SYMBOL INDEX (221 symbols across 17 files)

FILE: D.cpp
  type option (line 41) | struct option
  type opt (line 49) | namespace opt
  function doAbbaBaba (line 63) | void doAbbaBaba() {
  function abbaBabaMain (line 250) | int abbaBabaMain(int argc, char** argv) {
  function parseAbbaBabaOptions (line 317) | void parseAbbaBabaOptions(int argc, char** argv) {

FILE: D.h
  function class (line 13) | class TestTrioInfo {

FILE: Dmin.cpp
  type option (line 51) | struct option
  type opt (line 68) | namespace opt
  function DminMain (line 89) | int DminMain(int argc, char** argv) {
  function parseDminOptions (line 586) | void parseDminOptions(int argc, char** argv) {

FILE: Dmin_combine.cpp
  type option (line 34) | struct option
  type opt (line 43) | namespace opt
  function DminCombineMain (line 54) | int DminCombineMain(int argc, char** argv) {
  function parseDminCombineOptions (line 231) | void parseDminCombineOptions(int argc, char** argv) {

FILE: Dquartets.cpp
  type option (line 40) | struct option
  type opt (line 53) | namespace opt
  function DquartetsMain (line 70) | int DquartetsMain(int argc, char** argv) {
  function parseDquartetsOptions (line 442) | void parseDquartetsOptions(int argc, char** argv) {

FILE: Dsuite.cpp
  function main (line 42) | int main(int argc, char **argv) {

FILE: Dsuite_common.cpp
  function string (line 46) | string makeHeader(bool quartet, bool includeFstats, bool includeKSstats) {
  function string (line 55) | string prepareOutFileRootString(const string& providedPrefix, const stri...
  function printMissingLikelihoodsWarning (line 62) | void printMissingLikelihoodsWarning(const string& chr, const string& pos) {
  function duplicateTreeValueError (line 67) | void duplicateTreeValueError(const string& duplicate) {
  function printInitialMessageTriosQuartets (line 73) | void printInitialMessageTriosQuartets(const int regionLengthOpt, const i...
  function assignTreeLevelsAndLinkToTaxa (line 79) | void assignTreeLevelsAndLinkToTaxa(string& treeLine, std::map<string,std...
  function assignNumLinesToAnalyse (line 124) | int assignNumLinesToAnalyse(const int providedNumLinesOpt, const int reg...

FILE: Dsuite_common.h
  function notEnoughPopulationsError (line 30) | inline void notEnoughPopulationsError(const int minPopulations) {
  function outgroupNeededError (line 35) | inline void outgroupNeededError(const string& setsFileName) {
  function outgroupNotUsedInQuartetsWarning (line 40) | inline void outgroupNotUsedInQuartetsWarning(const string& setsFileName) {
  function wrongNumberOfColumnsError (line 44) | inline void wrongNumberOfColumnsError(const string& setsFileName, int li...
  function lineEmptyError (line 50) | inline void lineEmptyError(const string& setsFileName, int lineNum) {
  function class (line 56) | class SetInformation {
  function reportProgessVCF (line 114) | inline void reportProgessVCF(const int variantsProcessed, const std::clo...
  function reportProgessVCF (line 119) | inline void reportProgessVCF(const int variantsProcessed, const int VCFl...

FILE: Dsuite_fBranch.cpp
  type option (line 35) | struct option
  type opt (line 43) | namespace opt
  function fBranchMain (line 53) | int fBranchMain(int argc, char** argv) {
  function parseFbranchOptions (line 182) | void parseFbranchOptions(int argc, char** argv) {

FILE: Dsuite_fBranch.h
  function class (line 20) | class Branch {
  function class (line 58) | class Tree {

