| AVERAGE enum value | WeightWrapper |  | 
  | findFirst_(const std::vector< DoubleReal > &spec, DoubleReal &m) | SuffixArrayTrypticCompressed | protected | 
  | findFirst_(const std::vector< DoubleReal > &spec, DoubleReal &m, SignedSize start, SignedSize end) | SuffixArrayTrypticCompressed | protected | 
  | findSpec(std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &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(DoubleReal 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 |  | 
  | WeightWrapper(const WeightWrapper &source) | WeightWrapper |  | 
  | ~SuffixArray()=0 | SuffixArray | pure virtual | 
  | ~SuffixArrayTrypticCompressed() | SuffixArrayTrypticCompressed | virtual | 
  | ~WeightWrapper() | WeightWrapper | virtual |