| 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 |