FILE: Dsuite_utils.cpp
  function normalCDF (line 10) | long double normalCDF(double x) // Phi(-∞, x) aka N(x)
  function Fd_Denom_perVariant (line 15) | double Fd_Denom_perVariant(double p1, double p2, double p3, double pO) {
  function fG_Denom_perVariant (line 22) | double fG_Denom_perVariant(double p1, double p3a, double p3b, double pO) {
  function f4_perVariant (line 28) | double f4_perVariant(double p1, double p2, double p3, double p4) {
  function FdM_Denom_perVariant (line 33) | double FdM_Denom_perVariant(double p1, double p2, double p3, double pO) {
  function getExpectedGenotype (line 109) | double getExpectedGenotype(const std::vector<double>& thisProbabilities) {
  function transformFromPhred (line 114) | void transformFromPhred(std::vector<double>& thisLikelihoods) {
  function transformFromGL (line 121) | void transformFromGL(std::vector<double>& thisLikelihoods) {
  function calculateOneDs (line 626) | double calculateOneDs(double ABBAtotal, double BABAtotal) {
  function stringToDouble (line 651) | double stringToDouble(std::string s) {
  function stripExtension (line 660) | std::string stripExtension(const std::string& filename)
  function split (line 670) | void split(const std::string &s, char delim, std::vector<std::string> &e...
  function split (line 678) | std::vector<std::string> split(const std::string &s, char delim) {
  function splitToDouble (line 685) | void splitToDouble(const std::string &s, char delim, std::vector<double>...
  function splitToDouble (line 693) | std::vector<double> splitToDouble(const std::string &s, char delim) {
  function split2 (line 699) | std::vector<std::string> split2(std::string s, string delim) {
  function locateSet (line 713) | std::vector<size_t> locateSet(const std::vector<std::string>& sample_nam...
  function suffix (line 730) | std::string suffix(const std::string& seq, size_t len)
  function isGzip (line 737) | bool isGzip(const std::string& filename)
  function assertFileOpen (line 750) | void assertFileOpen(std::ifstream& fh, const std::string& fn)
  function assertFileOpen (line 759) | void assertFileOpen(std::ofstream& fh, const std::string& fn)
  function assertGZOpen (line 769) | void assertGZOpen(gzstreambase& gh, const std::string& fn)
  function checkGenotypesExist (line 778) | void checkGenotypesExist(const std::vector<std::string>& fields, const i...
  function file_exists (line 823) | bool file_exists(const std::string& name) {
  function assignSplits01FromAlleleFrequency (line 829) | void assignSplits01FromAlleleFrequency(const double p, double& splitA, d...

FILE: Dsuite_utils.h
  function string (line 93) | string numToString(T i) {
  function class (line 102) | class median_of_empty_list_exception:public std::exception{
  function copy_except (line 162) | inline void copy_except(int i, std::vector<double>& inVec, std::vector<d...
  function nChoosek (line 169) | inline unsigned nChoosek( unsigned n, unsigned k )
  function class (line 206) | class GeneralSetCounts {
  function class (line 269) | class GeneralSetCountsWithSplits : public GeneralSetCounts {
  function class (line 321) | class TrioDinfo {
  function addRegionDs (line 622) | void addRegionDs(const int arrangement) {
  function class (line 644) | class QuartetDinfo: public TrioDinfo {

FILE: KolmogorovSmirnovDist.cpp
  function log1p (line 63) | double log1p(double x)
  function getLogFactorial (line 155) | static double getLogFactorial (int n)
  function DeleteMatrixD (line 187) | static void DeleteMatrixD (double **T)
  function KSPlusbarAsymp (line 196) | static double KSPlusbarAsymp (int n, double x)
  function KSPlusbarUpper (line 214) | static double KSPlusbarUpper (int n, double x)
  function Pelz (line 280) | static double Pelz (int n, double x)
  function CalcFloorCeil (line 383) | static void CalcFloorCeil (
  function Pomeranz (line 442) | static double Pomeranz (int n, double x)
  function cdfSpecial (line 560) | static double cdfSpecial (int n, double x)
  function KScdf (line 595) | double KScdf (int n, double x)
  function fbarSpecial (line 620) | static double fbarSpecial (int n, double x)
  function KSfbar (line 651) | double KSfbar (int n, double x)
  function DurbinMatrix (line 708) | static double DurbinMatrix (int n, double d)
  function mMultiply (line 757) | static void mMultiply (double *A, double *B, double *C, int m)
  function renormalize (line 771) | static void renormalize (double *V, int m, int *p)
  function mPower (line 780) | static void mPower (double *A, int eA, double *V, int *eV, int m, int n)
  function main (line 816) | int main(void)

FILE: gzstream.cpp
  type GZSTREAM_NAMESPACE (line 41) | namespace GZSTREAM_NAMESPACE {
    function gzstreambuf (line 52) | gzstreambuf* gzstreambuf::open( const char* name, int open_mode) {
    function gzstreambuf (line 75) | gzstreambuf * gzstreambuf::close() {

FILE: gzstream.h
  function class (line 50) | class gzstreambuf : public std::streambuf {
  function class (line 79) | class gzstreambase : virtual public std::ios {

FILE: kstest.cpp
  function mMultiply (line 246) | void mMultiply(double *A,double *B,double *C,int m)
  function mPower (line 253) | void mPower(double *A,int eA,double *V,int *eV,int m,int n)
  function K (line 266) | double K(int n,double d)
  function ks_test (line 338) | double ks_test (std::list<int64_t> sample1, std::list<int64_t> sample2,
  function ks_test_of_uniformity (line 475) | double ks_test_of_uniformity(std::vector<double> sampleVect0to1, std::os...

