, including all inherited members.
| _check() const (defined in MyGraph) | MyGraph | [protected] |
| _checkDegree() const (defined in MyGraph) | MyGraph | [protected] |
| _checkNodeTotalEdgeWeight() (defined in MyGraph) | MyGraph | |
| _computeDensestSubgraphApprox(MyGraph &subgraph, bool hide=false, ostream *fstr=NULL) (defined in MyGraph) | MyGraph | [protected] |
| _computeDensestWeightedSubgraphApprox(MyGraph &subgraph, bool optimiseStouffersZscore=false, bool hide=false, ostream *fstr=NULL) (defined in MyGraph) | MyGraph | [protected] |
| _copyEdges(const MyGraph ©) (defined in MyGraph) | MyGraph | [protected] |
| _copyNodes(const MyGraph ©) (defined in MyGraph) | MyGraph | [protected] |
| _core(unsigned int k, bool hide, ostream *fstr) (defined in MyGraph) | MyGraph | [protected] |
| _createDegreeLists(unsigned int &minDegree, vector< list< MyNodeId > > °reeLists, map< MyNodeId, list< MyNodeId >::iterator > &nodePositions) const (defined in MyGraph) | MyGraph | |
| _decrementDegrees(vector< list< MyNodeId > > °reeLists, map< MyNodeId, list< MyNodeId >::iterator > &nodePositions, const set< MyNodeId > &neighbours) const (defined in MyGraph) | MyGraph | |
| _find_cores(vector< MyGraph > &cores) (defined in MyGraph) | MyGraph | [protected] |
| _findCliques(vector< MyGraph > &cliques, ostream &ostr) (defined in MyGraph) | MyGraph | [protected] |
| _getNode(MyNodeId id) const (defined in MyGraph) | MyGraph | [inline] |
| _getNode(MyNodeId id) (defined in MyGraph) | MyGraph | [inline] |
| _getNode(MyNodePtr &nptr) (defined in MyGraph) | MyGraph | [inline, protected] |
| _getNode(MyConstNodePtr &nptr) const (defined in MyGraph) | MyGraph | [inline, protected] |
| _getNodeId(MyNodePtr &nptr) (defined in MyGraph) | MyGraph | [inline, protected] |
| _getNodeId(MyConstNodePtr &nptr) const (defined in MyGraph) | MyGraph | [inline, protected] |
| _tryAddingNode(MyNodeId nid, const set< MyNodeId > ¤tClique) (defined in MyGraph) | MyGraph | [protected] |
| add(MyGraph &other) | MyGraph | [virtual] |
| addEdge(const MyEdge &edge) (defined in MyGraph) | MyGraph | |
| addEdge(MyNodeId nodeId1, MyNodeId nodeId2, MyNT weight=1, set< string > *types=NULL, bool keepGraphSimple=true) | MyGraph | |
| addInduced(MyGraph &other) | MyGraph | [virtual] |
| addNode(MyNodeId id) (defined in MyGraph) | MyGraph | [inline] |
| addNode(const MyNode &node) (defined in MyGraph) | MyGraph | [inline] |
| addNodeFunction(MyNodeId id, string function) (defined in MyGraph) | MyGraph | [inline] |
| addNodes(set< MyNodeId > ids) | MyGraph | [inline] |
| assignEdgeWeightFromDepth(const MyGainParams &gainParams, string annotationType, string category, unsigned int depth, MyEdge &edge) (defined in MyGainGraph) | MyGainGraph | |
| assignEdgeWeightsFromEdgeTypeWeights(const map< string, MyNT > &edgeTypeWeights) (defined in MyGraph) | MyGraph | |
| clear() (defined in MyGraph) | MyGraph | [virtual] |
| components(vector< MyGraph > *comps=NULL) | MyGraph | |
| computeBinaryVector(const map< string, unsigned int > &edgeToColumn, vector< unsigned int > &binaryVector) const | MyGraph | |
| computeChangeInEnergy(MyNodeStatesType &nodeStates, string changedNodeId) (defined in MyGainGraph) | MyGainGraph | |
| computeClosestNode(const MyNode &rootNode, MyNodeIdSet &nodeSet, MyNodeId &closest) | MyGraph | |
