- c -

• candidateRotate() : PosLattice
• candidateRotateZero() : PosLattice
• candidateRotorStart() : PosLattice
• candidateRotorStartZero() : PosLattice
• candidateTick() : GenericLattice , PosLattice
• check() : Enrichment< S, T >
• checkEvidenceCodeWeights() : GOEvidenceCodes
• checkIfClosed() : Apriori
• checkTruePathRule() : MyAnnotations
• checkTruePathRuleForPredictions() : Reporter
• ChisqFilter() : ChisqFilter
• clear() : DAG< NodeType > , Itemset , DAG< NodeType > , Enrichment< S, T >
• clearColumns() : Itemset
• clearEdgeEnrichments() : ActiveNetwork , SetOfActiveNetworks
• clearNodeEnrichments() : ActiveNetwork , SetOfActiveNetworks
• ClearResults() : Enrichment< S, T >
• ClearUniverse() : Enrichment< S, T >
• clone() : MyAbstractGraphModification , MyGraphEdgeDeletion , MyGraphEdgeInsertion , MyGraphNodeDeletion , MyGraphNodeInsertion
• collapse() : MyGainState< StateType >
• compareNetworkLegosToActiveNetworks() : SetOfActiveNetworks , SetOfNetworkLegos
• comparePredictions() : Reporter
• compareTTest() : MyPointSet
• components() : MyGraph
• compute() : SetOfNetworkLegos
• computeAverageExpressionValue() : MyPointSet
• computeBinaryMatrix() : SetOfActiveNetworks
• computeBinaryVector() : MyGraph
• computeClassIndexForSamples() : motifDataset , readfile
• computeClassNameForSamples() : motifDataset , readfile
• computeClosestNode() : MyGraph
• computeCommonNeighbours() : MyNode , MyGraph
• computeCompleteness() : MyGraph
• computeCoordinateDistribution() : MyPointSet
• computeCorrelations() : NetMan , MyPointSet
• computeCorrelationsHistogram() : MyPointSet
• computeCrossValidationResults() : MyAbstractGainAlgo< StateType > , MyOneVersusAllGainAlgo , MyOneVersusAllSinkSourceGainAlgo , MyOneVersusAllGeneManiaGainAlgo
• computeCut() : MyAbstractGainAlgo< StateType > , MyOneVersusAllGainAlgo
• computeDenseFunctions() : NetMan
• computeDenseSubgraphs() : MyGraph
• computeDensity() : MyGraph
• computeDifference() : DAG< NodeType > , MyAnnotations , DAG< NodeType >
• computeDiscreteCorrelation() : MyPoint
• computeEdgeBetweenessCentrality() : SetOfActiveNetworks , MyGraph
• computeEdgeCDWeights() : MyGraph
• computeEdgeEnrichments() : ActiveNetwork , SetOfActiveNetworks
• computeEdgeFSWeights() : MyGraph
• computeEdgeSimilarityGraph() : SetOfActiveNetworks
• computeEdgeTypeCounts() : MyGraph
• computeEdgeTypeOverlaps() : MyGraph
• computeEdgeTypeSubgraphs() : MyGraph
• computeEnergy() : MyOneVersusAllGainAlgo
• computeEnrichedFunctions() : FunctionalEnrichmentAlgorithm , RandomFunctionNetworkBasedEnrichmentAlgorithm , RandomUniverseNetworkBasedEnrichmentAlgorithm , GenGOAlgorithm , GroupHypAlgorithm , EdgeGroupHyp , FuncAssociate , SetCoverEnrichment
• computeEnrichmentForFunction() : FunctionalEnrichmentAlgorithm , RandomFunctionNetworkBasedEnrichmentAlgorithm , RandomUniverseNetworkBasedEnrichmentAlgorithm , HypergeometricAlgorithm , PAGEAlgorithm , GenGOAlgorithm , GroupHypAlgorithm , EdgeGroupHyp , FuncAssociate , SetCoverEnrichment
• computeEnrichments() : MyAnnotations
• computeEnrichmentsGenGO() : MyAnnotations
• computeEnrichmentsOntologizer() : GeneOntology
• computeExpansionNodeBased() : MyGraph
• computeFunctionDepths() : GeneOntology
• computeFunctionFrequency() : MyAnnotations
• computeFunctionsWithNoChildren() : GeneOntology
• computeGraphScore() : MCODE
• computeHistogramEdgeWeights() : MyGraph
• computeHistogramNodeWeights() : MyGraph
• computeHyperGeometricProbability() : Enrichment< S, T >
• computeInducedSubgraph() : MyGraph
• computeIntersection() : MyGraph
• computeItemsetFromRows() : Apriori
• computeItemsets() : Apriori , AprioriWithComplement
• computeItemsetsLowRAM() : Apriori
• computeLattice() : Apriori
• computeLatticeEdgeType() : Apriori , AprioriWithComplement
• computeLeaves() : DAG< NodeType >
• computeMaximallySignificantItemsets() : SetOfNetworkLegos