FILE: utils/dtools.py
  function set_float_format (line 72) | def set_float_format(formatter):
  function format_node (line 140) | def format_node(node, node_type, format, dist_formatter=None,
  function print_supported_formats (line 204) | def print_supported_formats():
  class NewickError (line 213) | class NewickError(Exception):
    method __init__ (line 216) | def __init__(self, value):
  function read_newick (line 223) | def read_newick(newick, root_node=None, format=0, quoted_names=False):
  function _read_newick_from_string (line 264) | def _read_newick_from_string(nw, root_node, matcher, formatcode, quoted_...
  function _parse_extra_features (line 346) | def _parse_extra_features(node, NHX_string):
  function compile_matchers (line 359) | def compile_matchers(formatcode):
  function _read_node_data (line 403) | def _read_node_data(subnw, current_node, node_type, matcher, formatcode):
  function write_newick (line 444) | def write_newick(rootnode, features=None, format=1, format_root_node=True,
  function _get_features_string (line 479) | def _get_features_string(self, features=None):
  class TreeError (line 524) | class TreeError(Exception):
    method __init__ (line 529) | def __init__(self, value=''):
    method __str__ (line 532) | def __str__(self):
  class TreeNode (line 536) | class TreeNode(object):
    method _get_dist (line 577) | def _get_dist(self):
    method _set_dist (line 580) | def _set_dist(self, value):
    method _get_support (line 586) | def _get_support(self):
    method _set_support (line 589) | def _set_support(self, value):
    method _get_up (line 595) | def _get_up(self):
    method _set_up (line 598) | def _set_up(self, value):
    method _get_children (line 604) | def _get_children(self):
    method _set_children (line 607) | def _set_children(self, value):
    method _get_style (line 614) | def _get_style(self):
    method _set_style (line 620) | def _set_style(self, value):
    method _set_face_areas (line 635) | def _set_face_areas(self, value):
    method _get_face_areas (line 641) | def _get_face_areas(self):
    method __init__ (line 649) | def __init__(self, newick=None, format=0, dist=None, support=None,
    method __nonzero__ (line 672) | def __nonzero__(self):
    method __bool__ (line 675) | def __bool__(self):
    method __repr__ (line 683) | def __repr__(self):
    method __and__ (line 686) | def __and__(self, value):
    method __add__ (line 696) | def __add__(self, value):
    method __str__ (line 707) | def __str__(self):
    method __contains__ (line 712) | def __contains__(self, item):
    method __len__ (line 720) | def __len__(self):
    method __iter__ (line 724) | def __iter__(self):
    method add_feature (line 728) | def add_feature(self, pr_name, pr_value):
    method add_features (line 735) | def add_features(self, **features):
    method del_feature (line 742) | def del_feature(self, pr_name):
    method add_child (line 751) | def add_child(self, child=None, name=None, dist=None, support=None):
    method remove_child (line 778) | def remove_child(self, child):
    method add_sister (line 791) | def add_sister(self, sister=None, name=None, dist=None):
    method remove_sister (line 802) | def remove_sister(self, sister=None):
    method delete (line 820) | def delete(self, prevent_nondicotomic=True, preserve_branch_length=Fal...
    method detach (line 874) | def detach(self):
    method prune (line 889) | def prune(self, nodes, preserve_branch_length=False):
    method swap_children (line 1026) | def swap_children(self):
    method get_children (line 1037) | def get_children(self):
    method get_sisters (line 1043) | def get_sisters(self):
    method iter_leaves (line 1052) | def iter_leaves(self, is_leaf_fn=None):
    method get_leaves (line 1067) | def get_leaves(self, is_leaf_fn=None):
    method iter_leaf_names (line 1076) | def iter_leaf_names(self, is_leaf_fn=None):
    method get_leaf_names (line 1086) | def get_leaf_names(self, is_leaf_fn=None):
    method iter_descendants (line 1096) | def iter_descendants(self, strategy="levelorder", is_leaf_fn=None):
    method get_descendants (line 1107) | def get_descendants(self, strategy="levelorder", is_leaf_fn=None):
    method traverse (line 1117) | def traverse(self, strategy="levelorder", is_leaf_fn=None):
    method iter_prepostorder (line 1143) | def iter_prepostorder(self, is_leaf_fn=None):
    method _iter_descendants_postorder (line 1170) | def _iter_descendants_postorder(self, is_leaf_fn=None):
    method _iter_descendants_levelorder (line 1192) | def _iter_descendants_levelorder(self, is_leaf_fn=None):
    method _iter_descendants_preorder (line 1203) | def _iter_descendants_preorder(self, is_leaf_fn=None):
    method iter_ancestors (line 1218) | def iter_ancestors(self):
    method get_ancestors (line 1230) | def get_ancestors(self):
    method describe (line 1239) | def describe(self):
