
  function GStr (line 331) | GStr GStr::copy() const {
  function GStr (line 336) | GStr& GStr::clear() {
  function GStr (line 378) | GStr& GStr::format(const char *fmt,...) {
  function GStr (line 395) | GStr& GStr::appendfmt(const char *fmt,...) {
  function GStr (line 410) | GStr& GStr::trim(char c) {
  function GStr (line 430) | GStr& GStr::trim(const char* c) {
  function GStr (line 449) | GStr& GStr::trimR(char c) {
  function GStr (line 469) | GStr& GStr::trimR(const char* c) {
  function GStr (line 487) | GStr& GStr::chomp(const char* cstr) {
  function GStr (line 510) | GStr& GStr::trimL(char c) {
  function GStr (line 527) | GStr& GStr::trimL(const char* c) {
  function GStr (line 545) | GStr& GStr::padR(int len, char c) {
  function GStr (line 556) | GStr& GStr::padL(int len, char c) { //align left the string
  function GStr (line 566) | GStr& GStr::padC(int len, char c) {
  function GStr (line 581) | GStr operator+(const char *s1, const GStr& s2) {
  function GStr (line 597) | GStr GStr::operator+(const GStr& s) const {
  function GStr (line 613) | GStr GStr::operator+(const char *s) const {
  function GStr (line 628) | GStr GStr::operator+(const int i) const {
  function GStr (line 639) | GStr GStr::operator+(const char c) const {
  function GStr (line 650) | GStr GStr::operator+(const double f) const {
  function GStr (line 678) | GStr GStr::substr(int idx, int len) const {
  function GStr (line 696) | GStr& GStr::reverse() {
  function GStr (line 714) | GStr&  GStr::tr(const char *rfrom, const char* rto) {
  function GStr (line 755) | GStr&  GStr::replace(const char *rfrom, const char* rto) {
  function GStr (line 809) | GStr&  GStr::cut(int idx, int len) {
  function GStr (line 838) | GStr&  GStr::paste(const GStr& s, int idx, int len) {
  function GStr (line 868) | GStr& GStr::paste(const char *s, int idx, int len) {
  function GStr (line 901) | GStr& GStr::insert(const GStr& s, int idx) {
  function GStr (line 925) | GStr& GStr::insert(const char *s, int idx) {
  function GStr (line 949) | GStr& GStr::append(const char* s) {
  function GStr (line 967) | GStr& GStr::append(const GStr& s) {
  function GStr (line 972) | GStr& GStr::upper() {
  function GStr (line 982) | GStr& GStr::lower() {
  function GStr (line 1054) | GStr GStr::split(const char* delim) {
  function GStr (line 1071) | GStr GStr::split(char c) {
  function GStr (line 1088) | GStr GStr::splitr(const char* delim) {
  function GStr (line 1099) | GStr GStr::splitr(char c) {
  function GStr (line 1322) | GStr GStr::to(char c) { //return the first part up to first occurence of c
  function GStr (line 1328) | GStr GStr::from(char c) { //same as to, but starting from the right side

FILE: src/GStr.h
  type enTokenizeMode (line 16) | enum enTokenizeMode {
  function class (line 21) | class GStr {
  function is_empty (line 73) | bool is_empty() const;
  function asDouble (line 114) | double asDouble() { return asReal(); }
  function asDouble (line 116) | bool asDouble(double& r) { return asReal(r); }
  function Gswap (line 218) | inline void Gswap(GStr& s1, GStr& s2) {

FILE: src/GVec.hh
  type IsPrimitiveType (line 26) | struct IsPrimitiveType {
  type IsPrimitiveType<bool> (line 30) | struct IsPrimitiveType<bool> { enum { VAL = 1 }; }
  type IsPrimitiveType<void*> (line 31) | struct IsPrimitiveType<void*> { enum { VAL = 1 }; }
  type IsPrimitiveType<char*> (line 32) | struct IsPrimitiveType<char*> { enum { VAL = 1 }; }
  type IsPrimitiveType<float> (line 33) | struct IsPrimitiveType<float> { enum { VAL = 1 }; }
  type IsPrimitiveType<double> (line 34) | struct IsPrimitiveType<double> { enum { VAL = 1 }; }
  type IsPrimitiveType<int> (line 36) | struct IsPrimitiveType<int> { enum { VAL = 1 }; }
  type IsPrimitiveType<unsigned int> (line 37) | struct IsPrimitiveType<unsigned int> { enum { VAL = 1 }; }
  type IsPrimitiveType<char> (line 38) | struct IsPrimitiveType<char> { enum { VAL = 1 }; }
  type IsPrimitiveType<unsigned char> (line 39) | struct IsPrimitiveType<unsigned char> { enum { VAL = 1 }; }
  type IsPrimitiveType<short> (line 40) | struct IsPrimitiveType<short> { enum { VAL = 1 }; }
  type IsPrimitiveType<unsigned short> (line 41) | struct IsPrimitiveType<unsigned short> { enum { VAL = 1 }; }
  type IsPrimitiveType<long> (line 42) | struct IsPrimitiveType<long> { enum { VAL = 1 }; }
  type IsPrimitiveType<unsigned long> (line 43) | struct IsPrimitiveType<unsigned long> { enum { VAL = 1 }; }
  type IsPrimitiveType<long long> (line 44) | struct IsPrimitiveType<long long> { enum { VAL = 1 }; }
  type IsPrimitiveType<unsigned long long> (line 45) | struct IsPrimitiveType<unsigned long long> { enum { VAL = 1 }; }
  function DefLTCompareProc (line 59) | int DefLTCompareProc(const pointer p1, const pointer p2) {
  class GVec (line 68) | class GVec {
    method Insert (line 81) | void Insert(int idx, OBJ item) { Insert(idx, &item); }
    method idxInsert (line 83) | void idxInsert(int idx, OBJ& item) { Insert(idx, &item); }
    method Add (line 88) | int Add(OBJ& item) { return Add(&item); }
    method cAdd (line 89) | int cAdd(OBJ item) { return Add(&item); }
    method Push (line 93) | int Push(OBJ& item) { return Add(&item); }
    method cPush (line 94) | int cPush(OBJ item) { return Add(&item); }
    method OBJ (line 100) | OBJ& Get(int idx) {
    method OBJ (line 104) | inline OBJ& operator[](int i) {
    method OBJ (line 108) | OBJ& Last() {
    method OBJ (line 112) | OBJ& First() {
    method Swap (line 120) | void Swap(int idx1, int idx2)  { Exchange(idx1, idx2); }
    method Capacity (line 121) | int  Capacity() { return fCapacity; }
    method Count (line 124) | int  Count() { return fCount; }
    method Resize (line 129) | void Resize(int NewCount) { setCount(NewCount); }
    method Resize (line 131) | void Resize(int NewCount, OBJ v) { setCount(NewCount, &v); }
    method isEmpty (line 134) | bool isEmpty() { return fCount==0; }
    method notEmpty (line 135) | bool notEmpty() { return fCount>0; }
  class GPVec (line 143) | class GPVec {
    method DefaultFreeProc (line 155) | static void DefaultFreeProc(pointer item) {
    method OBJ (line 165) | OBJ* operator[](int i) { return this->Get(i); }
    method setFreeItem (line 169) | void setFreeItem(GFreeProc *freeProc) { fFreeProc=freeProc; }
    method setFreeItem (line 170) | void setFreeItem(bool doFree) {
    method Push (line 175) | int Push(OBJ* item) { return Add(item); }
    method Swap (line 181) | void Swap(int idx1, int idx2)  { Exchange(idx1, idx2); }
    method OBJ (line 182) | OBJ* First() { return (fCount>0)?fList[0]:NULL; }
    method OBJ (line 183) | OBJ* Last()  { return (fCount>0)?fList[fCount-1]:NULL;}
    method isEmpty (line 184) | bool isEmpty() { return fCount==0; }
    method notEmpty (line 185) | bool notEmpty() { return fCount>0; }
    method Capacity (line 186) | int Capacity() { return fCapacity; }
    method Count (line 187) | int Count()   { return fCount; }
  function OBJ (line 410) | OBJ GVec<OBJ>::Pop() {
  function OBJ (line 420) | OBJ GVec<OBJ>::Shift() {
  function OBJ (line 696) | OBJ* GPVec<OBJ>::Get(int idx) {
  function OBJ (line 833) | OBJ* GPVec<OBJ>::Pop() {
  function OBJ (line 842) | OBJ* GPVec<OBJ>::Shift() {

FILE: src/abundances.cpp
  function digamma (line 85) | double digamma(double x)
  function trigamma (line 178) | double trigamma(double x)
  function negbin_log_likelihood (line 232) | long double negbin_log_likelihood(const vector<double>& samples, long do...
  function poisson_log_likelihood (line 267) | long double poisson_log_likelihood(const vector<double>& samples, long d...
  function negbin_log_likelihood_helper (line 290) | long double negbin_log_likelihood_helper(const vector<double>& samples, ...
  function negbin_log_likelihood_prime_helper (line 334) | long double negbin_log_likelihood_prime_helper(const vector<double>& sam...
  type negbin_ll_functor (line 357) | struct negbin_ll_functor
    method negbin_ll_functor (line 359) | negbin_ll_functor(const vector<double>& count_samples) : samples(count...
  function fit_negbin_dist (line 371) | bool fit_negbin_dist(const vector<double> samples, double& r, double& p)
  function compute_compatibilities (line 420) | void compute_compatibilities(const vector<boost::shared_ptr<Abundance> >...
  function AbundanceStatus (line 524) | AbundanceStatus AbundanceGroup::status() const
  function BOOST_FOREACH (line 564) | BOOST_FOREACH(boost::shared_ptr<Abundance> ab, _abundances)
  function BOOST_FOREACH (line 578) | BOOST_FOREACH(boost::shared_ptr<Abundance> ab, _abundances)
  function CountPerReplicateTable (line 586) | CountPerReplicateTable AbundanceGroup::num_fragments_by_replicate() const
  function FPKMPerReplicateTable (line 614) | FPKMPerReplicateTable AbundanceGroup::FPKM_by_replicate() const
  function StatusPerReplicateTable (line 638) | StatusPerReplicateTable AbundanceGroup::status_by_replicate() const
  function BOOST_FOREACH (line 688) | BOOST_FOREACH(boost::shared_ptr<Abundance> ab, _abundances)
  function BOOST_FOREACH (line 727) | BOOST_FOREACH(boost::shared_ptr<Abundance> ab, _abundances)
  function BOOST_FOREACH (line 739) | BOOST_FOREACH(boost::shared_ptr<Abundance> ab, _abundances)
  function BOOST_FOREACH (line 789) | BOOST_FOREACH(bool keeper, to_keep)
  function BOOST_FOREACH (line 858) | BOOST_FOREACH(boost::shared_ptr<Abundance> pA, _abundances)
  function BOOST_FOREACH (line 872) | BOOST_FOREACH (boost::shared_ptr<Abundance> pA, _abundances)
  function BOOST_FOREACH (line 885) | BOOST_FOREACH (boost::shared_ptr<Abundance> pA, _abundances)
  function BOOST_FOREACH (line 899) | BOOST_FOREACH (boost::shared_ptr<Abundance> pA, _abundances)
  function BOOST_FOREACH (line 912) | BOOST_FOREACH (boost::shared_ptr<Abundance> pA, _abundances)
  function string (line 921) | const string& AbundanceGroup::locus_tag() const
  function string (line 945) | const string& AbundanceGroup::reference_tag() const
  function BOOST_FOREACH (line 975) | BOOST_FOREACH (boost::shared_ptr<Abundance> ab, _abundances)
  function collapse_equivalent_hits (line 1140) | void collapse_equivalent_hits(const vector<MateHit>& alignments,
  function collapse_equivalent_hits_helper (line 1360) | void collapse_equivalent_hits_helper(const vector<MateHit>& alignments,
  function generate_count_assignment_samples (line 1429) | bool generate_count_assignment_samples(int num_draws,
  function calculate_gamma_mle_covariance (line 1518) | void calculate_gamma_mle_covariance(const std::map<boost::shared_ptr<Rea...
  function calculate_fragment_assignment_distribution (line 1597) | void calculate_fragment_assignment_distribution(const std::map<boost::sh...
  function solve_beta (line 2008) | long double solve_beta(long double A, long double B, long double C)
  function estimate_count_variance (line 2043) | bool estimate_count_variance(long double& variance,
  function simulate_count_covariance (line 2157) | bool simulate_count_covariance(const vector<double>& num_fragments,
  function BOOST_FOREACH (line 2747) | BOOST_FOREACH(boost::shared_ptr<Abundance> pA, _abundances)
  function compute_cond_probs_and_effective_lengths (line 2861) | void compute_cond_probs_and_effective_lengths(const vector<MateHit>& ali...
  function trace (line 2896) | double trace(const ublas::matrix<double>& m)
  function BOOST_FOREACH (line 2919) | BOOST_FOREACH (boost::shared_ptr<Abundance> ab, _abundances)
  function BOOST_FOREACH (line 2969) | BOOST_FOREACH (boost::shared_ptr<Abundance> ab, _abundances)
  function calculate_assignment_probs (line 3136) | void calculate_assignment_probs(const Eigen::VectorXd& alignment_multipl...
  function calculate_average_assignment_probs (line 3168) | void calculate_average_assignment_probs(const Eigen::VectorXd& alignment...
  function calculate_iterated_exp_count_covariance (line 3225) | void calculate_iterated_exp_count_covariance(const vector<double>& gammas,
  function BOOST_FOREACH (line 3370) | BOOST_FOREACH (boost::shared_ptr<Abundance> pA, _abundances)
  function BOOST_FOREACH (line 3379) | BOOST_FOREACH (boost::shared_ptr<Abundance> pA, _abundances)
  function get_alignments_from_scaffolds (line 3473) | void get_alignments_from_scaffolds(const vector<boost::shared_ptr<Abunda...
  function Estep (line 3506) | void Estep (int N,
  function Mstep (line 3607) | void Mstep (int N,
  function logLike (line 3630) | double logLike (int N,
  function EM (line 3661) | double EM(int N, int M,
  function compute_fisher (line 3718) | void compute_fisher(const vector<boost::shared_ptr<Abundance> >& transcr...
  function AbundanceStatus (line 3771) | AbundanceStatus compute_posterior_expectation(const vector<ublas::vector...
  function AbundanceStatus (line 3842) | AbundanceStatus AbundanceGroup::calculate_per_replicate_abundances(vecto...
  function AbundanceStatus (line 3903) | AbundanceStatus calculate_inverse_fisher(const vector<boost::shared_ptr<...
  function AbundanceStatus (line 3958) | AbundanceStatus revise_map_mean_and_cov_estimate(double log_total_weight,
  function AbundanceStatus (line 4032) | AbundanceStatus calc_is_scale_factor(const ublas::matrix<double>& covari...
  function is_identifiable (line 4053) | bool is_identifiable(M &m, PM &pm)
  function AbundanceStatus (line 4085) | AbundanceStatus gamma_mle(const vector<boost::shared_ptr<Abundance> >& t...
  function calc_isoform_fpkm_conf_intervals (line 4240) | void calc_isoform_fpkm_conf_intervals(double FPKM,
  function not_intronic (line 4251) | bool not_intronic(int p, vector<float>& depth_of_coverage, vector<float>...
  function compute_doc (line 4261) | double compute_doc(int bundle_origin,
  function major_isoform_intron_doc (line 4376) | double major_isoform_intron_doc(map<pair<int, int>, float>& intron_doc)
  function record_min_doc_for_scaffolds (line 4418) | void record_min_doc_for_scaffolds(int bundle_origin,
  function record_doc_for_scaffolds (line 4437) | void record_doc_for_scaffolds(int bundle_origin,
  function record_doc_for_scaffolds (line 4452) | void record_doc_for_scaffolds(int bundle_origin,
  function get_intron_doc (line 4471) | double get_intron_doc(const Scaffold& s,
  function get_scaffold_doc (line 4503) | double get_scaffold_doc(int bundle_origin,
  function get_scaffold_min_doc (line 4526) | double get_scaffold_min_doc(int bundle_origin,
  function tss_analysis (line 4549) | void tss_analysis(const string& locus_tag, SampleAbundances& sample)
  function cds_analyis (line 4632) | void cds_analyis(const string& locus_tag, SampleAbundances& sample)
  function sample_abundance_worker (line 4711) | void sample_abundance_worker(const string& locus_tag,
  function merge_precomputed_expression_worker (line 4838) | void merge_precomputed_expression_worker(const string& locus_tag,

FILE: src/abundances.h
  type ConfidenceInterval (line 30) | struct ConfidenceInterval
  type AbundanceStatus (line 46) | enum AbundanceStatus { NUMERIC_OK, NUMERIC_FAIL, NUMERIC_LOW_DATA, NUMER...
  type map (line 48) | typedef map<boost::shared_ptr<ReadGroupProperties const>, double> CountP...
  type map (line 49) | typedef map<boost::shared_ptr<ReadGroupProperties const>, double> FPKMPe...
  type map (line 50) | typedef map<boost::shared_ptr<ReadGroupProperties const>, AbundanceStatu...
  function class (line 58) | class Abundance
  function class (line 154) | class TranscriptAbundance : public Abundance
  function status (line 182) | void status(AbundanceStatus s)			{ _status = s; }
  function FPKM (line 185) | void FPKM(double fpkm)
  function FPKM_conf (line 195) | void FPKM_conf(const ConfidenceInterval& cf) { _FPKM_conf = cf; }
  function gamma (line 198) | void gamma(double g)					{ assert(!isnan(g)); _gamma = g; }
  function kappa (line 201) | void kappa(double k)					{ _kappa = k; }
  function num_fragments (line 205) | void num_fragments(double nf)
  function num_fragment_var (line 215) | void num_fragment_var(double nfv)		{ assert (!isnan(nfv)); _num_fragment...
  function num_fragment_uncertainty_var (line 220) | void            num_fragment_uncertainty_var(double nfv) { assert (!isna...
  function num_fragments_by_replicate (line 223) | void num_fragments_by_replicate(CountPerReplicateTable& cpr) { _num_frag...
  function FPKM_by_replicate (line 226) | void FPKM_by_replicate(FPKMPerReplicateTable& fpr) { _fpkm_per_replicate...
  function status_by_replicate (line 229) | void status_by_replicate(StatusPerReplicateTable& fpr) { _status_per_rep...
  function mass_variance (line 232) | void mass_variance(double mv)			{ _sample_mass_variance = mv; }
  function transfrag (line 234) | void transfrag(boost::shared_ptr<Scaffold> tf)		{ _transfrag = tf; }
  function effective_length (line 238) | void effective_length(double el)		{ _eff_len = el; }
  function vector (line 240) | const vector<double>* cond_probs() const	{ return _cond_probs; }
  function cond_probs (line 241) | void cond_probs(vector<double>* cp)
  function fpkm_samples (line 248) | void  fpkm_samples(const vector<double>& s) { _fpkm_samples = s; }
  function virtual (line 311) | virtual void			description(const string& d) { _description = d; }
  function virtual (line 314) | virtual void			locus_tag(const string& L) { _locus_tag = L; }
  function virtual (line 317) | virtual void			reference_tag(const string& r) { _ref_tag = r; }
  function class (line 379) | class AbundanceGroup : public Abundance
  type SampleAbundances (line 688) | struct SampleAbundances

FILE: src/assemble.cpp
  function weight_of_merge (line 65) | long long weight_of_merge(Scaffold& lhs,
  function create_reachability_bp_graph (line 115) | void create_reachability_bp_graph(DAG& dag,
  function add_weights_to_reachability_bp_graph (line 201) | void add_weights_to_reachability_bp_graph(ReachGraph& bp,
  function holdout_transitivity_hazards (line 293) | void holdout_transitivity_hazards(vector<Scaffold>& hits,
  function make_scaffolds (line 371) | bool make_scaffolds(int bundle_left,

FILE: src/biascorrection.cpp
  function output_vector (line 21) | void output_vector(vector<double>& v, char* fname)
  function colSums (line 34) | double colSums(const ublas::matrix<long double>& A, vector<long double>&...
  function fourSums (line 47) | double fourSums(const ublas::matrix<long double>& A, ublas::matrix<long ...
  function ones (line 61) | void ones(ublas::matrix<long double>& A)
  function get_compatibility_list (line 68) | void get_compatibility_list(const vector<boost::shared_ptr<Scaffold> >& ...
  function learn_bias (line 97) | void learn_bias(BundleFactory& bundle_factory, BiasLearner& bl, bool pro...
  function BOOST_FOREACH (line 215) | BOOST_FOREACH (const MateHit* hit_p, transcript.mate_hits())

FILE: src/biascorrection.h
  function class (line 33) | class BiasLearner{
  function class (line 81) | class BiasCorrectionHelper{

FILE: src/bundles.cpp
  type ScaffoldSorter (line 49) | struct ScaffoldSorter
    method ScaffoldSorter (line 51) | ScaffoldSorter(RefSequenceTable& _rt) : rt(_rt) {}
  function load_ref_rnas (line 78) | void load_ref_rnas(FILE* ref_mRNA_file,
  type HitlessScaffold (line 273) | struct HitlessScaffold
  function unmapped_hit (line 281) | bool unmapped_hit(const MateHit& x)
  function BOOST_FOREACH (line 595) | BOOST_FOREACH (MateHit& hit, _hits)
  function print_sort_error (line 646) | void print_sort_error(const char* last_chr_name,
  type IntronSpanCounter (line 1175) | struct IntronSpanCounter
    method IntronSpanCounter (line 1177) | IntronSpanCounter() : left_reads(0), little_reads(0), total_reads(0), ...
  function count_introns_in_read (line 1188) | void count_introns_in_read(const ReadHit& read,
  function minor_introns (line 1273) | void minor_introns(int bundle_length,
  function multimapping_introns (line 1345) | void multimapping_introns(int bundle_length,
  function identify_bad_splices (line 1385) | void identify_bad_splices(const HitBundle& bundle,
  function inspect_map (line 1623) | void inspect_map(boost::shared_ptr<BundleFactory> bundle_factory,

FILE: src/bundles.h
  type BundleStats (line 32) | struct BundleStats
  function add_raw_mass (line 110) | void add_raw_mass(double rm) { _raw_mass += rm; }
  function rem_raw_mass (line 111) | void rem_raw_mass(double rm) { _raw_mass -= rm; }
  function raw_mass (line 112) | double raw_mass() { return _raw_mass; }
  function compatible_mass (line 119) | void compatible_mass(double c) { _compatible_mass = c; }
  function clear_hits (line 121) | void clear_hits()
  function id (line 145) | void id(int i) { _id = i; }
  function add_ref_scaffold (line 147) | void add_ref_scaffold(boost::shared_ptr<Scaffold> scaff)
  function mass (line 178) | double mass() const
  type identity_hash (line 208) | struct identity_hash {
  type boost (line 212) | typedef boost::unordered_multimap<uint64_t, MateHit, identity_hash> Open...
  function class (line 228) | class BundleFactory
  function virtual (line 240) | virtual ~BundleFactory() {}
  function bundles_remain (line 243) | bool bundles_remain()
  function num_bundles (line 261) | void num_bundles(int n) { _num_bundles = n; }
  function virtual (line 263) | virtual void reset()
  function bad_intron_table (line 336) | void bad_intron_table(const BadIntronTable& bad_introns)
  function read_group_properties (line 344) | void read_group_properties(boost::shared_ptr<ReadGroupProperties> rg)
  function class (line 402) | class PrecomputedExpressionBundleFactory : public BundleFactory
  function class (line 429) | class IdToLocusMap

FILE: src/clustering.h
  type boost (line 40) | typedef boost::adjacency_list <boost::vecS, boost::vecS, boost::undirect...
  type ConnectByExonOverlap (line 42) | struct ConnectByExonOverlap
  type ConnectByAnnotatedGeneId (line 48) | struct ConnectByAnnotatedGeneId
  type ConnectByAnnotatedTssId (line 54) | struct ConnectByAnnotatedTssId
  type ConnectByAnnotatedProteinId (line 60) | struct ConnectByAnnotatedProteinId
  type ConnectByStrand (line 66) | struct ConnectByStrand

FILE: src/codons.cpp
  function packCodon (line 49) | unsigned short packCodon(char n1, char n2, char n3) {
  function codonTableInit (line 59) | bool codonTableInit() {

FILE: src/codons.h
  function else (line 9) | struct Codon {
  function const (line 37) | char operator[](int idx) const {

FILE: src/common.cpp
  function gaurd_assembly (line 176) | bool gaurd_assembly()
  function asm_verbose (line 181) | void asm_verbose(const char* fmt,...)
  function verbose_msg (line 192) | void verbose_msg(const char* fmt,...) {
  function parseInt (line 211) | int parseInt(int lower, const char *errmsg, void (*print_usage)()) {
  function parseFloat (line 234) | float parseFloat(float lower, float upper, const char *errmsg, void (*pr...
  function mkpath (line 261) | int mkpath(const char *s, mode_t mode)
  function init_library_table (line 286) | void init_library_table()
  function print_library_table (line 348) | void print_library_table()
  function init_dispersion_method_table (line 366) | void init_dispersion_method_table()
  function print_dispersion_method_table (line 374) | void print_dispersion_method_table()
  function init_lib_norm_method_table (line 393) | void init_lib_norm_method_table()
  function init_cufflinks_lib_norm_method_table (line 400) | void init_cufflinks_lib_norm_method_table()
  function print_lib_norm_method_table (line 408) | void print_lib_norm_method_table()
  function init_output_format_table (line 429) | void init_output_format_table()
  function print_output_format_table (line 435) | void print_output_format_table()
  function encode_seq (line 456) | void encode_seq(const string seqStr, char* seq, char* c_seq)

