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SuffixArraySeqan Member List

This is the complete list of members for SuffixArraySeqan, including all inherited members.

AVERAGE enum valueWeightWrapper
findFirst_(const std::vector< DoubleReal > &spec, DoubleReal &m)SuffixArraySeqanprotected
findFirst_(const std::vector< DoubleReal > &spec, DoubleReal &m, SignedSize start, SignedSize end)SuffixArraySeqanprotected
findSpec(std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec)SuffixArraySeqanvirtual
getNumberOfModifications()SuffixArraySeqanvirtual
getTags()SuffixArraySeqanvirtual
getTolerance() const SuffixArraySeqanvirtual
getUseTags()SuffixArraySeqanvirtual
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)SuffixArraySeqaninlineprotected
goNextSubTree_(TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map)SuffixArraySeqaninlineprotected
goNextSubTree_(TIter &it)SuffixArraySeqaninlineprotected
index_SuffixArraySeqanprotected
isDigestingEnd(const char aa1, const char aa2) const SuffixArraySeqanvirtual
it_SuffixArraySeqanprotected
masse_SuffixArraySeqanprotected
MONO enum valueWeightWrapper
number_of_modifications_SuffixArraySeqanprotected
open(const String &filename)SuffixArraySeqanvirtual
parseTree_(TIter &it, std::vector< std::pair< SignedSize, SignedSize > > &out_number, std::vector< std::pair< SignedSize, SignedSize > > &edge_length, std::vector< SignedSize > &leafe_depth)SuffixArraySeqaninlineprotected
printStatistic()SuffixArraySeqanvirtual
s_SuffixArraySeqanprotected
save(const String &filename)SuffixArraySeqanvirtual
setNumberOfModifications(Size number_of_mods)SuffixArraySeqanvirtual
setTags(const std::vector< OpenMS::String > &tags)SuffixArraySeqanvirtual
setTolerance(DoubleReal t)SuffixArraySeqanvirtual
setUseTags(bool use_tags)SuffixArraySeqanvirtual
setWeightMode(const WEIGHTMODE mode)WeightWrapper
SIZE_OF_WEIGHTMODE enum valueWeightWrapper
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
tags_SuffixArraySeqanprotected
TIndex typedefSuffixArraySeqanprivate
TIter typedefSuffixArraySeqanprivate
TIterSpec typedefSuffixArraySeqanprivate
tol_SuffixArraySeqanprotected
toString()SuffixArraySeqanvirtual
use_tags_SuffixArraySeqanprotected
WEIGHTMODE enum nameWeightWrapper
WeightWrapper()WeightWrapper
WeightWrapper(const WEIGHTMODE weight_mode)WeightWrapper
WeightWrapper(const WeightWrapper &source)WeightWrapper
~SuffixArray()=0SuffixArraypure virtual
~SuffixArraySeqan()SuffixArraySeqanvirtual
~WeightWrapper()WeightWrappervirtual

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5