HashTableFred Member List

This is the complete list of members for HashTableFred, including all inherited members.

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

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