TwoPassD2 Member List

This is the complete list of members for TwoPassD2, including all inherited members.

alignmentMetric	TwoPassD2	[private]
analyze()	TwoPassD2	[inline, virtual]
ESTAnalyzer::analyze(const int otherEST, const bool useHeuristics=true, const bool useHeavyWeight=true)	ESTAnalyzer
analyzeFrame(const std::string &refFrame, const std::string &otherFrame, const int wordSize)	FWAnalyzer	[protected, virtual]
analyzerName	ESTAnalyzer	[protected]
argsList	TwoPassD2	[private, static]
argumentFrameSize	FWAnalyzer	[protected, static]
BitMask	TwoPassD2	[private, static]
bitShift	TwoPassD2	[protected, static]
buildWordTable(int *wordTable, const char *estSeq, Encoder encoder)	TwoPassD2	[inline, protected]
chain	ESTAnalyzer	[protected]
compareMetrics(const float metric1, const float metric2) const	TwoPassD2	[inline, protected, virtual]
delta	TwoPassD2	[protected]
displayStats(std::ostream &os)	ESTAnalyzer	[inline, virtual]
dumpEST(ResultLog &log, const EST *est, const bool isReference=false)	FWAnalyzer	[protected, virtual]
dumpESTList(const std::vector< EST * > &estList, const EST *refEST, ResultLog &log)	FWAnalyzer	[protected, virtual]
dumpHeader(ResultLog &log, const double mean, const double variance)	FWAnalyzer	[protected, virtual]
ESTAnalyzer(const std::string &analyzerName, const int refESTidx, const std::string &outputFileName)	ESTAnalyzer	[protected]
ESTAnalyzerFactory class	TwoPassD2	[friend]
estFileName	ESTAnalyzer	[protected, static]
frameShift	TwoPassD2	[protected]
frameSize	FWAnalyzer	[protected]
FWAnalyzer(const std::string &analyzerName, const int refESTidx, const std::string &outputFile)	FWAnalyzer	[protected]
getAlignmentData(int &alignmentData)	TwoPassD2	[protected, virtual]
getFrame(const EST *est, bool start=true)	FWAnalyzer
getHeuristicChain() const	ESTAnalyzer	[inline, virtual]
getInputFileName() const	ESTAnalyzer	[inline]
getInvalidMetric() const	TwoPassD2	[inline, protected, virtual]
getMetric(const int otherEST)	TwoPassD2	[protected, virtual]
getName() const	TwoPassD2	[inline, virtual]
getPreferredDummyESTLength() const	FWAnalyzer	[inline, virtual]
getValidMetric() const	ESTAnalyzer	[inline, virtual]
hintKey	TwoPassD2	[private]
htmlLog	ESTAnalyzer	[protected, static]
initialize()	TwoPassD2	[virtual]
isDistanceMetric() const	TwoPassD2	[inline, protected, virtual]
loadFASTAFile(const char *fileName, const bool unpopulate=false)	ESTAnalyzer
maxThreshold	TwoPassD2	[protected]
minThreshold	TwoPassD2	[protected, static]
NHash	TwoPassD2	[private, static]
noMaskBases	ESTAnalyzer	[protected, static]
noNormalize	TwoPassD2	[private, static]
numWordsInWindow	TwoPassD2	[private]
outputFileName	ESTAnalyzer	[protected]
parseArguments(int &argc, char **argv)	TwoPassD2	[virtual]
readAhead	ESTAnalyzer	[protected, static]
referenceFrame	FWAnalyzer	[protected]
refESTidx	ESTAnalyzer	[protected]
runD2Asymmetric(int *s1MinScoreIdx, int *s2MinScoreIdx)	TwoPassD2	[private]
runD2Bounded(int sq1Start, int sq1End, int sq2Start, int sq2End)	TwoPassD2	[private]
s1WordTable	TwoPassD2	[protected]
s2WordTable	TwoPassD2	[protected]
setHeuristicChain(HeuristicChain *chain)	ESTAnalyzer	[virtual]
setReferenceEST(const int estIdx)	TwoPassD2	[virtual]
showArguments(std::ostream &os)	TwoPassD2	[virtual]
sq1Len	TwoPassD2	[private]
sq2Len	TwoPassD2	[private]
threshold	TwoPassD2	[protected]
TwoPassD2(const int refESTidx, const std::string &outputFileName)	TwoPassD2	[private]
updateParameters()	TwoPassD2	[private]
updateWindow(const int wordIn, const int wordOut, int &score, int &minScore, const int windowDistance)	TwoPassD2	[inline, private]
updateWindowAsym(const int wordIn, const int wordOut, int &score, int &minScore, const int s1CurWindowIdx, const int s2CurWindowIdx, int *s1MinScoreIdx, int *s2MinScoreIdx)	TwoPassD2	[inline, private]
wordSize	FWAnalyzer	[protected, static]
~ESTAnalyzer()	ESTAnalyzer	[virtual]
~FWAnalyzer()	FWAnalyzer	[virtual]
~TwoPassD2()	TwoPassD2	[virtual]