FILE: src/common.h
  type BundleMode (line 204) | enum BundleMode
  type BiasMode (line 213) | enum BiasMode
  type Strandedness (line 223) | enum Strandedness
  type StandardMateOrientation (line 230) | enum StandardMateOrientation
  type MateStrandMapping (line 239) | enum MateStrandMapping
  type Platform (line 247) | enum Platform
  type FLDSource (line 254) | enum FLDSource
  type DispersionMethod (line 261) | enum DispersionMethod
  type LibNormalizationMethod (line 270) | enum LibNormalizationMethod
  type OutputFormat (line 280) | enum OutputFormat
  function class (line 288) | class EmpDist
  function pdf (line 322) | double pdf(int l) const
  function npdf (line 330) | double npdf(int l, int r) const
  function cdf (line 341) | void cdf(std::vector<double>& cdf)	{ _cdf = cdf; }
  function cdf (line 342) | double cdf(int l) const
  function valid_len (line 351) | bool valid_len(int l) const { return (l >= _min && l <= _max); }
  function too_short (line 352) | bool too_short(int l) const { return (l < _min); }
  function mode (line 354) | void mode(int mode)				{ _mode = mode; }
  function max (line 357) | void max(int max)				{ _max = max;  }
  function min (line 360) | void min(int min)				{ _min = min;  }
  function mean (line 363) | void mean(double mean)				{ _mean = mean;  }
  function std_dev (line 366) | void std_dev(double std_dev)				{ _std_dev = std_dev;  }
  function source (line 370) | void source(FLDSource source)   { _source = source; }
  function load (line 379) | struct LocusCount
  function mate_strand_mapping (line 434) | struct CheckedParameters
  function platform (line 542) | void platform(Platform p)  { _platform = p; }
  function total_map_mass (line 545) | void total_map_mass(long double p)  { _total_map_mass = p; }
  function normalized_map_mass (line 548) | void normalized_map_mass(long double p)  { _norm_map_mass = p; }
  function frag_len_dist (line 551) | void frag_len_dist(boost::shared_ptr<EmpDist const> p)  { _frag_len_dist...
  function bias_learner (line 554) | void bias_learner(boost::shared_ptr<BiasLearner const> bl)  { _bias_lear...
  function internal_scale_factor (line 559) | void internal_scale_factor(double sf) { _internal_scale_factor = sf; }
  function external_scale_factor (line 562) | void external_scale_factor(double sf) { _external_scale_factor = sf; }
  function complete_fragments (line 565) | void complete_fragments(bool c)  { _complete_fragments = c; }
  function internally_scale_mass (line 568) | double internally_scale_mass(double unscaled_mass) const
  function mass_dispersion_model (line 581) | void mass_dispersion_model(boost::shared_ptr<const MassDispersionModel> nm)
  function mle_error_model (line 591) | void mle_error_model(boost::shared_ptr<const MleErrorModel> nm)
  function std (line 596) | const std::vector<LocusCount>& common_scale_compatible_counts() { return...
  function common_scale_compatible_counts (line 597) | void common_scale_compatible_counts(const std::vector<LocusCount>& count...
  function std (line 599) | const std::vector<LocusCount>& common_scale_total_counts() { return _com...
  function common_scale_total_counts (line 600) | void common_scale_total_counts(const std::vector<LocusCount>& counts) { ...
  function std (line 602) | const std::vector<LocusCount>& raw_compatible_counts() { return _raw_com...
  function raw_compatible_counts (line 603) | void raw_compatible_counts(const std::vector<LocusCount>& counts) { _raw...
  function std (line 605) | const std::vector<LocusCount>& raw_total_counts() { return _raw_total_co...
  function raw_total_counts (line 606) | void raw_total_counts(const std::vector<LocusCount>& counts) { _raw_tota...
  function clear_count_tables (line 608) | void clear_count_tables() {
  function multi_read_table (line 623) | void multi_read_table(boost::shared_ptr<MultiReadTable> mrt) { _multi_re...
  function condition_name (line 629) | void condition_name(const std::string& cd) { _condition_name = cd; }
  function file_path (line 632) | void file_path(const std::string& fp) { _file_path = fp; }
  function replicate_num (line 635) | void replicate_num(int rn) { _replicate_num = rn; }
  function ref_gtf (line 637) | void ref_gtf(const std::string& file_path, const boost::crc_32_type& gtf...
  function mask_gtf (line 643) | void mask_gtf(const std::string& file_path, const boost::crc_32_type& gt...
  function checked_parameters (line 651) | void checked_parameters(const CheckedParameters& rhs) { _checked_params ...
  function collect_checked_parameters (line 654) | void collect_checked_parameters() {
  type LibNormStandards (line 767) | struct LibNormStandards

FILE: src/compress_gtf.cpp
  type option (line 44) | struct option
  function print_usage (line 54) | void print_usage()
  function parse_options (line 68) | int parse_options(int argc, char** argv)
  function compress_genes (line 114) | void compress_genes(FILE* ftranscripts,
  function driver (line 336) | void driver(vector<FILE*> ref_gtf_files, FILE* gtf_out)
  function main (line 361) | int main(int argc, char** argv)

FILE: src/cuffcluster.cpp
  type option (line 48) | struct option
  function print_usage (line 61) | void print_usage()
  function parse_options (line 77) | int parse_options(int argc, char** argv)
  type ExprRecord (line 137) | struct ExprRecord
    method ExprRecord (line 139) | ExprRecord() :
  type ClusterStats (line 186) | struct ClusterStats
    method ClusterStats (line 188) | ClusterStats(int dim)
  type SortByVariance (line 199) | struct SortByVariance
  function assign_to_nearest_cluster (line 212) | void assign_to_nearest_cluster(vector<ExprRecord>& expr_records, vector<...
  function get_assignments (line 311) | void get_assignments(const vector<ClusterStats>& clusters,
  function split_cluster (line 329) | void split_cluster(const vector<ExprRecord>& expr_records,
  function kmeans (line 436) | void kmeans(vector<ExprRecord>& expr_records, int num_clusters, int num_...
  function driver (line 554) | void driver(FILE* fpkm_file, FILE* spec_out, FILE* row_matrix_out, FILE*...
  function main (line 874) | int main(int argc, char** argv)

FILE: src/cuffcompare.cpp
  function openfwrite (line 94) | void openfwrite(FILE* &f, GArgs& args, char opt) {
  class GSeqTrack (line 107) | class GSeqTrack {
    method get_gseqid (line 118) | int get_gseqid() { return gseq_id; }
    method GSeqTrack (line 119) | GSeqTrack(int gid=-1):xloci_f(true,true,false),
  function cmpGTrackByName (line 172) | int cmpGTrackByName(const pointer p1, const pointer p2) {
  function show_usage (line 177) | void show_usage() {
  function main (line 183) | int main(int argc, char * const argv[]) {
  function show_exons (line 467) | void show_exons(FILE* f, GffObj& m) {
  function ichainMatch (line 476) | bool ichainMatch(GffObj* t, GffObj* r, bool& exonMatch, int fuzz=0) {
  function exon_match (line 539) | bool exon_match(GXSeg& r, GXSeg& q, uint fuzz=0) {
  function compareLoci2R (line 559) | void compareLoci2R(GList<GLocus>& loci, GList<GSuperLocus>& cmpdata,
  function GSeqData (line 833) | GSeqData* getQryData(int gid, GList<GSeqData>& qdata) {
  function writeLoci (line 868) | void writeLoci(FILE* f, GList<GLocus> & loci) {
  function printXQ1 (line 888) | void printXQ1(FILE* f, int qidx, GList<GLocus>& qloci) {
  function numXLoci (line 902) | void numXLoci(GList<GXLocus>& xloci, int& last_id) {
  class GProtCl (line 911) | class GProtCl {
    method GProtCl (line 914) | GProtCl(GXConsensus* c=NULL):protcl(true,false,false) {
    method add_Pcons (line 918) | bool add_Pcons(GXConsensus* c) {
    method addMerge (line 930) | void addMerge(GProtCl& pcl, GXConsensus* pclnk) {
    method aalen (line 938) | int aalen() {
  class GTssCl (line 950) | class GTssCl:public GSeg { //experiment cluster of ref loci (isoforms)
    method GTssCl (line 955) | GTssCl(GXConsensus* c=NULL):tsscl(true,false,false) {
    method addFirst (line 963) | void addFirst(GXConsensus* c) {
    method add_Xcons (line 972) | bool add_Xcons(GXConsensus* c) {
    method addMerge (line 1015) | void addMerge(GTssCl& cl, GXConsensus* clnk) {
  function printConsGTF (line 1068) | void printConsGTF(FILE* fc, GXConsensus* xc, int xlocnum) {
  function tssCluster (line 1107) | void tssCluster(GXLocus& xloc)
  function protCluster (line 1155) | void protCluster(GXLocus& xloc, GFaSeqGet *faseq) {
  function printXLoci (line 1204) | void printXLoci(FILE* f, FILE* fc, int qcount, GList<GXLocus>& xloci, GF...
  function writeIntron (line 1244) | void writeIntron(FILE* f, char strand, GFaSeqGet* faseq, GSeg& iseg,
  function reportMIntrons (line 1278) | void reportMIntrons(FILE* fm, FILE* fn, FILE* fq, char strand,
  function processLoci (line 1303) | void processLoci(GSeqData& seqdata, GSeqData* refdata, int qfidx) {
  function collectRLocData (line 1323) | void collectRLocData(GSuperLocus& stats, GLocus& loc) {
  function collectRData (line 1338) | void collectRData(GSuperLocus& stats, GList<GLocus>& loci) {
  function collectQLocData (line 1344) | void collectQLocData(GSuperLocus& stats, GLocus& loc) {
  function collectQData (line 1361) | void collectQData(GSuperLocus& stats, GList<GLocus>& loci) {
  function collectQNOvl (line 1369) | void collectQNOvl(GSuperLocus& stats, GList<GLocus>& loci, GList<GLocus>...
  function collectQU (line 1378) | void collectQU(GSuperLocus& stats, GList<GLocus>& nloci) {
  function printLocus (line 1385) | void printLocus(FILE* f, GLocus& loc, const char* gseqname) {
  function collectRNOvl (line 1392) | void collectRNOvl(GSuperLocus& stats, GList<GLocus>& loci) { //, const c...
  function collectCmpData (line 1403) | void collectCmpData(GSuperLocus& stats, GList<GSuperLocus>& cmpdata) { /...
  function printLociQ (line 1417) | void printLociQ(FILE* f, GList<GLocus>& loci, char c=' ') {
  function printLocQ (line 1426) | void printLocQ(FILE *f, GLocus& loc) {
  function collectStats (line 1433) | void collectStats(GSuperLocus& stats, GSeqData* seqdata, GSeqData* refda...
  function reportStats (line 1473) | void reportStats(FILE* fout, const char* setname, GSuperLocus& stotal,
  function loadRefDescr (line 1605) | void loadRefDescr(const char* fname) {
  function GSeqTrack (line 1624) | GSeqTrack* findGSeqTrack(int gsid) {
    method get_gseqid (line 118) | int get_gseqid() { return gseq_id; }
    method GSeqTrack (line 119) | GSeqTrack(int gid=-1):xloci_f(true,true,false),
  function GffObj (line 1633) | GffObj* findRefMatch(GffObj& m, GLocus& rloc, int& ovlen) {
  function addXCons (line 1668) | void addXCons(GXLocus* xloc, GffObj* ref, char ovlcode, GffObj* tcons, C...
  function getOvlCode (line 1678) | char getOvlCode(GffObj& m, GffObj& r, int& ovlen) {
  function getRefOvl (line 1772) | char getRefOvl(GffObj& m, GLocus& rloc, GffObj*& rovl, int& ovlen) {
  function findTMatches (line 1802) | void findTMatches(GTrackLocus& loctrack, int qcount) {
  function cmpTData_qset (line 1832) | int cmpTData_qset(const pointer* p1, const pointer* p2) {
  function printITrack (line 1838) | void printITrack(FILE* ft, GList<GffObj>& mrnas, int qcount, int& cnum) {
  function findTRMatch (line 1979) | void findTRMatch(GTrackLocus& loctrack, int qcount, GLocus& rloc) {
  function inPolyRun (line 2040) | bool inPolyRun(char strand, GffObj& m, GList<GLocus>* rloci, int& rlocid...
  function CTData (line 2071) | CTData* getBestOvl(GffObj& m) {
  function reclass_XStrand (line 2079) | void reclass_XStrand(GList<GffObj>& mrnas, GList<GLocus>* rloci) {
  function reclass_mRNAs (line 2159) | void reclass_mRNAs(char strand, GList<GffObj>& mrnas, GList<GLocus>* rlo...
  function reclassLoci (line 2187) | void reclassLoci(char strand, GList<GLocus>& qloci, GList<GLocus>* rloci...
  function umrnaReclass (line 2196) | void umrnaReclass(int qcount,  GSeqTrack& gtrack, FILE** ftr, GFaSeqGet*...
  function buildXLoci (line 2240) | void buildXLoci(GTrackLocus& loctrack, int qcount, GSeqTrack& gtrack, ch...
  function singleQData (line 2318) | void singleQData(GList<GLocus>& qloci, GList<GTrackLocus>& loctracks) {
  function umrnasXStrand (line 2376) | void umrnasXStrand(GList<GXLocus>& xloci, GSeqTrack& gtrack) {
  function xclusterLoci (line 2414) | void xclusterLoci(int qcount, char strand, GSeqTrack& gtrack) {
  function printRefMap (line 2514) | void printRefMap(FILE** frs, int qcount, GList<GLocus>* rloci) {
  function trackGData (line 2563) | void trackGData(int qcount, GList<GSeqTrack>& gtracks, GStr& fbasename, ...

FILE: src/cuffdiff.cpp
  type option (line 60) | struct option
  function print_usage (line 123) | void print_usage()
  function parse_options (line 184) | int parse_options(int argc, char** argv)
  function print_tests (line 547) | void print_tests(FILE* fout,
  function print_FPKM_tracking (line 607) | void print_FPKM_tracking(FILE* fout,
  function print_count_tracking (line 698) | void print_count_tracking(FILE* fout,
  function print_read_group_tracking (line 765) | void print_read_group_tracking(FILE* fout,
  function print_read_group_info (line 829) | void print_read_group_info(FILE* fout,
  function print_run_info (line 848) | void print_run_info(FILE* fout)
  function p_value_lt (line 857) | bool p_value_lt(const SampleDifference* lhs, const SampleDifference* rhs)
  function fdr_significance (line 863) | int fdr_significance(double fdr,
  function extract_sample_diffs (line 906) | void extract_sample_diffs(SampleDiffs& diff_map,
  function inspect_map_worker (line 921) | void inspect_map_worker(ReplicatedBundleFactory& fac,
  function learn_bias_worker (line 945) | void learn_bias_worker(boost::shared_ptr<BundleFactory> fac)
  function quantitate_next_locus (line 959) | bool quantitate_next_locus(const RefSequenceTable& rt,
  function parse_contrast_file (line 1031) | void parse_contrast_file(FILE* contrast_file,
  function parse_sample_sheet_file (line 1123) | void parse_sample_sheet_file(FILE* sample_sheet_file,
  function init_default_contrasts (line 1182) | void init_default_contrasts(const vector<boost::shared_ptr<ReplicatedBun...
  function parse_norm_standards_file (line 1203) | void parse_norm_standards_file(FILE* norm_standards_file)
  function print_variability_models (line 1245) | void print_variability_models(FILE* var_model_out, const vector<boost::s...
  type DispModelAverageContext (line 1283) | struct DispModelAverageContext
  function fit_dispersions (line 1294) | void fit_dispersions(vector<boost::shared_ptr<ReplicatedBundleFactory> >...
  function driver (line 1554) | void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* no...
  function main (line 2236) | int main(int argc, char** argv)

FILE: src/cuffdiff_to_gct.py
  class Usage (line 22) | class Usage(Exception):
    method __init__ (line 23) | def __init__(self, msg):
  function main (line 27) | def main(argv=None):

FILE: src/cufflinks.cpp
  type option (line 38) | struct option
  function print_usage (line 105) | void print_usage()
  function parse_options (line 172) | int parse_options(int argc, char** argv)
  function combine_strand_assemblies (line 509) | void combine_strand_assemblies(vector<Scaffold>& lhs,
  function guess_strand (line 653) | void guess_strand(int bundle_origin,
  function CuffStrand (line 669) | CuffStrand guess_strand_for_interval(const vector<uint8_t>& strand_guess,
  function scaffolds_for_bundle (line 685) | bool scaffolds_for_bundle(const HitBundle& bundle,
  function decr_pool_count (line 922) | void decr_pool_count()
  function quantitate_transcript_cluster (line 930) | void quantitate_transcript_cluster(AbundanceGroup& transfrag_cluster,
  function quantitate_transcript_clusters (line 1114) | void quantitate_transcript_clusters(vector<boost::shared_ptr<Scaffold> >...
  function assemble_bundle (line 1167) | void assemble_bundle(const RefSequenceTable& rt,
  function assemble_hits (line 1431) | bool assemble_hits(BundleFactory& bundle_factory, boost::shared_ptr<Bias...
  function driver (line 1582) | void driver(const string& hit_file_name, FILE* ref_gtf, FILE* mask_gtf)
  function main (line 1698) | int main(int argc, char** argv)

FILE: src/cuffnorm.cpp
  type option (line 60) | struct option
  function print_usage (line 83) | void print_usage()
  function parse_options (line 114) | int parse_options(int argc, char** argv)
  function inspect_map_worker (line 318) | void inspect_map_worker(ReplicatedBundleFactory& fac,
  function quantitate_next_locus (line 344) | bool quantitate_next_locus(const RefSequenceTable& rt,
  function parse_sample_sheet_file (line 416) | void parse_sample_sheet_file(FILE* sample_sheet_file,
  function parse_norm_standards_file (line 474) | void parse_norm_standards_file(FILE* norm_standards_file)
  function print_variability_models (line 516) | void print_variability_models(FILE* var_model_out, const vector<boost::s...
  function driver (line 554) | void driver(FILE* ref_gtf, FILE* mask_gtf, FILE* contrast_file, FILE* no...
  function open_outfiles_for_writing_cuffdiff_format (line 775) | void open_outfiles_for_writing_cuffdiff_format(Outfiles& outfiles)
  function open_outfiles_for_writing_simple_table_format (line 936) | void open_outfiles_for_writing_simple_table_format(Outfiles& outfiles)
  function open_outfiles_for_writing (line 1096) | void open_outfiles_for_writing(Outfiles& outfiles)
  function main (line 1113) | int main(int argc, char** argv)

FILE: src/cuffquant.cpp
  type option (line 56) | struct option
  function print_usage (line 85) | void print_usage()
  function parse_options (line 126) | int parse_options(int argc, char** argv)
  type Outfiles (line 379) | struct Outfiles
  function print_FPKM_tracking (line 397) | void print_FPKM_tracking(FILE* fout,
  function print_count_tracking (line 488) | void print_count_tracking(FILE* fout,
  function print_run_info (line 555) | void print_run_info(FILE* fout)
  function decr_pool_count (line 573) | void decr_pool_count()
  function inspect_map_worker (line 584) | void inspect_map_worker(ReplicatedBundleFactory& fac,
  function learn_bias_worker (line 608) | void learn_bias_worker(boost::shared_ptr<BundleFactory> fac)
  type AbundanceRecorder (line 622) | struct AbundanceRecorder
    method AbundanceRecorder (line 625) | AbundanceRecorder(AbundanceRecorder& rhs) {}
    method AbundanceRecorder (line 628) | AbundanceRecorder(int num_samples,
    method clear_tracking_data (line 649) | void clear_tracking_data() { _tracking->clear(); }
    method light_ab_group_tracking_table (line 653) | const light_ab_group_tracking_table& get_sample_table() const { return...
  function BOOST_FOREACH (line 716) | BOOST_FOREACH (boost::shared_ptr<SampleAbundances> ab, abundances)
  function sample_worker (line 834) | void sample_worker(const RefSequenceTable& rt,
  function quantitate_next_locus (line 921) | bool quantitate_next_locus(const RefSequenceTable& rt,
  function parse_norm_standards_file (line 966) | void parse_norm_standards_file(FILE* norm_standards_file)
  function driver (line 1009) | void driver(const std::string& ref_gtf_filename, const std::string& mask...
  function main (line 1462) | int main(int argc, char** argv)

FILE: src/differential.cpp
  function decr_pool_count (line 36) | void decr_pool_count()
  function BOOST_FOREACH (line 102) | BOOST_FOREACH (boost::shared_ptr<SampleAbundances> ab, abundances)
  function SampleDifference (line 257) | SampleDifference test_diffexp(const FPKMContext& curr,
  function get_metadata (line 462) | boost::shared_ptr<SampleDifferenceMetaData> get_metadata(const string de...
  function SampleDifference (line 474) | SampleDifference get_de_tests(const string& description,
  function test_js (line 558) | bool test_js(const AbundanceGroup& prev_abundance,
  function SampleDifference (line 722) | SampleDifference get_ds_tests(const AbundanceGroup& prev_abundance,
  function string (line 821) | string make_ref_tag(const string& ref, char classcode)
  function string (line 833) | string bundle_locus_tag(const RefSequenceTable& rt,
  type LocusVarianceInfo (line 850) | struct LocusVarianceInfo
  function sample_worker (line 882) | void sample_worker(bool non_empty,
  function dump_locus_variance_info (line 1007) | void dump_locus_variance_info(const string& filename)
  function filter_group_for_js_testing (line 1031) | void filter_group_for_js_testing(vector<vector<AbundanceGroup> >& source...
  function clear_samples_from_fpkm_tracking_table (line 1072) | void clear_samples_from_fpkm_tracking_table(const string& locus_desc, FP...
  function clear_samples_from_tracking_table (line 1087) | void clear_samples_from_tracking_table(boost::shared_ptr<SampleAbundance...
  function test_differential (line 1119) | void test_differential(const string& locus_tag,
  function print_checked_params_table (line 1517) | void print_checked_params_table(const vector<boost::shared_ptr<ReadGroup...
  function validate_cross_sample_parameters (line 1544) | void validate_cross_sample_parameters(const vector<boost::shared_ptr<Rea...

FILE: src/differential.h
  type TestStatus (line 34) | enum TestStatus {
  type SampleDifferenceMetaData (line 42) | struct SampleDifferenceMetaData
  function class (line 53) | class SampleDifference
  type map (line 84) | typedef map<string, SampleDifference > SampleDiffs;
  type map (line 85) | typedef map<string, boost::shared_ptr<SampleDifferenceMetaData> > Sample...
  type Outfiles (line 87) | struct Outfiles
  type Tests (line 124) | struct Tests
  type TestLauncher (line 144) | struct TestLauncher
  function class (line 200) | class TrackingDataWriter : public TestLauncher

FILE: src/filters.cpp
  function filter_introns (line 22) | void filter_introns(int bundle_length,
  function background_rate (line 135) | double background_rate(const vector<float> depth_of_coverage,
  function pre_mrna_filter (line 160) | void pre_mrna_filter(int bundle_length,
  function filter_hits (line 332) | void filter_hits(int bundle_length,
  function filter_junk_isoforms (line 575) | void filter_junk_isoforms(vector<boost::shared_ptr<Abundance> >& transcr...
  function filter_junk_genes (line 689) | void filter_junk_genes(vector<Gene>& genes)
  function clip_by_3_prime_dropoff (line 746) | void clip_by_3_prime_dropoff(vector<Scaffold>& scaffolds)

FILE: src/gdna.cpp
  function byte (line 24) | byte gdna2bit(char* &nt, int n) {
  function ntComplement (line 42) | char ntComplement(char c) {
  function g2bit2base (line 46) | char g2bit2base(byte v2bit) {
  function gDnaInit (line 66) | bool gDnaInit() {

FILE: src/genes.cpp
  function get_next_isoform_id (line 20) | int get_next_isoform_id()
  function get_next_gene_id (line 130) | int get_next_gene_id()
  function get_next_skipped_region_id (line 145) | int get_next_skipped_region_id()

FILE: src/genes.h
  function class (line 33) | class Isoform
  function FPKM (line 80) | void   FPKM(double fpkm) { _FPKM = fpkm; }
  function effective_length (line 83) | void   effective_length(double eff_len) { _eff_len = eff_len; }
  function status (line 86) | void   status(AbundanceStatus status) { _status = status; }
  function fraction (line 89) | void fraction(double f) { _fraction = f; }
  function confidence (line 92) | void   confidence(ConfidenceInterval c) { _confidence = c; }
  function coverage (line 95) | void   coverage(double cov) { _coverage = cov; }
  function FMI (line 99) | void   FMI(double fmi) { _FMI = fmi; }
  function gene_id (line 107) | void gene_id(string& gid) { _gene_id = gid; }
  function estimated_count (line 114) | void estimated_count(double est) { _estimated_count = est; }
  function class (line 131) | class Gene

FILE: src/gff.cpp
  function gffnames_ref (line 26) | void gffnames_ref(GffNames* &n) {
  function gffnames_unref (line 31) | void gffnames_unref(GffNames* &n) {
  function gfo_cmpByLoc (line 45) | int gfo_cmpByLoc(const pointer p1, const pointer p2) {
  function GffLine (line 865) | GffLine* GffReader::nextGffLine() {
  function GffObj (line 916) | GffObj* GffReader::gfoAdd(GffObj* gfo) {
  function GffObj (line 926) | GffObj* GffReader::gfoAdd(GPVec<GffObj>& glst, GffObj* gfo) {
  function GffObj (line 936) | GffObj* GffReader::gfoFind(const char* id, GPVec<GffObj>*& glst,
  function GffObj (line 981) | GffObj* GffReader::updateParent(GffObj* newgfo, GffObj* parent) {
  function GffObj (line 997) | GffObj* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExo...
  function GffObj (line 1023) | GffObj* GffReader::updateGffRec(GffObj* prevgfo, GffLine* gffline,
  function CNonExon (line 1070) | CNonExon* GffReader::subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pe...
  function GffObj (line 1094) | GffObj* GffReader::promoteFeature(CNonExon* subp, char*& subp_name, GHas...
  function GffObj (line 1301) | GffObj* GffObj::finalize(GffReader* gfr, bool mergeCloseExons, bool keep...
  function decodeHexChars (line 1887) | void decodeHexChars(char* dbuf, const char* s, int maxlen=1023) {