| computeCommonNeighbours(MyNode &node1, MyNode &node2, set< MyNodeId > &common) | MyGraph | |
| computeCompleteness() const | MyGraph | [inline] |
| computeDenseFunctions(ostream *fstr, MyAnnotations &annotations, GeneOntology &go, map< string, MyGraph > &denseFunctionSubgraphs) (defined in MyGainGraph) | MyGainGraph | |
| computeDensestSubgraphApprox(MyGraph &subgraph, bool optimiseStouffersZscore=false, ostream *fstr=NULL) const (defined in MyGraph) | MyGraph | |
| computeDenseSubgraphs(ostream &logStream, vector< MyGraph > &denseSubgraphs, bool computeDenseSubgraphsTillTheBitterEnd=false, bool splitDenseSubgraphsIntoComponents=false, bool suppressDetails=false) | MyGraph | |
| computeDensity() const | MyGraph | |
| computeEdgeBetweenessCentrality(ostream *fstr, map< MyEdge, MyNT > *bets) | MyGraph | |
| computeEdgeCDWeights() | MyGraph | |
| computeEdgeFSWeights() | MyGraph | |
| computeEdgeProbabilitiesPerDepth(MyGainParams ¶ms, const map< unsigned int, set< GOFunction * > > &functionsByDepth, MyAnnotations &annotations, map< BioFunction, MyHistogram > &probabilities) (defined in MyGainGraph) | MyGainGraph | |
| computeEdgeProbabilitiesPerParent(MyGainParams ¶ms, GeneOntology &go, MyAnnotations &annotations, map< BioFunction, MyHistogram > &probs) (defined in MyGainGraph) | MyGainGraph | |
| computeEdgeTypeCounts(map< string, unsigned int > &counts) const | MyGraph | |
| computeEdgeTypeOverlaps() const | MyGraph | |
| computeEdgeTypeSubgraphs(ostream &logStream, map< string, MyGraph > &edgeTypeSubgraphs, bool useShared=1) | MyGraph | |
| computeEdgeTypeWeightsByCutoffFromSharedFunctionRatio(MyAnnotations &annotations, GeneOntology &go, MyGainParams &gainParams) (defined in MyGainGraph) | MyGainGraph | |
| computeEdgeTypeWeightsByDepthFromSharedFunctionRatio(MyAnnotations &annotations, GeneOntology &go, MyGainParams &gainParams) (defined in MyGainGraph) | MyGainGraph | |
| computeEdgeTypeWeightsJaccard(ostream &logStream, MyAnnotations &annotations) (defined in MyGainGraph) | MyGainGraph | |
| computeEnergy(MyNodeStatesType &nodeStates) (defined in MyGainGraph) | MyGainGraph | |
| computeExpansionNodeBased(MyGraph &superGraph) | MyGraph | |
| computeHistogramEdgeWeights(MyHistogram &hist, bool cumulative=false, bool reverse=false) | MyGraph | |
| computeHistogramNodeWeights(MyHistogram &hist, bool cumulative=false, bool reverse=false) | MyGraph | |
| computeInducedSubgraph(const set< MyNodeId > &subgraphNodes, MyGraph &subgraph) const | MyGraph | |
| computeInput(string nodeId, MyNodeStatesType &nodeStates) const (defined in MyGainGraph) | MyGainGraph | |
| computeIntersection(const vector< MyGraph > &others) | MyGraph | |
| computeMaximumSpanningTreePrim(MyGraph &mst) | MyGraph | |
| computeMinimumSpanningTreePrim(MyGraph &mst) | MyGraph | |
| computeMostPerturbedSubgraph(MyGraph &subgraph, unsigned int numIterationsFactor, ostream &logStream, bool runOnCopy=true) | MyGraph | |
| computeMostSimilarGraphEdges(const vector< MyGraph > &others, unsigned int &bestIndex) const | MyGraph | |
| computeMostSimilarGraphNodes(const vector< MyGraph > &others, unsigned int &bestIndex) const | MyGraph | |
| computeMSTPrim(MyGraph &mst) (defined in MyGraph) | MyGraph | |
| computeNodeBetweenessCentrality(ostream *fstr, map< MyNodeId, MyNT > *bets) (defined in MyGraph) | MyGraph | |
| computeNumCommonEdges(const MyGraph &other) const | MyGraph | |
