, including all inherited members.
| computeEnrichmentsOntologizer(const set< string > &geneSet, MyAnnotations &annotations, vector< EnrichmentRecord< string, string > > &rejalts) const | GeneOntology | |
| computeFunctionDepths(unsigned int type=0) | GeneOntology | |
| computeFunctionsWithNoChildren(set< string > &functions, set< string > &childless) | GeneOntology | |
| computeFunctionsWithNoChildren(set< GOFunction * > &functions, set< GOFunction * > &childless) | GeneOntology | |
| computeLeastCommonAncestors(GOFunction *function1, GOFunction *function2, vector< GOLCATuple > &lcas) (defined in GeneOntology) | GeneOntology | |
| computeMostSpecificFunctions(set< GOFunction * > &functions, set< GOFunction * > &specificFunctions) | GeneOntology | |
| computeMostSpecificFunctions(set< string > &functions, set< string > &specificFunctions) | GeneOntology | |
| computeMostSpecificFunctionsTemplated(InputIterator functionsBegin, InputIterator functionsEnd, OutputIterator specificFunctionsBegin, Extractor _extractor) (defined in GeneOntology) | GeneOntology | |
| computeSiblings(unsigned int type=0) | GeneOntology | |
| computeTopologicalSort(vector< GOFunction * > &sortedFunctions, unsigned int type=0) | GeneOntology | |
| GeneOntology() | GeneOntology | [inline] |
| GeneOntology(istream *in) | GeneOntology | |
| getAncestors(GOFunction *obj, int type=0) | GeneOntology | |
| getAncestorsWithDistance(GOFunction *obj, int type=0) | GeneOntology | |
| getChildren(GOFunction *obj, int type=0) | GeneOntology | |
| getDescendants(GOFunction *obj, int type=0) | GeneOntology | |
| getDescendantsWithDistance(GOFunction *obj, int type=0) | GeneOntology | |
| getFunctionById(int id) const | GeneOntology | |
| getFunctionById(string id) const | GeneOntology | [inline] |
| getFunctionByName(string name) const | GeneOntology | |
| getParents(GOFunction *obj, int type=0) | GeneOntology | |
| GOLCATuple typedef | GeneOntology | |
| groupFunctionsByCutoff(map< string, map< unsigned int, set< GOFunction * > > > &functionsByCutoff, const vector< unsigned int > &cutoffs, const map< BioFunction, unsigned int > &geneCounts, bool allowDescendants=false) (defined in GeneOntology) | GeneOntology | |
| groupFunctionsByDepth(map< unsigned int, set< GOFunction * > > &functionsByDepth, string functionCategory="biological_process", GOGroupByDepthType groupingType=GO_GROUP_BY_MINIMUM_DEPTH) | GeneOntology | |
| groupFunctionsByDepth2(map< string, map< unsigned int, set< GOFunction * > > > &functionsByDepth, bool allowDescendants=false) (defined in GeneOntology) | GeneOntology | |
| groupFunctionsByDepth2(map< string, map< unsigned int, set< BioFunction > > > &functionsByDepth, bool allowDescendants=false) (defined in GeneOntology) | GeneOntology | |
| isKnownFunctionId(string id) const (defined in GeneOntology) | GeneOntology | [inline] |
| printFunctionDepths(ostream &fstr, unsigned int type=0) | GeneOntology | |
| printFunctionDescendants(ostream &fstr, unsigned int type=0) | GeneOntology | |
| printRelationships() | GeneOntology | |
| read(string file) | GeneOntology | |
| read(istream *in) | GeneOntology | |
| readTerms(string file, vector< GOFunction * > &functions) | GeneOntology | |
| setBoolRelationship(bool r) (defined in GeneOntology) | GeneOntology | [inline] |
| setStrRelationshipFile(string file) (defined in GeneOntology) | GeneOntology | [inline] |
| ~GeneOntology() | GeneOntology | |
1.7.6.1
