, including all inherited members.
| addAnnotation(string gene, const BioFunction &function, string evidenceCode, MyGainAnnotationType status=ANNOTATED_STATE, bool msa=false) | MyAnnotations | |
| addAnnotation(string gene, string function, string funcType, string evidenceCode, MyGainAnnotationType status=ANNOTATED_STATE, bool msa=false) | MyAnnotations | |
| applyTruePathRule(GeneOntology &go, bool applyUpward=true, bool applyDownward=true, bool applySideways=true) | MyAnnotations | |
| checkTruePathRule(GeneOntology &go, ostream *ostr=NULL, bool *annotationsOK=NULL, bool *unknownOK=NULL) | MyAnnotations | |
| computeDifference(MyAnnotations &other, MyAnnotations &difference, bool restrictToCommonGenes=false) | MyAnnotations | |
| computeEnrichments(const set< string > &geneSet, const GeneOntology *go, vector< EnrichmentRecord< string, string > > &rejalts) | MyAnnotations | |
| computeEnrichmentsGenGO(const set< string > &geneSet, vector< EnrichmentRecord< string, string > > &rejalts, const GeneOntology *go=NULL, GenGOParametersOptimisationType optType=GENGO_PARAMETER_OPTIMISATION_NONE) const | MyAnnotations | |
| computeEnrichmentsGenGO(const set< string > &geneSet, string functionType, vector< EnrichmentRecord< string, string > > &rejalts, const GeneOntology *go=NULL, GenGOParametersOptimisationType optType=GENGO_PARAMETER_OPTIMISATION_NONE) const | MyAnnotations | |
| computeFunctionFrequency(string funcType, string func) | MyAnnotations | |
| computeGeneCounts(map< BioFunction, unsigned int > &geneCounts) (defined in MyAnnotations) | MyAnnotations | |
| computeStatistics() (defined in MyAnnotations) | MyAnnotations | |
| copyAnnotationsForFunctions(const set< BioFunction > &functions, MyAnnotations &annotations) (defined in MyAnnotations) | MyAnnotations | |
| functions(string type) | MyAnnotations | [inline, virtual] |
| functionsMultiIndex() const | MyAnnotations | [inline, virtual] |
| functionTypes() const | MyAnnotations | [inline] |
| getAnnotatedFunctionWeight(string gene, string func, string type) | MyAnnotations | |
| getAnnotatedFunctionWeightProbabilisticOr(string gene, string func, string type) | MyAnnotations | |
| getAnnotatedFunctionWeights(string gene, string func, string type) | MyAnnotations | |
| getAnnotatedGenes(string functype, set< string > &annotatedGenes) | MyAnnotations | |
| getAnnotatedWeights(string gene, string type) | MyAnnotations | |
| getAnnotations(string type, map< string, set< string > > &annotations) const | MyAnnotations | |
| getAnnotations(string type, string function, set< string > &annotations) const | MyAnnotations | [virtual] |
| getAnnotations(const GOFunction *function, set< string > &annotations) const | MyAnnotations | |
| getAnnotations(const set< GOFunction * > &functions, set< string > &annotations) const | MyAnnotations | |
| getAnnotationsByGene(string type, map< string, set< string > > &annotations) const | MyAnnotations | |
| getAnnotationsForGene(string type, string gene, set< string > &annotations) const | MyAnnotations | [virtual] |
| getEvidenceCodeCounts(map< string, unsigned int > &ecCounts) const | MyAnnotations | [inline] |
| getEvidenceCodeCounts(string funcType, string funcId, map< string, unsigned int > &ecCounts) const | MyAnnotations | |
| getFunctionFrequency(string function) const | MyAnnotations | [inline] |
| getFunctionType(string functionName) const | MyAnnotations | |
| hasAnnotatedFunction(string gene) const | MyAnnotations | [inline] |
| hasAnnotatedFunction(string gene, string category) const | MyAnnotations | [inline] |
| hasAnnotatedGene(string func, string type) const | MyAnnotations | [inline] |