| computeNumCommonEdgesWeighted(const MyGraph &other) const | MyGraph | |
| computeNumCommonNodes(const MyGraph &other) const | MyGraph | |
| computeNumCommonNodesWeighted(const MyGraph &other) const | MyGraph | |
| computeProbabilitiesFromEdgeWeights(ostream &fstr, const MyPointSet &geData, string experimentName, MyHistogram &edgeWeightsToProbabilities) (defined in MyGainGraph) | MyGainGraph | |
| computeProbabilitiesFromEdgeWeights(ostream &fstr, MyAnnotations &annotations, const vector< BioFunction > *functionVector, MyHistogram &edgeWeightsToProbabilities) | MyGainGraph | |
| computeSegregation(MyNodeIdList &nodes) | MyGraph | [inline] |
| computeSeparator(const set< MyNodeId > &nodes, set< MyNodeId > &separator) | MyGraph | |
| computeSeparatorRatio(MyGraph subgraph) | MyGraph | |
| computeShortestPathDAG(const MyNode &node, map< MyNodeId, MyNT > &distance, map< MyNodeId, unsigned int > &count) | MyGraph | |
| computeShortestPathDAG(const MyNodeId nodeid, map< MyNodeId, MyNT > &distance, map< MyNodeId, unsigned int > &count) | MyGraph | |
| computeShortestPathDAG(const MyNode &node, map< MyNodeId, MyNT > &distance, map< MyNodeId, unsigned int > &count, stack< MyNodeId > &descendents, map< MyNodeId, vector< MyNodeId > > &predecessors) (defined in MyGraph) | MyGraph | |
| computeShortestPathDAG(const MyNode &node, map< MyNodeId, MyNT > &distance, map< MyNodeId, unsigned int > &count, stack< MyNodeId > &descendents, map< MyNodeId, vector< MyNodeId > > &predecessors, map< MyNodeId, vector< MyNodeId > > &successors) (defined in MyGraph) | MyGraph | |
| computeSimilarityEdges(const MyGraph &other, bool jacquard=true, bool asymmetric=false) const | MyGraph | |
| computeSimilarityEdgesWeighted(const MyGraph &other, bool jacquard=true, bool asymmetric=false) const | MyGraph | |
| computeSimilarityNodes(const MyGraph &other, bool jacquard=true, bool asymmetric=false) const | MyGraph | |
| computeSimilarityNodesWeighted(const MyGraph &other, bool jacquard=true, bool asymmetric=false) const | MyGraph | |
| computeStouffersZScore() const | MyGraph | |
| computeStouffersZScoreSlowly() const | MyGraph | |
| computeWeightedDensity() | MyGraph | |
| ConstIncidentEdgeIterator typedef (defined in MyGraph) | MyGraph | |
| construct(const map< string, map< string, MyNT > > &allEdgeWeights) | MyGraph | [virtual] |
| copyEdgeWeights(MyGraph &other) | MyGraph | |
| core(unsigned int k, MyGraph &subgraph, bool hide, ostream *fstr=NULL) const (defined in MyGraph) | MyGraph | |
| createErdosRenyiNPGraph(MyGraph &graph, unsigned long numNodes, MyNT prob=0.5) | MyGraph | [static] |
| createSubgraph(const vector< MyNodeId > &deletedNodes, MyGraph &subgraph) const | MyGraph | |
| degree(MyNodeId nid) const | MyGraph | [inline] |
| degrees(map< unsigned int, unsigned int > &distribution) const | MyGraph | |
| deleteDisconnectedNodes() | MyGraph | |
| deleteEdge(MyNodeId node1, MyNodeId node2) | MyGraph | |
| deleteNode(MyNodeId id, set< MyNodeId > *neighbours=NULL) | MyGraph | |
| deleteNodeSet(const set< MyNodeId > ids) | MyGraph | |
| deleteSubgraphEdges(MyGraph &subgraph) | MyGraph | |
| deleteSubgraphNodes(MyGraph &subgraph) | MyGraph | |
| Edge typedef (defined in MyGraph) | MyGraph | |
| EdgeIterator typedef (defined in MyGraph) | MyGraph | |
| edges() | MyGraph | [inline, virtual] |
| edges() const | MyGraph | [inline, virtual] |
