, including all inherited members.
| _anetIdToIndex (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [protected] |
| _anets (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [protected] |
| _combinedAnet (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [protected] |
| _edgeCentralities (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [protected] |
| _nodeCentralities (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [protected] |
| _nodeCounts (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [protected] |
| add(ActiveNetwork &anet) | SetOfActiveNetworks | [inline] |
| add(vector< ActiveNetwork > &nets) | SetOfActiveNetworks | [inline] |
| add(Itemset &itemset, unsigned int index) | SetOfActiveNetworks | [inline] |
| add(vector< Itemset > &itemsets) | SetOfActiveNetworks | [inline] |
| addCondition(string condition) | SetOfActiveNetworks | [inline] |
| clearEdgeEnrichments() | SetOfActiveNetworks | |
| clearNodeEnrichments() | SetOfActiveNetworks | |
| compareNetworkLegosToActiveNetworks() | SetOfNetworkLegos | [virtual] |
| compute(ostream &logStream, unsigned int minNumberConditions=1, unsigned int minNumberInteractions=1) | SetOfNetworkLegos | [virtual] |
| computeBinaryMatrix(vector< vector< unsigned int > > &binaryMatrix, map< unsigned int, string > &rowNames, map< unsigned int, string > &columnNames, bool addComplements=false, set< unsigned int > *complementRows=NULL) | SetOfActiveNetworks | |
| computeEdgeBetweenessCentrality() | SetOfActiveNetworks | |
| computeEdgeEnrichments(const MyAnnotations &annotations) | SetOfActiveNetworks | |
| computeEdgeSimilarityGraph(MyGraph &graph) const | SetOfActiveNetworks | |
| computeMaximallySignificantItemsets(const vector< Itemset > &allSignificantItemsets, vector< Itemset > &maximallySignificantItemsets, vector< Itemset > &significantLatticeRoots, vector< Itemset > &significantLatticeLeaves) | SetOfNetworkLegos | |
| computeMostSimilarEdges(const MyGraph &other, unsigned int &bestIndex) const | SetOfActiveNetworks | |
| computeMostSimilarNodes(const MyGraph &other, unsigned int &bestIndex) const | SetOfActiveNetworks | |
| computeNodeBetweenessCentrality() | SetOfActiveNetworks | |
| computeNodeCounts() | SetOfActiveNetworks | |
| computeNodeSimilarityGraph(MyGraph &graph) const | SetOfActiveNetworks | |
| computeNodeWeights(const GEData &gedata) | SetOfActiveNetworks | |
| computePvalues(const MyHistogram &histogram) | SetOfActiveNetworks | |
| computeRecoverability(ostream &logStream) (defined in SetOfNetworkLegos) | SetOfNetworkLegos | [virtual] |
| computeSignificantLegos(ostream &logStream, unsigned int numRandomTrials=100000, MyNT pvalueThreshold=0.01) | SetOfNetworkLegos | [virtual] |
| computeSNetwork() | SetOfActiveNetworks | |
| computeStability(ostream &logStream) | SetOfNetworkLegos | [virtual] |
| computeTrivialLegos(ostream &logStream) | SetOfNetworkLegos | [virtual] |
| computeUnion(string name, ActiveNetwork &unionActiveNetwork) | SetOfActiveNetworks | [inline] |
| computeUnion(string name) | SetOfActiveNetworks | |
| expand(const GEData &expression, string id, MyNT correlationThreshold) | SetOfActiveNetworks | |
| getActiveNetworks() | SetOfActiveNetworks | [inline] |
| getNumActiveNetworks() const | SetOfActiveNetworks | [inline] |
| getSignificantLegos(SetOfActiveNetworks &legos) | SetOfNetworkLegos | [inline, virtual] |
| getUnion(ActiveNetwork &unionActiveNetwork) | SetOfActiveNetworks | [inline] |
| printBinaryMatrix(ostream &ostr, bool transposed=false) const | SetOfNetworkLegos | |
| printClosedLattice(ostream &ostr) const | SetOfNetworkLegos | [inline] |
| printConditions(ostream &conditionStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printEdgeBetweenessCentrality(ostream &edgeCentralityStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printEdgeEnrichments(ostream &edgeEnrichmentStream, ostream &edgeEnrichedFunctionStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printEdges(ostream &edgeStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printEdgesItemset(ostream &itemsetStream, string id) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printEdgeTypeCounts(ostream &edgeTypesCountStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printEdgeWeightsHistograms(ostream &edgeWeightsHistogramStream, string fileName) | SetOfActiveNetworks | |
| printLattice(ostream &ostr) const | SetOfNetworkLegos | [inline] |
| printNodeBetweenessCentrality(ostream &nodeCentralityStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printNodeEnrichments(ostream &nodeEnrichmentStream, ostream &nodeEnrichedFunctionStream, GeneOntology *go) | SetOfActiveNetworks | |
| printNodes(ostream &nodeStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| printNodeWeightsHistograms(ostream &nodeWeightsHistogramStream, string fileName) | SetOfActiveNetworks | |
| printStatistics(ostream &statStream) (defined in SetOfActiveNetworks) | SetOfActiveNetworks | |
| processNodeEnrichments(ostream &processNodeEnrichmentsStream, const GeneOntology *go) | SetOfActiveNetworks | |
| read(const vector< string > &activeNetworkFiles) | SetOfActiveNetworks | |
| read(string activeNetworkFile) | SetOfActiveNetworks | |
| readEdges(string edgesFile) | SetOfActiveNetworks | |
| readMappingFromNetworkLegosToActiveNetworks(string nlsToRNsFile) | SetOfNetworkLegos | [virtual] |
| readNodeEnrichedFunctions(string nodeEnrichedFunctionsFile) | SetOfActiveNetworks | |
| readNodeEnrichments(string nodeEnrichmentsFile) | SetOfActiveNetworks | |
| readNodes(string nodesFile, MyGraph &superGraph) | SetOfActiveNetworks | |
| SetOfActiveNetworks() (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [inline] |
| SetOfNetworkLegos() (defined in SetOfNetworkLegos) | SetOfNetworkLegos | [inline] |
| SetOfNetworkLegos(SetOfActiveNetworks &anetSet) (defined in SetOfNetworkLegos) | SetOfNetworkLegos | [inline] |
| ~SetOfActiveNetworks() (defined in SetOfActiveNetworks) | SetOfActiveNetworks | [inline, virtual] |
| ~SetOfNetworkLegos() (defined in SetOfNetworkLegos) | SetOfNetworkLegos | [inline, virtual] |
1.7.6.1