    method write (line 1258) | def write(self, features=None, outfile=None, format=0, is_leaf_fn=None,
    method get_tree_root (line 1306) | def get_tree_root(self):
    method get_common_ancestor (line 1315) | def get_common_ancestor(self, *target_nodes, **kargs):
    method iter_search_nodes (line 1377) | def iter_search_nodes(self, **conditions):
    method search_nodes (line 1393) | def search_nodes(self, **conditions):
    method get_leaves_by_name (line 1409) | def get_leaves_by_name(self, name):
    method is_leaf (line 1415) | def is_leaf(self):
    method is_root (line 1421) | def is_root(self):
    method get_distance (line 1433) | def get_distance(self, target, target2=None, topology_only=False):
    method get_farthest_node (line 1475) | def get_farthest_node(self, topology_only=False):
    method _get_farthest_and_closest_leaves (line 1518) | def _get_farthest_and_closest_leaves(self, topology_only=False, is_lea...
    method get_farthest_leaf (line 1546) | def get_farthest_leaf(self, topology_only=False, is_leaf_fn=None):
    method get_closest_leaf (line 1563) | def get_closest_leaf(self, topology_only=False, is_leaf_fn=None):
    method get_midpoint_outgroup (line 1581) | def get_midpoint_outgroup(self):
    method populate (line 1603) | def populate(self, size, names_library=None, reuse_names=False,
    method set_outgroup (line 1677) | def set_outgroup(self, outgroup):
    method unroot (line 1762) | def unroot(self):
    method _asciiArt (line 1830) | def _asciiArt(self, char1='-', show_internal=True, compact=False, attr...
    method get_ascii (line 1874) | def get_ascii(self, show_internal=True, compact=False, attributes=None):
    method ladderize (line 1889) | def ladderize(self, direction=0):
    method sort_descendants (line 1947) | def sort_descendants(self, attr="name"):
    method get_cached_content (line 1968) | def get_cached_content(self, store_attr=None, container_type=set, leav...
    method robinson_foulds (line 2029) | def robinson_foulds(self, t2, attr_t1="name", attr_t2="name",
    method compare (line 2200) | def compare(self, ref_tree, use_collateral=False, min_support_source=0...
    method _diff (line 2365) | def _diff(self, t2, output='topology', attr_t1='name', attr_t2='name',...
    method iter_edges (line 2388) | def iter_edges(self, cached_content=None):
    method get_edges (line 2403) | def get_edges(self, cached_content=None):
    method standardize (line 2414) | def standardize(self, delete_orphan=True, preserve_branch_length=True):
    method convert_to_ultrametric (line 2483) | def convert_to_ultrametric(self, tree_length=None, strategy='balanced'):
    method check_monophyly (line 2527) | def check_monophyly(self, values, target_attr, ignore_missing=False,
    method get_monophyletic (line 2622) | def get_monophyletic(self, values, target_attr):
    method expand_polytomies (line 2650) | def expand_polytomies(self, map_attr="name", polytomy_size_limit=5,
    method resolve_polytomy (line 2714) | def resolve_polytomy(self, default_dist=0.0, default_support=0.0,
    method add_face (line 2757) | def add_face(self, face, column, position="branch-right"):
    method from_parent_child_table (line 2785) | def from_parent_child_table(parent_child_table):
    method from_skbio (line 2826) | def from_skbio(skbio_tree, map_attributes=None):
    method phonehome (line 2866) | def phonehome(self):
  function _translate_nodes (line 2871) | def _translate_nodes(root, *nodes):
  class HsTree (line 2899) | class HsTree(TreeNode):
    method __init__ (line 2902) | def __init__(tree, *args, **kwa):
    method get_time (line 2937) | def get_time(node):
    method get_name (line 2942) | def get_name(tree):
    method write (line 2951) | def write(tree, **kwa):
    method add_mass_migration (line 2977) | def add_mass_migration(tree, source, destination, fraction, time):
    method add_property_to_nodes (line 2991) | def add_property_to_nodes(tree, property_name, property_node_dict):
    method add_properties_to_nodes (line 3031) | def add_properties_to_nodes(tree, properties, properties_node_dict):
    method get_nodes_at_time (line 3066) | def get_nodes_at_time(tree, time):
    method plot (line 3078) | def plot(tree, ax=None, style='orthogonal',
    method search_node_by_newick (line 3395) | def search_node_by_newick(tree, newick):
    method set_leaf_order (line 3401) | def set_leaf_order(tree, order, check_consistent=True):
    method set_outgroup (line 3430) | def set_outgroup(tree, outgroup, end_at_present=True):
    method reverse (line 3448) | def reverse(tree):
  function align_fbranch_with_tree (line 3454) | def align_fbranch_with_tree(fbranch, tree, outgroup, ladderize=False):
  function plot_fbranch (line 3487) | def plot_fbranch(fbranch, tree_no_outgroup, leaves_to_present=True,
  function main (line 3589) | def main():