| find_cores(vector< MyGraph > &cores) const (defined in MyGraph) | MyGraph | |
| findCliques(vector< MyGraph > &cliques, ostream &ostr) const (defined in MyGraph) | MyGraph | |
| getAverageNodeWeight() | MyGraph | |
| getEdge(MyNodeId node1, MyNodeId node2) const | MyGraph | [inline] |
| getEdge(MyNodeId node1, MyNodeId node2, MyEdgePtr &ptr) (defined in MyGraph) | MyGraph | [inline] |
| getEdgeSet(set< string > &edgeSet) const | MyGraph | [inline] |
| getId() const (defined in MyGraph) | MyGraph | [inline] |
| getName() const (defined in MyGraph) | MyGraph | [inline] |
| getNodeSet(set< MyNodeId > &nodeSet) const | MyGraph | [inline] |
| getNodeVec(vector< MyNodeId > &nodeVec) const | MyGraph | [inline] |
| getTotalAbsoluteEdgeWeight() const | MyGraph | |
| getTotalAbsoluteNodeWeight() const | MyGraph | |
| getTotalEdgeWeight() const | MyGraph | |
| getTotalNodeWeight() const | MyGraph | |
| getTotalSquaredNodeDegrees() const | MyGraph | |
| IncidentEdgeIterator typedef (defined in MyGraph) | MyGraph | |
| incidentEdges(MyNodeId nodeId) (defined in MyGraph) | MyGraph | [inline, virtual] |
| incidentEdges(MyNode &node) (defined in MyGraph) | MyGraph | [inline, virtual] |
| isConnected() | MyGraph | |
| isEdge(MyNodeId node1, MyNodeId node2) const | MyGraph | [inline] |
| isEdge(const MyNode &node1, const MyNode &node2) const | MyGraph | [inline] |
| isEdgeValid(MyEdgePtr eptr) | MyGraph | [inline] |
| isHiddenNode(MyNodeId id) const | MyGraph | [inline] |
| isInduced(const MyGraph &subgraph) | MyGraph | |
| isNode(const MyNode &node) const | MyGraph | [inline] |
| isNode(MyNodeId id) const | MyGraph | [inline] |
| isValidEdge(const MyEdgePtr &eptr) const | MyGraph | [inline] |
| isVisibleNode(MyNodeId id) const | MyGraph | [inline] |
| MyConstEdgeIterator typedef (defined in MyGraph) | MyGraph | |
| MyConstEdgePtr typedef (defined in MyGraph) | MyGraph | |
| MyConstNodeIterator typedef (defined in MyGraph) | MyGraph | |
| MyConstNodePtr typedef (defined in MyGraph) | MyGraph | |
| MyEdgeIterator typedef (defined in MyGraph) | MyGraph | |
| MyEdgeList typedef (defined in MyGraph) | MyGraph | |
| MyEdgePtr typedef (defined in MyGraph) | MyGraph | |
| MyGainGraph() (defined in MyGainGraph) | MyGainGraph | [inline] |
| MyGainGraph(string infile, string type, string outputDir, string commandLine, MyNT minEdgeWeight=0) (defined in MyGainGraph) | MyGainGraph | [inline] |
| MyGraph() (defined in MyGraph) | MyGraph | [inline] |
| MyGraph(string infile, string type, MyNT minEdgeWeight=0) (defined in MyGraph) | MyGraph | [inline] |
| MyGraph(const MyGraph ©) (defined in MyGraph) | MyGraph | |
| MyNodeList typedef (defined in MyGraph) | MyGraph | |
| MyNodePtr typedef (defined in MyGraph) | MyGraph | |
| Node typedef (defined in MyGraph) | MyGraph | |
| nodeFunctions(MyNodeId id, vector< string > &fns) const (defined in MyGraph) | MyGraph | [inline] |
| NodeIterator typedef (defined in MyGraph) | MyGraph | |
| nodes() | MyGraph | [inline, virtual] |
| nodes() const | MyGraph | [inline, virtual] |
| numEdges() const | MyGraph | [inline] |
| numHiddenEdges() const | MyGraph | [inline] |
| numHiddenNodes() const | MyGraph | [inline] |
| numNodes() const | MyGraph | [inline] |
| operator<(const MyGraph &rhs) const | MyGraph | |
| operator=(const MyGraph &rhs) (defined in MyGraph) | MyGraph | |