FILE: src/gff.h
  type GffExonType (line 53) | enum GffExonType {
  function class (line 68) | class GffLine {
  function class (line 173) | class GffAttr {
  function setValue (line 185) | void setValue(const char* av) {
  function operator (line 209) | bool operator==(GffAttr& d){
  function operator (line 212) | bool operator>(GffAttr& d){
  function operator (line 215) | bool operator<(GffAttr& d){
  function class (line 224) | class GffNameInfo {
  function d (line 237) | bool operator==(GffNameInfo& d){
  function d (line 240) | bool operator<(GffNameInfo& d){
  function class (line 245) | class GffNameList:public GList<GffNameInfo> {
  function lastNameId (line 263) | int lastNameId() { return idlast; }
  function addName (line 270) | int addName(const char* tname) {//returns or create an id for the given ...
  function addNewName (line 287) | int addNewName(const char* tname) {
  function getId (line 295) | int getId(const char* tname) { //only returns a name id# if found
  function removeName (line 300) | int removeName() {
  function class (line 306) | class GffNames {
  type GffPrintMode (line 327) | enum GffPrintMode {
  function class (line 338) | class GffAttrs:public GList<GffAttr> {
  function class (line 376) | class GffExon : public GSeg {
  function class (line 425) | class GffCDSeg:public GSeg {
  function class (line 431) | class GffObj:public GSeg {
  function exonOverlap (line 676) | bool exonOverlap(uint s, uint e) {//check if ANY exon overlaps given seg...
  function exonOverlap (line 684) | bool exonOverlap(GffObj& m) {//check if ANY exon overlaps given segment
  function exonOverlapLen (line 718) | int exonOverlapLen(GffObj& m) {
  function exonOverlap (line 744) | bool exonOverlap(GffObj* m) {
  function xcoordseg (line 775) | void xcoordseg(uint& segstart, uint &segend) {
  function unxcoord (line 789) | void unxcoord() { //revert back to absolute genomic/gff coordinates if x...
  function unxcoordseg (line 808) | void unxcoordseg(uint& astart, uint &aend) {
  function operator (line 822) | bool operator==(GffObj& d){
  function operator (line 825) | bool operator>(GffObj& d){
  function operator (line 834) | bool operator<(GffObj& d){
  function setGeneName (line 846) | void setGeneName(const char* gname) {
  function setGeneID (line 850) | void setGeneID(const char* gene_id) {
  function empty (line 884) | bool empty() { return (start==0); }
  function class (line 897) | class GSeqStat {
  function operator (line 915) | bool operator>(GSeqStat& g) {
  function operator (line 918) | bool operator<(GSeqStat& g) {
  function operator (line 921) | bool operator==(GSeqStat& g) {
  function freeAll (line 948) | void freeAll() {
  function freeUnused (line 955) | void freeUnused() {
  function class (line 979) | class CNonExon { //utility class used in subfeature promotion
  function class (line 998) | class GffReader {

FILE: src/gff_utils.cpp
  function printFasta (line 8) | void printFasta(FILE* f, GStr& defline, char* seq, int seqlen) {
  function qsearch_gloci (line 25) | int qsearch_gloci(uint x, GList<GffLocus>& loci) {
  function qsearch_rnas (line 58) | int qsearch_rnas(uint x, GList<GffObj>& rnas) {
  function cmpRedundant (line 91) | int cmpRedundant(GffObj& a, GffObj& b) {
  function tMatch (line 102) | bool tMatch(GffObj& a, GffObj& b) {
  function unsplContained (line 139) | bool unsplContained(GffObj& ti, GffObj&  tj, bool fuzzSpan) {
  function GffObj (line 169) | GffObj* redundantTranscripts(GffObj& ti, GffObj&  tj, bool matchAllIntro...
  function gseqCmpName (line 315) | int gseqCmpName(const pointer p1, const pointer p2) {
  function printLocus (line 320) | void printLocus(GffLocus* loc, const char* pre) {
  function preserveContainedCDS (line 330) | void preserveContainedCDS(GffObj* t, GffObj* tfrom) {
  function exonOverlap2Gene (line 344) | bool exonOverlap2Gene(GffObj* t, GffObj& g) {
  function collectLocusData (line 514) | void collectLocusData(GList<GenomicSeqData>& ref_data) {

FILE: src/gff_utils.h
  function class (line 10) | class GeneInfo { //for Ensembl GTF conversion
  function class (line 94) | class GFastaDb {
  function init (line 124) | void init(const char* fpath) {
  function class (line 213) | class GTData { //transcript associated data
  function class (line 235) | class CGeneSym {
  function operator (line 242) | bool operator<(CGeneSym& b) {
  function operator (line 246) | bool operator==(CGeneSym& b) { return name==b.name; }
  function class (line 253) | class GffLocus:public GSeg {
  function class (line 470) | class GenomicSeqData {
  function d (line 486) | bool operator==(GenomicSeqData& d){
  function d (line 489) | bool operator<(GenomicSeqData& d){
  function class (line 496) | class GSpliceSite {
  function canonicalDonor (line 538) | bool canonicalDonor() {
  function c (line 541) | bool operator==(GSpliceSite& c) {
  function else (line 558) | struct GffLoader {

FILE: src/gffread.cpp
  class SeqInfo (line 88) | class SeqInfo { //populated from the -s option of gffread
    method SeqInfo (line 92) | SeqInfo( int l, char* s) {
  class RefTran (line 105) | class RefTran {
    method RefTran (line 108) | RefTran(char *ns) {
  function loadSeqInfo (line 178) | void loadSeqInfo(FILE* f, GHash<SeqInfo> &si) {
  function loadRefTable (line 208) | void loadRefTable(FILE* f, GHash<RefTran>& rt) {
  function GFaSeqGet (line 262) | GFaSeqGet* fastaSeqGet(GFastaDb& gfasta, GffObj& gffrec) {
  function adjust_stopcodon (line 268) | int adjust_stopcodon(GffObj& gffrec, int adj, GList<GSeg>* seglst=NULL) {
  function process_transcript (line 312) | bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {
  function openfw (line 592) | void openfw(FILE* &f, GArgs& args, char opt) {
  function printGff3Header (line 607) | void printGff3Header(FILE* f, GArgs& args) {
  function validateGffRec (line 616) | bool validateGffRec(GffObj* gffrec, GList<GffObj>* gfnew) {
  function main (line 681) | int main(int argc, char * const argv[]) {

FILE: src/graph_optimize.cpp
  function fill_gaps (line 30) | void fill_gaps(vector<Scaffold>& scaffolds, int fill_size)
  type ConflictState (line 36) | enum ConflictState { UNKNOWN_CONFLICTS = 0, SAME_CONFLICTS, DIFF_CONFLIC...
  function scaff_left_lt_right_gt (line 38) | bool scaff_left_lt_right_gt(const Scaffold& lhs, const Scaffold& rhs)
  function op_left_lt_right_lt (line 45) | bool op_left_lt_right_lt(const AugmentedCuffOp& lhs, const AugmentedCuff...
  function extract_conflicting_ops (line 58) | void extract_conflicting_ops(const vector<AugmentedCuffOp>& ops,
  function collect_non_redundant_ops (line 91) | void collect_non_redundant_ops(const vector<Scaffold>& scaffolds,
  function fill_unambiguous_unknowns (line 108) | void fill_unambiguous_unknowns(vector<Scaffold>& to_fill,
  function add_non_constitutive_to_scaffold_mask (line 140) | void add_non_constitutive_to_scaffold_mask(const vector<Scaffold>& scaff...
  function collapse_contained_transfrags (line 212) | bool collapse_contained_transfrags(vector<Scaffold>& scaffolds,
  function scaff_smaller_lt_rt (line 294) | bool scaff_smaller_lt_rt(const Scaffold& lhs, const Scaffold& rhs)
  type FragIndexSortSmallerLR (line 310) | struct FragIndexSortSmallerLR
    method FragIndexSortSmallerLR (line 312) | FragIndexSortSmallerLR(const vector<Scaffold>& frags) : fragments(frag...
  function collapse_equivalent_transfrags (line 336) | bool collapse_equivalent_transfrags(vector<Scaffold>& fragments,
  function compress_consitutive (line 601) | void compress_consitutive(vector<Scaffold>& hits)
  function compress_redundant (line 650) | void compress_redundant(vector<Scaffold>& fragments)
  function compress_fragments (line 691) | void compress_fragments(vector<Scaffold>& fragments)
  function compress_overlap_dag_paths (line 705) | void compress_overlap_dag_paths(DAG& bundle_dag,

FILE: src/gtf_reads.cpp
  type option (line 32) | struct option
  function print_usage (line 36) | void print_usage()
  function parse_options (line 42) | int parse_options(int argc, char** argv)
  function driver (line 61) | void driver(FILE* ref_gtf, FILE* sam_hit_file)
  function main (line 127) | int main(int argc, char** argv)

FILE: src/gtf_to_sam.cpp
  type option (line 39) | struct option
  function print_usage (line 45) | void print_usage()
  function parse_options (line 57) | int parse_options(int argc, char** argv)
  function print_scaff_as_sam (line 85) | void print_scaff_as_sam(FILE* sam_out,
  function set_relative_fpkms (line 184) | void set_relative_fpkms(vector<boost::shared_ptr<Scaffold> >& ref_mRNAs)
  function driver (line 252) | void driver(vector<FILE*> ref_gtf_files, FILE* sam_out)
  function main (line 282) | int main(int argc, char** argv)

FILE: src/gtf_tracking.cpp
  function cmpByPtr (line 21) | int cmpByPtr(const pointer p1, const pointer p2) {
  function betterRef (line 25) | bool betterRef(GffObj* a, GffObj* b) {
  function GffObj (line 36) | GffObj* is_RefDup(GffObj* m, GList<GffObj>& mrnas, int& dupidx) {
  function intronRedundant (line 61) | bool intronRedundant(GffObj& ti, GffObj&  tj, bool no5share=false) {
  function t_contains (line 140) | bool t_contains(GffObj& a, GffObj& b) {
  function is_Redundant (line 158) | int is_Redundant(GffObj*m, GList<GffObj>* mrnas, bool no5share=false) {
  function t_dominates (line 178) | bool t_dominates(GffObj* a, GffObj* b) {
  function betterDupRef (line 186) | bool betterDupRef(GffObj* a, GffObj* b) {
  function parse_mRNAs (line 198) | int parse_mRNAs(GfList& mrnas,
  function singleExonTMatch (line 376) | bool singleExonTMatch(GffObj& m, GffObj& r, int& ovlen) {
  function tMatch (line 385) | bool tMatch(GffObj& a, GffObj& b, int& ovlen, bool fuzzunspl, bool conta...
  function cluster_mRNAs (line 431) | void cluster_mRNAs(GList<GffObj> & mrnas, GList<GLocus> & loci, int qfid...
  function fix_umrnas (line 474) | int fix_umrnas(GSeqData& seqdata, GSeqData* rdata, FILE* fdis=NULL) {
  function GSeqData (line 581) | GSeqData* getRefData(int gid, GList<GSeqData>& ref_data) {
  function read_transcripts (line 590) | void read_transcripts(FILE* f, GList<GSeqData>& seqdata,
  function cmpGSeqByName (line 608) | int cmpGSeqByName(const pointer p1, const pointer p2) {
  function sort_GSeqs_byName (line 612) | void sort_GSeqs_byName(GList<GSeqData>& seqdata) {
  function read_mRNAs (line 616) | void read_mRNAs(FILE* f, GList<GSeqData>& seqdata, GList<GSeqData>* ref_...
  function qsearch_mrnas (line 712) | int qsearch_mrnas(uint x, GList<GffObj>& mrnas) {
  function qsearch_loci (line 745) | int qsearch_loci(uint x, GList<GLocus>& loci) {

FILE: src/gtf_tracking.h
  function class (line 33) | class GFastaHandler {
  function init (line 58) | void init(const char* fpath) {
  function class (line 149) | class COvLink {
  function operator (line 178) | bool operator<(COvLink& b) {
  function operator (line 183) | bool operator==(COvLink& b) {
  function class (line 188) | class GISeg: public GSeg {
  function class (line 194) | class GIArray:public GArray<GISeg> {
  function class (line 216) | class CEqList: public GList<GffObj> {
  function class (line 224) | class CTData { //transcript associated data
  function joinEqList (line 270) | void joinEqList(GffObj* m) { //add list from m
  function getBestCode (line 348) | char getBestCode() {
  function operator (line 351) | bool operator<(CTData& b) { return (mrna < b.mrna); }
  function operator (line 352) | bool operator==(CTData& b) { return (mrna==b.mrna); }
  function class (line 359) | class GXSeg : public GSeg {
  function class (line 862) | class GSeqData {
  function operator (line 894) | bool operator==(GSeqData& d){
  function operator (line 897) | bool operator>(GSeqData& d){
  function operator (line 900) | bool operator<(GSeqData& d){
  function class (line 907) | class GQCluster : public GList<GffObj> {
  function class (line 1076) | class GXConsensus:public GSeg {
  function class (line 1112) | class GXLocus:public GSeg {

FILE: src/hits.cpp
  function hit_insert_id_lt (line 167) | bool hit_insert_id_lt(const ReadHit& h1, const ReadHit& h2)
  function hits_eq_mod_id (line 172) | bool hits_eq_mod_id(const ReadHit& lhs, const ReadHit& rhs)
  function hits_eq_non_multi (line 182) | bool hits_eq_non_multi(const MateHit& lhs, const MateHit& rhs)
  function hits_eq_non_multi_non_replicate (line 191) | bool hits_eq_non_multi_non_replicate(const MateHit& lhs, const MateHit& ...
  function hits_equals (line 199) | bool hits_equals(const MateHit& lhs, const MateHit& rhs)
  function has_no_collapse_mass (line 221) | bool has_no_collapse_mass(const MateHit& hit)
  function collapse_hits (line 228) | void collapse_hits(const vector<MateHit>& hits,
  function mate_hit_lt (line 265) | bool mate_hit_lt(const MateHit& lhs, const MateHit& rhs)
  function ReadHit (line 327) | ReadHit HitFactory::create_hit(const string& insert_name,
  function ReadHit (line 356) | ReadHit HitFactory::create_hit(const string& insert_name,
  function CuffStrand (line 385) | CuffStrand use_stranded_protocol(uint32_t sam_flag,  MateStrandMapping msm)
  function Platform (line 604) | Platform str_to_platform(const string pl_str)
  function BOOST_FOREACH (line 1040) | BOOST_FOREACH(const LocusCount& c, rg_props.raw_compatible_counts())
  function BOOST_FOREACH (line 1047) | BOOST_FOREACH(const LocusCount& c, rg_props.raw_total_counts())
  function HitFactory (line 1210) | HitFactory* createSamHitFactory(const string& hit_file_name, ReadTable& ...
  function HitFactory (line 1278) | HitFactory* createSamHitFactory(const string& hit_file_name, ReadTable& ...

FILE: src/hits.h
  type CuffStrand (line 45) | enum CuffStrand { CUFF_STRAND_UNKNOWN = 0, CUFF_FWD = 1, CUFF_REV = 2, C...
  type CigarOpCode (line 48) | enum CigarOpCode
  type CigarOp (line 59) | struct CigarOp
  type InsertID (line 69) | typedef uint64_t InsertID;
  type RefID (line 70) | typedef uint64_t RefID;
  type ReadHit (line 77) | struct ReadHit
  function read_len (line 167) | int read_len() const
  function operator (line 205) | bool operator==(const ReadHit& rhs) const
  function gaps (line 241) | void gaps(vector<pair<int,int> >& gaps_out) const
  function class (line 334) | class ReadTable
  function class (line 380) | class RefSequenceTable
  function RefID (line 418) | RefID get_id(const string& name,
  function Sequence (line 460) | Sequence* get_seq(RefID ID) const
  function SequenceInfo (line 469) | const SequenceInfo* get_info(RefID ID) const
  function observation_order (line 481) | int observation_order(RefID ID) const
  function order_recs_lexicographically (line 492) | void order_recs_lexicographically()
  function print_rec_ordering (line 510) | void print_rec_ordering()
  function iterator (line 518) | iterator begin() { return _by_id.begin(); }
  function iterator (line 519) | iterator end() { return _by_id.end(); }
  function clear (line 526) | void clear()
  function class (line 562) | class HitFactory
  function class (line 674) | class SAMHitFactory : public HitFactory
  function class (line 726) | class BAMHitFactory : public HitFactory
  function class (line 753) | class SamtoolsHitFactory : public BAMHitFactory
  function class (line 819) | class HTSHitFactory : public BAMHitFactory
  function class (line 900) | class PrecomputedExpressionHitFactory : public HitFactory
  function class (line 1030) | class MateHit
  function ReadHit (line 1062) | const ReadHit* left_alignment() const {return _left_alignment;}
  function left_alignment (line 1063) | void left_alignment(const ReadHit* left_alignment)
  function ReadHit (line 1068) | const ReadHit* right_alignment() const {return _right_alignment;}
  function right_alignment (line 1069) | void right_alignment(const ReadHit* right_alignment)
  function is_mapped (line 1075) | void is_mapped(bool mapped)
  function num_hits (line 1080) | int num_hits() const
  function CuffStrand (line 1122) | CuffStrand strand() const
  function mass (line 1196) | double mass() const
  function edit_dist (line 1219) | unsigned int  edit_dist() const
  function collapse_mass (line 1230) | void collapse_mass(double m) { _collapse_mass = m; }
  function incr_collapse_mass (line 1231) | void incr_collapse_mass(double incr) { _collapse_mass += incr; }

FILE: src/jensen_shannon.cpp
  function entropy (line 18) | double entropy(const Eigen::VectorXd& p)
  function jensen_shannon_distance (line 34) | double jensen_shannon_distance(std::vector<Eigen::VectorXd>& sample_kappas)
  function jensen_shannon_gradient (line 70) | void jensen_shannon_gradient(vector<Eigen::VectorXd>& sample_kappas,
  function make_js_covariance_matrix (line 142) | void make_js_covariance_matrix(vector<ublas::matrix<double> >& kappa_cov...

FILE: src/lemon/bfs.h
  type GR (line 45) | typedef GR Graph;
  type typename (line 53) | typedef typename Graph::template
  function PredMap (line 59) | static PredMap *createPredMap(const GR &G)
  type NullMap (line 68) | typedef NullMap<typename
  function ProcessedMap (line 77) | static ProcessedMap *createProcessedMap(const GR &)
  type typename (line 87) | typedef typename Graph::template
  function ReachedMap (line 93) | static ReachedMap *createReachedMap(const GR &G)
  type typename (line 102) | typedef typename Graph::template
  function DistMap (line 107) | static DistMap *createDistMap(const GR &G)
  type TR (line 151) | typedef TR Traits;
  type typename (line 153) | typedef typename TR::Graph Graph;
  type typename (line 157) | typedef typename TR::PredMap PredMap;
  type typename (line 159) | typedef typename TR::ReachedMap ReachedMap;
  type typename (line 161) | typedef typename TR::ProcessedMap ProcessedMap;
  type typename (line 163) | typedef typename TR::DistMap DistMap;
  type typename (line 167) | typedef typename Graph::NodeIt NodeIt;
  type typename (line 168) | typedef typename Graph::Edge Edge;
  type typename (line 169) | typedef typename Graph::OutEdgeIt OutEdgeIt;
  function create_maps (line 197) | void create_maps()
  type T (line 231) | typedef T PredMap;
  function PredMap (line 232) | static PredMap *createPredMap(const Graph &)
  type T (line 249) | typedef T DistMap;
  function DistMap (line 250) | static DistMap *createDistMap(const Graph &)
  type T (line 267) | typedef T ReachedMap;
  function ReachedMap (line 268) | static ReachedMap *createReachedMap(const Graph &)
  type T (line 285) | typedef T ProcessedMap;
  function ProcessedMap (line 286) | static ProcessedMap *createProcessedMap(const Graph &)
  function Traits (line 301) | struct DefGraphProcessedMapTraits : public Traits {
  function addSource (line 447) | void addSource(Node s)
  function Node (line 466) | Node processNextNode()
  function Node (line 497) | Node processNextNode(Node target, bool& reach)
  function Node (line 556) | Node nextNode()
  function emptyQueue (line 566) | bool emptyQueue() { return _queue_tail==_queue_head; }
  function queueSize (line 570) | int queueSize() { return _queue_head-_queue_tail; }
  function start (line 585) | void start()
  function start (line 602) | void start(Node dest)
  function run (line 646) | void run(Node s) {
  function run (line 665) | int run(Node s,Node t) {
  type PredMapPath (line 682) | typedef PredMapPath<Graph, PredMap> Path;
  function Path (line 688) | Path path(Node t)
  function dist (line 699) | int dist(Node v) const { return (*_dist)[v]; }
  function Edge (line 712) | Edge predEdge(Node v) const { return (*_pred)[v];}
  function Node (line 726) | Node predNode(Node v) const { return (*_pred)[v]==INVALID ? INVALID:
  function reached (line 751) | bool reached(Node v) { return (*_reached)[v]; }
  type GR (line 764) | typedef GR Graph;
  type NullMap (line 772) | typedef NullMap<typename
  function PredMap (line 781) | static PredMap *createPredMap(const GR &)
  type NullMap (line 792) | typedef NullMap<typename
  function ProcessedMap (line 801) | static ProcessedMap *createProcessedMap(const GR &)
  type typename (line 811) | typedef typename Graph::template
  function ReachedMap (line 817) | static ReachedMap *createReachedMap(const GR &G)
  type NullMap (line 826) | typedef NullMap<typename
  function DistMap (line 834) | static DistMap *createDistMap(const GR &)
  type BfsWizardDefaultTraits (line 853) | typedef BfsWizardDefaultTraits<GR> Base;
  type TR (line 914) | typedef TR Base;
  type typename (line 917) | typedef typename TR::Graph Graph;
  type typename (line 919) | typedef typename Graph::Node Node;
  type typename (line 921) | typedef typename Graph::NodeIt NodeIt;
  type typename (line 923) | typedef typename Graph::Edge Edge;
  type typename (line 925) | typedef typename Graph::OutEdgeIt OutEdgeIt;
  type typename (line 929) | typedef typename TR::ReachedMap ReachedMap;
  type typename (line 932) | typedef typename TR::ProcessedMap ProcessedMap;
  type typename (line 935) | typedef typename TR::PredMap PredMap;
  type typename (line 937) | typedef typename TR::DistMap DistMap;
  function TR (line 951) | BfsWizard(const TR &b) : TR(b) {}
  function run (line 959) | void run()
  function run (line 978) | void run(Node s)
  type T (line 986) | typedef T PredMap;
  function PredMap (line 987) | static PredMap *createPredMap(const Graph &) { return 0; }
  function TR (line 988) | DefPredMapBase(const TR &b) : TR(b) {}
  type T (line 1007) | typedef T ReachedMap;
  function ReachedMap (line 1008) | static ReachedMap *createReachedMap(const Graph &) { return 0; }
  function TR (line 1009) | DefReachedMapBase(const TR &b) : TR(b) {}
  type T (line 1028) | typedef T ProcessedMap;
  function ProcessedMap (line 1029) | static ProcessedMap *createProcessedMap(const Graph &) { return 0; }
  function TR (line 1030) | DefProcessedMapBase(const TR &b) : TR(b) {}
  type T (line 1049) | typedef T DistMap;
  function DistMap (line 1050) | static DistMap *createDistMap(const Graph &) { return 0; }
  function TR (line 1051) | DefDistMapBase(const TR &b) : TR(b) {}
  type _Graph (line 1110) | typedef _Graph Graph;
  type typename (line 1111) | typedef typename Graph::Edge Edge;
  type typename (line 1112) | typedef typename Graph::Node Node;
  function discover (line 1117) | void discover(const Edge& edge) {}
  function reach (line 1121) | void reach(const Node& node) {}
  function examine (line 1127) | void examine(const Edge& edge) {}
  function start (line 1131) | void start(const Node& node) {}
  function process (line 1135) | void process(const Node& node) {}
  type _Graph (line 1140) | typedef _Graph Graph;
  type typename (line 1141) | typedef typename Graph::Edge Edge;
  type typename (line 1142) | typedef typename Graph::Node Node;
  function discover (line 1143) | void discover(const Edge&) {}
  function reach (line 1144) | void reach(const Node&) {}
  function examine (line 1145) | void examine(const Edge&) {}
  function start (line 1146) | void start(const Node&) {}
  function process (line 1147) | void process(const Node&) {}
  function constraints (line 1151) | void constraints() {
  type _Graph (line 1173) | typedef _Graph Graph;
  type typename (line 1180) | typedef typename Graph::template
  function ReachedMap (line 1187) | static ReachedMap *createReachedMap(const Graph &graph) {
  function class (line 1232) | class UninitializedParameter : public lemon::UninitializedParameter {
  type _Traits (line 1240) | typedef _Traits Traits;
  type typename (line 1242) | typedef typename Traits::Graph Graph;
  type _Visitor (line 1244) | typedef _Visitor Visitor;
  type typename (line 1247) | typedef typename Traits::ReachedMap ReachedMap;
  type typename (line 1252) | typedef typename Graph::NodeIt NodeIt;
  type typename (line 1253) | typedef typename Graph::Edge Edge;
  type typename (line 1254) | typedef typename Graph::OutEdgeIt OutEdgeIt;
  function create_maps (line 1271) | void create_maps() {
  type T (line 1291) | typedef T ReachedMap;
  function ReachedMap (line 1292) | static ReachedMap *createReachedMap(const Graph &graph) {
  function addSource (line 1371) | void addSource(Node s) {
  function Node (line 1387) | Node processNextNode() {
  function Node (line 1417) | Node processNextNode(Node target, bool& reach) {
  function Node (line 1474) | Node nextNode() {
  function emptyQueue (line 1483) | bool emptyQueue() { return _list_front == _list_back; }
  function queueSize (line 1488) | int queueSize() { return _list_back - _list_front; }
  function start (line 1496) | void start() {
  function start (line 1506) | void start(Node dest) {
  function run (line 1542) | void run(Node s) {
  function run (line 1565) | void run() {
  function reached (line 1590) | bool reached(Node v) { return (*_reached)[v]; }

