findFirst_(const std::vector< double > &spec, double &m) | SuffixArrayTrypticCompressed | [protected] |
findFirst_(const std::vector< double > &spec, double &m, int start, int end) | SuffixArrayTrypticCompressed | [protected] |
findSpec(std::vector< std::vector< std::pair< std::pair< int, int >, float > > > &candidates, const std::vector< double > &spec) | SuffixArrayTrypticCompressed | [virtual] |
getLCP_(const std::pair< int, int > &last_point, const std::pair< int, int > ¤t_point) | SuffixArrayTrypticCompressed | [protected] |
getNextSep_(const int p) const | SuffixArrayTrypticCompressed | [protected] |
getNumberOfModifications() | SuffixArrayTrypticCompressed | [virtual] |
getTags() | SuffixArrayTrypticCompressed | [virtual] |
getTolerance() const | SuffixArrayTrypticCompressed | [virtual] |
getUseTags() | SuffixArrayTrypticCompressed | [virtual] |
hasMoreOutgoings_(int start_index, int stop_index, int walked_in) | SuffixArrayTrypticCompressed | [protected] |
indices_ | SuffixArrayTrypticCompressed | [protected] |
isDigestingEnd(const char aa1, const char aa2) const | SuffixArrayTrypticCompressed | [virtual] |
lcp_ | SuffixArrayTrypticCompressed | [protected] |
masse_ | SuffixArrayTrypticCompressed | [protected] |
number_of_modifications_ | SuffixArrayTrypticCompressed | [protected] |
open(const String &file_name) | SuffixArrayTrypticCompressed | [virtual] |
parseTree_(int start_index, int stop_index, int depth, int walked_in, int edge_len, std::vector< std::pair< int, int > > &out_number, std::vector< std::pair< int, int > > &edge_length, std::vector< int > &leafe_depth) | SuffixArrayTrypticCompressed | [protected] |
printStatistic() | SuffixArrayTrypticCompressed | [virtual] |
progress_ | SuffixArrayTrypticCompressed | [protected] |
s_ | SuffixArrayTrypticCompressed | [protected] |
save(const String &file_name) | SuffixArrayTrypticCompressed | [virtual] |
setNumberOfModifications(unsigned int number_of_mods) | SuffixArrayTrypticCompressed | [virtual] |
setTags(const std::vector< String > &tags) | SuffixArrayTrypticCompressed | [virtual] |
setTolerance(double t) | SuffixArrayTrypticCompressed | [virtual] |
setUseTags(bool use_tags) | SuffixArrayTrypticCompressed | [virtual] |
skip_ | SuffixArrayTrypticCompressed | [protected] |
SuffixArray(const String &st, const String &sa_file_name) | SuffixArray | |
SuffixArray(const SuffixArray &sa) | SuffixArray | |
SuffixArray() | SuffixArray | |
SuffixArrayTrypticCompressed(const String &st, const String &sa_file_name) | SuffixArrayTrypticCompressed | |
SuffixArrayTrypticCompressed(const SuffixArrayTrypticCompressed &sa) | SuffixArrayTrypticCompressed | |
SuffixArrayTrypticCompressed() | SuffixArrayTrypticCompressed | [protected] |
tags_ | SuffixArrayTrypticCompressed | [protected] |
tol_ | SuffixArrayTrypticCompressed | [protected] |
toString() | SuffixArrayTrypticCompressed | [virtual] |
use_tags_ | SuffixArrayTrypticCompressed | [protected] |
~SuffixArray()=0 | SuffixArray | [pure virtual] |
~SuffixArrayTrypticCompressed() | SuffixArrayTrypticCompressed | [virtual] |