AVERAGE enum value | WeightWrapper | |
findFirst_(const std::vector< DoubleReal > &spec, DoubleReal &m) | SuffixArraySeqan | protected |
findFirst_(const std::vector< DoubleReal > &spec, DoubleReal &m, SignedSize start, SignedSize end) | SuffixArraySeqan | protected |
findSpec(std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec) | SuffixArraySeqan | virtual |
getNumberOfModifications() | SuffixArraySeqan | virtual |
getTags() | SuffixArraySeqan | virtual |
getTolerance() const | SuffixArraySeqan | virtual |
getUseTags() | SuffixArraySeqan | 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 | |
goNext_(TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map) | SuffixArraySeqan | inlineprotected |
goNextSubTree_(TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map) | SuffixArraySeqan | inlineprotected |
goNextSubTree_(TIter &it) | SuffixArraySeqan | inlineprotected |
index_ | SuffixArraySeqan | protected |
isDigestingEnd(const char aa1, const char aa2) const | SuffixArrayTrypticSeqan | virtual |
it_ | SuffixArraySeqan | protected |
masse_ | SuffixArraySeqan | protected |
MONO enum value | WeightWrapper | |
number_of_modifications_ | SuffixArraySeqan | protected |
open(const String &filename) | SuffixArraySeqan | virtual |
parseTree_(TIter &it, std::vector< std::pair< SignedSize, SignedSize > > &out_number, std::vector< std::pair< SignedSize, SignedSize > > &edge_length, std::vector< SignedSize > &leafe_depth) | SuffixArraySeqan | inlineprotected |
printStatistic() | SuffixArraySeqan | virtual |
s_ | SuffixArraySeqan | protected |
save(const String &filename) | SuffixArraySeqan | virtual |
setNumberOfModifications(Size number_of_mods) | SuffixArraySeqan | virtual |
setTags(const std::vector< OpenMS::String > &tags) | SuffixArraySeqan | virtual |
setTolerance(DoubleReal t) | SuffixArraySeqan | virtual |
setUseTags(bool use_tags) | SuffixArraySeqan | virtual |
setWeightMode(const WEIGHTMODE mode) | WeightWrapper | |
SIZE_OF_WEIGHTMODE enum value | WeightWrapper | |
SuffixArray(const String &st, const String &filename) | SuffixArray | |
SuffixArray(const SuffixArray &sa) | SuffixArray | |
SuffixArray() | SuffixArray | |
SuffixArraySeqan(const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | SuffixArraySeqan | |
SuffixArraySeqan(const SuffixArraySeqan &source) | SuffixArraySeqan | |
SuffixArrayTrypticSeqan(const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO) | SuffixArrayTrypticSeqan | |
tags_ | SuffixArraySeqan | protected |
tol_ | SuffixArraySeqan | protected |
toString() | SuffixArraySeqan | virtual |
use_tags_ | SuffixArraySeqan | protected |
WEIGHTMODE enum name | WeightWrapper | |
WeightWrapper() | WeightWrapper | |
WeightWrapper(const WEIGHTMODE weight_mode) | WeightWrapper | |
WeightWrapper(const WeightWrapper &source) | WeightWrapper | |
~SuffixArray()=0 | SuffixArray | pure virtual |
~SuffixArraySeqan() | SuffixArraySeqan | virtual |
~WeightWrapper() | WeightWrapper | virtual |