Inheritance diagram for MyGainGraph:

Public Member Functions
	MyGainGraph (string infile, string type, string outputDir, string commandLine, MyNT minEdgeWeight=0)
void	setUseDegree (bool ud)
void	resetThreshold ()
void	setNodeWeights ()
unsigned int	printStates (ofstream &ostr, const MyNodeStatesType &states, string currentFunc, string algorithm="Hopfield", bool printAll=false)
void	reduce2 (ostream &hopstr, map< MyNodeId, MyGainTriStateType > &nodeStates, const MyGainParams &params, MyGainGraph &reducedGraph, MyNodeIdSet &unpredictableNodes)
	"Reduce" the graph, i.e., remove connected components that do not contain nodes in HYPOTHETICAL_STATE, ANNOTATED_STATE, and NOT_ANNOTATED_STATE.
void	setEdgeWeightsCorrelations (ostream &fstr, const MyPointSet &geData)
void	computeDenseFunctions (ostream *fstr, MyAnnotations &annotations, GeneOntology &go, map< string, MyGraph > &denseFunctionSubgraphs)
void	computeProbabilitiesFromEdgeWeights (ostream &fstr, const MyPointSet &geData, string experimentName, MyHistogram &edgeWeightsToProbabilities)
void	computeEdgeProbabilitiesPerDepth (MyGainParams &params, const map< unsigned int, set< GOFunction * > > &functionsByDepth, MyAnnotations &annotations, map< BioFunction, MyHistogram > &probabilities)
void	computeEdgeProbabilitiesPerParent (MyGainParams &params, GeneOntology &go, MyAnnotations &annotations, map< BioFunction, MyHistogram > &probs)
void	computeProbabilitiesFromEdgeWeights (ostream &fstr, MyAnnotations &annotations, const vector< BioFunction > *functionVector, MyHistogram &edgeWeightsToProbabilities)
void	setEdgeWeights (ostream &fstr, const MyHistogram &edgeWeightsToProbabilities)
MyNT	computeInput (string nodeId, MyNodeStatesType &nodeStates) const
MyNT	computeEnergy (MyNodeStatesType &nodeStates)
MyNT	computeChangeInEnergy (MyNodeStatesType &nodeStates, string changedNodeId)
void	printDimacs (string filename, MyNodeStatesType &nodeStates, string format)
void	runMinCut (string outfile, MyNodeStatesType &nodeStates, const MyGainParams &params)
void	computeEdgeTypeWeightsByCutoffFromSharedFunctionRatio (MyAnnotations &annotations, GeneOntology &go, MyGainParams &gainParams)
void	computeEdgeTypeWeightsByDepthFromSharedFunctionRatio (MyAnnotations &annotations, GeneOntology &go, MyGainParams &gainParams)
void	computeEdgeTypeWeightsJaccard (ostream &logStream, MyAnnotations &annotations)
void	assignEdgeWeightFromDepth (const MyGainParams &gainParams, string annotationType, string category, unsigned int depth, MyEdge &edge)

Member Function Documentation

void MyGainGraph::computeProbabilitiesFromEdgeWeights	(	ostream &	fstr,
		MyAnnotations &	annotations,
		const vector< BioFunction > *	functionVector,
		MyHistogram &	edgeWeightsToProbabilities
	)

void MyGainGraph::reduce2	(	ostream &	hopstr,
		map< MyNodeId, MyGainTriStateType > &	nodeStates,
		const MyGainParams &	params,
		MyGainGraph &	reducedGraph,
		MyNodeIdSet &	unpredictableNodes
	)

"Reduce" the graph, i.e., remove connected components that do not contain nodes in HYPOTHETICAL_STATE, ANNOTATED_STATE, and NOT_ANNOTATED_STATE.

Parameters:

[in]	hopstr,an	output stream to print logging information to.
[in]	nodeStates,a	map from MyNodeId to the initial state type (either HYPOTHETICAL_STATE, ANNOTATED_STATE, or NOT_ANNOTATED_STATE) of the node.
[in]	params,an	instance of MyGainParams. CURRENTLY NOT USED.
[out]	reducedGraph,a	subgraph of *this that contains only trichromatic components (see below).
[out]	unpredictableNodes,a	set of MyNodeIds that the method thinks are no predictable.

This method partitions *this into maximal connected components: two nodes (in HYPOTHETICAL_STATE) are in different components iff all paths between them contain at least one node whose state is ANNOTATED_STATE or NOT_ANNOTATED_STATE.

Such a component is "trichromatic" if it contains nodes in all three states (HYPOTHETICAL_STATE, ANNOTATED_STATE, and NOT_ANNOTATED_STATE). Those are the only components that some algorithms (e.g., Hopfield and SinkSource) can reliably make predictions for. For a non-trichromatic component, running these algorithms will make the component "monochromatic", i.e., all nodes in HYPOTHETICAL_STATE in that component will become annotated either with ANNOTATED_STATE or NOT_ANNOTATED_STATE.

The documentation for this class was generated from the following files:

/home/poirel/src/c++/biorithm/gain/gain.h
/home/poirel/src/c++/biorithm/gain/gain.C

Public Member Functions

Member Function Documentation