, including all inherited members.
| 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 | |
| OpenMS::SuffixArray::findSpec(std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec)=0 | SuffixArray | [pure virtual] |
| getNumberOfModifications() | SuffixArraySeqan | |
| OpenMS::SuffixArray::getNumberOfModifications()=0 | SuffixArray | [pure virtual] |
| getTags() | SuffixArraySeqan | |
| OpenMS::SuffixArray::getTags()=0 | SuffixArray | [pure virtual] |
| getTolerance() const | SuffixArraySeqan | |
| OpenMS::SuffixArray::getTolerance() const =0 | SuffixArray | [pure virtual] |
| getUseTags() | SuffixArraySeqan | |
| OpenMS::SuffixArray::getUseTags()=0 | SuffixArray | [pure 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 | [inline, protected] |
| goNextSubTree_(TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map) | SuffixArraySeqan | [inline, protected] |
| goNextSubTree_(TIter &it) | SuffixArraySeqan | [inline, protected] |
| index_ | SuffixArraySeqan | [protected] |
| isDigestingEnd(const char aa1, const char aa2) const | SuffixArrayTrypticSeqan | |
| OpenMS::SuffixArraySeqan::OpenMS::SuffixArray::isDigestingEnd(const char aa1, const char aa2) const =0 | SuffixArray | [pure virtual] |
| it_ | SuffixArraySeqan | [protected] |
| masse_ | SuffixArraySeqan | [protected] |
| MONO enum value | WeightWrapper | |
| number_of_modifications_ | SuffixArraySeqan | [protected] |
| open(const String &filename) | SuffixArraySeqan | |
| OpenMS::SuffixArray::open(const String &filename)=0 | SuffixArray | [pure 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 | [inline, protected] |
| printStatistic() | SuffixArraySeqan | |
| OpenMS::SuffixArray::printStatistic()=0 | SuffixArray | [pure virtual] |
| s_ | SuffixArraySeqan | [protected] |
| save(const String &filename) | SuffixArraySeqan | |
| OpenMS::SuffixArray::save(const String &filename)=0 | SuffixArray | [pure virtual] |
| setNumberOfModifications(Size number_of_mods) | SuffixArraySeqan | |
| OpenMS::SuffixArray::setNumberOfModifications(Size number_of_mods)=0 | SuffixArray | [pure virtual] |
| setTags(const std::vector< OpenMS::String > &tags) | SuffixArraySeqan | |
| OpenMS::SuffixArray::setTags(const std::vector< String > &tags)=0 | SuffixArray | [pure virtual] |
| setTolerance(DoubleReal t) | SuffixArraySeqan | |
| OpenMS::SuffixArray::setTolerance(DoubleReal t)=0 | SuffixArray | [pure virtual] |
| setUseTags(bool use_tags) | SuffixArraySeqan | |
| OpenMS::SuffixArray::setUseTags(bool use_tags)=0 | SuffixArray | [pure 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 | |
| OpenMS::SuffixArray::toString()=0 | SuffixArray | [pure 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] |