| AddSequence(SortedMerList *sar, genome::gnSequence *seq=NULL) | mems::MatchFinder | [virtual] |
| alpha_map | mems::MatchFinder | [protected] |
| alpha_map_size | mems::MatchFinder | [protected] |
| alphabet_bits | mems::MatchFinder | [protected] |
| ambiguity_tolerance | mems::MatchFinder | [protected] |
| AmbiguityTolerance() | mems::MatchFinder | [inline, virtual] |
| Clear() | mems::MatchFinder | [virtual] |
| EnumerateMatches(IdmerList &match_list) | mems::MatchFinder | [protected, virtual] |
| ExtendMatch(UngappedMatchType &mhe, std::vector< UngappedMatchType > &subset_matches, gnSeqI max_backward=GNSEQI_END, gnSeqI max_forward=GNSEQI_END) | mems::MatchFinder | [protected] |
| FindMatchSeeds() | mems::MatchFinder | [virtual] |
| FindMatchSeeds(const std::vector< gnSeqI > &start_offsets) | mems::MatchFinder | [virtual] |
| FindSubsets(const MatchType &mhe, std::vector< MatchType > &subset_matches) | mems::MatchFinder | [protected] |
| GetBreakpoint(uint32 sarI, gnSeqI startI, std::vector< gnSeqI > &breakpoints) const | mems::MatchFinder | [virtual] |
| GetProgress() const | mems::MatchFinder | [inline, virtual] |
| GetSar(uint32 sarI) const | mems::MatchFinder | [inline, protected, virtual] |
| HashMatch(IdmerList &match_list)=0 | mems::MatchFinder | [protected, pure virtual] |
| log_stream | mems::MatchFinder | [protected] |
| LogProgress(std::ostream *os) | mems::MatchFinder | [virtual] |
| m_progress | mems::MatchFinder | [protected] |
| MatchFinder() | mems::MatchFinder | |
| MatchFinder(const MatchFinder &mf) | mems::MatchFinder | |
| mer_size | mems::MatchFinder | [protected] |
| mers_processed | mems::MatchFinder | [protected] |
| Multiplicity(void) | mems::MatchFinder | [inline, virtual] |
| offset_stream | mems::MatchFinder | [protected] |
| sar_table | mems::MatchFinder | [protected] |
| SearchRange(std::vector< gnSeqI > &start_points, std::vector< gnSeqI > &search_len) | mems::MatchFinder | [protected, virtual] |
| seq_count | mems::MatchFinder | [protected] |
| seq_table | mems::MatchFinder | [protected] |
| SetAmbiguityTolerance(uint32 ambiguity_tol) | mems::MatchFinder | [inline, virtual] |
| SetOffsetLog(std::ostream *offset_stream) | mems::MatchFinder | [inline] |
| total_mers | mems::MatchFinder | [protected] |
| ~MatchFinder() | mems::MatchFinder | |