| hasAnnotatedGene(const BioFunction &function) const | MyAnnotations | [inline] |
| hasExperimentallyAnnotatedFunction(string gene, string category) const | MyAnnotations | [inline] |
| haveOverlappingFunction(string gene1, string function, string type) (defined in MyAnnotations) | MyAnnotations | |
| haveSameFunction(string gene1, string gene2, const BioFunction &function) (defined in MyAnnotations) | MyAnnotations | |
| haveSameFunction(string gene1, string gene2, const vector< BioFunction > &functionVector) (defined in MyAnnotations) | MyAnnotations | |
| haveSameFunction(string gene1, string gene2, InputIterator first, InputIterator last) (defined in MyAnnotations) | MyAnnotations | |
| haveSameFunction(string gene1, string gene2, string type) (defined in MyAnnotations) | MyAnnotations | |
| haveSameFunction(string gene1, string gene2) (defined in MyAnnotations) | MyAnnotations | |
| isAnnotatedWithFunction(string gene, string func, string type, bool beforeTruePathRule=false) | MyAnnotations | |
| isAnnotatedWithFunctionExperimentally(string gene, string func, string type) | MyAnnotations | |
| isNotKnownToBeAnnotatedWithFunction(string gene, string func, string type) | MyAnnotations | [inline] |
| isNotKnownToBeAnnotatedWithFunctionSansTruePathRule(string gene, string func, string type, GeneOntology &goDAG) | MyAnnotations | |
| isUnknownFunction(string func, string type) const | MyAnnotations | [inline] |
| keepAnnotationsForGenes(set< string > &geneSet) | MyAnnotations | |
| MyAnnotations() (defined in MyAnnotations) | MyAnnotations | [inline] |
| NewBioFunctionsIterator (defined in MyAnnotations) | MyAnnotations | [friend] |
| numAnnotatedGenes(string funcType, string function) | MyAnnotations | [inline] |
| numAnnotatedGenes(string funcType="") | MyAnnotations | [inline] |
| numAnnotatingFunctions(string gene, string funcType) | MyAnnotations | [inline] |
| numAnnotatingFunctions(string funcType="") | MyAnnotations | [inline] |
| numAnnotations(string category="") | MyAnnotations | |
| numNegativeGenes(string funcType, string function) (defined in MyAnnotations) | MyAnnotations | [inline] |
| numNonAnnotatedGenes(string funcType) | MyAnnotations | [inline] |
| numNonAnnotatedGenes(string funcType, string function) (defined in MyAnnotations) | MyAnnotations | [inline] |
| numTotalNonAnnotatedGenes(string function, string funcType) | MyAnnotations | [inline] |
| numUnknownAnnotatingFunctions(string gene, string funcType) | MyAnnotations | [inline] |
| numUnknownAnnotations(string category="") | MyAnnotations | |
| print(string fileName) | MyAnnotations | |
| printNumAnnotationsPerFunction(ostream &numFunStream) | MyAnnotations | |
| printWithName(string fileName) | MyAnnotations | |
| read(string fileName, string dataType="unweighted", const map< string, set< string > > *nodeAliases=NULL, bool mostSpecificAnnotations=false, const set< string > *evidenceCodesToIgnore=NULL) | MyAnnotations | |
| read(string fileName, unsigned int keySize) | MyAnnotations | |
| readEvidenceCodeWeights(string ecwFile) | MyAnnotations | [inline] |
| readGO(string fileName, unsigned int altSymbolCol=0) | MyAnnotations | |
| readOverlappingFunctions(string fileName) (defined in MyAnnotations) | MyAnnotations | |
| setOverlappingFunctionsFlag() (defined in MyAnnotations) | MyAnnotations | [inline] |
| storeGODAG(GeneOntology &go) | MyAnnotations | [inline] |
| subtract(MyAnnotations &other, MyAnnotations &difference) | MyAnnotations | |
| ~MyAnnotations() (defined in MyAnnotations) | MyAnnotations | [inline, virtual] |
1.7.6.1
