, including all inherited members.
| _closeOutputFiles() (defined in NetMan) | NetMan | |
| _nodeAliases | NetMan | |
| _openOutputFiles() | NetMan | |
| _outputFileNames (defined in NetMan) | NetMan | |
| _reversedNodeAliases (defined in NetMan) | NetMan | |
| addDirectory(char *dir) (defined in NetMan) | NetMan | [inline] |
| addIgnoredEdgeType(string type) (defined in NetMan) | NetMan | [inline] |
| allowNegativeEdgeWeight(set< string > &types) const | NetMan | [inline] |
| binaryMatrixStream | NetMan | |
| closedLatticeStream (defined in NetMan) | NetMan | |
| computeCorrelations(MyGraph &wiring) | NetMan | |
| computeDenseFunctions(ostream *fstr, map< string, MyGraph > &denseFunctionSubgraphs) | NetMan | |
| computeDenseFunctions(ostream *fstr=NULL) | NetMan | [inline] |
| computeDenseSubgraphs(vector< ActiveNetwork > &denseSubgraphs, bool randomRun=false) (defined in NetMan) | NetMan | |
| computePathwayPerturbation() | NetMan | |
| computePathwayPerturbation(const map< string, set< string > > &treatmentControlPairs, map< string, MyGraph > &pathways) | NetMan | |
| computePathwayPerturbation(MyGraph &pathway, const GEData &treatment, const GEData &control, string contrast, ActiveNetwork &subgraph) | NetMan | |
| computePathwayPerturbation(MyGraph &pathway, const GEData &geData) (defined in NetMan) | NetMan | |
| conditionStream (defined in NetMan) | NetMan | |
| createWebPages(SetOfActiveNetworks &anetSet) | NetMan | |
| edgeCentralityStream (defined in NetMan) | NetMan | |
| edgeEnrichedFunctionStream (defined in NetMan) | NetMan | |
| edgeEnrichmentStream (defined in NetMan) | NetMan | |
| edgeSimilarityGraphStream (defined in NetMan) | NetMan | |
| edgeStream (defined in NetMan) | NetMan | |
| edgeTypesCountStream (defined in NetMan) | NetMan | |
| edgeWeightsHistogramStream (defined in NetMan) | NetMan | |
| expressionValuesHistogramStream (defined in NetMan) | NetMan | |
| functionSubgraphsStream (defined in NetMan) | NetMan | |
| geData | NetMan | |
| getActiveNetworksEdgesFile() const | NetMan | [inline] |
| getActiveNetworksNodesFile() const | NetMan | [inline] |
| getClassFile(void) const (defined in NetMan) | NetMan | [inline] |
| getComputeActiveNetworks(void) const (defined in NetMan) | NetMan | [inline] |
| getComputeActiveNetworksTillTheBitterEnd() const (defined in NetMan) | NetMan | [inline] |
| getComputeBetweennessCentralities() const (defined in NetMan) | NetMan | [inline] |
| getComputeDenseFunctions() const (defined in NetMan) | NetMan | [inline] |
| getComputeNetworkLegos() const (defined in NetMan) | NetMan | [inline] |
| getComputeNetworkLegoStability() const (defined in NetMan) | NetMan | [inline] |
| getComputePathwayPerturbation() const (defined in NetMan) | NetMan | [inline] |
| getComputeTrivialNetworkLegos() const (defined in NetMan) | NetMan | [inline] |
| getCorrelationMethod() const (defined in NetMan) | NetMan | [inline] |
| getCorrelationThreshold() const (defined in NetMan) | NetMan | [inline] |
| getCreateWebPages() const (defined in NetMan) | NetMan | [inline] |
| getDirectory(unsigned int index) const (defined in NetMan) | NetMan | [inline] |
| getDownRegulationBound() const (defined in NetMan) | NetMan | [inline] |
| getEdgeAnnotationsFile(void) const | NetMan | [inline] |
| getEdgeWeightThreshold() const (defined in NetMan) | NetMan | [inline] |
| getEmbedActiveNetworkInSuperGraph() const | NetMan | [inline] |
