| allocateHitList(unsigned long size) | HashTableTranslated | [virtual] |
| bitsPerSymbol_ | HashTableGeneric | [protected] |
| cleanupTempData(void) | HashTableTranslated | [virtual] |
| codonEncoder_ | HashTableTranslated | [protected] |
| codons_ | HashTableTranslated | [protected] |
| computePointerArray(void) | HashTableTranslated | [virtual] |
| countWords(SequenceAdapter &thisSeq) | HashTableTranslated | [virtual] |
| countWordsAndGetNames(SequenceReader &sequenceReader, SequenceAdapter *seq) | HashTableTranslated | [virtual] |
| createHashTable(SequenceReader &sequenceReader, int wordLength, int maxNumHits, int stepLength=0) | HashTableGeneric | [virtual] |
| eDNAWordSizeForHashing enum value | HashTableTranslated | |
| getBitsPerSymbol(void) const | HashTableGeneric | [inline] |
| getHitListFormat(void) const | HashTableGeneric | [inline] |
| getHitListStart(void) const | HashTableTranslated | [virtual] |
| getHitTypeSize(void) const | HashTableTranslated | [virtual] |
| getMaxNumHits() const | HashTableTranslated | [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 | HashTableTranslated | [virtual] |
| getWordLength() const | HashTableGeneric | [inline] |
| hashAllWords(SequenceReader &sequenceReader, SequenceAdapter *seq, int numSeqs) | HashTableTranslated | [virtual] |
| hashFwd_ | HashTableTranslated | [protected] |
| hashRev_ | HashTableTranslated | [protected] |
| HashTableGeneric(ostream &monitoringStream, const string &name, Allocator< PositionInHitList > &arrayAllocator) | HashTableGeneric | |
| HashTableTranslated(ostream &monitoringStream=cerr, string name="", Allocator< PositionPacked > &hitListAllocator=HashTablePacked::defaultHitListAllocator, Allocator< PositionInHitList > &arrayAllocator=HashTablePacked::defaultArrayAllocator) | HashTableTranslated | |
| HashTableTranslated(const HashTableTranslated &) | HashTableTranslated | [private] |
| hashWords(SequenceAdapter &thisSeq, SequenceNumber seqNum) | HashTableTranslated | [virtual] |
| hitListFormat_ | HashTableGeneric | [protected] |
| isForward(void) const | HashTableTranslated | [inline] |
| isInitialized() const | HashTableGeneric | [inline] |
| isInitialized_ | HashTableGeneric | [protected] |
| loadHashTable(SourceReaderIndex *pSourceReader=NULL) | HashTableTranslated | [virtual] |
| loadHitList(unsigned long size) | HashTableTranslated | [virtual] |
| loadSequenceNames(void) | HashTableGeneric | [virtual] |
| matchSequence(WordSequence &seq, HitList &hitListFwd) | HashTableTranslated | [inline, virtual] |
| MatchSequencePointer typedef | HashTableTranslated | |
| matchSequenceProtein(WordSequence &seq, HitList &hitListFwd) | HashTableTranslated | |
| matchSequenceTranslatedDNA(WordSequence &seq, HitList &hitListFwd) | HashTableTranslated | |
| maxNumHits_ | HashTableGeneric | [protected] |
| monitoringStream_ | HashTableGeneric | [protected] |
| name_ | HashTableGeneric | [protected] |
| numDifferentWords_ | HashTableGeneric | [protected] |
| operator=(const HashTableTranslated &) | HashTableTranslated | [private] |
| pArrayAllocator_ | HashTableGeneric | [protected] |
| pHash_ | HashTableTranslated | [protected] |
| pHitsFoundSoFar_ | HashTableGeneric | [protected] |
| pMatchSequence_ | HashTableTranslated | [protected] |
| pNameReader_ | HashTableGeneric | [protected] |
| printHashStats(void) | HashTableTranslated | [virtual] |
| pSequenceSizes_ | HashTableGeneric | [protected] |
| pWordPositionInHitList_ | HashTableGeneric | [protected] |
| saveHashTable(void) | HashTableTranslated | [virtual] |
| saveHitList(void) | HashTableTranslated | [virtual] |
| saveSequenceNames(void) | HashTableGeneric | [virtual] |
| setForward(void) | HashTableTranslated | [inline] |
| setMaxNumHits(int mnh) | HashTableTranslated | [virtual] |
| setNumRepeats(int nr) | HashTableTranslated | [virtual] |
| setQueryProtein(void) | HashTableTranslated | [inline] |
| setQueryTranslatedDNA(void) | HashTableTranslated | [inline] |
| setReverse(void) | HashTableTranslated | [inline] |
| setSubstituteThreshold(int ns) | HashTableTranslated | [virtual] |
| setupHitList(void) | HashTableTranslated | [virtual] |
| setupPointerArray(void) | HashTableTranslated | [virtual] |
| sourceData_ | HashTableGeneric | [protected] |
| stepLength_ | HashTableGeneric | [protected] |
| tempAlloc_ | HashTableGeneric | |
| translatedWordLength_ | HashTableTranslated | [protected] |
| wordLength_ | HashTableGeneric | [protected] |
| wordsInDatabase_ | HashTableGeneric | [protected] |
| ~HashTableGeneric() | HashTableGeneric | [virtual] |
| ~HashTableTranslated() | HashTableTranslated | [inline, virtual] |
