SYMBOL INDEX (170 symbols across 12 files)

FILE: gflags.py
  function bool (line 323) | def bool(x):
  function _GetCallingModule (line 333) | def _GetCallingModule():
  class FlagsError (line 349) | class FlagsError(Exception):
  class DuplicateFlag (line 354) | class DuplicateFlag(FlagsError):
  class DuplicateFlagError (line 362) | class DuplicateFlagError(DuplicateFlag):
    method __init__ (line 364) | def __init__(self, flagname, flag_values):
  class IllegalFlagValue (line 377) | class IllegalFlagValue(FlagsError):
  class UnrecognizedFlag (line 382) | class UnrecognizedFlag(FlagsError):
  class UnrecognizedFlagError (line 390) | class UnrecognizedFlagError(UnrecognizedFlag):
    method __init__ (line 391) | def __init__(self, flagname):
  function GetHelpWidth (line 402) | def GetHelpWidth():
  function CutCommonSpacePrefix (line 407) | def CutCommonSpacePrefix(text):
  function TextWrap (line 450) | def TextWrap(text, length=None, indent='', firstline_indent=None, tabs='...
  function DocToHelp (line 563) | def DocToHelp(doc):
  function __GetModuleName (line 589) | def __GetModuleName(globals_dict):
  function _GetMainModule (line 608) | def _GetMainModule():
  class FlagValues (line 618) | class FlagValues:
    method __init__ (line 651) | def __init__(self):
    method FlagDict (line 664) | def FlagDict(self):
    method FlagsByModuleDict (line 667) | def FlagsByModuleDict(self):
    method KeyFlagsByModuleDict (line 676) | def KeyFlagsByModuleDict(self):
    method _RegisterFlagByModule (line 685) | def _RegisterFlagByModule(self, module_name, flag):
    method _RegisterKeyFlagForModule (line 698) | def _RegisterKeyFlagForModule(self, module_name, flag):
    method _GetFlagsDefinedByModule (line 712) | def _GetFlagsDefinedByModule(self, module):
    method _GetKeyFlagsForModule (line 728) | def _GetKeyFlagsForModule(self, module):
    method AppendFlagValues (line 753) | def AppendFlagValues(self, flag_values):
    method __setitem__ (line 768) | def __setitem__(self, name, flag):
    method __getitem__ (line 792) | def __getitem__(self, name):
    method __getattr__ (line 796) | def __getattr__(self, name):
    method __setattr__ (line 803) | def __setattr__(self, name, value):
    method _FlagIsRegistered (line 809) | def _FlagIsRegistered(self, flag_obj):
    method __delattr__ (line 838) | def __delattr__(self, flag_name):
    method __RemoveFlagFromDictByModule (line 871) | def __RemoveFlagFromDictByModule(self, flags_by_module_dict, flag_obj):
    method SetDefault (line 885) | def SetDefault(self, name, value):
    method __contains__ (line 892) | def __contains__(self, name):
    method __iter__ (line 898) | def __iter__(self):
    method __call__ (line 902) | def __call__(self, argv):
    method __call2__ (line 914) | def __call2__(self, argv):
    method Reset (line 1052) | def Reset(self):
    method RegisteredFlags (line 1057) | def RegisteredFlags(self):
    method FlagValuesDict (line 1061) | def FlagValuesDict(self):
    method __str__ (line 1071) | def __str__(self):
    method GetHelp (line 1075) | def GetHelp(self, prefix=''):
    method __RenderModuleFlags (line 1106) | def __RenderModuleFlags(self, module, flags, output_lines, prefix=""):
    method __RenderOurModuleFlags (line 1111) | def __RenderOurModuleFlags(self, module, output_lines, prefix=""):
    method __RenderOurModuleKeyFlags (line 1117) | def __RenderOurModuleKeyFlags(self, module, output_lines, prefix=""):
    method MainModuleHelp (line 1130) | def MainModuleHelp(self):
    method __RenderFlagList (line 1136) | def __RenderFlagList(self, flaglist, output_lines, prefix="  "):
    method get (line 1179) | def get(self, name, default):
    method ShortestUniquePrefixes (line 1193) | def ShortestUniquePrefixes(self, fl):
    method __IsFlagFileDirective (line 1229) | def __IsFlagFileDirective(self, flag_string):
    method ExtractFilename (line 1244) | def ExtractFilename(self, flagfile_str):
    method __GetFlagFileLines (line 1258) | def __GetFlagFileLines(self, filename, parsed_file_list):
    method ReadFlagsFromFiles (line 1314) | def ReadFlagsFromFiles(self, argv):
    method FlagsIntoString (line 1369) | def FlagsIntoString(self):
    method AppendFlagsIntoFile (line 1384) | def AppendFlagsIntoFile(self, filename):
    method WriteHelpInXMLFormat (line 1396) | def WriteHelpInXMLFormat(self, outfile=None):
  function _MakeXMLSafe (line 1448) | def _MakeXMLSafe(s):
  function _WriteSimpleXMLElement (line 1461) | def _WriteSimpleXMLElement(outfile, name, value, indent):
  class Flag (line 1479) | class Flag:
    method __init__ (line 1513) | def __init__(self, parser, serializer, name, default, help_string,
    method __GetParsedValueAsString (line 1531) | def __GetParsedValueAsString(self, value):
    method Parse (line 1543) | def Parse(self, argument):
    method Unparse (line 1550) | def Unparse(self):
    method Serialize (line 1557) | def Serialize(self):
    method SetDefault (line 1570) | def SetDefault(self, value):
    method Type (line 1584) | def Type(self):
    method WriteInfoInXMLFormat (line 1591) | def WriteInfoInXMLFormat(self, outfile, module_name, is_key=False, ind...
    method _WriteCustomInfoInXMLFormat (line 1625) | def _WriteCustomInfoInXMLFormat(self, outfile, indent):
