, including all inherited members.
| alignmentMetric | D2 | [private] |
| analyze() | D2 | [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 | D2 | [private, static] |
| argumentFrameSize | FWAnalyzer | [protected, static] |
| BitMask | D2 | [private, static] |
| bitShift | D2 | [protected, static] |
| buildWordTable(std::vector< int > &wordTable, const char *estSeq, Encoder encoder) | D2 | [inline, protected] |
| chain | ESTAnalyzer | [protected] |
| compareMetrics(const float metric1, const float metric2) const | D2 | [inline, protected, virtual] |
| D2(const int refESTidx, const std::string &outputFileName) | D2 | [private] |
| delta | D2 | [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 | D2 | [friend] |
| estFileName | ESTAnalyzer | [protected, static] |
| frameShift | D2 | [protected, static] |
| frameSize | FWAnalyzer | [protected] |
| FWAnalyzer(const std::string &analyzerName, const int refESTidx, const std::string &outputFile) | FWAnalyzer | [protected] |
| getAlignmentData(int &alignmentData) | D2 | [protected, virtual] |
| getFrame(const EST *est, bool start=true) | FWAnalyzer | |
| getHeuristicChain() const | ESTAnalyzer | [inline, virtual] |
| getInputFileName() const | ESTAnalyzer | [inline] |
| getInvalidMetric() const | D2 | [inline, protected, virtual] |
| getMetric(const int otherEST) | D2 | [protected, virtual] |
| getName() const | D2 | [inline, virtual] |
| getPreferredDummyESTLength() const | FWAnalyzer | [inline, virtual] |
| getValidMetric() const | ESTAnalyzer | [inline, virtual] |
| hintKey | D2 | [private] |
| htmlLog | ESTAnalyzer | [protected, static] |
| initialize() | D2 | [virtual] |
| isDistanceMetric() const | D2 | [inline, protected, virtual] |
| loadFASTAFile(const char *fileName, const bool unpopulate=false) | ESTAnalyzer | |
| noMaskBases | ESTAnalyzer | [protected, static] |
| numWordsInWindow | D2 | [private] |
| outputFileName | ESTAnalyzer | [protected] |
| parseArguments(int &argc, char **argv) | D2 | [virtual] |
| readAhead | ESTAnalyzer | [protected, static] |
| referenceFrame | FWAnalyzer | [protected] |
| refESTidx | ESTAnalyzer | [protected] |
| runD2(const int otherEST) | D2 | [private] |
| s1WordTable | D2 | [protected] |
| s2WordTable | D2 | [protected] |
| setHeuristicChain(HeuristicChain *chain) | ESTAnalyzer | [virtual] |
| setReferenceEST(const int estIdx) | D2 | [virtual] |
| showArguments(std::ostream &os) | D2 | [virtual] |
| threshold | D2 | [protected, static] |
| updateWindow(const int wordIn, const int wordOut, int &score, int &minScore) | D2 | [inline, private] |
| wordSize | FWAnalyzer | [protected, static] |
| ~D2() | D2 | [virtual] |
| ~ESTAnalyzer() | ESTAnalyzer | [virtual] |
| ~FWAnalyzer() | FWAnalyzer | [virtual] |
