| allocateHitList(unsigned long size)=0 | HashTableGeneric | [pure virtual] |
| bitsPerSymbol_ | HashTableGeneric | [protected] |
| cleanupTempData(void) | HashTableGeneric | [virtual] |
| computePointerArray(void) | HashTableGeneric | [virtual] |
| countWords(SequenceAdapter &thisSeq)=0 | HashTableGeneric | [pure virtual] |
| countWordsAndGetNames(SequenceReader &sequenceReader, SequenceAdapter *seq) | HashTableGeneric | [virtual] |
| createHashTable(SequenceReader &sequenceReader, int wordLength, int maxNumHits, int stepLength=0) | HashTableGeneric | [virtual] |
| getBitsPerSymbol(void) const | HashTableGeneric | [inline] |
| getHitListFormat(void) const | HashTableGeneric | [inline] |
| getHitListStart(void) const=0 | HashTableGeneric | [pure virtual] |
| getHitTypeSize(void) const=0 | HashTableGeneric | [pure virtual] |
| getMaxNumHits() const | HashTableGeneric | [inline, virtual] |
| getNameReader() const | HashTableGeneric | [inline] |
| getNumSequences() const | HashTableGeneric | |
| getSequenceName(string &seqName, SequenceNumber seqNum) const | HashTableGeneric | |
| getSequenceName(SequenceNumber seqNum) const | HashTableGeneric | |
| getSequenceSize(SequenceNumber seqNum) const | HashTableGeneric | |
| getSourceDataType(void) const | HashTableGeneric | [inline] |
| getStepLength() const | HashTableGeneric | [inline] |
| getTotalNumWords(void) const | HashTableGeneric | [inline, virtual] |
| getWordLength() const | HashTableGeneric | [inline] |
| hashAllWords(SequenceReader &sequenceReader, SequenceAdapter *seq, int numSeqs) | HashTableGeneric | [virtual] |
| HashTableFactory class | HashTableGeneric | [friend] |
| HashTableGeneric(ostream &monitoringStream, const string &name, Allocator< PositionInHitList > &arrayAllocator) | HashTableGeneric | |
| HashTableGeneric(const HashTableGeneric &) | HashTableGeneric | [private] |
| hashWords(SequenceAdapter &thisSeq, SequenceNumber seqNum)=0 | HashTableGeneric | [pure virtual] |
| hitListFormat_ | HashTableGeneric | [protected] |
| isInitialized() const | HashTableGeneric | [inline] |
| isInitialized_ | HashTableGeneric | [protected] |
| loadHashTable(SourceReaderIndex *pSourceReader=NULL) | HashTableGeneric | [virtual] |
| loadHitList(unsigned long size)=0 | HashTableGeneric | [pure virtual] |
| loadSequenceNames(void) | HashTableGeneric | [virtual] |
| matchSequence(WordSequence &seq, HitList &hitListFwd)=0 | HashTableGeneric | [pure virtual] |
| maxNumHits_ | HashTableGeneric | [protected] |
| monitoringStream_ | HashTableGeneric | [protected] |
| name_ | HashTableGeneric | [protected] |
| numDifferentWords_ | HashTableGeneric | [protected] |
| operator=(const HashTableGeneric &) | HashTableGeneric | [private] |
| pArrayAllocator_ | HashTableGeneric | [protected] |
| pHitsFoundSoFar_ | HashTableGeneric | [protected] |
| pNameReader_ | HashTableGeneric | [protected] |
| printHashStats(void) | HashTableGeneric | [virtual] |
| pSequenceSizes_ | HashTableGeneric | [protected] |
| pWordPositionInHitList_ | HashTableGeneric | [protected] |
| saveHashTable(void) | HashTableGeneric | [virtual] |
| saveHitList(void)=0 | HashTableGeneric | [pure virtual] |
| saveSequenceNames(void) | HashTableGeneric | [virtual] |
| setMaxNumHits(int mnh) | HashTableGeneric | [inline, virtual] |
| setNumRepeats(int nr)=0 | HashTableGeneric | [pure virtual] |
| setSubstituteThreshold(int ns) | HashTableGeneric | [inline, virtual] |
| setupHitList(void) | HashTableGeneric | [virtual] |
| setupPointerArray(void) | HashTableGeneric | [virtual] |
| sourceData_ | HashTableGeneric | [protected] |
| stepLength_ | HashTableGeneric | [protected] |
| tempAlloc_ | HashTableGeneric | |
| wordLength_ | HashTableGeneric | [protected] |
| wordsInDatabase_ | HashTableGeneric | [protected] |
| ~HashTableGeneric() | HashTableGeneric | [virtual] |