  class ArgumentParser (line 1640) | class ArgumentParser:
    method Parse (line 1653) | def Parse(self, argument):
    method Type (line 1657) | def Type(self):
    method WriteCustomInfoInXMLFormat (line 1660) | def WriteCustomInfoInXMLFormat(self, outfile, indent):
  class ArgumentSerializer (line 1664) | class ArgumentSerializer:
    method Serialize (line 1667) | def Serialize(self, value):
  class ListSerializer (line 1671) | class ListSerializer(ArgumentSerializer):
    method __init__ (line 1673) | def __init__(self, list_sep):
    method Serialize (line 1676) | def Serialize(self, value):
  function DEFINE (line 1683) | def DEFINE(parser, name, default, help, flag_values=FLAGS, serializer=None,
  function DEFINE_flag (line 1707) | def DEFINE_flag(flag, flag_values=FLAGS):
  function _InternalDeclareKeyFlags (line 1731) | def _InternalDeclareKeyFlags(flag_names, flag_values=FLAGS):
  function DECLARE_key_flag (line 1756) | def DECLARE_key_flag(flag_name, flag_values=FLAGS):
  function ADOPT_module_key_flags (line 1779) | def ADOPT_module_key_flags(module, flag_values=FLAGS):
  function DEFINE_string (line 1807) | def DEFINE_string(name, default, help, flag_values=FLAGS, **args):
  class BooleanParser (line 1819) | class BooleanParser(ArgumentParser):
    method Convert (line 1822) | def Convert(self, argument):
    method Parse (line 1838) | def Parse(self, argument):
    method Type (line 1842) | def Type(self):
  class BooleanFlag (line 1846) | class BooleanFlag(Flag):
    method __init__ (line 1859) | def __init__(self, name, default, help, short_name=None, **args):
  function DEFINE_boolean (line 1865) | def DEFINE_boolean(name, default, help, flag_values=FLAGS, **args):
  class HelpFlag (line 1881) | class HelpFlag(BooleanFlag):
    method __init__ (line 1888) | def __init__(self):
    method Parse (line 1891) | def Parse(self, arg):
  class HelpXMLFlag (line 1903) | class HelpXMLFlag(BooleanFlag):
    method __init__ (line 1906) | def __init__(self):
    method Parse (line 1911) | def Parse(self, arg):
  class HelpshortFlag (line 1917) | class HelpshortFlag(BooleanFlag):
    method __init__ (line 1925) | def __init__(self):
    method Parse (line 1928) | def Parse(self, arg):
  class FloatParser (line 1943) | class FloatParser(ArgumentParser):
    method __init__ (line 1952) | def __init__(self, lower_bound=None, upper_bound=None):
    method Convert (line 1970) | def Convert(self, argument):
    method Parse (line 1974) | def Parse(self, argument):
    method Type (line 1981) | def Type(self):
    method WriteCustomInfoInXMLFormat (line 1984) | def WriteCustomInfoInXMLFormat(self, outfile, indent):
  function DEFINE_float (line 1992) | def DEFINE_float(name, default, help, lower_bound=None, upper_bound=None,
  class IntegerParser (line 2009) | class IntegerParser(FloatParser):
    method Convert (line 2018) | def Convert(self, argument):
    method Type (line 2036) | def Type(self):
  function DEFINE_integer (line 2040) | def DEFINE_integer(name, default, help, lower_bound=None, upper_bound=None,
  class EnumParser (line 2057) | class EnumParser(ArgumentParser):
    method __init__ (line 2063) | def __init__(self, enum_values=None):
    method Parse (line 2066) | def Parse(self, argument):
    method Type (line 2072) | def Type(self):
  class EnumFlag (line 2076) | class EnumFlag(Flag):
    method __init__ (line 2079) | def __init__(self, name, default, help, enum_values=None,
    method _WriteCustomInfoInXMLFormat (line 2088) | def _WriteCustomInfoInXMLFormat(self, outfile, indent):
  function DEFINE_enum (line 2093) | def DEFINE_enum(name, default, enum_values, help, flag_values=FLAGS,
  class BaseListParser (line 2105) | class BaseListParser(ArgumentParser):
    method __init__ (line 2116) | def __init__(self, token=None, name=None):
    method Parse (line 2122) | def Parse(self, argument):
    method Type (line 2128) | def Type(self):
  class ListParser (line 2132) | class ListParser(BaseListParser):
    method __init__ (line 2135) | def __init__(self):
    method WriteCustomInfoInXMLFormat (line 2138) | def WriteCustomInfoInXMLFormat(self, outfile, indent):
  class WhitespaceSeparatedListParser (line 2143) | class WhitespaceSeparatedListParser(BaseListParser):
    method __init__ (line 2146) | def __init__(self):
    method WriteCustomInfoInXMLFormat (line 2149) | def WriteCustomInfoInXMLFormat(self, outfile, indent):
  function DEFINE_list (line 2157) | def DEFINE_list(name, default, help, flag_values=FLAGS, **args):
  function DEFINE_spaceseplist (line 2164) | def DEFINE_spaceseplist(name, default, help, flag_values=FLAGS, **args):
  class MultiFlag (line 2179) | class MultiFlag(Flag):
    method __init__ (line 2196) | def __init__(self, *args, **kwargs):
    method Parse (line 2200) | def Parse(self, arguments):
    method Serialize (line 2229) | def Serialize(self):
    method Type (line 2247) | def Type(self):
  function DEFINE_multi (line 2251) | def DEFINE_multi(parser, serializer, name, default, help, flag_values=FL...
  function DEFINE_multistring (line 2265) | def DEFINE_multistring(name, default, help, flag_values=FLAGS, **args):
  function DEFINE_multi_int (line 2278) | def DEFINE_multi_int(name, default, help, lower_bound=None, upper_bound=...

