MyOneVersusNoneGainAlgo Class Reference

Inheritance diagram for MyOneVersusNoneGainAlgo:

List of all members.

Public Member Functions
	MyOneVersusNoneGainAlgo (MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL)
virtual void	initialiseNodeStates (const BioFunction &function, MyNodeIdList &nodesToAnnotate)
virtual void	setCrossValidationList (MyNodeIdList &nodesToAnnotate, const MyNodeIdList &cvList)
virtual string	getName ()

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Member Function Documentation

virtual string MyOneVersusNoneGainAlgo::getName

(

)

[inline, virtual]

Return the name of the algorithm.

Reimplemented from MyOneVersusAllGainAlgo.

Reimplemented in MyOneVersusNoneLocalGainAlgo, and MyOneVersusNoneFunctionalFlowGainAlgo.

void MyOneVersusNoneGainAlgo::initialiseNodeStates	(	const BioFunction &	function,
		MyNodeIdList &	nodesToAnnotate
	)		[virtual]

Initialise the states of the nodes in the graph. Each node annotated with function gets the state ANNOTATED_STATE; these nodes are "clamped," i.e., the algorithm will not change their states. All other nodes get the state HYPOTHETICAL_STATE. The algorithm may change the states of these nodes. In other words, these nodes are not clamped. The argument nodesToAnnotate contains the IDs of the unclamped nodes.

For every node ID in nodes, "remember" its state information and clamp it, so that MyOneVersusNoneGainAlgo::run() can't modify the state of that node.

Parameters:

[in]

nodes,the

list of node whose initial state must be unmasked.

Reimplemented from MyOneVersusAllGainAlgo.

void MyOneVersusNoneGainAlgo::setCrossValidationList	(	MyNodeIdList &	nodesToAnnotate,
		const MyNodeIdList &	cvList
	)		[virtual]

Given a list of unannotated nodes (nodesToAnnotate) and a list of nodes to cross validate (cvList),update nodesToAnnotate to include nodes in cvList, so that the annotation algorithm also annotates the nodes in cvList.

Warning:

Call this method only after invoking maskNodeStates().

Note:

This method is virtual since some algorithms can set nodesToAnnotate to be equal to cvList, for example, algorithms that use only one round of "guilt-by-association," where each node computes its state from the states of its neighbours.

Reimplemented from MyAbstractGainAlgo< MyGainTriStateType >.

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

• /home/poirel/src/c++/biorithm/gain/gain-algorithm.h
• /home/poirel/src/c++/biorithm/gain/gain-algorithm.C