| getExpandActiveNetworks() const (defined in NetMan) | NetMan | [inline] |
| getExperimentName() const (defined in NetMan) | NetMan | [inline] |
| getFunctionSubgraphsFile() const (defined in NetMan) | NetMan | [inline] |
| getGEfile(void) const (defined in NetMan) | NetMan | [inline] |
| getLayoutConstraintsFile() const (defined in NetMan) | NetMan | [inline] |
| getMinNumberConditions() const (defined in NetMan) | NetMan | [inline] |
| getMinNumberInteractions() const (defined in NetMan) | NetMan | [inline] |
| getMultipleHypothesesCorrectionTest() const (defined in NetMan) | NetMan | [inline] |
| getNetworkFile(void) const (defined in NetMan) | NetMan | [inline] |
| getNodeAliasFile() const | NetMan | [inline] |
| getNodeAnnotationsFile(unsigned int index) const (defined in NetMan) | NetMan | [inline] |
| getNodeAnnotationsFiles(vector< string > &files) const (defined in NetMan) | NetMan | |
| getNumDirectories() const (defined in NetMan) | NetMan | [inline] |
| getNumNodeAnnotationsFiles() const (defined in NetMan) | NetMan | [inline] |
| getNumRandomRuns() const (defined in NetMan) | NetMan | [inline] |
| getOBOFile(void) const (defined in NetMan) | NetMan | [inline] |
| getOnlyRandomRuns() const (defined in NetMan) | NetMan | [inline] |
| getProcessComputedActiveNetworks() const | NetMan | [inline] |
| getProcessNetwork() const | NetMan | [inline] |
| getPvalueThreshold() const (defined in NetMan) | NetMan | [inline] |
| getRegulationBound() const (defined in NetMan) | NetMan | [inline] |
| getRegulationMethod() const (defined in NetMan) | NetMan | [inline] |
| getSimulatedAnnealingFactorNumberIterations() const (defined in NetMan) | NetMan | [inline] |
| getSparsificationMethod() const (defined in NetMan) | NetMan | [inline] |
| getSparsifyNetwork() const (defined in NetMan) | NetMan | [inline] |
| getSplitActiveNetworksIntoComponents() const (defined in NetMan) | NetMan | [inline] |
| getSplitGEData() const (defined in NetMan) | NetMan | [inline] |
| getTranslateAnnotations() const (defined in NetMan) | NetMan | [inline] |
| getTreatmentControlFile() const | NetMan | [inline] |
| getUpRegulationBound() const (defined in NetMan) | NetMan | [inline] |
| getUseRandomisedGEData() const (defined in NetMan) | NetMan | [inline] |
| getUseStudentsTDistribution() const (defined in NetMan) | NetMan | [inline] |
| getWiringDiagram(MyGraph &wd) | NetMan | [inline] |
| getWiringDiagramNodes(set< string > &nodes) const | NetMan | [inline] |
| getWWWParametersDir() const (defined in NetMan) | NetMan | [inline] |
| histogramStream (defined in NetMan) | NetMan | |
| itemsetStream (defined in NetMan) | NetMan | |
| latticeStream (defined in NetMan) | NetMan | |
| logStream (defined in NetMan) | NetMan | |
| logStringStream (defined in NetMan) | NetMan | |
| NetMan(void) (defined in NetMan) | NetMan | |
| nodeCentralityStream (defined in NetMan) | NetMan | |
| nodeEnrichedFunctionStream (defined in NetMan) | NetMan | |
| nodeEnrichmentOntologizerStream (defined in NetMan) | NetMan | |
| nodeEnrichmentStream (defined in NetMan) | NetMan | |
| nodeSimilarityGraphStream (defined in NetMan) | NetMan | |
| nodeStream (defined in NetMan) | NetMan | |
| nodeWeightsHistogramStream (defined in NetMan) | NetMan | |
| outputStreams (defined in NetMan) | NetMan | |
| plotExpressionCorrelationsHistogram() | NetMan | |
| plotExpressionValuesHistogram() | NetMan | |
