AVERAGE enum value | WeightWrapper | |
findFirst_(const std::vector< double > &spec, double &m) | SuffixArrayTrypticCompressed | protected |
findFirst_(const std::vector< double > &spec, double &m, SignedSize start, SignedSize end) | SuffixArrayTrypticCompressed | protected |
findSpec(std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, double > > > &candidates, const std::vector< double > &spec) | SuffixArrayTrypticCompressed | virtual |
getLCP_(const std::pair< SignedSize, SignedSize > &last_point, const std::pair< SignedSize, SignedSize > ¤t_point) | SuffixArrayTrypticCompressed | protected |
getNextSep_(const SignedSize p) const | SuffixArrayTrypticCompressed | protected |
getNumberOfModifications() | SuffixArrayTrypticCompressed | virtual |
getTags() | SuffixArrayTrypticCompressed | virtual |
getTolerance() const | SuffixArrayTrypticCompressed | virtual |
getUseTags() | SuffixArrayTrypticCompressed | virtual |
getWeight(const AASequence &aa) const | WeightWrapper | |
getWeight(const EmpiricalFormula &ef) const | WeightWrapper | |
getWeight(const Residue &r, Residue::ResidueType res_type=Residue::Full) const | WeightWrapper | |
getWeightMode() const | WeightWrapper | |
hasMoreOutgoings_(SignedSize start_index, SignedSize stop_index, SignedSize walked_in) | SuffixArrayTrypticCompressed | protected |
indices_ | SuffixArrayTrypticCompressed | protected |
isDigestingEnd(const char aa1, const char aa2) const | SuffixArrayTrypticCompressed | virtual |
lcp_ | SuffixArrayTrypticCompressed | protected |
masse_ | SuffixArrayTrypticCompressed | protected |
MONO enum value | WeightWrapper | |
number_of_modifications_ | SuffixArrayTrypticCompressed | protected |
open(const String &file_name) | SuffixArrayTrypticCompressed | virtual |
parseTree_(SignedSize start_index, SignedSize stop_index, SignedSize depth, SignedSize walked_in, SignedSize edge_len, std::vector< std::pair< SignedSize, SignedSize > > &out_number, std::vector< std::pair< SignedSize, SignedSize > > &edge_length, std::vector< SignedSize > &leafe_depth) | SuffixArrayTrypticCompressed | protected |
printStatistic() | SuffixArrayTrypticCompressed | virtual |
progress_ | SuffixArrayTrypticCompressed | protected |
s_ | SuffixArrayTrypticCompressed | protected |
save(const String &file_name) | SuffixArrayTrypticCompressed | virtual |
setNumberOfModifications(Size number_of_mods) | SuffixArrayTrypticCompressed | virtual |
setTags(const std::vector< String > &tags) | SuffixArrayTrypticCompressed | virtual |
setTolerance(double t) | SuffixArrayTrypticCompressed | virtual |
setUseTags(bool use_tags) | SuffixArrayTrypticCompressed | virtual |
setWeightMode(const WEIGHTMODE mode) | WeightWrapper | |
SIZE_OF_WEIGHTMODE enum value | WeightWrapper | |
skip_ | SuffixArrayTrypticCompressed | protected |
SuffixArray(const String &st, const String &filename) | SuffixArray | |
SuffixArray(const SuffixArray &sa) | SuffixArray | |
SuffixArray() | SuffixArray | |
SuffixArrayTrypticCompressed(const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | SuffixArrayTrypticCompressed | |
SuffixArrayTrypticCompressed(const SuffixArrayTrypticCompressed &sa) | SuffixArrayTrypticCompressed | |
SuffixArrayTrypticCompressed() | SuffixArrayTrypticCompressed | protected |
tags_ | SuffixArrayTrypticCompressed | protected |
tol_ | SuffixArrayTrypticCompressed | protected |
toString() | SuffixArrayTrypticCompressed | virtual |
use_tags_ | SuffixArrayTrypticCompressed | protected |
WEIGHTMODE enum name | WeightWrapper | |
WeightWrapper() | WeightWrapper | |
WeightWrapper(const WEIGHTMODE weight_mode) | WeightWrapper | explicit |
WeightWrapper(const WeightWrapper &source) | WeightWrapper | |
~SuffixArray()=0 | SuffixArray | pure virtual |
~SuffixArrayTrypticCompressed() | SuffixArrayTrypticCompressed | virtual |
~WeightWrapper() | WeightWrapper | virtual |