MatrixFileAnalyzer Member List

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

analyze()	MatrixFileAnalyzer	`[virtual]`
ESTAnalyzer::analyze(const int otherEST, const bool useHeuristics=true, const bool useHeavyWeight=true)	ESTAnalyzer
analyzerName	ESTAnalyzer	`[protected]`
argsList	MatrixFileAnalyzer	`[private, static]`
chain	ESTAnalyzer	`[protected]`
compareMetrics(const float metric1, const float metric2) const	MatrixFileAnalyzer	`[inline, protected, virtual]`
dataFileName	MatrixFileAnalyzer	`[private, static]`
displayStats(std::ostream &os)	ESTAnalyzer	`[inline, virtual]`
distanceValues	MatrixFileAnalyzer	`[protected]`
ESTAnalyzer(const std::string &analyzerName, const int refESTidx, const std::string &outputFileName)	ESTAnalyzer	`[protected]`
ESTAnalyzerFactory class	MatrixFileAnalyzer	`[friend]`
estCount	MatrixFileAnalyzer	`[protected]`
estFileName	ESTAnalyzer	`[protected, static]`
getAlignmentData(int &alignmentData)	ESTAnalyzer	`[inline, virtual]`
getHeuristicChain() const	ESTAnalyzer	`[inline, virtual]`
getInputFileName() const	ESTAnalyzer	`[inline]`
getInvalidMetric() const	MatrixFileAnalyzer	`[inline, protected, virtual]`
getMetric(const int otherEST)	MatrixFileAnalyzer	`[protected, virtual]`
getName() const	MatrixFileAnalyzer	`[inline, virtual]`
getPreferredDummyESTLength() const	ESTAnalyzer	`[inline, virtual]`
getValidMetric() const	ESTAnalyzer	`[inline, virtual]`
htmlLog	ESTAnalyzer	`[protected, static]`
initialize()	MatrixFileAnalyzer	`[virtual]`
inputFileName	MatrixFileAnalyzer	`[protected]`
isDistanceMetric() const	MatrixFileAnalyzer	`[inline, protected, virtual]`
loadFASTAFile(const char *fileName, const bool unpopulate=false)	ESTAnalyzer
MatrixFileAnalyzer(const int refESTidx, const std::string &outputFileName)	MatrixFileAnalyzer	`[private]`
noMaskBases	ESTAnalyzer	`[protected, static]`
outputFileName	ESTAnalyzer	`[protected]`
parseArguments(int &argc, char **argv)	MatrixFileAnalyzer	`[virtual]`
parseESTCount(const char *line)	MatrixFileAnalyzer	`[private]`
parseMetrics(const char line, float values, const int startPos, const int maxValues)	MatrixFileAnalyzer	`[private]`
readAhead	ESTAnalyzer	`[protected, static]`
readLine(FILE *fp)	MatrixFileAnalyzer	`[private]`
refESTidx	ESTAnalyzer	`[protected]`
setHeuristicChain(HeuristicChain *chain)	ESTAnalyzer	`[virtual]`
setReferenceEST(const int estIdx)	MatrixFileAnalyzer	`[virtual]`
showArguments(std::ostream &os)	MatrixFileAnalyzer	`[virtual]`
~ESTAnalyzer()	ESTAnalyzer	`[virtual]`
~MatrixFileAnalyzer()	MatrixFileAnalyzer	`[virtual]`