FILE: src/lemon/bin_heap.h
  function namespace (line 30) | namespace lemon {

FILE: src/lemon/bipartite_matching.h
  function namespace (line 37) | namespace lemon {
  type typename (line 586) | typedef typename _WeightMap::Value Value;
  type _BpUGraph (line 589) | typedef _BpUGraph BpUGraph;
  type _WeightMap (line 592) | typedef _WeightMap WeightMap;
  type typename (line 598) | typedef typename BpUGraph::template ANodeMap<int> HeapCrossRef;
  function HeapCrossRef (line 605) | static HeapCrossRef *createHeapCrossRef(const BpUGraph &graph) {
  type FibHeap (line 617) | typedef FibHeap<Value, HeapCrossRef> Heap;
  function Heap (line 623) | static Heap *createHeap(HeapCrossRef& crossref) {
  type typename (line 658) | typedef typename Traits::BpUGraph BpUGraph;
  type typename (line 659) | typedef typename Traits::WeightMap WeightMap;
  type typename (line 660) | typedef typename Traits::Value Value;
  type typename (line 665) | typedef typename Traits::Heap Heap;
  type typename (line 668) | typedef typename BpUGraph::Node Node;
  type typename (line 669) | typedef typename BpUGraph::ANodeIt ANodeIt;
  type typename (line 670) | typedef typename BpUGraph::BNodeIt BNodeIt;
  type typename (line 671) | typedef typename BpUGraph::UEdge UEdge;
  type typename (line 672) | typedef typename BpUGraph::UEdgeIt UEdgeIt;
  type typename (line 673) | typedef typename BpUGraph::IncEdgeIt IncEdgeIt;
  type typename (line 675) | typedef typename BpUGraph::template ANodeMap<UEdge> ANodeMatchingMap;
  type typename (line 676) | typedef typename BpUGraph::template BNodeMap<UEdge> BNodeMatchingMap;
  type typename (line 678) | typedef typename BpUGraph::template ANodeMap<Value> ANodePotentialMap;
  type typename (line 679) | typedef typename BpUGraph::template BNodeMap<Value> BNodePotentialMap;
  type CR (line 701) | typedef CR HeapCrossRef;
  type H (line 702) | typedef H Heap;
  function HeapCrossRef (line 703) | static HeapCrossRef *createHeapCrossRef(const BpUGraph &) {
  function Heap (line 706) | static Heap *createHeap(HeapCrossRef &) {
  type DefHeap (line 717) | struct DefHeap
  type CR (line 726) | typedef CR HeapCrossRef;
  type H (line 727) | typedef H Heap;
  function HeapCrossRef (line 728) | static HeapCrossRef *createHeapCrossRef(const BpUGraph &graph) {
  function Heap (line 731) | static Heap *createHeap(HeapCrossRef &crossref) {
  type DefStandardHeap (line 744) | struct DefStandardHeap
  function init (line 808) | void init() {
  function matchingEdge (line 1052) | bool matchingEdge(const UEdge& edge) const {
  function UEdge (line 1060) | UEdge matchingEdge(const Node& node) const {
  function destroyStructures (line 1097) | void destroyStructures() {
  type typename (line 1187) | typedef typename _CostMap::Value Value;
  type _BpUGraph (line 1190) | typedef _BpUGraph BpUGraph;
  type _CostMap (line 1193) | typedef _CostMap CostMap;
  type typename (line 1199) | typedef typename BpUGraph::template NodeMap<int> HeapCrossRef;
  function HeapCrossRef (line 1206) | static HeapCrossRef *createHeapCrossRef(const BpUGraph &graph) {
  type FibHeap (line 1218) | typedef FibHeap<Value, HeapCrossRef> Heap;
  function Heap (line 1224) | static Heap *createHeap(HeapCrossRef& crossref) {
  type typename (line 1257) | typedef typename Traits::BpUGraph BpUGraph;
  type typename (line 1258) | typedef typename Traits::CostMap CostMap;
  type typename (line 1259) | typedef typename Traits::Value Value;
  type typename (line 1264) | typedef typename Traits::Heap Heap;
  type typename (line 1267) | typedef typename BpUGraph::Node Node;
  type typename (line 1268) | typedef typename BpUGraph::ANodeIt ANodeIt;
  type typename (line 1269) | typedef typename BpUGraph::BNodeIt BNodeIt;
  type typename (line 1270) | typedef typename BpUGraph::UEdge UEdge;
  type typename (line 1271) | typedef typename BpUGraph::UEdgeIt UEdgeIt;
  type typename (line 1272) | typedef typename BpUGraph::IncEdgeIt IncEdgeIt;
  type typename (line 1274) | typedef typename BpUGraph::template ANodeMap<UEdge> ANodeMatchingMap;
  type typename (line 1275) | typedef typename BpUGraph::template BNodeMap<UEdge> BNodeMatchingMap;
  type typename (line 1277) | typedef typename BpUGraph::template ANodeMap<Value> ANodePotentialMap;
  type typename (line 1278) | typedef typename BpUGraph::template BNodeMap<Value> BNodePotentialMap;
  type CR (line 1300) | typedef CR HeapCrossRef;
  type H (line 1301) | typedef H Heap;
  function HeapCrossRef (line 1302) | static HeapCrossRef *createHeapCrossRef(const BpUGraph &) {
  function Heap (line 1305) | static Heap *createHeap(HeapCrossRef &) {
  type DefHeap (line 1316) | struct DefHeap
  type CR (line 1325) | typedef CR HeapCrossRef;
  type H (line 1326) | typedef H Heap;
  function HeapCrossRef (line 1327) | static HeapCrossRef *createHeapCrossRef(const BpUGraph &graph) {
  function Heap (line 1330) | static Heap *createHeap(HeapCrossRef &crossref) {
  type DefStandardHeap (line 1343) | struct DefStandardHeap
  function init (line 1407) | void init() {
  function augment (line 1432) | bool augment() {
  function start (line 1538) | void start() {
  function run (line 1545) | void run() {
  function matchingEdge (line 1632) | bool matchingEdge(const UEdge& edge) const {
  function UEdge (line 1640) | UEdge matchingEdge(const Node& node) const {
  function destroyStructures (line 1677) | void destroyStructures() {

FILE: src/lemon/bits/alteration_notifier.h
  function namespace (line 31) | namespace lemon {
  function erase (line 429) | void erase(const std::vector<Item>& items) {
  function build (line 448) | void build() {
  function clear (line 468) | void clear() {

FILE: src/lemon/bits/array_map.h
  function namespace (line 33) | namespace lemon {

FILE: src/lemon/bits/base_extender.h
  function namespace (line 34) | namespace lemon {
  function first (line 350) | void first(BNode& node) const {
  function next (line 353) | void next(BNode& node) const {
  function id (line 357) | int id(const BNode& node) const {
  function Node (line 361) | Node source(const UEdge& edge) const {
  function Node (line 364) | Node target(const UEdge& edge) const {
  function firstInc (line 368) | void firstInc(UEdge& edge, bool& dir, const Node& node) const {
  function nextInc (line 377) | void nextInc(UEdge& edge, bool& dir) const {
  function class (line 386) | class Edge : public UEdge {
  function first (line 409) | void first(Edge& edge) const {
  function next (line 414) | void next(Edge& edge) const {
  function firstOut (line 421) | void firstOut(Edge& edge, const Node& node) const {
  function nextOut (line 430) | void nextOut(Edge& edge) const {
  function firstIn (line 439) | void firstIn(Edge& edge, const Node& node) const {
  function nextIn (line 448) | void nextIn(Edge& edge) const {
  function Node (line 457) | Node source(const Edge& edge) const {
  function Node (line 460) | Node target(const Edge& edge) const {
  function id (line 464) | int id(const Edge& edge) const {
  function Edge (line 468) | Edge edgeFromId(int ix) const {
  function direction (line 475) | bool direction(const Edge& edge) const {
  function Edge (line 479) | Edge direct(const UEdge& edge, bool dir) const {

FILE: src/lemon/bits/debug_map.h
  function namespace (line 38) | namespace lemon {
  type _Graph (line 84) | typedef _Graph Graph;
  type _Item (line 86) | typedef _Item Item;
  type True (line 88) | typedef True ReferenceMapTag;
  type _Item (line 91) | typedef _Item Key;
  type _Value (line 93) | typedef _Value Value;
  type typename (line 96) | typedef typename ItemSetTraits<_Graph, _Item>::ItemNotifier Notifier;
  type DebugMap (line 99) | typedef DebugMap Map;
  type typename (line 101) | typedef typename Notifier::ObserverBase Parent;
  type typename (line 104) | typedef typename Container::reference Reference;
  type typename (line 106) | typedef typename Container::const_reference ConstReference;
  function Parent (line 142) | DebugMap(const DebugMap& _copy) : Parent() {
  function ConstReference (line 217) | ConstReference operator[](const Key& key) const {
  function set (line 226) | void set(const Key& key, const Value& value) {
  function virtual (line 260) | virtual void add(const std::vector<Key>& keys) {
  function virtual (line 290) | virtual void erase(const Key& key) {
  function virtual (line 310) | virtual void erase(const std::vector<Key>& keys) {
  function virtual (line 332) | virtual void build() {
  function virtual (line 356) | virtual void clear() {

FILE: src/lemon/bits/default_map.h
  function namespace (line 31) | namespace lemon {

FILE: src/lemon/bits/graph_adaptor_extender.h
  function namespace (line 31) | namespace lemon {
  function Node (line 170) | Node baseNode(const OutEdgeIt &e) const {
  function Node (line 177) | Node runningNode(const OutEdgeIt &e) const {
  function Node (line 184) | Node baseNode(const InEdgeIt &e) const {
  function Node (line 191) | Node runningNode(const InEdgeIt &e) const {
  type _UGraph (line 206) | typedef _UGraph UGraph;
  type UGraphAdaptorExtender (line 207) | typedef UGraphAdaptorExtender Adaptor;
  type typename (line 209) | typedef typename Parent::Node Node;
  type typename (line 210) | typedef typename Parent::Edge Edge;
  type typename (line 211) | typedef typename Parent::UEdge UEdge;
  function maxId (line 215) | int maxId(Node) const {
  function maxId (line 219) | int maxId(Edge) const {
  function maxId (line 223) | int maxId(UEdge) const {
  function Node (line 227) | Node fromId(int id, Node) const {
  function Edge (line 231) | Edge fromId(int id, Edge) const {
  function UEdge (line 235) | UEdge fromId(int id, UEdge) const {
  function Node (line 239) | Node oppositeNode(const Node &n, const UEdge &e) const {
  function Edge (line 248) | Edge oppositeEdge(const Edge &e) const {
  function Edge (line 253) | Edge direct(const UEdge &ue, const Node &s) const {
  function class (line 258) | class NodeIt : public Node {
  function class (line 281) | class EdgeIt : public Edge {
  function class (line 304) | class OutEdgeIt : public Edge {
  function class (line 328) | class InEdgeIt : public Edge {
  function class (line 351) | class UEdgeIt : public Parent::UEdge {
  function class (line 373) | class IncEdgeIt : public Parent::UEdge {
  function Node (line 401) | Node baseNode(const OutEdgeIt &e) const {
  function Node (line 408) | Node runningNode(const OutEdgeIt &e) const {
  function Node (line 415) | Node baseNode(const InEdgeIt &e) const {
  function Node (line 422) | Node runningNode(const InEdgeIt &e) const {
  function Node (line 429) | Node baseNode(const IncEdgeIt &e) const {
  function Node (line 435) | Node runningNode(const IncEdgeIt &e) const {
  type BpUGraphAdaptorExtender (line 448) | typedef BpUGraphAdaptorExtender Graph;
  type typename (line 450) | typedef typename Parent::Node Node;
  type typename (line 451) | typedef typename Parent::BNode BNode;
  type typename (line 452) | typedef typename Parent::ANode ANode;
  type typename (line 453) | typedef typename Parent::Edge Edge;
  type typename (line 454) | typedef typename Parent::UEdge UEdge;
  function maxId (line 457) | int maxId(Node) const {
  function maxId (line 460) | int maxId(BNode) const {
  function maxId (line 463) | int maxId(ANode) const {
  function maxId (line 466) | int maxId(Edge) const {
  function maxId (line 469) | int maxId(UEdge) const {
  function Node (line 474) | Node fromId(int id, Node) const {
  function ANode (line 477) | ANode fromId(int id, ANode) const {
  function BNode (line 480) | BNode fromId(int id, BNode) const {
  function Edge (line 483) | Edge fromId(int id, Edge) const {
  function UEdge (line 486) | UEdge fromId(int id, UEdge) const {
  function class (line 490) | class NodeIt : public Node {
  function class (line 512) | class ANodeIt : public Node {
  function class (line 534) | class BNodeIt : public Node {
  function class (line 556) | class EdgeIt : public Edge {
  function class (line 579) | class UEdgeIt : public UEdge {
  function class (line 601) | class OutEdgeIt : public Edge {
  function class (line 626) | class InEdgeIt : public Edge {
  function Node (line 653) | Node baseNode(const OutEdgeIt &e) const {
  function Node (line 660) | Node runningNode(const OutEdgeIt &e) const {
  function Node (line 667) | Node baseNode(const InEdgeIt &e) const {
  function Node (line 674) | Node runningNode(const InEdgeIt &e) const {
  function class (line 678) | class IncEdgeIt : public Parent::UEdge {
  function Node (line 707) | Node baseNode(const IncEdgeIt &e) const {
  function Node (line 714) | Node runningNode(const IncEdgeIt &e) const {
  function Node (line 718) | Node oppositeNode(const Node &n, const UEdge &e) const {
  function Edge (line 727) | Edge oppositeEdge(const Edge &e) const {
  function Edge (line 732) | Edge direct(const UEdge &ue, const Node &s) const {

FILE: src/lemon/bits/graph_extender.h
  function namespace (line 35) | namespace lemon {
  function Node (line 194) | Node baseNode(const OutEdgeIt &e) const {
  function Node (line 201) | Node runningNode(const OutEdgeIt &e) const {
  function Node (line 208) | Node baseNode(const InEdgeIt &e) const {
  function Node (line 215) | Node runningNode(const InEdgeIt &e) const {
  type GraphExtender (line 224) | typedef GraphExtender Graph;
  type MapExtender (line 225) | typedef MapExtender<DefaultMap<Graph, Node, _Value> > Parent;
  function explicit (line 227) | explicit NodeMap(const Graph& graph)
  type GraphExtender (line 248) | typedef GraphExtender Graph;
  type MapExtender (line 249) | typedef MapExtender<DefaultMap<Graph, Edge, _Value> > Parent;
  function explicit (line 251) | explicit EdgeMap(const Graph& graph)
  function Node (line 268) | Node addNode() {
  function Edge (line 274) | Edge addEdge(const Node& from, const Node& to) {
  function clear (line 280) | void clear() {
  function erase (line 293) | void erase(const Node& node) {
  function erase (line 311) | void erase(const Edge& edge) {
  type UGraphExtender (line 336) | typedef UGraphExtender Graph;
  type True (line 338) | typedef True UndirectedTag;
  type typename (line 340) | typedef typename Parent::Node Node;
  type typename (line 341) | typedef typename Parent::Edge Edge;
  type typename (line 342) | typedef typename Parent::UEdge UEdge;
  function maxId (line 346) | int maxId(Node) const {
  function maxId (line 350) | int maxId(Edge) const {
  function maxId (line 354) | int maxId(UEdge) const {
  function Node (line 358) | Node fromId(int id, Node) const {
  function Edge (line 362) | Edge fromId(int id, Edge) const {
  function UEdge (line 366) | UEdge fromId(int id, UEdge) const {
  function Node (line 370) | Node oppositeNode(const Node &n, const UEdge &e) const {
  function Edge (line 379) | Edge oppositeEdge(const Edge &e) const {
  function Edge (line 384) | Edge direct(const UEdge &ue, const Node &s) const {
  type AlterationNotifier (line 390) | typedef AlterationNotifier<UGraphExtender, Node> NodeNotifier;
  type AlterationNotifier (line 391) | typedef AlterationNotifier<UGraphExtender, Edge> EdgeNotifier;
  type AlterationNotifier (line 392) | typedef AlterationNotifier<UGraphExtender, UEdge> UEdgeNotifier;
  function class (line 417) | class NodeIt : public Node {
  function class (line 440) | class EdgeIt : public Edge {
  function class (line 463) | class OutEdgeIt : public Edge {
  function class (line 487) | class InEdgeIt : public Edge {
  function class (line 511) | class UEdgeIt : public Parent::UEdge {
  function class (line 533) | class IncEdgeIt : public Parent::UEdge {
  function Node (line 561) | Node baseNode(const OutEdgeIt &e) const {
  function Node (line 568) | Node runningNode(const OutEdgeIt &e) const {
  function Node (line 575) | Node baseNode(const InEdgeIt &e) const {
  function Node (line 582) | Node runningNode(const InEdgeIt &e) const {
  function Node (line 589) | Node baseNode(const IncEdgeIt &e) const {
  function Node (line 595) | Node runningNode(const IncEdgeIt &e) const {
  type UGraphExtender (line 605) | typedef UGraphExtender Graph;
  type MapExtender (line 606) | typedef MapExtender<DefaultMap<Graph, Node, _Value> > Parent;
  function Parent (line 608) | NodeMap(const Graph& graph)
  type UGraphExtender (line 629) | typedef UGraphExtender Graph;
  type MapExtender (line 630) | typedef MapExtender<DefaultMap<Graph, Edge, _Value> > Parent;
  function Parent (line 632) | EdgeMap(const Graph& graph)
  type UGraphExtender (line 653) | typedef UGraphExtender Graph;
  type MapExtender (line 654) | typedef MapExtender<DefaultMap<Graph, UEdge, _Value> > Parent;
  function Parent (line 656) | UEdgeMap(const Graph& graph)
  function Node (line 676) | Node addNode() {
  function UEdge (line 682) | UEdge addEdge(const Node& from, const Node& to) {
  function clear (line 692) | void clear() {
  function erase (line 708) | void erase(const Node& node) {
  function erase (line 726) | void erase(const UEdge& uedge) {
  type BpUGraphExtender (line 757) | typedef BpUGraphExtender Graph;
  type True (line 759) | typedef True UndirectedTag;
  type typename (line 761) | typedef typename Parent::Node Node;
  type typename (line 762) | typedef typename Parent::ANode ANode;
  type typename (line 763) | typedef typename Parent::BNode BNode;
  type typename (line 764) | typedef typename Parent::Edge Edge;
  type typename (line 765) | typedef typename Parent::UEdge UEdge;
  function Node (line 768) | Node oppositeNode(const Node& node, const UEdge& edge) const {
  function Edge (line 774) | Edge direct(const UEdge& edge, const Node& node) const {
  function Edge (line 778) | Edge oppositeEdge(const Edge& edge) const {
  function maxId (line 782) | int maxId(Node) const {
  function maxId (line 785) | int maxId(BNode) const {
  function maxId (line 788) | int maxId(ANode) const {
  function maxId (line 791) | int maxId(Edge) const {
  function maxId (line 794) | int maxId(UEdge) const {
  function Node (line 799) | Node fromId(int id, Node) const {
  function ANode (line 802) | ANode fromId(int id, ANode) const {
  function BNode (line 805) | BNode fromId(int id, BNode) const {
  function Edge (line 808) | Edge fromId(int id, Edge) const {
  function UEdge (line 811) | UEdge fromId(int id, UEdge) const {
  type AlterationNotifier (line 815) | typedef AlterationNotifier<BpUGraphExtender, ANode> ANodeNotifier;
  type AlterationNotifier (line 816) | typedef AlterationNotifier<BpUGraphExtender, BNode> BNodeNotifier;
  type AlterationNotifier (line 817) | typedef AlterationNotifier<BpUGraphExtender, Node> NodeNotifier;
  type AlterationNotifier (line 818) | typedef AlterationNotifier<BpUGraphExtender, Edge> EdgeNotifier;
  type AlterationNotifier (line 819) | typedef AlterationNotifier<BpUGraphExtender, UEdge> UEdgeNotifier;
  function class (line 851) | class NodeIt : public Node {
  function class (line 873) | class ANodeIt : public Node {
  function class (line 895) | class BNodeIt : public Node {
  function class (line 917) | class EdgeIt : public Edge {
  function class (line 940) | class UEdgeIt : public UEdge {
  function class (line 962) | class OutEdgeIt : public Edge {
  function class (line 987) | class InEdgeIt : public Edge {
  function Node (line 1014) | Node baseNode(const OutEdgeIt &e) const {
  function Node (line 1021) | Node runningNode(const OutEdgeIt &e) const {
  function Node (line 1028) | Node baseNode(const InEdgeIt &e) const {
  function Node (line 1035) | Node runningNode(const InEdgeIt &e) const {
  function class (line 1039) | class IncEdgeIt : public Parent::UEdge {
  function Node (line 1068) | Node baseNode(const IncEdgeIt &e) const {
  function Node (line 1075) | Node runningNode(const IncEdgeIt &e) const {
  type BpUGraphExtender (line 1083) | typedef BpUGraphExtender Graph;
  type MapExtender (line 1084) | typedef MapExtender<DefaultMap<Graph, ANode, _Value> > Parent;
  function Parent (line 1086) | ANodeMap(const Graph& graph)
  type BpUGraphExtender (line 1107) | typedef BpUGraphExtender Graph;
  type MapExtender (line 1108) | typedef MapExtender<DefaultMap<Graph, BNode, _Value> > Parent;
  function Parent (line 1110) | BNodeMap(const Graph& graph)
  type Node (line 1134) | typedef Node Key;
  type _Value (line 1135) | typedef _Value Value;
  type typename (line 1138) | typedef typename ANodeMap<_Value>::Reference Reference;
  type typename (line 1140) | typedef typename ANodeMap<_Value>::ConstReference ConstReference;
  type True (line 1142) | typedef True ReferenceMapTag;
  function ConstReference (line 1161) | ConstReference operator[](const Key& node) const {
  function Reference (line 1169) | Reference operator[](const Key& node) {
  function set (line 1177) | void set(const Key& node, const Value& value) {
  function class (line 1185) | class MapIt : public NodeIt {
  function class (line 1209) | class ConstMapIt : public NodeIt {
  function class (line 1225) | class ItemIt : public NodeIt {
  type BpUGraphExtender (line 1246) | typedef BpUGraphExtender Graph;
  type MapExtender (line 1247) | typedef MapExtender<DefaultMap<Graph, Edge, _Value> > Parent;
  function Parent (line 1249) | EdgeMap(const Graph& graph)
  type BpUGraphExtender (line 1269) | typedef BpUGraphExtender Graph;
  type MapExtender (line 1270) | typedef MapExtender<DefaultMap<Graph, UEdge, _Value> > Parent;
  function Parent (line 1272) | UEdgeMap(const Graph& graph)
  function Node (line 1289) | Node addANode() {
  function Node (line 1296) | Node addBNode() {
  function UEdge (line 1303) | UEdge addEdge(const Node& s, const Node& t) {
  function clear (line 1315) | void clear() {
  function erase (line 1336) | void erase(const Node& node) {
  function erase (line 1358) | void erase(const UEdge& uedge) {
  function Edge (line 1384) | Edge findEdge(Node u, Node v, Edge prev = INVALID) const {

FILE: src/lemon/bits/invalid.h
  function namespace (line 25) | namespace lemon {

FILE: src/lemon/bits/map_extender.h
  function namespace (line 32) | namespace lemon {

FILE: src/lemon/bits/path_dump.h
  function namespace (line 22) | namespace lemon {
  type _Graph (line 100) | typedef _Graph Graph;
  type typename (line 101) | typedef typename Graph::Edge Edge;
  type _PredMatrixMap (line 102) | typedef _PredMatrixMap PredMatrixMap;
  function length (line 111) | int length() const {
  function class (line 126) | class RevEdgeIt {

FILE: src/lemon/bits/traits.h
  function namespace (line 28) | namespace lemon {

FILE: src/lemon/bits/utility.h
  function namespace (line 45) | namespace lemon
  type T (line 118) | typedef T type;

FILE: src/lemon/bits/variant.h
  function namespace (line 27) | namespace lemon {
  function First (line 189) | const First& first() const {
  type typename (line 251) | typedef typename _TypeMap::template Map<_idx>::Type Current;
  function destroy (line 253) | static void destroy(int index, char* place) {
  function copy (line 261) | static void copy(int index, char* to, const char* from) {
  function destroy (line 275) | static void destroy(int, char*) {
  function copy (line 279) | static void copy(int, char*, const char*) {
  type _TypeMap (line 339) | typedef _TypeMap TypeMap;
  type WrongStateError (line 341) | struct WrongStateError
  function namespace (line 446) | namespace _variant_bits {

FILE: src/lemon/bits/vector_map.h
  function namespace (line 37) | namespace lemon {

FILE: src/lemon/bucket_heap.h
  function namespace (line 30) | namespace lemon {

FILE: src/lemon/concept_check.h
  function namespace (line 39) | namespace lemon {

FILE: src/lemon/concepts/bpugraph.h
  function namespace (line 33) | namespace lemon {
  function class (line 616) | class OutEdgeIt : public Edge {
  function class (line 668) | class InEdgeIt : public Edge {
  function Edge (line 845) | Edge direct(const UEdge&, const Node&) const {
  function Edge (line 855) | Edge direct(const UEdge&, bool) const {
  function aNode (line 862) | bool aNode(Node) const { return true;}
  function bNode (line 867) | bool bNode(Node) const { return true;}
  function Node (line 872) | Node aNode(UEdge) const { return INVALID;}
  function Node (line 877) | Node bNode(UEdge) const { return INVALID;}
  function direction (line 883) | bool direction(Edge) const { return true; }
  function Edge (line 888) | Edge oppositeEdge(Edge) const { return INVALID; }
  function Node (line 893) | Node oppositeNode(Node, UEdge) const { return INVALID; }
  function Node (line 906) | Node source(UEdge) const { return INVALID; }
  function Node (line 909) | Node target(UEdge) const { return INVALID; }
  function Node (line 912) | Node source(Edge) const { return INVALID; }
  function Node (line 915) | Node target(Edge) const { return INVALID; }
  function Node (line 920) | Node baseNode(OutEdgeIt e) const {
  function Node (line 928) | Node runningNode(OutEdgeIt e) const {
  function Node (line 935) | Node baseNode(InEdgeIt e) const {
  function Node (line 942) | Node runningNode(InEdgeIt e) const {
  function Node (line 949) | Node baseNode(IncEdgeIt) const {
  function Node (line 956) | Node runningNode(IncEdgeIt) const {
  function first (line 960) | void first(Node&) const {}
  function next (line 961) | void next(Node&) const {}
  function first (line 963) | void first(Edge&) const {}
  function next (line 964) | void next(Edge&) const {}
  function first (line 966) | void first(UEdge&) const {}
  function next (line 967) | void next(UEdge&) const {}
  function firstANode (line 969) | void firstANode(Node&) const {}
  function nextANode (line 970) | void nextANode(Node&) const {}
  function firstBNode (line 972) | void firstBNode(Node&) const {}
  function nextBNode (line 973) | void nextBNode(Node&) const {}
  function firstIn (line 975) | void firstIn(Edge&, const Node&) const {}
  function nextIn (line 976) | void nextIn(Edge&) const {}
  function firstOut (line 978) | void firstOut(Edge&, const Node&) const {}
  function nextOut (line 979) | void nextOut(Edge&) const {}