| power(unsigned int distance) (defined in MyGraph) | MyGraph | |
| print(ostream &fstr=cout, string name="") | MyGraph | [virtual] |
| printAllPairsShortestPathDistances(ostream &ostr) | MyGraph | |
| printAllPairsShortestPathDistances(string outfile) | MyGraph | |
| printDimacs(string filename, MyNodeStatesType &nodeStates, string format) (defined in MyGainGraph) | MyGainGraph | |
| printEdges(ostream &fstr=cout, string name="") const | MyGraph | [virtual] |
| printEdgesItemset(ostream &fstr, vector< string > types) (defined in MyGraph) | MyGraph | [virtual] |
| printEdgeTypeCounts(ostream &ostr) const | MyGraph | |
| printNodes(ostream &fstr=cout, string name="") | MyGraph | [virtual] |
| printStates(ofstream &ostr, const MyNodeStatesType &states, string currentFunc, string algorithm="Hopfield", bool printAll=false) (defined in MyGainGraph) | MyGainGraph | |
| randomise(MyGraph &random, map< MyNodeId, bool > *vertexcover=NULL) | MyGraph | |
| randomiseErdosRenyiSubgraph(MyGraph &random, const vector< MyNodeId > &subgraphNodes, MyNT prob=0.5) | MyGraph | |
| randomiseErdosRenyiSubgraph(MyGraph &random, const set< MyNodeId > &subgraphNodes, MyNT prob=0.5) | MyGraph | |
| randomiseErdosRenyiSubgraph(const set< MyNodeId > &subgraphNodes, MyNT prob) | MyGraph | |
| randomiseVectorOfEdges(MyGraph &random, unsigned int numIterations) | MyGraph | |
| read(string fileName, string type="", MyNT minEdgeWeight=0, ostream &logStream=cout) | MyGraph | [virtual] |
| read2(string fileName, string type="", MyNT minEdgeWeight=0, ostream &logstream=cout) | MyGraph | [virtual] |
| readEdgeTypeGroups(string fileName) (defined in MyGraph) | MyGraph | |
| readEdgeWeights(string weightsFile) (defined in MyGraph) | MyGraph | [virtual] |
| readNodeTypes(string file) | MyGraph | [virtual] |
| reduce2(ostream &hopstr, map< MyNodeId, MyGainTriStateType > &nodeStates, const MyGainParams ¶ms, MyGainGraph &reducedGraph, MyNodeIdSet &unpredictableNodes) | MyGainGraph | |
| resetThreshold() (defined in MyGainGraph) | MyGainGraph | [inline] |
| runMinCut(string outfile, MyNodeStatesType &nodeStates, const MyGainParams ¶ms) (defined in MyGainGraph) | MyGainGraph | |
| setEdgeWeight(MyNodeId node1, MyNodeId node2, MyNT weight) (defined in MyGraph) | MyGraph | |
| setEdgeWeight(MyEdge *edge, MyNT weight) (defined in MyGraph) | MyGraph | |
| setEdgeWeights(ostream &fstr, const MyHistogram &edgeWeightsToProbabilities) (defined in MyGainGraph) | MyGainGraph | |
| setEdgeWeightsCorrelations(ostream &fstr, const MyPointSet &geData) (defined in MyGainGraph) | MyGainGraph | |
| setName(string name) (defined in MyGraph) | MyGraph | [inline] |
| setNodeWeights() (defined in MyGainGraph) | MyGainGraph | |
| setUseDegree(bool ud) (defined in MyGainGraph) | MyGainGraph | [inline] |
| sparsify(string method) | MyGraph | [virtual] |
| subtract(MyGraph &other) | MyGraph | [virtual] |
| transformEdgeWeights(_Transform function) | MyGraph | |
| transformEdgeWeightsString(string transform) | MyGraph | [virtual] |
| translateTypes(const set< string > &types, set< string > &workingTypes, bool useShared=1) (defined in MyGraph) | MyGraph | |
| weightedDegree(MyNodeId nid) const | MyGraph | [inline] |
| ~MyGainGraph() (defined in MyGainGraph) | MyGainGraph | [inline, virtual] |
| ~MyGraph() (defined in MyGraph) | MyGraph | [inline, virtual] |
1.7.6.1