• computeMaximumSpanningTreePrim() : MyGraph
• computeMean() : MyHistogram , MyPointSet
• computeMeanAndStandardDeviation() : MyPointSet
• computeMeanAndVariance() : MyPointSet
• computeMinimumSpanningTreePrim() : MyGraph
• computeMostPerturbedSubgraph() : MyGraph
• computeMostSimilarEdges() : SetOfActiveNetworks
• computeMostSimilarGraphEdges() : MyGraph
• computeMostSimilarGraphNodes() : MyGraph
• computeMostSimilarNodes() : SetOfActiveNetworks
• computeMostSpecificFunctions() : GeneOntology
• computeNodeBetweenessCentrality() : SetOfActiveNetworks
• computeNodeCounts() : SetOfActiveNetworks
• computeNodeEnrichments() : ActiveNetwork
• computeNodeSimilarityGraph() : SetOfActiveNetworks
• computeNodeWeights() : SetOfActiveNetworks , ActiveNetwork
• computeNorm() : MyPoint
• computeNumCommonEdges() : MyGraph
• computeNumCommonEdgesWeighted() : MyGraph
• computeNumCommonNodes() : MyGraph
• computeNumCommonNodesWeighted() : MyGraph
• computePathwayPerturbation() : NetMan
• computePearsonsCorrelation() : MyPoint
• computePower() : DAG< NodeType >
• computePredictionRanks() : Reporter
• computePredictions() : MyAbstractGainAlgo< StateType > , MyOneVersusAllGainAlgo , MyOneVersusAllSinkSourceGainAlgo , MyOneVersusNoneFunctionalFlowGainAlgo , MyOneVersusAllGeneManiaGainAlgo , MyOneVersusAllSemiHierarchicalHopfieldGainAlgo
• computeProbabilitiesFromEdgeWeights() : MyGainGraph
• computePvalues() : SetOfActiveNetworks
• computeRandomDistribution() : Apriori
• computeRandomisedCorrelationsHistogram() : MyPointSet
• computeRandomNeighbour() : MyDensestSubgraphAnnealState , MyAbstractAnnealState , MyDensestSubgraphConnectedBruteForceAnnealState
• computeRanks() : MyPoint
• computeRoots() : DAG< NodeType >
• computeScore() : MyAbstractAnnealState , MyDensestSubgraphAnnealState
• computeSegregation() : MyGraph
• computeSemanticValue() : GOFunction
• computeSeparator() : MyGraph
• computeSeparatorRatio() : MyGraph
• computeShortestPathDAG() : MyGraph
• computeSiblings() : GOFunction , GeneOntology
• computeSignificantLegos() : SetOfNetworkLegos
• computeSimilarityEdges() : MyGraph
• computeSimilarityEdgesWeighted() : MyGraph
• computeSimilarityNodes() : MyGraph
• computeSimilarityNodesWeighted() : MyGraph
• computeSNetwork() : SetOfActiveNetworks
• computeSparsityHoyer() : MyPoint
• computeStability() : SetOfNetworkLegos
• computeStandardDeviation() : MyHistogram
• computeState() : MyOneVersusAllSinkSourceGainAlgo , MyOneVersusAllHopfieldGainAlgo , MyAbstractGainAlgo< StateType > , MyOneVersusAllGainAlgo , MyOneVersusAllLocalGainAlgo , MyOneVersusNoneFunctionalFlowGainAlgo , MyOneVersusNoneLocalGainAlgo , MyOneVersusAllGeneManiaGainAlgo
• computeStouffersZScore() : MyGraph
• computeStouffersZScoreSlowly() : MyGraph
• computeTopologicalSort() : DAG< NodeType > , GeneOntology , DAG< NodeType >
• computeTransitiveClosure() : DAG< NodeType >
• computeTransitiveReduction() : DAG< NodeType >
• computeTrivialLegos() : SetOfNetworkLegos
• computeUnion() : SetOfActiveNetworks
• computeVariance() : MyHistogram
• computeWeightedDensity() : MyGraph
• construct() : MyGraph
• constructCrossValidationLists() : MyOneVersusAllGainAlgo , MyAbstractGainAlgo< StateType >
• constructTDistributionHistogram() : MyHistogram
• containsColumn() : Itemset , Apriori
• containsRow() : Apriori , Itemset
• containsRows() : Itemset
• convertToPvalues() : MyHistogram
• convertToRanks() : MyPointSet
• copy() : MyNode
• copyEdgeWeights() : MyGraph
• correct() : Enrichment< S, T >
• countSets() : PosLattice
• countSubsets() : PosLattice
• countTable() : HPosMiner , PosMiner , TreeMiner
• createCandidate() : GenericLattice , PosLattice
• createCandidateRotate() : PosLattice
• createCandidateRotorStart() : PosLattice
• createErdosRenyiNPGraph() : MyGraph
• createSubgraph() : MyGraph
• createWebPages() : NetMan