FILE: src/lemon/concepts/graph.h
  function namespace (line 33) | namespace concepts {

FILE: src/lemon/concepts/graph_components.h
  function namespace (line 32) | namespace lemon {
  type typename (line 1814) | typedef typename _Base::Node Node;
  type typename (line 1815) | typedef typename _Base::Edge Edge;
  function Node (line 1821) | Node addNode() {
  function Edge (line 1828) | Edge addEdge(const Node&, const Node&) {
  function constraints (line 1834) | void constraints() {
  type typename (line 1859) | typedef typename _Base::Node Node;
  type typename (line 1860) | typedef typename _Base::UEdge UEdge;
  function Node (line 1866) | Node addNode() {
  function UEdge (line 1873) | UEdge addEdge(const Node&, const Node&) {
  function constraints (line 1879) | void constraints() {
  function constraints (line 1907) | void constraints() {
  type typename (line 1924) | typedef typename Base::Node Node;
  type typename (line 1925) | typedef typename Base::Edge Edge;
  function erase (line 1931) | void erase(const Node&) {}
  function erase (line 1937) | void erase(const Edge&) {}
  function constraints (line 1941) | void constraints() {
  type typename (line 1964) | typedef typename Base::Node Node;
  type typename (line 1965) | typedef typename Base::UEdge UEdge;
  function erase (line 1971) | void erase(const Node&) {}
  function erase (line 1977) | void erase(const UEdge&) {}
  function constraints (line 1981) | void constraints() {
  type _Base (line 2004) | typedef _Base Base;
  function constraints (line 2008) | void constraints() {
  function clear (line 2030) | void clear() {}
  function constraints (line 2034) | void constraints() {
  type _Base (line 2053) | typedef _Base Base;
  function constraints (line 2057) | void constraints() {
  type _Base (line 2077) | typedef _Base Base;
  function constraints (line 2081) | void constraints() {

FILE: src/lemon/concepts/heap.h
  function namespace (line 29) | namespace lemon {

FILE: src/lemon/concepts/maps.h
  function namespace (line 29) | namespace lemon {

FILE: src/lemon/concepts/matrix_maps.h
  function namespace (line 29) | namespace lemon {

FILE: src/lemon/concepts/path.h
  function namespace (line 32) | namespace lemon {

FILE: src/lemon/concepts/ugraph.h
  function class (line 69) | class UGraph {
  function class (line 409) | class OutEdgeIt : public Edge {
  function class (line 461) | class InEdgeIt : public Edge {
  function Edge (line 575) | Edge direct(const UEdge&, const Node&) const {
  function Edge (line 585) | Edge direct(const UEdge&, bool) const {
  function direction (line 593) | bool direction(Edge) const { return true; }
  function Edge (line 598) | Edge oppositeEdge(Edge) const { return INVALID; }
  function Node (line 603) | Node oppositeNode(Node, UEdge) const { return INVALID; }
  function Node (line 616) | Node source(UEdge) const { return INVALID; }
  function Node (line 619) | Node target(UEdge) const { return INVALID; }
  function Node (line 622) | Node source(Edge) const { return INVALID; }
  function Node (line 625) | Node target(Edge) const { return INVALID; }
  function first (line 627) | void first(Node&) const {}
  function next (line 628) | void next(Node&) const {}
  function first (line 630) | void first(UEdge&) const {}
  function next (line 631) | void next(UEdge&) const {}
  function first (line 633) | void first(Edge&) const {}
  function next (line 634) | void next(Edge&) const {}
  function firstOut (line 636) | void firstOut(Edge&, Node) const {}
  function nextOut (line 637) | void nextOut(Edge&) const {}
  function firstIn (line 639) | void firstIn(Edge&, Node) const {}
  function nextIn (line 640) | void nextIn(Edge&) const {}
  function firstInc (line 643) | void firstInc(UEdge &, bool &, const Node &) const {}
  function Node (line 663) | Node baseNode(InEdgeIt e) const {
  function Node (line 670) | Node runningNode(InEdgeIt e) const {
  function Node (line 677) | Node baseNode(IncEdgeIt) const {
  function Node (line 684) | Node runningNode(IncEdgeIt) const {
  function constraints (line 690) | void constraints() {

FILE: src/lemon/dfs.h
  type GR (line 46) | typedef GR Graph;
  type typename (line 54) | typedef typename Graph::template
  function PredMap (line 60) | static PredMap *createPredMap(const GR &G)
  type NullMap (line 70) | typedef NullMap<typename
  function ProcessedMap (line 79) | static ProcessedMap *createProcessedMap(const GR &)
  type typename (line 89) | typedef typename Graph::template
  function ReachedMap (line 95) | static ReachedMap *createReachedMap(const GR &G)
  type typename (line 104) | typedef typename Graph::template
  function DistMap (line 109) | static DistMap *createDistMap(const GR &G)
  type TR (line 152) | typedef TR Traits;
  type typename (line 154) | typedef typename TR::Graph Graph;
  type typename (line 156) | typedef typename Graph::Node Node;
  type typename (line 158) | typedef typename Graph::NodeIt NodeIt;
  type typename (line 160) | typedef typename Graph::Edge Edge;
  type typename (line 162) | typedef typename Graph::OutEdgeIt OutEdgeIt;
  type typename (line 166) | typedef typename TR::PredMap PredMap;
  type typename (line 168) | typedef typename TR::ReachedMap ReachedMap;
  type typename (line 170) | typedef typename TR::ProcessedMap ProcessedMap;
  type typename (line 172) | typedef typename TR::DistMap DistMap;
  function create_maps (line 199) | void create_maps()
  type T (line 233) | typedef T PredMap;
  function PredMap (line 234) | static PredMap *createPredMap(const Graph &G)
  type T (line 252) | typedef T DistMap;
  function DistMap (line 253) | static DistMap *createDistMap(const Graph &)
  type Dfs (line 265) | typedef Dfs<Graph, DefDistMapTraits<T> > Create;
  type T (line 270) | typedef T ReachedMap;
  function ReachedMap (line 271) | static ReachedMap *createReachedMap(const Graph &)
  type T (line 288) | typedef T ProcessedMap;
  function ProcessedMap (line 289) | static ProcessedMap *createProcessedMap(const Graph &)
  function Traits (line 304) | struct DefGraphProcessedMapTraits : public Traits {
  function addSource (line 452) | void addSource(Node s)
  function Edge (line 477) | Edge processNextEdge()
  function OutEdgeIt (line 508) | OutEdgeIt nextEdge()
  function emptyQueue (line 518) | bool emptyQueue() { return _stack_head<0; }
  function queueSize (line 522) | int queueSize() { return _stack_head+1; }
  function start (line 538) | void start()
  function start (line 557) | void start(Node dest)
  function run (line 604) | void run() {
  function run (line 629) | void run(Node s) {
  function run (line 648) | int run(Node s,Node t) {
  type PredMapPath (line 665) | typedef PredMapPath<Graph, PredMap> Path;
  function Path (line 671) | Path path(Node t)
  function dist (line 682) | int dist(Node v) const { return (*_dist)[v]; }
  function Edge (line 695) | Edge predEdge(Node v) const { return (*_pred)[v];}
  function Node (line 709) | Node predNode(Node v) const { return (*_pred)[v]==INVALID ? INVALID:
  function reached (line 734) | bool reached(Node v) { return (*_reached)[v]; }
  type GR (line 747) | typedef GR Graph;
  type NullMap (line 755) | typedef NullMap<typename
  function PredMap (line 764) | static PredMap *createPredMap(const GR &)
  type NullMap (line 775) | typedef NullMap<typename
  function ProcessedMap (line 784) | static ProcessedMap *createProcessedMap(const GR &)
  type typename (line 794) | typedef typename Graph::template
  function ReachedMap (line 800) | static ReachedMap *createReachedMap(const GR &G)
  type NullMap (line 809) | typedef NullMap<typename
  function DistMap (line 817) | static DistMap *createDistMap(const GR &)
  type DfsWizardDefaultTraits (line 836) | typedef DfsWizardDefaultTraits<GR> Base;
  type TR (line 897) | typedef TR Base;
  type typename (line 900) | typedef typename TR::Graph Graph;
  type typename (line 902) | typedef typename Graph::Node Node;
  type typename (line 904) | typedef typename Graph::NodeIt NodeIt;
  type typename (line 906) | typedef typename Graph::Edge Edge;
  type typename (line 908) | typedef typename Graph::OutEdgeIt OutEdgeIt;
  type typename (line 912) | typedef typename TR::ReachedMap ReachedMap;
  type typename (line 915) | typedef typename TR::ProcessedMap ProcessedMap;
  type typename (line 918) | typedef typename TR::PredMap PredMap;
  type typename (line 920) | typedef typename TR::DistMap DistMap;
  function TR (line 934) | DfsWizard(const TR &b) : TR(b) {}
  function run (line 942) | void run()
  function run (line 961) | void run(Node s)
  type T (line 969) | typedef T PredMap;
  function PredMap (line 970) | static PredMap *createPredMap(const Graph &) { return 0; }
  function TR (line 971) | DefPredMapBase(const TR &b) : TR(b) {}
  type T (line 990) | typedef T ReachedMap;
  function ReachedMap (line 991) | static ReachedMap *createReachedMap(const Graph &) { return 0; }
  function TR (line 992) | DefReachedMapBase(const TR &b) : TR(b) {}
  type T (line 1011) | typedef T ProcessedMap;
  function ProcessedMap (line 1012) | static ProcessedMap *createProcessedMap(const Graph &) { return 0; }
  function TR (line 1013) | DefProcessedMapBase(const TR &b) : TR(b) {}
  type T (line 1031) | typedef T DistMap;
  function DistMap (line 1032) | static DistMap *createDistMap(const Graph &) { return 0; }
  function TR (line 1033) | DefDistMapBase(const TR &b) : TR(b) {}
  type _Graph (line 1092) | typedef _Graph Graph;
  type typename (line 1093) | typedef typename Graph::Edge Edge;
  type typename (line 1094) | typedef typename Graph::Node Node;
  function discover (line 1099) | void discover(const Edge& edge) {}
  function reach (line 1103) | void reach(const Node& node) {}
  function backtrack (line 1107) | void backtrack(const Edge& edge) {}
  function leave (line 1111) | void leave(const Node& node) {}
  function examine (line 1117) | void examine(const Edge& edge) {}
  function start (line 1121) | void start(const Node& node) {}
  function stop (line 1125) | void stop(const Node& node) {}
  type _Graph (line 1131) | typedef _Graph Graph;
  type typename (line 1132) | typedef typename Graph::Edge Edge;
  type typename (line 1133) | typedef typename Graph::Node Node;
  function discover (line 1134) | void discover(const Edge&) {}
  function reach (line 1135) | void reach(const Node&) {}
  function backtrack (line 1136) | void backtrack(const Edge&) {}
  function leave (line 1137) | void leave(const Node&) {}
  function examine (line 1138) | void examine(const Edge&) {}
  function start (line 1139) | void start(const Node&) {}
  function stop (line 1140) | void stop(const Node&) {}
  function constraints (line 1144) | void constraints() {
  type _Graph (line 1168) | typedef _Graph Graph;
  type typename (line 1175) | typedef typename Graph::template
  function ReachedMap (line 1182) | static ReachedMap *createReachedMap(const Graph &graph) {
  function class (line 1226) | class UninitializedParameter : public lemon::UninitializedParameter {
  type _Traits (line 1234) | typedef _Traits Traits;
  type typename (line 1236) | typedef typename Traits::Graph Graph;
  type _Visitor (line 1238) | typedef _Visitor Visitor;
  type typename (line 1241) | typedef typename Traits::ReachedMap ReachedMap;
  type typename (line 1246) | typedef typename Graph::NodeIt NodeIt;
  type typename (line 1247) | typedef typename Graph::Edge Edge;
  type typename (line 1248) | typedef typename Graph::OutEdgeIt OutEdgeIt;
  function create_maps (line 1265) | void create_maps() {
  type T (line 1285) | typedef T ReachedMap;
  function ReachedMap (line 1286) | static ReachedMap *createReachedMap(const Graph &graph) {
  function addSource (line 1365) | void addSource(Node s) {
  function Edge (line 1387) | Edge processNextEdge() {
  function Edge (line 1420) | Edge nextEdge() {
  function emptyQueue (line 1429) | bool emptyQueue() { return _stack_head < 0; }
  function queueSize (line 1434) | int queueSize() { return _stack_head + 1; }
  function start (line 1442) | void start() {
  function start (line 1452) | void start(Node dest) {
  function run (line 1488) | void run(Node s) {
  function run (line 1511) | void run() {
  function reached (line 1535) | bool reached(Node v) { return (*_reached)[v]; }

FILE: src/lemon/error.h
  function namespace (line 33) | namespace lemon {
  function class (line 101) | class ErrorMessage {
  function class (line 173) | class Exception : public std::exception {
  function class (line 194) | class LogicError : public Exception {
  function class (line 207) | class UninitializedParameter : public LogicError {
  function class (line 222) | class RuntimeError : public Exception {
  function class (line 230) | class RangeError : public RuntimeError {
  function class (line 238) | class IoError : public RuntimeError {
  function class (line 246) | class DataFormatError : public IoError {
  function line (line 269) | void line(int ln) { _line = ln; }
  function message (line 271) | void message(const std::string& msg) { _message.set(msg); }
  function file (line 273) | void file(const std::string &fl) { _file.set(fl); }
  function virtual (line 298) | virtual const char* what() const throw() {
  function virtual (line 317) | virtual ~DataFormatError() throw() {}
  function class (line 321) | class FileOpenError : public IoError {
  function class (line 365) | class IoParameterError : public IoError {
  function file (line 387) | void file(const std::string &fl) { _file.set(fl); }
  function virtual (line 410) | virtual const char* what() const throw() {
  function virtual (line 421) | virtual ~IoParameterError() throw() {}
  function class (line 426) | class AssertionFailedError : public LogicError {
  function virtual (line 454) | virtual const char* what() const throw() {
  function virtual (line 470) | virtual ~AssertionFailedError() throw() {}

FILE: src/lemon/fib_heap.h
  function namespace (line 30) | namespace lemon {

FILE: src/lemon/graph_adaptor.h
  function namespace (line 41) | namespace lemon {
  type GraphAdaptorBase (line 228) | typedef GraphAdaptorBase<_Graph> Parent;
  type typename (line 233) | typedef typename Parent::Edge Edge;
  function firstIn (line 235) | void firstIn(Edge& i, const Node& n) const { Parent::firstOut(i, n); }
  function firstOut (line 236) | void firstOut(Edge& i, const Node& n ) const { Parent::firstIn(i, n); }
  function nextIn (line 238) | void nextIn(Edge& i) const { Parent::nextOut(i); }
  function nextOut (line 239) | void nextOut(Edge& i) const { Parent::nextIn(i); }
  function Node (line 241) | Node source(const Edge& e) const { return Parent::target(e); }
  function Node (line 242) | Node target(const Edge& e) const { return Parent::source(e); }
  type FindEdgeTagIndicator (line 244) | typedef FindEdgeTagIndicator<Graph> FindEdgeTag;
  function Edge (line 245) | Edge findEdge(const Node& u, const Node& v,
  type GraphAdaptorExtender (line 306) | typedef GraphAdaptorExtender<
  type SubGraphAdaptorBase (line 328) | typedef SubGraphAdaptorBase Adaptor;
  type GraphAdaptorBase (line 329) | typedef GraphAdaptorBase<_Graph> Parent;
  function setNodeFilterMap (line 336) | void setNodeFilterMap(NodeFilterMap& _node_filter_map) {
  function setEdgeFilterMap (line 339) | void setEdgeFilterMap(EdgeFilterMap& _edge_filter_map) {
  type typename (line 346) | typedef typename Parent::Edge Edge;
  function first (line 348) | void first(Node& i) const {
  function first (line 353) | void first(Edge& i) const {
  function firstIn (line 360) | void firstIn(Edge& i, const Node& n) const {
  function firstOut (line 366) | void firstOut(Edge& i, const Node& n) const {
  function next (line 372) | void next(Node& i) const {
  function next (line 377) | void next(Edge& i) const {
  function nextIn (line 384) | void nextIn(Edge& i) const {
  function nextOut (line 390) | void nextOut(Edge& i) const {
  function hide (line 401) | void hide(const Node& n) const { node_filter_map->set(n, false); }
  function hide (line 408) | void hide(const Edge& e) const { edge_filter_map->set(e, false); }
  function unHide (line 415) | void unHide(const Node& n) const { node_filter_map->set(n, true); }
  function unHide (line 422) | void unHide(const Edge& e) const { edge_filter_map->set(e, true); }
  function hidden (line 428) | bool hidden(const Node& n) const { return !(*node_filter_map)[n]; }
  function hidden (line 434) | bool hidden(const Edge& e) const { return !(*edge_filter_map)[e]; }
  type False (line 436) | typedef False NodeNumTag;
  type False (line 437) | typedef False EdgeNumTag;
  type FindEdgeTagIndicator (line 439) | typedef FindEdgeTagIndicator<Graph> FindEdgeTag;
  function Edge (line 440) | Edge findEdge(const Node& source, const Node& target,
  function Parent (line 462) | NodeMap(const Graph& g)
  function Parent (line 488) | EdgeMap(const Graph& g)
  type SubGraphAdaptorBase (line 511) | typedef SubGraphAdaptorBase Adaptor;
  type GraphAdaptorBase (line 512) | typedef GraphAdaptorBase<_Graph> Parent;
  function setNodeFilterMap (line 519) | void setNodeFilterMap(NodeFilterMap& _node_filter_map) {
  function setEdgeFilterMap (line 522) | void setEdgeFilterMap(EdgeFilterMap& _edge_filter_map) {
  type typename (line 529) | typedef typename Parent::Edge Edge;
  function first (line 531) | void first(Node& i) const {
  function first (line 536) | void first(Edge& i) const {
  function firstIn (line 541) | void firstIn(Edge& i, const Node& n) const {
  function firstOut (line 546) | void firstOut(Edge& i, const Node& n) const {
  function next (line 551) | void next(Node& i) const {
  function next (line 555) | void next(Edge& i) const {
  function nextIn (line 559) | void nextIn(Edge& i) const {
  function nextOut (line 564) | void nextOut(Edge& i) const {
  function hide (line 574) | void hide(const Node& n) const { node_filter_map->set(n, false); }
  function hide (line 581) | void hide(const Edge& e) const { edge_filter_map->set(e, false); }
  function unHide (line 588) | void unHide(const Node& n) const { node_filter_map->set(n, true); }
  function unHide (line 595) | void unHide(const Edge& e) const { edge_filter_map->set(e, true); }
  function hidden (line 601) | bool hidden(const Node& n) const { return !(*node_filter_map)[n]; }
  function hidden (line 607) | bool hidden(const Edge& e) const { return !(*edge_filter_map)[e]; }
  type False (line 609) | typedef False NodeNumTag;
  type False (line 610) | typedef False EdgeNumTag;
  type FindEdgeTagIndicator (line 612) | typedef FindEdgeTagIndicator<Graph> FindEdgeTag;
  function Edge (line 613) | Edge findEdge(const Node& source, const Node& target,
  function Parent (line 635) | NodeMap(const Graph& g)
  function Parent (line 661) | EdgeMap(const Graph& g)
  type GraphAdaptorExtender (line 745) | typedef GraphAdaptorExtender< SubGraphAdaptorBase<_Graph, NodeFilterMap,
  function const_true_map (line 823) | const_true_map(true) {
  function const_true_map (line 999) | const_true_map(true) {
  type UndirGraphAdaptorBase (line 1034) | typedef UndirGraphAdaptorBase Adaptor;
  type UndirGraphExtender (line 1035) | typedef UndirGraphExtender<GraphAdaptorBase<_Graph> > Parent;
  type typename (line 1044) | typedef typename Parent::Edge Edge;
  type _Value (line 1058) | typedef _Value Value;
  type Edge (line 1059) | typedef Edge Key;
  function typename (line 1075) | typename MapTraits<MapImpl>::ConstReturnValue operator[](Edge e) const {
  function typename (line 1083) | typename MapTraits<MapImpl>::ReturnValue operator[](Edge e) {
  type Adaptor (line 1104) | typedef Adaptor Graph;
  type SubMapExtender (line 1105) | typedef SubMapExtender<Adaptor, EdgeMapBase<_Value> > Parent;
  function Parent (line 1107) | EdgeMap(const Graph& g)
  function explicit (line 1129) | explicit UEdgeMap(const Adaptor& ga)
  type InvalidType (line 1162) | typedef InvalidType EdgeNotifier;
  type _Graph (line 1174) | typedef _Graph Graph;
  type typename (line 1175) | typedef typename _Graph::Edge GraphEdge;
  function setGraph (line 1182) | void setGraph(_Graph& g) {
  type typename (line 1193) | typedef typename Parent::UEdge UEdge;
  type typename (line 1194) | typedef typename Parent::Edge Edge;
  type typename (line 1196) | typedef typename Parent::EdgeNotifier UEdgeNotifier;
  type AlterationNotifier (line 1200) | typedef AlterationNotifier<AlterableUndirGraphAdaptor,
  type AlterableUndirGraphAdaptor (line 1210) | typedef AlterableUndirGraphAdaptor AdaptorBase;
  function setNotifier (line 1222) | void setNotifier(typename Graph::EdgeNotifier& nf) {
  function virtual (line 1235) | virtual void add(const std::vector<GraphEdge>& ge) {
  function virtual (line 1243) | virtual void erase(const GraphEdge& ge) {
  function virtual (line 1249) | virtual void erase(const std::vector<GraphEdge>& ge) {
  function virtual (line 1257) | virtual void build() {
  function virtual (line 1260) | virtual void clear() {
  type AlterableUndirGraphAdaptor (line 1323) | typedef AlterableUndirGraphAdaptor<_Graph> Parent;
  type _BackwardMap (line 1344) | typedef _BackwardMap BackwardMap;
  type typename (line 1346) | typedef typename MapTraits<ForwardMap>::ReferenceMapTag ReferenceMapTag;
  type typename (line 1348) | typedef typename ForwardMap::Value Value;
  type typename (line 1349) | typedef typename Parent::Edge Key;
  function set (line 1366) | void set(const Key& e, const Value& a) {
  function typename (line 1377) | typename MapTraits<ForwardMap>::ConstReturnValue
  function typename (line 1389) | typename MapTraits<ForwardMap>::ReturnValue
  function setForwardMap (line 1401) | void setForwardMap(ForwardMap& _forward_map) {
  function setBackwardMap (line 1408) | void setBackwardMap(BackwardMap& _backward_map) {
  type Value (line 1439) | typedef bool Value;
  function setCapacity (line 1448) | void setCapacity(const CapacityMap& _capacity) { capacity = &_capacity; }
  function setFlow (line 1449) | void setFlow(const FlowMap& _flow) { flow = &_flow; }
  function const (line 1451) | bool operator[](const typename Graph::Edge& e) const {
  type Value (line 1465) | typedef bool Value;
  function setCapacity (line 1472) | void setCapacity(const CapacityMap& _capacity) { capacity = &_capacity; }
  function setFlow (line 1473) | void setFlow(const FlowMap& _flow) { flow = &_flow; }
  function const (line 1474) | bool operator[](const typename Graph::Edge& e) const {
  type ResForwardFilter (line 1529) | typedef ResForwardFilter<const Graph, Number, CapacityMap, FlowMap>
  type ResBackwardFilter (line 1532) | typedef ResBackwardFilter<const Graph, Number, CapacityMap, FlowMap>
  type typename (line 1535) | typedef typename UGraph::
  type EdgeSubGraphAdaptor (line 1539) | typedef EdgeSubGraphAdaptor<UGraph, EdgeFilter> Parent;
  function setCapacityMap (line 1551) | void setCapacityMap(const CapacityMap& _capacity) {
  function setFlowMap (line 1557) | void setFlowMap(FlowMap& _flow) {
  type typename (line 1580) | typedef typename Parent::Edge Edge;
  function Number (line 1585) | Number rescap(const Edge& edge) const {
  function augment (line 1598) | void augment(const Edge& e, Number a) const {
  function forward (line 1609) | static bool forward(const Edge& e) {
  function backward (line 1616) | static bool backward(const Edge& e) {
  function Edge (line 1623) | static Edge forward(const typename Graph::Edge& e) {
  function Edge (line 1630) | static Edge backward(const typename Graph::Edge& e) {
  function class (line 1638) | class ResCap {
  type GraphAdaptorBase (line 1661) | typedef GraphAdaptorBase<_Graph> Parent;
  function setFirstOutEdgesMap (line 1667) | void setFirstOutEdgesMap(FirstOutEdgesMap& _first_out_edges) {
  type typename (line 1674) | typedef typename Parent::Edge Edge;
  function firstOut (line 1676) | void firstOut(Edge& i, const Node& n) const {
  function erase (line 1680) | void erase(const Edge& e) const {
  type _Graph (line 1708) | typedef _Graph Graph;
  type GraphAdaptorExtender (line 1709) | typedef GraphAdaptorExtender<
  type GraphAdaptorBase (line 1732) | typedef GraphAdaptorBase<const _Graph> Parent;
  type typename (line 1734) | typedef typename Graph::Node GraphNode;
  type typename (line 1735) | typedef typename Graph::Edge GraphEdge;
  function class (line 1744) | class Node : public GraphNode {
  function operator (line 1762) | bool operator!=(const Node& node) const {
  function operator (line 1766) | bool operator<(const Node& node) const {
  function class (line 1772) | class Edge {
  function first (line 1823) | void first(Node& n) const {
  function next (line 1828) | void next(Node& n) const {
  function first (line 1837) | void first(Edge& e) const {
  function next (line 1846) | void next(Edge& e) const {
  function firstOut (line 1858) | void firstOut(Edge& e, const Node& n) const {
  function nextOut (line 1867) | void nextOut(Edge& e) const {
  function firstIn (line 1875) | void firstIn(Edge& e, const Node& n) const {
  function nextIn (line 1884) | void nextIn(Edge& e) const {
  function Node (line 1892) | Node source(const Edge& e) const {
  function Node (line 1900) | Node target(const Edge& e) const {
  function id (line 1908) | int id(const Node& n) const {
  function Node (line 1911) | Node nodeFromId(int ix) const {
  function id (line 1918) | int id(const Edge& e) const {
  function Edge (line 1925) | Edge edgeFromId(int ix) const {
  function maxEdgeId (line 1932) | int maxEdgeId() const {
  function outNode (line 1947) | static bool outNode(const Node& n) {
  function origEdge (line 1954) | static bool origEdge(const Edge& e) {
  function bindEdge (line 1961) | static bool bindEdge(const Edge& e) {
  function Node (line 1968) | static Node inNode(const GraphNode& n) {
  function Node (line 1975) | static Node outNode(const GraphNode& n) {
  function Edge (line 1982) | static Edge edge(const GraphNode& n) {
  function Edge (line 1989) | static Edge edge(const GraphEdge& e) {
  type True (line 1993) | typedef True NodeNumTag;
  type True (line 1999) | typedef True EdgeNumTag;
  function edgeNum (line 2001) | int edgeNum() const {
  type typename (line 2027) | typedef typename Parent::template
  function set (line 2042) | void set(const Node& key, const T& val) {
  function typename (line 2047) | typename MapTraits<NodeImpl>::ReturnValue
  function typename (line 2053) | typename MapTraits<NodeImpl>::ConstReturnValue
  type typename (line 2065) | typedef typename Parent::template
  type typename (line 2066) | typedef typename Parent::template
  function set (line 2082) | void set(const Edge& key, const T& val) {
  function typename (line 2090) | typename MapTraits<EdgeMapImpl>::ReturnValue
  function typename (line 2099) | typename MapTraits<EdgeMapImpl>::ConstReturnValue
  type _Graph (line 2123) | typedef _Graph Graph;
  type typename (line 2125) | typedef typename Graph::Node GraphNode;
  type typename (line 2126) | typedef typename Graph::Node GraphEdge;
  type InvalidType (line 2135) | typedef InvalidType EdgeNotifier;
  type _Graph (line 2148) | typedef _Graph Graph;
  type typename (line 2150) | typedef typename Graph::Node GraphNode;
  type typename (line 2151) | typedef typename Graph::Edge GraphEdge;
  type typename (line 2153) | typedef typename Parent::Node Node;
  type typename (line 2154) | typedef typename Parent::Edge Edge;
  function setGraph (line 2161) | void setGraph(_Graph& graph) {
  type AlterationNotifier (line 2172) | typedef AlterationNotifier<AlterableSplitGraphAdaptor, Node> NodeNotifier;
  type InvalidType (line 2173) | typedef InvalidType EdgeNotifier;
  type AlterableSplitGraphAdaptor (line 2183) | typedef AlterableSplitGraphAdaptor AdaptorBase;
  function setNotifier (line 2195) | void setNotifier(typename Graph::NodeNotifier& graph_notifier) {
  function virtual (line 2209) | virtual void add(const std::vector<GraphNode>& gn) {
  function virtual (line 2218) | virtual void erase(const GraphNode& gn) {
  function virtual (line 2225) | virtual void erase(const std::vector<GraphNode>& gn) {
  function virtual (line 2233) | virtual void build() {
  function virtual (line 2236) | virtual void clear() {
  type _Graph (line 2259) | typedef _Graph Graph;
  type typename (line 2261) | typedef typename Graph::Node GraphNode;
  type typename (line 2262) | typedef typename Graph::Edge GraphEdge;
  type typename (line 2264) | typedef typename Parent::Node Node;
  type typename (line 2265) | typedef typename Parent::Edge Edge;
  function setGraph (line 2273) | void setGraph(_Graph& g) {
  type AlterationNotifier (line 2286) | typedef AlterationNotifier<AlterableSplitGraphAdaptor, Node> NodeNotifier;
  type AlterationNotifier (line 2287) | typedef AlterationNotifier<AlterableSplitGraphAdaptor, Edge> EdgeNotifier;
  type AlterableSplitGraphAdaptor (line 2298) | typedef AlterableSplitGraphAdaptor AdaptorBase;
  function setNotifier (line 2310) | void setNotifier(typename Graph::NodeNotifier& graph_notifier) {
  function virtual (line 2324) | virtual void add(const std::vector<GraphNode>& gn) {
  function virtual (line 2335) | virtual void erase(const GraphNode& gn) {
  function virtual (line 2342) | virtual void erase(const std::vector<GraphNode>& gn) {
  function virtual (line 2353) | virtual void build() {
  function virtual (line 2363) | virtual void clear() {
  function class (line 2377) | class EdgeNotifierProxy : public Graph::EdgeNotifier::ObserverBase {
  function setNotifier (line 2393) | void setNotifier(typename Graph::EdgeNotifier& graph_notifier) {
  function virtual (line 2403) | virtual void add(const std::vector<GraphEdge>& ge) {
  function virtual (line 2410) | virtual void erase(const GraphEdge& ge) {
  function virtual (line 2413) | virtual void erase(const std::vector<GraphEdge>& ge) {
  function virtual (line 2420) | virtual void build() {
  function virtual (line 2429) | virtual void clear() {
  type typename (line 2523) | typedef typename Parent::Node Node;
  type typename (line 2524) | typedef typename Parent::Edge Edge;
  type typename (line 2542) | typedef typename InNodeMap::Value Value;
  function Value (line 2564) | Value operator[](const Key& key) const {
  function set (line 2575) | void set(const Key& key, const Value& value) {
  type typename (line 2628) | typedef typename GraphEdgeMap::Value Value;
  function set (line 2639) | void set(const Edge& edge, const Value& val) {
  function Value (line 2650) | Value operator[](const Key& edge) const {