| postProcess(SetOfActiveNetworks &anetSet) | NetMan | |
| process() | NetMan | |
| processComputedActiveNetworks() | NetMan | |
| processedNodeEnrichmentsOntologizerStream (defined in NetMan) | NetMan | |
| processedNodeEnrichmentsStream (defined in NetMan) | NetMan | |
| processFunctionSubgraphs() | NetMan | |
| processNetwork() | NetMan | |
| processNetworkLegos(SetOfActiveNetworks &anetSet) | NetMan | |
| randomise(MyHistogram &histogram) (defined in NetMan) | NetMan | |
| randomPvaluesStream (defined in NetMan) | NetMan | |
| randomStream (defined in NetMan) | NetMan | |
| readDirectories() (defined in NetMan) | NetMan | |
| readEdgeAnnotations(string name) | NetMan | |
| readFunctionSubgraphs(string) (defined in NetMan) | NetMan | |
| readGEData(string) (defined in NetMan) | NetMan | |
| readNetwork(string, MyNT minimumEdgeWeight=0) (defined in NetMan) | NetMan | |
| readNodeAliases(string file) | NetMan | |
| readNodeAnnotations(string name, set< string > *geneSet=NULL) | NetMan | |
| readOBO(string name) (defined in NetMan) | NetMan | [inline] |
| removeUnresponsiveGenes(GEData &gedata) | NetMan | |
| separateDenseFunctions() | NetMan | |
| setActiveNetworksEdgesFile(string file) | NetMan | [inline] |
| setActiveNetworksNodesFile(string file) | NetMan | [inline] |
| setClassFile(string name) (defined in NetMan) | NetMan | [inline] |
| setComputeActiveNetworksTillTheBitterEnd() (defined in NetMan) | NetMan | [inline] |
| setComputeBetweennessCentralities() (defined in NetMan) | NetMan | [inline] |
| setComputeDenseFunctions() (defined in NetMan) | NetMan | [inline] |
| setComputeNetworkLegos() (defined in NetMan) | NetMan | [inline] |
| setCorrelationThreshold(float arg) (defined in NetMan) | NetMan | [inline] |
| setEdgeWeightThreshold(string optarg) (defined in NetMan) | NetMan | [inline] |
| setEdgeWeightThreshold(MyNT thresh) (defined in NetMan) | NetMan | [inline] |
| setExpandActiveNetworks() (defined in NetMan) | NetMan | [inline] |
| setFunctionSubgraphsFile(string arg) (defined in NetMan) | NetMan | [inline] |
| setGEfile(char *name) (defined in NetMan) | NetMan | [inline] |
| setMinNumberConditions(unsigned int min) (defined in NetMan) | NetMan | [inline] |
| setMinNumberInteractions(unsigned int min) (defined in NetMan) | NetMan | [inline] |
| setMultipleHypothesesCorrectionTest(string optarg) (defined in NetMan) | NetMan | [inline] |
| setNetworkFile(char *file) (defined in NetMan) | NetMan | [inline] |
| setNodeAnnotationsFile(char *name) (defined in NetMan) | NetMan | [inline] |
| setNumRandomRuns(unsigned int num) (defined in NetMan) | NetMan | [inline] |
| setOBOFile(char *file) (defined in NetMan) | NetMan | [inline] |
| setOnlyRandomRuns() (defined in NetMan) | NetMan | [inline] |
| setParameters(int argc, char **argv) | NetMan | [virtual] |
| setPvalueThreshold(float thresh) (defined in NetMan) | NetMan | [inline] |
| setSplitActiveNetworksIntoComponents() (defined in NetMan) | NetMan | [inline] |
| setUseRandomisedGEData() (defined in NetMan) | NetMan | [inline] |
| setUseStudentsTDistribution() (defined in NetMan) | NetMan | [inline] |
| setWiringDiagramEdgeWeightsCD() | NetMan | [inline] |
| setWiringDiagramEdgeWeightsFS() | NetMan | [inline] |
| statsStream (defined in NetMan) | NetMan | |
| treatAliases(MyGraph &pathway, const GEData &geData) (defined in NetMan) | NetMan | |
| ~NetMan(void) (defined in NetMan) | NetMan | |
1.7.6.1
