| 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 |