FILE: src/lemon/graph_utils.h
  function namespace (line 40) | namespace lemon {
  function _map (line 645) | _map(map) {}
  function virtual (line 647) | virtual void copy(const Graph& graph, const RefMap& refMap) {
  function _cmap (line 663) | _cmap(cmap) {}
  function virtual (line 665) | virtual void copy(const Graph& graph, const RefMap& refMap) {
  type typename (line 776) | typedef typename From::NodeIt NodeIt;
  type typename (line 777) | typedef typename From::Edge Edge;
  type typename (line 778) | typedef typename From::EdgeIt EdgeIt;
  type typename (line 780) | typedef typename To::Node TNode;
  type typename (line 781) | typedef typename To::Edge TEdge;
  type typename (line 783) | typedef typename From::template
  type typename (line 784) | typedef typename From::template
  function run (line 899) | void run() {
  type typename (line 955) | typedef typename From::NodeIt NodeIt;
  type typename (line 956) | typedef typename From::Edge Edge;
  type typename (line 957) | typedef typename From::EdgeIt EdgeIt;
  type typename (line 958) | typedef typename From::UEdge UEdge;
  type typename (line 959) | typedef typename From::UEdgeIt UEdgeIt;
  type typename (line 961) | typedef typename To::Node TNode;
  type typename (line 962) | typedef typename To::Edge TEdge;
  type typename (line 963) | typedef typename To::UEdge TUEdge;
  type typename (line 965) | typedef typename From::template
  type typename (line 966) | typedef typename From::template
  type EdgeRefMap (line 968) | struct EdgeRefMap {
  function run (line 1150) | void run() {
  type typename (line 1214) | typedef typename From::ANode ANode;
  type typename (line 1215) | typedef typename From::BNode BNode;
  type typename (line 1216) | typedef typename From::NodeIt NodeIt;
  type typename (line 1217) | typedef typename From::Edge Edge;
  type typename (line 1218) | typedef typename From::EdgeIt EdgeIt;
  type typename (line 1219) | typedef typename From::UEdge UEdge;
  type typename (line 1220) | typedef typename From::UEdgeIt UEdgeIt;
  type typename (line 1222) | typedef typename To::Node TNode;
  type typename (line 1223) | typedef typename To::Edge TEdge;
  type typename (line 1224) | typedef typename To::UEdge TUEdge;
  type typename (line 1226) | typedef typename From::template
  type typename (line 1227) | typedef typename From::template
  type typename (line 1228) | typedef typename From::template
  type NodeRefMap (line 1230) | struct NodeRefMap {
  type EdgeRefMap (line 1247) | struct EdgeRefMap {
  function run (line 1501) | void run() {
  type Value (line 1589) | typedef int Value;
  type _Item (line 1590) | typedef _Item Item;
  type _Item (line 1591) | typedef _Item Key;
  function explicit (line 1596) | explicit IdMap(const Graph& _graph) : graph(&_graph) {}
  function const (line 1601) | int operator[](const Item& item) const { return graph->id(item);}
  function Item (line 1606) | Item operator()(int id) { return graph->fromId(id, Item()); }
  function explicit (line 1628) | explicit InverseMap(const IdMap& idMap) : graph(idMap.graph) {}
  function Item (line 1634) | Item operator[](int id) const { return graph->fromId(id, Item());}
  type _Graph (line 1668) | typedef _Graph Graph;
  type std (line 1670) | typedef std::map<_Value, _Item> Container;
  type typename (line 1678) | typedef typename Map::Value Value;
  function explicit (line 1686) | explicit InvertableMap(const Graph& graph) : Map(graph) {}
  function set (line 1744) | void set(const Key& key, const Value& val) {
  function typename (line 1757) | typename MapTraits<Map>::ConstReturnValue
  function Key (line 1765) | Key operator()(const Value& key) const {
  function virtual (line 1789) | virtual void erase(const std::vector<Key>& keys) {
  function virtual (line 1804) | virtual void clear() {
  type typename (line 1824) | typedef typename InvertableMap::Key Value;
  type typename (line 1826) | typedef typename InvertableMap::Value Key;
  function Value (line 1832) | Value operator[](const Key& key) const {
  type DefaultMap (line 1870) | typedef DefaultMap<_Graph, _Item, int> Map;
  type typename (line 1877) | typedef typename Map::Key Key;
  type typename (line 1879) | typedef typename Map::Value Value;
  function explicit (line 1884) | explicit DescriptorMap(const Graph& _graph) : Map(_graph) {
  function virtual (line 1909) | virtual void add(const std::vector<Item>& items) {
  function virtual (line 1921) | virtual void erase(const Item& item) {
  function virtual (line 1932) | virtual void erase(const std::vector<Item>& items) {
  function virtual (line 1945) | virtual void build() {
  function virtual (line 1959) | virtual void clear() {
  function swap (line 1976) | void swap(const Item& p, const Item& q) {
  function const (line 1988) | int operator[](const Item& item) const {
  function Item (line 1995) | Item operator()(int id) const {
  type typename (line 2018) | typedef typename DescriptorMap::Key Value;
  type typename (line 2020) | typedef typename DescriptorMap::Value Key;
  function Value (line 2026) | Value operator[](const Key& key) const {
  function InverseMap (line 2044) | const InverseMap inverse() const {
  function Value (line 2072) | Value operator[](const Key& edge) const {
  type typename (line 2099) | typedef typename Graph::Edge Key;
  function explicit (line 2105) | explicit TargetMap(const Graph& _graph) : graph(_graph) {}
  function Value (line 2112) | Value operator[](const Key& e) const {
  type typename (line 2139) | typedef typename Graph::UEdge Key;
  function explicit (line 2145) | explicit ForwardMap(const Graph& _graph) : graph(_graph) {}
  function Value (line 2152) | Value operator[](const Key& key) const {
  type typename (line 2179) | typedef typename Graph::UEdge Key;
  function explicit (line 2185) | explicit BackwardMap(const Graph& _graph) : graph(_graph) {}
  function Value (line 2192) | Value operator[](const Key& key) const {
  type typename (line 2218) | typedef typename NodeMap::Value Value;
  function explicit (line 2223) | explicit PotentialDifferenceMap(const Graph& _graph,
  function Value (line 2230) | Value operator[](const Key& edge) const {
  type Value (line 2274) | typedef int Value;
  type typename (line 2275) | typedef typename Graph::Node Key;
  type typename (line 2277) | typedef typename ItemSetTraits<_Graph, typename
  type typename (line 2286) | typedef typename Parent::Graph Graph;
  function Parent (line 2288) | AutoNodeMap(const Graph& graph) : Parent(graph, 0) {}
  function virtual (line 2290) | virtual void add(const Key& key) {
  function virtual (line 2295) | virtual void add(const std::vector<Key>& keys) {
  function virtual (line 2302) | virtual void build() {
  function const (line 2326) | int operator[](const Key& key) const {
  function virtual (line 2334) | virtual void add(const Edge& edge) {
  function virtual (line 2338) | virtual void add(const std::vector<Edge>& edges) {
  function virtual (line 2344) | virtual void erase(const Edge& edge) {
  function virtual (line 2348) | virtual void erase(const std::vector<Edge>& edges) {
  function virtual (line 2354) | virtual void build() {
  function virtual (line 2360) | virtual void clear() {
  type _Graph (line 2398) | typedef _Graph Graph;
  type Value (line 2399) | typedef int Value;
  type typename (line 2400) | typedef typename Graph::Node Key;
  type typename (line 2408) | typedef typename Parent::Graph Graph;
  function Parent (line 2410) | AutoNodeMap(const Graph& graph) : Parent(graph, 0) {}
  function virtual (line 2412) | virtual void add(const Key& key) {
  function virtual (line 2416) | virtual void add(const std::vector<Key>& keys) {
  function virtual (line 2422) | virtual void build() {
  function const (line 2446) | int operator[](const Key& key) const {
  function virtual (line 2454) | virtual void add(const Edge& edge) {
  function virtual (line 2458) | virtual void add(const std::vector<Edge>& edges) {
  function virtual (line 2464) | virtual void erase(const Edge& edge) {
  function virtual (line 2468) | virtual void erase(const std::vector<Edge>& edges) {
  function virtual (line 2474) | virtual void build() {
  function virtual (line 2480) | virtual void clear() {
  type G (line 2524) | typedef G Graph;
  function Parent (line 2533) | AutoNodeMap(const G& graph) : Parent(graph, INVALID) {}
  function virtual (line 2535) | virtual void add(const Node& node) {
  function virtual (line 2540) | virtual void add(const std::vector<Node>& nodes) {
  function virtual (line 2547) | virtual void build() {
  function class (line 2563) | class EdgeLess {
  function virtual (line 2599) | virtual void erase(const Edge& edge) {
  function virtual (line 2603) | virtual void erase(const std::vector<Edge>& edges) {
  function virtual (line 2609) | virtual void build() {
  function virtual (line 2613) | virtual void clear() {
  function insert (line 2619) | void insert(Edge edge) {
  function remove (line 2654) | void remove(Edge edge) {
  function Edge (line 2723) | Edge refreshRec(std::vector<Edge> &v,int a,int b)
  function refresh (line 2744) | void refresh() {
  function zig (line 2758) | void zig(Edge v) {
  function zag (line 2776) | void zag(Edge v) {
  function splay (line 2794) | void splay(Edge v) {
  function Edge (line 2870) | Edge findFirst(Node s, Node t) const
  function Edge (line 2911) | Edge findNext(Node, Node t, Edge e) const
  type G (line 2961) | typedef G Graph;
  function class (line 2969) | class EdgeLess {
  function refresh (line 3024) | void refresh()
  function Edge (line 3043) | Edge operator()(Node s, Node t) const
  type G (line 3078) | typedef G Graph;
  function Edge (line 3082) | Edge refreshNext(Edge head,Edge next=INVALID)
  function refreshNext (line 3094) | void refreshNext()
  function refresh (line 3115) | void refresh(Node n)
  function refresh (line 3130) | void refresh()
  function Edge (line 3164) | Edge operator()(Node s, Node t, Edge prev=INVALID) const {}
  function Edge (line 3167) | Edge operator()(Node s, Node t, Edge prev) const

FILE: src/lemon/list_graph.h
  function namespace (line 34) | namespace lemon {
  function Node (line 480) | Node split(Edge e) {
  function class (line 498) | class Snapshot {
  function class (line 725) | class ListUGraphBase {
  type UGraphExtender (line 1098) | typedef UGraphExtender<ListUGraphBase> ExtendedListUGraphBase;
  function class (line 1117) | class ListUGraph : public ExtendedListUGraphBase {
  function class (line 1242) | class Snapshot {
  function class (line 1467) | class ListBpUGraphBase {
  type BpUGraphExtender (line 1854) | typedef BpUGraphExtender<BidirBpUGraphExtender<ListBpUGraphBase> >
  function class (line 1869) | class ListBpUGraph : public ExtendedListBpUGraphBase {

FILE: src/lemon/maps.h
  function namespace (line 35) | namespace lemon {
  type typename (line 181) | typedef typename Parent::Key Key;
  type typename (line 183) | typedef typename Parent::Value Value;
  type T (line 185) | typedef T& Reference;
  type T (line 187) | typedef const T& ConstReference;
  type True (line 189) | typedef True ReferenceMapTag;
  function ConstReference (line 228) | ConstReference operator[](const Key &k) const {
  function set (line 237) | void set(const Key &k, const T &t) {
  function setAll (line 246) | void setAll(const T &t) {
  type rebind (line 252) | struct rebind {
  type typename (line 299) | typedef typename Parent::Key Key;
  type typename (line 301) | typedef typename Parent::Value Value;
  type T (line 303) | typedef T& Reference;
  type T (line 305) | typedef const T& ConstReference;
  type True (line 307) | typedef True ReferenceMapTag;
  function ConstReference (line 346) | ConstReference operator[](Key k) const {
  function set (line 351) | void set(const Key &k, const T& t) {
  type typename (line 379) | typedef typename Parent::Key Key;
  type typename (line 380) | typedef typename Parent::Value Value;
  function T (line 383) | const T& operator[](const T& t) const {
  type typename (line 409) | typedef typename Parent::Key Key;
  type typename (line 410) | typedef typename Parent::Value Value;
  function m (line 416) | ConvertMap(const M &_m) : m(_m) {}
  function Value (line 419) | Value operator[](const Key& k) const {return m[k];}
  type typename (line 447) | typedef typename Parent::Key Key;
  type typename (line 448) | typedef typename Parent::Value Value;
  function m (line 451) | SimpleMap(const M &_m) : m(_m) {}
  function Value (line 453) | Value operator[](Key k) const {return m[k];}
  type typename (line 481) | typedef typename Parent::Key Key;
  type typename (line 482) | typedef typename Parent::Value Value;
  function m (line 485) | m(_m) {}
  function Value (line 487) | Value operator[](Key k) const {return m[k];}
  function set (line 489) | void set(Key k, const Value& c) { m.set(k, c); }
  type typename (line 514) | typedef typename Parent::Key Key;
  type typename (line 515) | typedef typename Parent::Value Value;
  function Value (line 520) | Value operator[](Key k) const {return m1[k]+m2[k];}
  type typename (line 557) | typedef typename Parent::Key Key;
  type typename (line 558) | typedef typename Parent::Value Value;
  function Value (line 567) | Value operator[](Key k) const {return m[k] + v;}
  type typename (line 583) | typedef typename Parent::Key Key;
  type typename (line 584) | typedef typename Parent::Value Value;
  function Value (line 593) | Value operator[](Key k) const {return m[k] + v;}
  function set (line 595) | void set(Key k, const Value& c) { m.set(k, c - v); }
  type typename (line 629) | typedef typename Parent::Key Key;
  type typename (line 630) | typedef typename Parent::Value Value;
  function Value (line 635) | Value operator[](Key k) const {return m1[k]-m2[k];}
  type typename (line 660) | typedef typename Parent::Key Key;
  type typename (line 661) | typedef typename Parent::Value Value;
  function Value (line 666) | Value operator[](Key k) const {return m1[k]*m2[k];}
  type typename (line 701) | typedef typename Parent::Key Key;
  type typename (line 702) | typedef typename Parent::Value Value;
  function Value (line 711) | Value operator[](Key k) const {return v * m[k];}
  type typename (line 729) | typedef typename Parent::Key Key;
  type typename (line 730) | typedef typename Parent::Value Value;
  function Value (line 739) | Value operator[](Key k) const {return v * m[k];}
  function set (line 741) | void set(Key k, const Value& c) { m.set(k, c / v);}
  type typename (line 774) | typedef typename Parent::Key Key;
  type typename (line 775) | typedef typename Parent::Value Value;
  function Value (line 780) | Value operator[](Key k) const {return m1[k]/m2[k];}
  type typename (line 815) | typedef typename Parent::Key Key;
  type typename (line 816) | typedef typename Parent::Value Value;
  function typename (line 821) | typename MapTraits<M1>::ConstReturnValue
  type typename (line 865) | typedef typename Parent::Key Key;
  type typename (line 866) | typedef typename Parent::Value Value;
  function Value (line 872) | Value operator[](Key k) const {return f(m1[k],m2[k]);}
  type typename (line 923) | typedef typename Parent::Key Key;
  type typename (line 924) | typedef typename Parent::Value Value;
  function m (line 927) | NegMap(const M &_m) : m(_m) {}
  function Value (line 929) | Value operator[](Key k) const {return -m[k];}
  type typename (line 945) | typedef typename Parent::Key Key;
  type typename (line 946) | typedef typename Parent::Value Value;
  function m (line 949) | m(_m) {}
  function Value (line 951) | Value operator[](Key k) const {return -m[k];}
  function set (line 953) | void set(Key k, const Value& v) { m.set(k, -v); }
  type typename (line 1000) | typedef typename Parent::Key Key;
  type typename (line 1001) | typedef typename Parent::Value Value;
  function m (line 1004) | AbsMap(const M &_m) : m(_m) {}
  function Value (line 1006) | Value operator[](Key k) const {
  type typename (line 1043) | typedef typename Parent::Key Key;
  type typename (line 1044) | typedef typename Parent::Value Value;
  function f (line 1047) | f(_f) {}
  function Value (line 1049) | Value operator[](Key k) const { return f(k);}
  type typename (line 1093) | typedef typename Parent::Key Key;
  type typename (line 1094) | typedef typename Parent::Value Value;
  type typename (line 1096) | typedef typename M::Key argument_type;
  type typename (line 1097) | typedef typename M::Value result_type;
  function m (line 1100) | MapFunctor(const M &_m) : m(_m) {}
  function Value (line 1102) | Value operator()(Key k) const {return m[k];}
  function Value (line 1104) | Value operator[](Key k) const {return m[k];}
  type typename (line 1133) | typedef typename Parent::Key Key;
  type typename (line 1134) | typedef typename Parent::Value Value;
  function Value (line 1139) | Value operator[](Key k) const {return m1[k];}
  type typename (line 1161) | typedef typename Parent::Key Key;
  type typename (line 1162) | typedef typename Parent::Value Value;
  function Value (line 1167) | Value operator[](Key k) const {return m1[k];}
  function set (line 1169) | void set(Key k, const Value &v) {m1.set(k,v); m2.set(k,v);}
  type typename (line 1206) | typedef typename Parent::Key Key;
  type typename (line 1207) | typedef typename Parent::Value Value;
  function m (line 1210) | NotMap(const M &_m) : m(_m) {}
  function Value (line 1212) | Value operator[](Key k) const {return !m[k];}
  type typename (line 1228) | typedef typename Parent::Key Key;
  type typename (line 1229) | typedef typename Parent::Value Value;
  function m (line 1232) | m(_m) {}
  function Value (line 1234) | Value operator[](Key k) const {return !m[k];}
  function set (line 1236) | void set(Key k, bool v) { m.set(k, !v); }
  function namespace (line 1257) | namespace _maps_bits {
  type typename (line 1318) | typedef typename _Functor::argument_type Key;
  type Value (line 1319) | typedef bool Value;
  type _Functor (line 1321) | typedef _Functor Functor;
  function set (line 1338) | void set(const Key& key, Value value) const {
  type Value (line 1374) | typedef bool Value;
  function set (line 1382) | void set(const Key& key, Value value) {
  type Value (line 1409) | typedef bool Value;
  function set (line 1417) | void set(const Key& key, Value value) {
  type Value (line 1452) | typedef bool Value;
  function set (line 1474) | void set(const Key& key, Value value) {
  type Value (line 1516) | typedef bool Value;
  function typename (line 1532) | typename Map::Value& fillValue() {
  function fillValue (line 1537) | void fillValue(const typename Map::Value& _fill) {
  function set (line 1542) | void set(const Key& key, Value value) {
  type Value (line 1607) | typedef bool Value;
  function set (line 1619) | void set(const Key& key, Value value) {