FILE: src/Utils/base.h
  function namespace (line 48) | namespace LinearDesign {
  function namespace (line 104) | namespace Hash {

FILE: src/Utils/codon.h
  function rtrim (line 21) | static inline void rtrim(std::string &s) {
  function calc_cai (line 73) | float calc_cai(const std::string& rna_seq) const {

FILE: src/Utils/common.h
  type class (line 33) | enum class
  function Beam_type (line 50) | enum class Beam_type : std::uint8_t {

FILE: src/Utils/constants.h
  function namespace (line 6) | namespace LinearDesign {

FILE: src/Utils/flat.h
  function namespace (line 9) | namespace detail {
  function LINEAR_DESIGN_INLINE (line 29) | LINEAR_DESIGN_INLINE iterator begin() {
  function LINEAR_DESIGN_INLINE (line 33) | LINEAR_DESIGN_INLINE iterator end() {
  function LINEAR_DESIGN_INLINE (line 41) | LINEAR_DESIGN_INLINE void reserve(const size_t n) {
  function LINEAR_DESIGN_INLINE (line 45) | LINEAR_DESIGN_INLINE void resize(const size_t n) {
  function reference (line 50) | reference operator[](size_t index) {
  function const_reference (line 55) | const_reference operator[](size_t index) const {
  function LINEAR_DESIGN_INLINE (line 59) | LINEAR_DESIGN_INLINE reference operator[](key_type key) {
  function LINEAR_DESIGN_INLINE (line 63) | LINEAR_DESIGN_INLINE const_reference operator[](key_type key) const {

FILE: src/Utils/network.h
  function namespace (line 26) | namespace LinearDesign {
  function add_node (line 74) | void add_node(NodeType n1){

FILE: src/Utils/reader.h
  type Reader (line 13) | struct Reader {
  function Reader (line 19) | struct Fasta : public Reader {

FILE: src/backtrace_iter.cc
  type LinearDesign (line 8) | namespace LinearDesign {
    function BacktraceResult (line 11) | BacktraceResult BeamCKYParser<ScoreType, IndexType, NodeType>::backtra...

FILE: src/beam_cky_parser.cc
  type LinearDesign (line 28) | namespace LinearDesign {

FILE: src/beam_cky_parser.h
  function namespace (line 18) | namespace LinearDesign {
  type NodeIndex (line 35) | struct NodeIndex {
  type NodeNucReverseIndex2 (line 41) | struct NodeNucReverseIndex2 {
  function update_if_better (line 200) | void update_if_better(State_t &state, const ScoreType newscore, const do...
  function update_if_better (line 207) | void update_if_better(State_t &state, const ScoreType newscore, const do...

FILE: src/linear_design.cpp
  function output_result (line 19) | bool output_result(const DecoderResult<ScoreType, IndexType>& result,
  function show_usage (line 38) | void show_usage() {
  function main (line 45) | int main(int argc, char** argv) {