| allocateHitList(unsigned long size) | HashTableView< PositionPacked, HashTablePacked > | [inline, virtual] |
| begin(Word w) const | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| bitsPerSymbol_ | HashTableGeneric | [protected] |
| cleanupTempData(void) | HashTableGeneric | [virtual] |
| computePointerArray(void) | HashTableGeneric | [virtual] |
| const_iterator typedef | HashTableView< PositionPacked, HashTablePacked > | |
| convertHits(PackedHitStore &hits, HitList &hitListFwd) | HashTableComponent | [virtual] |
| countWords(SequenceAdapter &thisSeq) | HashTablePacked | [virtual] |
| countWordsAndGetNames(SequenceReader &sequenceReader, SequenceAdapter *seq) | HashTableGeneric | [virtual] |
| createHashTable(SequenceReader &sequenceReader, int wordLength, int maxNumHits, int stepLength=0) | HashTableGeneric | [virtual] |
| defaultArrayAllocator | HashTablePacked | [static] |
| defaultHitListAllocator | HashTablePacked | [static] |
| end(Word w) const | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| GenerateSubstitutesPointer typedef | HashTablePacked | |
| getBitsPerSymbol(void) const | HashTableGeneric | [inline] |
| getHitListFormat(void) const | HashTableGeneric | [inline] |
| getHitListStart(void) const | HashTableView< PositionPacked, HashTablePacked > | [inline, virtual] |
| getHitTypeSize(void) const | HashTableView< PositionPacked, HashTablePacked > | [inline, virtual] |
| getMaxNumHits() const | HashTableGeneric | [inline, virtual] |
| getNameReader() const | HashTableGeneric | [inline] |
| getNumSequences() const | HashTableGeneric | |
| getOffset(const_iterator i) | HashTablePacked | [inline, static] |
| getSequence(const_iterator i) | HashTablePacked | [inline, static] |
| 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] |
| HashTableComponent(ostream &monitoringStream, string name, Allocator< PositionPacked > &hitListAllocator=defaultHitListAllocator, Allocator< PositionInHitList > &arrayAllocator=defaultArrayAllocator) | HashTableComponent | |
| HashTableFactory class | HashTableView< PositionPacked, HashTablePacked > | [friend] |
| HashTableGeneric(ostream &monitoringStream, const string &name, Allocator< PositionInHitList > &arrayAllocator) | HashTableGeneric | |
| HashTablePacked(ostream &monitoringStream=cerr, string name="", Allocator< PositionPacked > &hitListAllocator=defaultHitListAllocator, Allocator< PositionInHitList > &arrayAllocator=defaultArrayAllocator) | HashTablePacked | [inline] |
| HashTableView(ostream &monitoringStream, string name, Allocator< HitType > &hitListAllocator, Allocator< PositionInHitList > &arrayAllocator) | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| hashWords(SequenceAdapter &thisSeq, SequenceNumber seqNum) | HashTablePacked | [virtual] |
| hitListFormat_ | HashTableGeneric | [protected] |
| HitType typedef | HashTableView< PositionPacked, HashTablePacked > | |
| isInitialized() const | HashTableGeneric | [inline] |
| isInitialized_ | HashTableGeneric | [protected] |
| iterator typedef | HashTableView< PositionPacked, HashTablePacked > | |
| last(Word w) const | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| loadHashTable(SourceReaderIndex *pSourceReader=NULL) | HashTableGeneric | [virtual] |
| loadHitList(unsigned long size) | HashTablePacked | [virtual] |
| loadSequenceNames(void) | HashTableGeneric | [virtual] |
| matchSequence(WordSequence &seq, HitList &hitListFwd) | HashTablePacked | [inline, virtual] |
| MatchSequencePointer typedef | HashTablePacked | |
| matchSequenceRepeated(WordSequence &seq, HitList &hitListFwd) | HashTablePacked | |
| matchSequenceStandard(WordSequence &seq, HitList &hitListFwd) | HashTablePacked | |
| matchWord(Word queryWord, HITLIST &hitsFound, int baseOffset=0) const | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| matchWord(const WordSequence &queryWords, HITLIST &hitsFound, int baseOffset=0) const | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| matchWordDeluxe(Word w, PackedHitStore &hitList, int offset) | HashTablePacked | [inline] |
| MatchWordPointer typedef | HashTablePacked | |
| matchWordStandard(Word w, PackedHitStore &hitList, int offset) | HashTablePacked | [inline] |
| matchWordSubstitute(Word w, PackedHitStore &hitList, int offset) | HashTablePacked | |
| maxNumHits_ | HashTableGeneric | [protected] |
| monitoringStream_ | HashTableGeneric | [protected] |
| name_ | HashTableGeneric | [protected] |
| numDifferentWords_ | HashTableGeneric | [protected] |
| numRepeats_ | HashTablePacked | [protected] |
| pArrayAllocator_ | HashTableGeneric | [protected] |
| pGenerateSubstitutes_ | HashTablePacked | [protected] |
| pHitListAllocator_ | HashTableView< PositionPacked, HashTablePacked > | [protected] |
| pHitListForAllWords_ | HashTableView< PositionPacked, HashTablePacked > | [protected] |
| pHitsFoundSoFar_ | HashTableGeneric | [protected] |
| pMatchSequence_ | HashTablePacked | [protected] |
| pMatchWord_ | HashTablePacked | [protected] |
| pNameReader_ | HashTableGeneric | [protected] |
| printHashStats(void) | HashTableGeneric | [virtual] |
| pSequenceSizes_ | HashTableGeneric | [protected] |
| pWordPositionInHitList_ | HashTableGeneric | [protected] |
| queryFrame_ | HashTableComponent | [private] |
| saveHashTable(void) | HashTableGeneric | [virtual] |
| saveHitList(void) | HashTablePacked | [virtual] |
| saveSequenceNames(void) | HashTableGeneric | [virtual] |
| seqStarts_ | HashTablePacked | [protected] |
| setMaxNumHits(int mnh) | HashTableGeneric | [inline, virtual] |
| setNumRepeats(int numRepeats) | HashTablePacked | [virtual] |
| setQueryFrame(int qf) | HashTableComponent | [inline] |
| setSubstituteThreshold(int ns) | HashTablePacked | [virtual] |
| setupHitList(void) | HashTableGeneric | [virtual] |
| setupPointerArray(void) | HashTableGeneric | [virtual] |
| size(Word w) const | HashTableView< PositionPacked, HashTablePacked > | [inline] |
| sorter_ | HashTablePacked | [protected] |
| sourceData_ | HashTableGeneric | [protected] |
| stepLength_ | HashTableGeneric | [protected] |
| substituteThreshold_ | HashTablePacked | [protected] |
| tempAlloc_ | HashTableGeneric | |
| wordLength_ | HashTableGeneric | [protected] |
| wordNum_ | HashTablePacked | [protected] |
| wordsInDatabase_ | HashTableGeneric | [protected] |
| ~HashTableGeneric() | HashTableGeneric | [virtual] |
| ~HashTableView() | HashTableView< PositionPacked, HashTablePacked > | [inline, virtual] |