FILE: src/lemon/math.h
  function namespace (line 32) | namespace lemon {

FILE: src/lemon/smart_graph.h
  function namespace (line 38) | namespace lemon {
  type GraphExtender (line 186) | typedef GraphExtender<SmartGraphBase> ExtendedSmartGraphBase;
  function class (line 204) | class SmartGraph : public ExtendedSmartGraphBase {
  function save (line 369) | void save(SmartGraph &_g)
  function restore (line 383) | void restore()
  function class (line 391) | class SmartUGraphBase {
  type UGraphExtender (line 589) | typedef UGraphExtender<SmartUGraphBase> ExtendedSmartUGraphBase;
  function class (line 608) | class SmartUGraph : public ExtendedSmartUGraphBase {
  function class (line 760) | class SmartBpUGraphBase {
  function class (line 804) | class UEdge {
  function firstANode (line 818) | void firstANode(Node& node) const {
  function nextANode (line 822) | void nextANode(Node& node) const {
  function firstBNode (line 827) | void firstBNode(Node& node) const {
  function nextBNode (line 830) | void nextBNode(Node& node) const {
  function first (line 834) | void first(Node& node) const {
  function next (line 841) | void next(Node& node) const {
  function first (line 848) | void first(UEdge& edge) const {
  function next (line 851) | void next(UEdge& edge) const {
  function firstFromANode (line 855) | void firstFromANode(UEdge& edge, const Node& node) const {
  function nextFromANode (line 859) | void nextFromANode(UEdge& edge) const {
  function firstFromBNode (line 863) | void firstFromBNode(UEdge& edge, const Node& node) const {
  function nextFromBNode (line 867) | void nextFromBNode(UEdge& edge) const {
  function id (line 871) | static int id(const Node& node) {
  function Node (line 874) | static Node nodeFromId(int id) {
  function id (line 882) | static int id(const UEdge& edge) {
  function UEdge (line 885) | static UEdge uEdgeFromId(int id) {
  function aNodeId (line 892) | static int aNodeId(const Node& node) {
  function Node (line 895) | static Node nodeFromANodeId(int id) {
  function bNodeId (line 902) | static int bNodeId(const Node& node) {
  function Node (line 905) | static Node nodeFromBNodeId(int id) {
  function Node (line 912) | Node aNode(const UEdge& edge) const {
  function Node (line 915) | Node bNode(const UEdge& edge) const {
  function aNode (line 919) | static bool aNode(const Node& node) {
  function bNode (line 923) | static bool bNode(const Node& node) {
  function Node (line 927) | Node addANode() {
  function Node (line 934) | Node addBNode() {
  function UEdge (line 941) | UEdge addEdge(const Node& source, const Node& target) {
  function reserveANode (line 959) | void reserveANode(int n) { aNodes.reserve(n); }
  function reserveBNode (line 960) | void reserveBNode(int n) { bNodes.reserve(n); }
  function reserveEdge (line 962) | void reserveEdge(int m) { edges.reserve(m); }
  function clear (line 964) | void clear() {
  type True (line 970) | typedef True NodeNumTag;
  type True (line 975) | typedef True EdgeNumTag;
  type BpUGraphExtender (line 981) | typedef BpUGraphExtender<BidirBpUGraphExtender<SmartBpUGraphBase> >
  function class (line 1000) | class SmartBpUGraph : public ExtendedSmartBpUGraphBase {

FILE: src/lemon/tolerance.h
  function namespace (line 30) | namespace lemon {

FILE: src/lemon/topology.h
  function namespace (line 44) | namespace lemon {

FILE: src/locfit/adap.c
  function acri (line 17) | double acri(lk,t0,t2,pen)
  function mmse (line 26) | double mmse(lf,des)
  function INT (line 55) | INT ainitband(des,lf)
  function aband2 (line 101) | double aband2(des,lf,h0)
  function aband3 (line 152) | double aband3(des,lf,h0)

FILE: src/locfit/ar_funs.c
  function vrexp (line 14) | double vrexp()  { return(rexp(1.0)); }
  function vrnorm (line 15) | double vrnorm() { return(rnorm(0.0,1.0)); }
  function vpnorm (line 16) | double vpnorm(double x){ return(pnorm(x,0.0,1.0)); }
  function vdnorm (line 17) | double vdnorm(double x){ return(exp(-x*x/2)/S2PI); }
  function dummyf (line 18) | double dummyf() { return(0.0); }
  function frac (line 19) | double frac(double x) { return(x-floor(x)); }
  function vmin (line 21) | double vmin(v)
  function vmax (line 33) | double vmax(v)
  function vsum (line 45) | double vsum(v)
  function vmean (line 53) | double vmean(vari *v) { return(vsum(v)/vlength(v)); }
  function ar_setfunction (line 55) | int ar_setfunction(rt,z,len)

FILE: src/locfit/arith.c
  function vadd (line 14) | double vadd(double e1,double e2) { return(e1+e2); }
  function vsub (line 15) | double vsub(double e1,double e2) { return(e1-e2); }
  function vmul (line 16) | double vmul(double e1,double e2) { return(e1*e2); }
  function vdiv (line 17) | double vdiv(double e1,double e2) { return(e1/e2); }
  function vpow (line 18) | double vpow(double e1,double e2)
  function vgt (line 23) | double vgt(double e1,double e2) { return((double)(e1>e2)); }
  function vlt (line 24) | double vlt(double e1,double e2) { return((double)(e1<e2)); }
  function vge (line 25) | double vge(double e1,double e2) { return((double)(e1>=e2)); }
  function vle (line 26) | double vle(double e1,double e2) { return((double)(e1<=e2)); }
  function veq (line 27) | double veq(double e1,double e2) { return((double)(e1==e2)); }
  function vne (line 28) | double vne(double e1,double e2) { return((double)(e1!=e2)); }
  function lf_exp (line 32) | double lf_exp(double x) { return (x<700.0) ? exp(x) : exp(700.0); }
  function vseq (line 34) | double vseq(double a,double b,int i,int n) { return(a+(b-a)*i/(n-1)); }
  function rsample (line 36) | double rsample(v)
  function setnext (line 74) | void setnext(va,n,p,k)
  function prars (line 86) | void prars(v,i)
  function isstring (line 100) | int isstring(z,i1,i2)
  function isname (line 109) | int isname(z,i1,i2)
  function isfunction (line 119) | int isfunction(z,i1,i2)
  function issubset (line 129) | int issubset(z,i1,i2)
  function isNumber (line 139) | int isNumber(z,i1,i2,val)
  function isoperator (line 148) | int isoperator(z,i1,i2)
  function dareval (line 553) | double dareval(v,k,x)
  function darith (line 578) | double darith(z)
  function INT (line 588) | INT arvect(z,res,c,a) /* c = no of items to read */

FILE: src/locfit/band.c
  function INT (line 18) | INT procvbind(des,lf,v)
  function bcri (line 38) | double bcri(h,c,cri)
  function bsel2 (line 66) | void bsel2(h0,g0,ifact,c,cri)
  function bsel3 (line 89) | void bsel3(h0,g0,ifact,c,cri)
  function bselect (line 103) | void bselect(c,cri,pn)
  function compsda (line 133) | double compsda(x,h,n)
  function widthsj (line 151) | double widthsj(x,lambda,n)
  function kdecri (line 177) | void kdecri(x,h,res,c,k,ker,n)
  function esolve (line 282) | double esolve(x,j,h0,h1,k,c,ker,n)
  function kdeselect (line 328) | void kdeselect(band,x,ind,h0,h1,meth,nm,ker,n)
  function band (line 342) | void band(v)
  function slscv (line 374) | void slscv(x,n,h,z)

FILE: src/locfit/c_args.c
  function getarg (line 16) | int getarg(v,s,un) /* un=1: unnamed permitted un=2: next unused */
  function readilist (line 55) | int readilist(ivec,z,n0,n1,pad)
  function getlogic (line 79) | int getlogic(v,i)

FILE: src/locfit/c_plot.c
  function plotopt (line 77) | void plotopt(v,re)
  function pvari (line 139) | void pvari(cmd,xyz,win,ax)
  function plotdata (line 166) | void plotdata(v)
  function plotfit (line 224) | void plotfit(v)
  function plottrack (line 391) | void plottrack(v)
  function setplot (line 436) | void setplot(v)

FILE: src/locfit/cmd.c
  type lfcol (line 26) | struct lfcol
  function savefit (line 44) | void savefit(v,mode)
  function readdata (line 60) | void readdata(v)
  function savedata (line 71) | void savedata(v)
  function recondat (line 80) | void recondat(xonly,n)
  function ckap (line 99) | void ckap(v)
  function crband (line 117) | void crband(v)
  function ckdeb (line 132) | void ckdeb(v)
  function docrit (line 168) | double docrit(v)
  function crit (line 178) | void crit(v)
  function backtr (line 187) | double backtr(th,mi,nd)
  function predict (line 194) | void predict(vc)
  function printfit (line 282) | void printfit(v)
  function knots (line 343) | void knots(v)
  function summfit (line 376) | void summfit(v)
  function AC (line 415) | void AC(name,r,g,b,p)
  function INT (line 422) | INT getcolidx(cname, def)
  function greyscale (line 433) | void greyscale(v)
  function setcolor (line 444) | void setcolor(v)
  function table (line 478) | void table(v)
  function setout (line 555) | void setout(v)
  function dosleep (line 580) | void dosleep(v)
  function setdef (line 589) | void setdef(v)
  function dcmdint (line 614) | void dcmdint(v)
  function cmdint (line 672) | void cmdint(v)
  function INT (line 736) | INT locfit_dispatch(char *z)
  function setuplf (line 752) | void setuplf()

FILE: src/locfit/dens_haz.c
  function INT (line 33) | INT haz_sph_int(lf,dfx,cf,h,r1)
  function INT (line 68) | INT hazint_sph(t,resp,r1,lf,cf,h)
  function INT (line 96) | INT hazint_prod(t,resp,x,lf,cf,h)
  function INT (line 172) | INT hazint(t,resp,resp1,lf,cf,h)
  function haz_init (line 181) | void haz_init(lf,des,il)

FILE: src/locfit/dens_int.c
  function lforder (line 29) | void lforder(ind,x,l,r)
  function estdiv (line 61) | double estdiv(x0,x1,f0,f1,d0,d1,link)
  function dens_integrate (line 104) | double dens_integrate(lf,des,z)
  function dens_renorm (line 185) | void dens_renorm(lf,des)
  function dens_lscv (line 196) | void dens_lscv(des,lf)

FILE: src/locfit/dens_odi.c
  function INT (line 23) | INT exbctay(b,c,n,z) /* n-term taylor series of e^(bx+cx^2) */
  function explinjtay (line 43) | double explinjtay(l0,l1,j,cf)
  function explint1 (line 60) | void explint1(l0,l1,cf,I,p) /* int x^j exp(a+bx); j=0..p-1 */
  function explintyl (line 92) | void explintyl(l0,l1,cf,I,p) /* small c, use taylor series and explint1 */
  function solvetrid (line 103) | void solvetrid(X,y,m)
  function initi0i1 (line 121) | void initi0i1(I,cf,y0,y1,l0,l1)
  function explinsid (line 142) | void explinsid(l0,l1,cf,I,p) /* large b; don't use fwd recursion */
  function explinbkr (line 192) | void explinbkr(l0,l1,cf,I,p) /* small b,c; use back recursion */
  function explinfbk0 (line 209) | void explinfbk0(l0,l1,cf,I,p) /* fwd and bac recur; b=0; c<0 */
  function explinfbk (line 260) | void explinfbk(l0,l1,cf,I,p) /* fwd and bac recur; b not too large */
  function recent (line 291) | void recent(I,resp,wt,p,s,x)
  function recurint (line 307) | void recurint(l0,l2,cf,resp,p,ker)
  function INT (line 418) | INT onedexpl(cf,mi,resp)
  function INT (line 436) | INT onedgaus(cf,mi,resp)
  function INT (line 463) | INT onedint(cf,mi,l0,l1,resp) /* int W(u)u^j exp(..), j=0..2*deg */

FILE: src/locfit/density.c
  function prresp (line 16) | void prresp(coef,resp,p)
  function INT (line 30) | INT multint(t,resp1,resp2,lf,cf,h)
  function INT (line 75) | INT mlinint(t,resp1,resp2,lf,cf,h)
  function prodint_resp (line 165) | void prodint_resp(resp,prod_wk,dim,deg,p)
  function INT (line 197) | INT prodint(t,resp,resp2,lf,coef,h)
  function INT (line 241) | INT gausint(t,resp,C,cf,h,mi,sca)
  function likeden (line 293) | int likeden(coef, lk0, f1, A)
  function INT (line 343) | INT inre(x,bound,d)
  function INT (line 354) | INT setintlimits(lf, x, h, ang, lset)
  function INT (line 386) | INT selectintmeth(mi,lset,ang)
  function INT (line 437) | INT densinit(lf,des,h,cf,m)

FILE: src/locfit/design.h
  type design (line 9) | typedef struct {

FILE: src/locfit/dist.c
  function dchisq (line 14) | double dchisq(x, df)
  function df (line 19) | double df(x, df1, df2)
  function ibeta (line 27) | double ibeta(x, a, b)
  function igamma (line 77) | double igamma(x, df)
  function pf (line 137) | double pf(q, df1, df2)
  function pchisq (line 142) | double pchisq(q, df)
  function pnorm (line 149) | double pnorm(x,mu,s)
  function pnorm (line 154) | double pnorm(x,mu,s)

FILE: src/locfit/ev_atree.c
  function atree_guessnv (line 16) | void atree_guessnv(nvm,ncm,vc,dp,mi)
  function INT (line 56) | INT atree_split(lf,ce,le,ll,ur)
  function atree_grow (line 87) | void atree_grow(des,lf,ce,ct,term,ll,ur)
  function atree_start (line 132) | void atree_start(des,lf)
  function atree_int (line 167) | double atree_int(tr,x,what)

FILE: src/locfit/ev_interp.c
  function linear_interp (line 8) | double linear_interp(h,d,f0,f1)
  function hermite2 (line 14) | void hermite2(x,z,phi)
  function cubic_interp (line 38) | double cubic_interp(h,f0,f1,d0,d1)
  function cubintd (line 45) | double cubintd(h,f0,f1,d0,d1)
  function rectcell_interp (line 65) | double rectcell_interp(x,xev,vv,ll,ur,d,nc)
  function INT (line 115) | INT exvval(lf,vv,nv,d,what,z)
  function exvvalpv (line 162) | void exvvalpv(vv,vl,vr,d,k,dl,nc)
  function gridint (line 181) | double gridint(tr,x,what)
  function fitpint (line 212) | double fitpint(lf,x,what,i)
  function dointpointpf (line 221) | double dointpointpf(lf,des,x,what)
  function xbarint (line 233) | double xbarint(lf,x,what)
  function dointpoint (line 247) | double dointpoint(lf,des,x,what,ev,j)

FILE: src/locfit/ev_kdtre.c
  function kdtre_guessnv (line 16) | void kdtre_guessnv(nvm,ncm,vc,dp,mi)
  function ksmall (line 50) | int ksmall(l, r, m, x, pi)
  function INT (line 101) | INT terminal(tr,p,pi,fc,d,m,split_val)
  function kdtre_start (line 141) | void kdtre_start(des,tr)
  function newcell (line 226) | void newcell(nv,vc,xev, d, k, split_val, cpar, clef, crig)
  function blend (line 254) | double blend(lf,s,x,ll,ur,j,nt,t,what)
  function kdtre_int (line 305) | double kdtre_int(lf,x,what)

FILE: src/locfit/ev_main.c
  function guessnv (line 33) | void guessnv(nvm,ncm,vc,dp,mi)
  function lfit_reqd (line 71) | int lfit_reqd(d,nvm,ncm)
  function lfit_reqi (line 75) | int lfit_reqi(nvm,ncm,vc)
  function trchck (line 80) | void trchck(tr,nvm,ncm,d,p,vc)
  function reassign (line 115) | void reassign(lf)
  function dataf (line 149) | void dataf(des,lf)
  function xbarf (line 167) | void xbarf(des,lf)
  function preset (line 181) | void preset(des,lf)
  function crossf (line 199) | void crossf(des,lf)
  function gridf (line 218) | void gridf(des,tr)
  function INT (line 248) | INT newsplit(des,lf,i0,i1,pv)

FILE: src/locfit/ev_trian.c
  function INT (line 8) | INT triang_split(tr,ce,le)
  function resort (line 26) | void resort(pv,xev,dig)
  function triang_grow (line 54) | void triang_grow(des,tr,ce,ct,term)
  function triang_descend (line 105) | void triang_descend(tr,xa,ce)
  function covrofdata (line 179) | void covrofdata(lf,V,mn) /* covar of data; mean in mn */
  function INT (line 195) | INT intri(x,w,xev,xa,d) /* is x in triangle bounded by xd[0..d-1]? */
  function triang_start (line 213) | void triang_start(des,tr) /* Triangulation with polyhedral start */
  function triang_cubicint (line 277) | double triang_cubicint(v,vv,w,d,nc,xxa)
  function triang_clotoch (line 317) | double triang_clotoch(xev,vv,ce,p,xxa)
  function INT (line 401) | INT triang_getvertexvals(lf,vv,i,what)
  function triang_int (line 428) | double triang_int(tr,x,what)

FILE: src/locfit/family.c
  function INT (line 12) | INT defaultlink(link,family)
  function INT (line 50) | INT validlinks(link,family)
  function INT (line 79) | INT famdens(mean,th,link,res,cens,w)
  function INT (line 91) | INT famgaus(y,mean,th,link,res,cens,w)
  function INT (line 133) | INT famrobu(y,mean,th,link,res,cens,w,rs)
  function INT (line 159) | INT famcauc(y,p,th,link,res,cens,w,rs)
  function INT (line 174) | INT famrbin(y,p,th,link,res,cens,w)
  function INT (line 200) | INT fambino(y,p,th,link,res,cens,w)
  function INT (line 259) | INT fampois(y,mean,th,link,res,cens,w)
  function INT (line 330) | INT famgamm(y,mean,th,link,res,cens,w)
  function INT (line 389) | INT famgeom(y,mean,th,link,res,cens,w)
  function INT (line 430) | INT famweib(y,mean,th,link,res,cens,w)
  function INT (line 451) | INT famcirc(y,mean,th,link,res,cens,w)
  function robustify (line 465) | void robustify(res,rs)
  function lf_link (line 476) | double lf_link(y,lin)
  function invlink (line 491) | double invlink(th,lin)
  function INT (line 507) | INT links(th,y,fam,lin,res,cd,w,rs) /* the link and various related func...
  function INT (line 552) | INT stdlinks(res,lf,i,th,rs)
  function b2 (line 564) | double b2(th,tg,w)
  function b3 (line 579) | double b3(th,tg,w)
  function b4 (line 594) | double b4(th,tg,w)

FILE: src/locfit/fitted.c
  function resid (line 20) | double resid(y,w,th,mi,ty,res)
  function studentize (line 52) | double studentize(res,inl,var,ty,link)
  function fitted (line 74) | void fitted(lf,des,fit,what,cv,st,ty)
  function cfitted (line 128) | void cfitted(v,ty)

FILE: src/locfit/frend.c
  function resp (line 11) | double resp(lf,i)
  function prwt (line 18) | double prwt(lf,i)
  function base (line 26) | double base(lf,i)
  function cens (line 33) | double cens(lf,i)
  function vocri (line 40) | double vocri(lk,t0,t2,pen)
  function INT (line 46) | INT procvraw(des,lf,v)
  function set_default_like (line 91) | void set_default_like(lf,nvm,v,d)
  function INT (line 102) | INT procv(des,lf,v)
  function intvo (line 180) | double intvo(des,lf,c0,c1,a,p,t0,t20,t21)
  function INT (line 197) | INT procvvord(des,lf,v)
  function ressummd (line 264) | void ressummd(lf,des)
  function ressumm (line 284) | void ressumm(lf,des)
  function rss (line 393) | double rss(lf,des,df)

FILE: src/locfit/help.c
  function example (line 18) | void example(v)

FILE: src/locfit/imatlb.h
  type vari (line 1) | typedef struct {
  type xtwxstruc (line 6) | typedef struct {
  type paramcomp (line 10) | typedef struct {
  type design (line 15) | typedef struct {
  type lfit (line 23) | typedef struct {

FILE: src/locfit/lf_dercor.c
  function dercor (line 21) | void dercor(des,lf,coef)

FILE: src/locfit/lf_fitfun.c
  function INT (line 25) | INT calcp(mi,deg)
  function INT (line 44) | INT coefnumber(deriv,nd,kt,d,deg)
  function makecfn (line 70) | void makecfn(des,lf)
  function fitfunangl (line 94) | void fitfunangl(dx,ff,sca,cd,deg)
  function fitfun (line 120) | void fitfun(lf,x,t,f,deriv,nd)
  function designmatrix (line 234) | void designmatrix(lf,des)

FILE: src/locfit/lf_robust.c
  function median (line 36) | double median(x,n)
  function nrobustscale (line 65) | double nrobustscale(lf,des,rs)
  function robustscale (line 89) | double robustscale(lf,des)
  function update_rs (line 106) | double update_rs(x)
  function lf_robust (line 117) | void lf_robust(lf,des)

FILE: src/locfit/lf_vari.c
  function vmat (line 21) | void vmat(lf, des, M12, M2, tr)
  function comp_infl (line 75) | double comp_infl(lf,des)
  function comp_vari (line 83) | void comp_vari(lf,des,tr,t0)
  function local_df (line 123) | void local_df(lf,des,tr)

FILE: src/locfit/lfd.c
  function closefile (line 18) | void closefile()
  function openfile (line 23) | void openfile(mode)
  function INT (line 40) | INT setfilename(name,ext,mode,fp)
  function readchar (line 108) | void readchar(c,n)
  function readstr (line 114) | void readstr(z)
  function dumpchar (line 123) | void dumpchar(c,n)
  function dumpstr (line 129) | void dumpstr(z)
  function dosavedata (line 136) | void dosavedata(v,fp)
  function doreaddata (line 178) | void doreaddata(name,fp)
  function dosavefit (line 233) | void dosavefit(lf,fi,mode,fp)

FILE: src/locfit/lfstr.c
  function INT (line 35) | INT lffamily(z)
  function getlffam (line 55) | void getlffam(z,x)
  function setstrval (line 88) | void setstrval(mi,v,z)
  function INT (line 134) | INT restyp(z)
  function INT (line 143) | INT ppwhat(z)

FILE: src/locfit/lfstruc.h
  type vari (line 19) | typedef struct {
  type vari (line 28) | typedef struct {
  type carg (line 39) | typedef struct {
  type device (line 44) | typedef struct {
  type paramcomp (line 50) | typedef struct {
  type lfit (line 55) | typedef struct {
  type pplot (line 72) | typedef struct {
  type arstruct (line 77) | typedef struct {
  type plxyz (line 83) | typedef struct {
  type plots (line 88) | typedef struct {
  type lfcol (line 99) | struct lfcol {

FILE: src/locfit/linalg.c
  function svd (line 8) | void svd(x,p,q,d,mxit)  /* svd of square matrix */
  function INT (line 83) | INT svdsolve(x,w,P,D,Q,d,tol) /* original X = PDQ^T; comp. QD^{-1}P^T x */
  function hsvdsolve (line 110) | void hsvdsolve(x,w,P,D,Q,d,tol) /* original X = PDQ^T; comp. D^{-1/2}P^T...
  function QRupd (line 128) | void QRupd(X,u,p,w,y)
  function QR1 (line 152) | void QR1(X,n,p,w)   /* QR of X (n*p); take w for the ride, if not NULL */
  function bacK (line 196) | void bacK(R,f,p)   /* R^{-1} f */
  function bacT (line 207) | void bacT(R,f,p,i0,i1)   /* R^{-1} (R^T)^{-1} f; p columns; use i0-(i1-1...
  function solve (line 225) | void solve(A,b,d) /* this is crude! A organized by column. */
  function grsc (line 244) | void grsc(X,d)
  function setzero (line 262) | void setzero(v,p)
  function unitvec (line 269) | void unitvec(x,k,p)
  function innerprod (line 276) | double innerprod(v1,v2,p)
  function addouter (line 286) | void addouter(re,v1,v2,p,c)
  function multmatscal (line 295) | void multmatscal(A,z,n)
  function transpose (line 309) | void transpose(x,m,n)
  function m_trace (line 328) | double m_trace(x,n)

FILE: src/locfit/local.h
  type INT (line 77) | typedef int INT;

FILE: src/locfit/locfit.c
  function likereg (line 16) | int likereg(coef, lk0, f1, Z)
  function INT (line 79) | INT robustinit(lf,des)
  function INT (line 91) | INT circinit(lf,des)
  function INT (line 108) | INT reginit(lf,des)
  function lfinit (line 165) | int lfinit(lf,des)
  function lfiter (line 195) | void lfiter(lf,des)
  function use_robust_scale (line 213) | int use_robust_scale(int tg)
  function locfit (line 219) | int locfit(lf,des,h,noit)

FILE: src/locfit/m_chol.c
  function chol_dec (line 9) | void chol_dec(A,n)
  function chol_solve (line 31) | int chol_solve(A,v,p)
  function chol_hsolve (line 47) | int chol_hsolve(A,v,p)
  function chol_qf (line 59) | double chol_qf(A,v,p)

FILE: src/locfit/m_eigen.c
  function e_tol (line 12) | double e_tol(D,p)
  function eig_dec (line 23) | void eig_dec(X,P,d)
  function eig_solve (line 66) | int eig_solve(J,x)
  function eig_hsolve (line 97) | int eig_hsolve(J,v)
  function eig_qf (line 124) | double eig_qf(J,v)

FILE: src/locfit/m_jacob.c
  function jac_reqd (line 13) | int jac_reqd(int p) { return(2*p*(p+1)); }
  function jacob_dec (line 28) | void jacob_dec(J, meth)
  function jacob_solve (line 57) | int jacob_solve(J,v) /* (X^T W X)^{-1} v */
  function jacob_hsolve (line 79) | int jacob_hsolve(J,v) /*  J^{-1/2} v */
  function jacob_qf (line 99) | double jacob_qf(J,v)  /* vT J^{-1} v */

FILE: src/locfit/m_max.c
  function max_grid (line 41) | double max_grid(f,xlo,xhi,n,flag)
  function max_golden (line 63) | double max_golden(f,xlo,xhi,n,tol,err,flag)
  function max_quad (line 104) | double max_quad(f,xlo,xhi,n,tol,err,flag)
  function max_nr (line 169) | double max_nr(F, coef, old_coef, f1, delta, J, p, maxit, tol, err)

FILE: src/locfit/makecmd.c
  type forvar (line 34) | typedef struct {
  function countfields (line 42) | int countfields(z)
  function makefields (line 66) | void makefields(z, va, n)
  function set_forvar (line 116) | void set_forvar(v,ct)
  function inc_forvar (line 135) | void inc_forvar()
  function dec_forvar (line 154) | void dec_forvar()
  function run (line 162) | void run(va)
  function makecmd (line 188) | void makecmd(cmdline)
  function del_lines (line 221) | void del_lines()
  function vari (line 233) | vari *getcmd()

