findFirst_(const std::vector< double > &spec, double &m) | SuffixArraySeqan | [protected] |
findFirst_(const std::vector< double > &spec, double &m, int start, int end) | SuffixArraySeqan | [protected] |
findSpec(std::vector< std::vector< std::pair< std::pair< int, int >, float > > > &candidates, const std::vector< double > &spec) | SuffixArraySeqan | [virtual] |
getNumberOfModifications() | SuffixArraySeqan | [virtual] |
getTags() | SuffixArraySeqan | [virtual] |
getTolerance() const | SuffixArraySeqan | [virtual] |
getUseTags() | SuffixArraySeqan | [virtual] |
goNext(seqan::Iter< TIndex, seqan::VSTree< seqan::TopDown< seqan::ParentLinks< TSpec > > > > &it, double &m, std::stack< double > &allm, std::stack< std::map< double, int > > &mod_map) | SuffixArraySeqan | [inline] |
goNextSubTree(seqan::Iter< TIndex, seqan::VSTree< seqan::TopDown< seqan::ParentLinks< TSpec > > > > &it, double &m, std::stack< double > &allm, std::stack< std::map< double, int > > &mod_map) | SuffixArraySeqan | [inline] |
goNextSubTree(seqan::Iter< TIndex, seqan::VSTree< seqan::TopDown< seqan::ParentLinks< TSpec > > > > &it) | SuffixArraySeqan | [inline] |
index_ | SuffixArraySeqan | [protected] |
isDigestingEnd(const char aa1, const char aa2) const | SuffixArraySeqan | [virtual] |
it_ | SuffixArraySeqan | [protected] |
masse_ | SuffixArraySeqan | [protected] |
number_of_modifications_ | SuffixArraySeqan | [protected] |
open(const String &file_name) | SuffixArraySeqan | [virtual] |
parseTree(seqan::Iter< TIndex, seqan::VSTree< seqan::TopDown< seqan::ParentLinks< TSpec > > > > &it, std::vector< std::pair< int, int > > &out_number, std::vector< std::pair< int, int > > &edge_length, std::vector< int > &leafe_depth) | SuffixArraySeqan | [inline] |
printStatistic() | SuffixArraySeqan | [virtual] |
s_ | SuffixArraySeqan | [protected] |
save(const String &file_name) | SuffixArraySeqan | [virtual] |
setNumberOfModifications(unsigned int number_of_mods) | SuffixArraySeqan | [virtual] |
setTags(const std::vector< OpenMS::String > &tags) | SuffixArraySeqan | [virtual] |
setTolerance(double t) | SuffixArraySeqan | [virtual] |
setUseTags(bool use_tags) | SuffixArraySeqan | [virtual] |
SuffixArray(const String &st, const String &sa_file_name) | SuffixArray | |
SuffixArray(const SuffixArray &sa) | SuffixArray | |
SuffixArray() | SuffixArray | |
SuffixArraySeqan(const String &st, const String &sa_file_name) | SuffixArraySeqan | |
SuffixArraySeqan(const SuffixArraySeqan &source) | SuffixArraySeqan | |
tags_ | SuffixArraySeqan | [protected] |
TIndex typedef | SuffixArraySeqan | [private] |
tol_ | SuffixArraySeqan | [protected] |
toString() | SuffixArraySeqan | [virtual] |
use_tags_ | SuffixArraySeqan | [protected] |
~SuffixArray()=0 | SuffixArray | [pure virtual] |
~SuffixArraySeqan() | SuffixArraySeqan | [virtual] |