| findMatchesInRange(HitListVector::iterator first, HitListVector::iterator last, MatchAdder &addMatch) | MatchAlgorithmGapped | |
| generateHits(WordSequence &querySeq, HitListVector &hitList, HashTableGeneric &subjectTable) | MatchAlgorithm | |
| generateMatches(HitListVector &hitList, MatchAdder &addMatch) | MatchAlgorithmGapped | [virtual] |
| MatchAlgorithm(int numRepeats) | MatchAlgorithm | [inline] |
| MatchAlgorithmGapped(int maxGap, int maxInsert, int minToProcess, int numRepeats) | MatchAlgorithmGapped | [inline] |
| maxGap_ | MatchAlgorithmGapped | [private] |
| maxInsert_ | MatchAlgorithmGapped | [private] |
| maxQueryDiff_ | MatchAlgorithmGapped | [private] |
| minHitsForMatch_ | MatchAlgorithmGapped | [private] |
| minToProcess_ | MatchAlgorithmGapped | [private] |
| numRepeats_ | MatchAlgorithm | [protected] |
| operator()(WordSequence &querySeq, MatchAdder &addMatch, HashTableGeneric &subjectTable, int wordLength=-1, int stepLength=-1) | MatchAlgorithm | |
| sortNeeded_ | MatchAlgorithm | [protected] |
| stepLength_ | MatchAlgorithm | [protected] |
| wordLength_ | MatchAlgorithm | [protected] |