FILE: src/locfit/math.c
  function lferf (line 25) | double lferf(x)
  function lferfc (line 51) | double lferfc(x)
  function lflgamma (line 58) | double lflgamma(x)
  function lfdaws (line 80) | double lfdaws(x)
  function ptail (line 125) | double ptail(x) /* exp(x*x/2)*int_{-\infty}^x exp(-u^2/2)du for x < -6 */
  function logit (line 139) | double logit(x)
  function expit (line 144) | double expit(x)
  function factorial (line 154) | int factorial(n)

FILE: src/locfit/minmax.c
  function ipower (line 22) | double ipower(x,n) /* use for n not too large!! */
  function setmmwt (line 30) | double setmmwt(des,lf,a,gam)
  function mmsums (line 51) | int mmsums(coef,f,z,J)
  function updatesd (line 84) | double updatesd(des,lf,z,p,a,a0,sw0,gam)
  function mm_initial (line 140) | int mm_initial(des,lf,z,p,coef)
  function mmax (line 159) | int mmax(coef, old_coef, f1, delta, J, p, maxit, tol, err)
  function findab (line 223) | double findab(double gam)
  function weightmm (line 249) | double weightmm(coef,di,ff,mi,gam)
  function minmax (line 259) | double minmax(lf,des)

FILE: src/locfit/mutil.h
  type jacobian (line 12) | typedef struct {

FILE: src/locfit/nbhd.c
  function rho (line 15) | double rho(x,sc,d,kt,sty) /* ||x|| for appropriate distance metric */
  function kordstat (line 51) | double kordstat(x,k,n,ind)
  function INT (line 78) | INT inlim(lf,xlim,i,d)
  function compbandwid (line 91) | double compbandwid(di,ind,x,n,d,nn,fxh)
  function nbhd1 (line 117) | double nbhd1(lf,des,k,fxh)
  function nbhd (line 184) | double nbhd(lf,des,nn,fxh,redo)

FILE: src/locfit/pcomp.c
  function INT (line 12) | INT noparcomp(lf)
  function INT (line 25) | INT hasparcomp(lf)
  function pc_reqd (line 31) | int pc_reqd(d,p)
  function pcchk (line 37) | void pcchk(pc,d,p,lc)
  function compparcomp (line 55) | void compparcomp(des,lf,nopc)
  function subparcomp (line 128) | void subparcomp(des,lf,coef)
  function subparcomp2 (line 149) | void subparcomp2(des,lf,vr,il)
  function addparcomp (line 178) | double addparcomp(lf,x,c)

FILE: src/locfit/pout.c
  function FILE (line 24) | FILE *popen(const char *cmd,const char *mode) { return(NULL); }
  function pclose (line 25) | int pclose(FILE *file) { return(0); }
  function f2 (line 30) | char f2(fmt)
  function INT (line 39) | INT pretty(xl,k,z)
  function isgrid (line 61) | void isgrid(xyz)
  function getxyzitem (line 93) | void getxyzitem(x,xyz,i)
  function project (line 107) | void project(z,x,theta,phi)
  function iproject (line 117) | void iproject(z,i,theta,phi)
  function line3d (line 125) | void line3d(z1,z2,theta,phi,dev,col)
  function xyztext (line 136) | void xyztext(tx,x,ah,av,theta,phi,dev,col)
  function getgreylevel (line 147) | int getgreylevel(z)
  function points3d (line 156) | void points3d(x,theta,phi,dev,type)
  function lines3d (line 175) | void lines3d(xyz,theta,phi,dev)
  function segments (line 194) | void segments(xyz0,xyz1,theta,phi,dev)
  function spl (line 209) | double spl(z0,z1)
  function contour3d (line 215) | void contour3d(x,theta,phi,dev,sl,nsl)
  function angle (line 303) | double angle(x0,x1,x2) /* rotation angle from (x0,x1) to (x0,x2) */
  function persp3d (line 318) | void persp3d(xyz,theta,phi,DP,sl,nsl)
  function updatelim (line 376) | void updatelim(v,xl)
  function axis (line 389) | void axis(z1,z2,zl,lab,theta,phi,a,s,dev)
  function plotxwin (line 442) | void plotxwin(pl,dev,wn,w,h,rd)
  function plotmaple (line 553) | void plotmaple(pl)
  function plotmathe (line 593) | void plotmathe(pl,fmt)
  function plotmatlb (line 645) | void plotmatlb(pl) /* Matlab */
  function plotgnup (line 687) | void plotgnup(pl,fmt)

FILE: src/locfit/preplot.c
  function predptall (line 32) | void predptall(lf,des,x,what,ev,i)
  function prepvector (line 57) | void prepvector(lf,des,x,n,what) /* interpolate a vector */
  function prepfitp (line 71) | void prepfitp(lf,des,what)
  function prepgrid (line 84) | void prepgrid(lf,des,x,mg,n,what) /* interpolate a grid given margins */
  function preplot (line 103) | void preplot(lf,des,x,f,se,band,mg,where,what)
  function cpreplot (line 153) | void cpreplot(pp,vc,band)
  function INT (line 169) | INT setpppoints(pp,where,mg,xl)

FILE: src/locfit/random.c
  function runif (line 15) | double runif()
  function rseed (line 26) | void rseed(seed)
  function rnorm (line 49) | double rnorm(mu,s)
  function rexp (line 62) | double rexp(lb)
  function rpois (line 74) | double rpois(lambda)

FILE: src/locfit/readfile.c
  function readfile (line 25) | void readfile(vc)

FILE: src/locfit/scb.c
  function covar_par (line 13) | double covar_par(lf,des,x1,x2)
  function cumulant (line 57) | void cumulant(lf,des,sd)
  function q2 (line 130) | double q2(u)
  function p2 (line 136) | double p2(u)
  function procvscb2 (line 143) | void procvscb2(des,lf,v)
  function scb (line 194) | void scb(des,lf)
  function scbsim_fun (line 238) | double scbsim_fun(x)
  function do_scbsim (line 273) | void do_scbsim(des,lf)
  function scbsim (line 287) | void scbsim(lf,des)
  function cscbsim (line 300) | void cscbsim(v)

FILE: src/locfit/scb_cons.c
  function assignk0 (line 15) | void assignk0(z,d,n) /* z should be n*(2*d*d+2*d+2); */
  function christ (line 23) | void christ(d,nn,nl)  /* lij[i][j] = res proj. of Tij to (T1...Td) */
  function d1 (line 45) | void d1(n,d)   /* d1[i][j] = e_i^T (A^T A)^{-1} B_j^T */
  function k2x (line 61) | void k2x(lf,des,kap)
  function l1x (line 91) | void l1x(lf,des,lap,re)
  function m0x (line 137) | void m0x(lf,des,m0,re,rg)
  function INT (line 159) | INT constants(des,lf,kap)
  function tailp (line 270) | double tailp(c,k0,m,d,nu)
  function taild (line 289) | double taild(c,k0,m,d,nu)
  function critval (line 308) | double critval(k0,m,d,al,it,s,nu)
  function scritval (line 336) | void scritval(k0,d,cov,m,rdf,z)

FILE: src/locfit/simul.c
  function goldensec (line 10) | void goldensec(f,des,tr,eps,xm,ym,meth)
  function dnk (line 53) | double dnk(x,k)
  function locai (line 70) | double locai(h,des,tr)
  function loccp (line 82) | double loccp(h,des,tr,m) /* m=1: cp    m=2: gcv */
  function cp (line 102) | double cp(des,tr,meth)
  function gkk (line 111) | double gkk(des,tr)
  function rsw (line 138) | double rsw(des,tr,kk)
  function rband (line 186) | void rband(des,tr,hhat,meth,nmeth,kk)

FILE: src/locfit/solve.c
  function solve_secant (line 47) | double solve_secant(f,c,xlo,xhi,tol,bd_flag,err)
  function solve_nr (line 96) | double solve_nr(f,f1,c,x0,tol,err)
  function solve_fp (line 107) | double solve_fp(f,x0,tol,maxit)

FILE: src/locfit/startlf.c
  function fitdefault (line 25) | void fitdefault(lf,n,d)
  function des_reqd (line 61) | int des_reqd(n,p)
  function des_reqi (line 66) | int des_reqi(INT n) { return(n); }
  function deschk (line 68) | void deschk(des,n,p)
  function bbox (line 120) | void bbox(lf,bx)
  function preproc (line 148) | void preproc(des,lf,nopc)
  function startlf (line 185) | void startlf(des,lf,vfun,nopc)
  function INT (line 239) | INT nofit()
  function endfit (line 244) | void endfit()
  function INT (line 253) | INT drl(key,dv,mi)
  function fitoptions (line 266) | void fitoptions(lf,vc,re)
  function clocfit (line 417) | void clocfit(v,re)

FILE: src/locfit/strings.c
  function stm (line 36) | int stm(char *u, char *v, int k) { return((strncmp(u,v,k)==0)); }
  function ct_match (line 38) | int ct_match(z1, z2)
  function pmatch (line 48) | int pmatch(z, strings, vals, n, def)
  function matchrt (line 64) | int matchrt(z,i,i2,op,cl)
  function matchlf (line 85) | int matchlf(z,i1,i,op,cl)
  function checkltor (line 106) | int checkltor(z,i1,i2,c)
  function checkrtol (line 122) | int checkrtol(z,i1,i2,c)
  function strip (line 137) | void strip(z)

FILE: src/locfit/vari.cpp
  function cleardb (line 34) | void cleardb()
  function initdb (line 47) | void initdb() /* initialize locfit's work space */
  function INT (line 76) | INT vbytes(int n, int mode)
  function vitem (line 103) | double vitem(vari* v, int i)
  function vassn (line 126) | void vassn(vari* v, int i, double x)
  function vari (line 131) | vari *growvar(vari* vold, int n)
  function setvarname (line 169) | void setvarname(vari* v, varname name)
  function vari (line 183) | vari *findvar(varname name, int err, int* n)
  function deletevar (line 219) | void deletevar(vari* v) /* delete variable, or top variable if NULL */
  function deleteifhidden (line 239) | void deleteifhidden(vari* v)
  function deletename (line 246) | void deletename(varname name) /* delete variable name, or top variable i...
  function vari (line 254) | vari *createvar(varname name, int status, int n, int mode)

FILE: src/locfit/wdiag.c
  function nnresproj (line 21) | void nnresproj(lf,des,u,m,p,mi)
  function wdexpand (line 38) | void wdexpand(l,n,ind,m)
  function INT (line 59) | INT wdiagp(lf,des,lx,deg,ty,exp)
  function INT (line 98) | INT wdiag(lf,des,lx,deg,ty,exp)
  function INT (line 224) | INT procvhatm(des,lf,v)
  function cwdiag (line 241) | void cwdiag(v)

FILE: src/locfit/weight.c
  function W (line 14) | double W(u,ker)
  function INT (line 43) | INT iscompact(ker)
  function weightprod (line 49) | double weightprod(lf,u,h)
  function weightsph (line 80) | double weightsph(lf,u,h,hasdi,di)
  function weight (line 97) | double weight(lf,x,t,h,hasdi,di)
  function sgn (line 112) | double sgn(x)
  function WdW (line 119) | double WdW(u,ker) /* W'(u)/W(u) */
  function weightd (line 143) | double weightd(u,sc,d,ker,kt,h,sty,di)
  function weightdd (line 159) | double weightdd(u,sc,d,ker,kt,h,sty,di,i0,i1)
  function Wd (line 174) | double Wd(u,ker)
  function Wdd (line 195) | double Wdd(u,ker)
  function wint (line 217) | double wint(d,j,nj,ker)
  function INT (line 258) | INT wtaylor(f,x,ker)
  function Wconv (line 331) | double Wconv(v,ker)
  function Wconv1 (line 359) | double Wconv1(v,ker)
  function Wconv4 (line 384) | double Wconv4(v,ker)
  function Wconv5 (line 400) | double Wconv5(v,ker) /* (d/dv)^5 int W(x)W(x+v)dx */
  function Wconv6 (line 416) | double Wconv6(v,ker)
  function Wikk (line 435) | double Wikk(ker,deg)

FILE: src/matching_merge.cpp
  function find_path (line 15) | void find_path(const DAG& bundle_dag,
  function extend_chains_to_paths (line 49) | void extend_chains_to_paths(const DAG& bundle_dag,
  function make_scaffolds_from_paths (line 78) | void make_scaffolds_from_paths(DAG& bundle_dag,

FILE: src/matching_merge.h
  type lemon (line 24) | typedef lemon::SmartBpUGraph ReachGraph;

FILE: src/multireads.cpp
  function MultiHit (line 19) | MultiHit* MultiRead::get_hit(RefID r_id, int left, int right)
  function MultiRead (line 61) | MultiRead* MultiReadTable::get_read(InsertID mr_id)

FILE: src/multireads.h
  type RefID (line 6) | typedef uint64_t RefID;
  type InsertID (line 7) | typedef uint64_t InsertID;
  type MultiHit (line 9) | struct MultiHit
  function class (line 22) | class MultiRead
  function num_hits (line 41) | size_t num_hits() { return (int)_hits.size(); }
  function class (line 49) | class MultiReadTable

FILE: src/negative_binomial_distribution.h
  type RealType (line 40) | typedef RealType input_type;
  function class (line 42) | class param_type {
  function param (line 151) | void param(const param_type& parm)
  function reset (line 161) | void reset() { }

FILE: src/progressbar.h
  function class (line 11) | class ProgressBar
  function update (line 49) | void update(const char* bundle_label_buf, double inc_amt)
  function remaining (line 75) | void remaining(int num_remaining)
  function complete (line 97) | void complete()

FILE: src/replicates.cpp
  function transform_counts_to_common_scale (line 297) | void transform_counts_to_common_scale(const vector<double>& scale_factors,
  function calc_geometric_scaling_factors (line 312) | void calc_geometric_scaling_factors(const vector<LocusCountList>& sample...
  function calc_classic_fpkm_scaling_factors (line 354) | void calc_classic_fpkm_scaling_factors(const vector<LocusCountList>& sam...
  function calc_quartile_scaling_factors (line 392) | void calc_quartile_scaling_factors(const vector<LocusCountList>& sample_...
  function calc_tmm_scaling_factors (line 445) | void calc_tmm_scaling_factors(const vector<LocusCountList>& sample_compa...
  type SCVInterpolator (line 453) | struct SCVInterpolator
    method add_scv_pair (line 455) | void add_scv_pair(double est_scv, double true_scv)
    method finalize (line 461) | void finalize()
    method interpolate_scv (line 473) | double interpolate_scv(double est_scv)
  function build_scv_correction_fit (line 587) | void build_scv_correction_fit(int nreps, int ngenes, int mean_count, SCV...
  function calculate_count_means_and_vars (line 729) | void calculate_count_means_and_vars(const vector<LocusCountList>& sample...
  function fit_dispersion_model_helper (line 757) | boost::shared_ptr<MassDispersionModel>
  function fit_dispersion_model (line 886) | boost::shared_ptr<MassDispersionModel>
  function build_norm_table (line 926) | void build_norm_table(const vector<LocusCountList>& full_count_table,
  function normalize_counts (line 980) | void normalize_counts(vector<boost::shared_ptr<ReadGroupProperties> > & ...

FILE: src/replicates.h
  function class (line 15) | class MassDispersionModel
  function class (line 79) | class PoissonDispersionModel : public MassDispersionModel
  function class (line 95) | class MleErrorModel
  type LocusCountList (line 117) | struct LocusCountList
  function class (line 153) | class ReplicatedBundleFactory
  function set_mask_rnas (line 456) | void set_mask_rnas(const vector<boost::shared_ptr<Scaffold> >& mRNAs)
  function mass_dispersion_model (line 469) | void mass_dispersion_model(boost::shared_ptr<MassDispersionModel const> ...
  function mle_error_model (line 485) | void mle_error_model(boost::shared_ptr<MleErrorModel const> mle_model)

FILE: src/rounding.h
  function namespace (line 57) | namespace rounding

FILE: src/sampling.cpp
  function generate_importance_samples (line 14) | void generate_importance_samples(multinormal_generator<double>& generator,

FILE: src/sampling.h
  function namespace (line 44) | namespace boost { namespace numeric { namespace ublas {
  type permutation_matrix (line 169) | typedef permutation_matrix<std::size_t> pmatrix;
  type boost (line 206) | typedef boost::mt19937 base_generator_type;
  type boost (line 207) | typedef boost::normal_distribution<> distribution_type;
  function boost (line 225) | const boost::numeric::ublas::vector<ValueType>& next_rand()
  function set_parameters (line 251) | void set_parameters(const boost::numeric::ublas::vector<ValueType>& mean,

FILE: src/scaffold_graph.cpp
  type HitBufBasket (line 24) | struct HitBufBasket
    method HitBufBasket (line 26) | HitBufBasket(int coord, Scaffold* h, DAGNode d)
  function right_lt (line 35) | bool right_lt (const HitBufBasket& lhs,
  type Expired (line 41) | struct Expired
    method Expired (line 43) | Expired(int ec) : expiration_coord(ec) {}
  type ConnectState (line 52) | enum ConnectState { UNKNOWN, CONNECT, DONT_CONNECT }
  type connect_visitor (line 55) | struct connect_visitor
    method connect_visitor (line 59) | connect_visitor(CompatibilityMap compatibility, ConnectMap connect, DA...
  function record_connections (line 98) | connect_visitor<CompatibilityMap, ConnectMap, Tag>
  function create_overlap_dag (line 108) | bool create_overlap_dag(vector<Scaffold>& hits,
  function add_terminal_nodes (line 246) | pair<DAGNode, DAGNode> add_terminal_nodes(DAG& bundle_dag)

FILE: src/scaffold_graph.h
  type boost (line 27) | typedef boost::adjacency_list<boost::vecS,
  type boost (line 32) | typedef boost::graph_traits<DAG>::vertex_descriptor DAGNode;
  type boost (line 34) | typedef boost::property_map<DAG, boost::vertex_name_t>::type HitsForNode...

FILE: src/scaffolds.cpp
  function disjoint_ops (line 93) | void disjoint_ops(vector<AugmentedCuffOp>& to_reduce)
  function record_gaps (line 120) | void record_gaps(const vector<AugmentedCuffOp>& to_fill,
  function is_known (line 424) | bool is_known(const AugmentedCuffOp& op)
  function check_merge_length (line 431) | bool check_merge_length(const vector<AugmentedCuffOp>& ops)
  function has_intron (line 455) | inline bool has_intron(const Scaffold& scaff)
  function BOOST_FOREACH (line 822) | BOOST_FOREACH (const Scaffold& sc, s)
  function BOOST_FOREACH (line 877) | BOOST_FOREACH(const AugmentedCuffOp& op, orig_ops)
  function BOOST_FOREACH (line 894) | BOOST_FOREACH (const AugmentedCuffOp& op, padded_filler)
  function intron_op (line 962) | bool intron_op(const AugmentedCuffOp& op)
  function overlap_in_genome (line 1102) | bool overlap_in_genome(int ll, int lr, int rl, int rr)
  function BOOST_FOREACH (line 1676) | BOOST_FOREACH(const MateHit* h, mate_hits())
  function BOOST_FOREACH (line 1700) | BOOST_FOREACH (const MateHit* h, mate_hits())
  function BOOST_FOREACH (line 1710) | BOOST_FOREACH (boost::shared_ptr<Scaffold const> ref_scaff, *ref_scaffs)
  function BOOST_FOREACH (line 1735) | BOOST_FOREACH(const MateHit* h, _mates_in_scaff)
  function BOOST_FOREACH (line 1746) | BOOST_FOREACH (AugmentedCuffOp a, _augmented_ops)
  function BOOST_FOREACH (line 1757) | BOOST_FOREACH(const AugmentedCuffOp& a, hit_introns)
  function BOOST_FOREACH (line 1763) | BOOST_FOREACH(const AugmentedCuffOp& a, scaffold_introns)
  function BOOST_FOREACH (line 1776) | BOOST_FOREACH (AugmentedCuffOp a, _augmented_ops)
  function scaff_lt (line 1787) | bool scaff_lt(const Scaffold& lhs, const Scaffold& rhs)
  function scaff_lt_rt (line 1792) | bool scaff_lt_rt(const Scaffold& lhs, const Scaffold& rhs)
  function scaff_lt_rt_oplt (line 1799) | bool scaff_lt_rt_oplt(const Scaffold& lhs, const Scaffold& rhs)
  function scaff_lt_sp (line 1824) | bool scaff_lt_sp(boost::shared_ptr<Scaffold> lhs, boost::shared_ptr<Scaf...
  function scaff_lt_rt_sp (line 1829) | bool scaff_lt_rt_sp(boost::shared_ptr<Scaffold> lhs, boost::shared_ptr<S...
  function scaff_lt_rt_oplt_sp (line 1834) | bool scaff_lt_rt_oplt_sp(boost::shared_ptr<Scaffold> lhs, boost::shared_...

FILE: src/scaffolds.h
  type CuffOpCode (line 26) | enum CuffOpCode { CUFF_MATCH, CUFF_INTRON, CUFF_UNKNOWN }
  function g_left (line 28) | struct AugmentedCuffOp
  function g_right (line 46) | void g_right(int right)
  function overlap_in_genome (line 52) | static bool overlap_in_genome(const AugmentedCuffOp& lhs,
  function contains (line 66) | bool contains(const AugmentedCuffOp& other) const
  function properly_contains (line 73) | bool properly_contains(const AugmentedCuffOp& other) const
  function match_length (line 81) | static int match_length(const AugmentedCuffOp& op, int left, int right)
  function class (line 159) | class Scaffold
  function vector (line 349) | const vector<const MateHit*>& mate_hits() const { return _mates_in_scaff; }
  function annotated_trans_id (line 355) | void annotated_trans_id(const string& ann_name) { _annotated_trans_id = ...
  function annotated_gene_id (line 358) | void annotated_gene_id(const string& ann_name) { _annotated_gene_id = an...
  function annotated_gene_name (line 361) | void annotated_gene_name(const string& ann_name) { _annotated_gene_name ...
  function annotated_protein_id (line 364) | void annotated_protein_id(const string& ann_name) { _annotated_protein_i...
  function annotated_tss_id (line 367) | void annotated_tss_id(const string& ann_name) { _annotated_tss_id = ann_...
  function nearest_ref_id (line 370) | void nearest_ref_id(const string& ann_name) { _nearest_ref_id = ann_name; }
  function fpkm (line 375) | void fpkm(double fpkm) { _fpkm = fpkm; }
  function num_fragments (line 378) | void num_fragments(double nf) { _num_fragments = nf; }
  function seq (line 381) | void seq(const string& s) {	_seq = s; }
  function nearest_ref_classcode (line 399) | void nearest_ref_classcode(char cc) { _classcode = cc; }
  function internal_exon_coverage (line 405) | double internal_exon_coverage() const;
  function is_ref (line 419) | void is_ref(bool ir) { _is_ref = ir; }
  function is_pseudo_primary (line 422) | void is_pseudo_primary(bool ip) { _is_pseudo_primary = ip; }
  function strand (line 429) | void strand(CuffStrand strand)
  type vector (line 655) | typedef vector<AugmentedCuffOp> OpList;
  type StructurallyEqualScaffolds (line 699) | struct StructurallyEqualScaffolds

FILE: src/tokenize.cpp
  function tokenize (line 15) | void tokenize(const string& s, const string& delims, vector<string>& ss) {
  function tokenize_strict (line 29) | void tokenize_strict(const string& s, const string& delims, vector<strin...

FILE: src/tracking.cpp
  function add_to_tracking_table (line 3) | void add_to_tracking_table(size_t sample_index,

FILE: src/tracking.h
  type TrackingInfoPerRep (line 3) | struct TrackingInfoPerRep
  type FPKMContext (line 11) | struct FPKMContext
  type FPKMTracking (line 81) | struct FPKMTracking
  type map (line 98) | typedef map<string,  FPKMTracking> FPKMTrackingTable;
  type Tracking (line 100) | struct Tracking

FILE: src/transitive_closure.h
  type v_id_size_type (line 37) | typedef uint16_t v_id_size_type;
  function union_successor_sets (line 39) | inline void
  type typename (line 82) | typedef typename boost::graph_traits < Graph >::vertex_descriptor vertex;
  type typename (line 83) | typedef typename boost::graph_traits < Graph >::edge_descriptor edge;
  type typename (line 84) | typedef typename boost::graph_traits < Graph >::vertex_iterator vertex_i...
  type typename (line 87) | typedef typename boost::graph_traits <
  type v_id_size_type (line 97) | typedef v_id_size_type cg_vertex;
  type std (line 115) | typedef std::vector<std::vector<cg_vertex> > CG_t;
  type typename (line 224) | typedef typename boost::graph_traits < GraphTC >::vertex_descriptor tc_v...
  type typename (line 274) | typedef typename boost::property_map<Graph, boost::vertex_index_t>::cons...
  type typename (line 278) | typedef typename boost::graph_traits<GraphTC>::vertex_descriptor tc_vertex;
  type typename (line 293) | typedef typename boost::graph_traits < GraphTC >::vertex_descriptor tc_v...
  type typename (line 321) | typedef typename boost::graph_traits < G >::vertex_descriptor vertex;
  type typename (line 322) | typedef typename boost::graph_traits < G >::vertex_iterator vertex_itera...
  type typename (line 347) | typedef typename boost::graph_traits < G >::vertex_descriptor vertex;
  type typename (line 348) | typedef typename boost::graph_traits < G >::vertex_iterator vertex_itera...

FILE: src/transitive_reduction.h
  function namespace (line 31) | namespace boost {

FILE: src/update_check.h
  function AlarmHandler (line 20) | static void AlarmHandler(int sig)
  function error (line 25) | bool error(const char *msg)
  function parse_version_str (line 30) | int parse_version_str(char* version_str)
  function get_current_version (line 41) | bool get_current_version(char* curr_version)
  function check_version (line 97) | void check_version(const char* this_version)

FILE: tests/unit_tests/test_main.cpp
  class CustomFormatter (line 32) | class CustomFormatter : public Outputter
  function CustomFormatter (line 141) | CustomFormatter* CustomFormatter::defaultOutputter( TestResultCollector ...
  function main (line 306) | int main(int argc, char* argv[])

FILE: tests/unit_tests/test_scaffolds.cpp
  class AugmentedCuffOpTests (line 17) | class AugmentedCuffOpTests : public CppUnit::TestFixture