MyOneVersusAllAbstractSVMGainAlgo Class Reference

Inheritance diagram for MyOneVersusAllAbstractSVMGainAlgo:

List of all members.

Public Member Functions
	MyOneVersusAllAbstractSVMGainAlgo (MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL)
virtual void	run (const MyNodeIdList &nodesToAnnotate)
virtual void	visualiseCut (const BioFunction &currentFunction, MyNodeIdList &predictedNodes)
	Layout a graph that highlights the cut seprating nodes annotated with or predicted to be annotated with currentFunction from all the other nodes.
virtual void	visualiseCVTemp (const BioFunction &currentFunction, MyNodeIdList &nodesToAnnotate)
virtual void	setCrossValidationList (MyNodeIdList &nodesToAnnotate, const MyNodeIdList &cvList)
Protected Member Functions
virtual void	_train (const MyNodeIdList &nodesToAnnotate)
virtual void	_predict (const MyNodeIdList &nodesToAnnotate)
virtual void	_createTrainInputFile (const MyNodeIdList &nodesToAnnotate)
virtual void	_createTestInputFile (const MyNodeIdList &nodesToAnnotate)
virtual void	_readTestOutputFile (const MyNodeIdList &nodesToAnnotate)
virtual void	_createSVMOutputLine (ostream &ostr, MyGainTriStateType state, MyNode &node, bool includeHypothetical)
virtual void	_addComment (ostream &ostr, MyNode &node)=0
virtual void	_readModelFile ()=0
virtual double	_calculateSVMResult (MyNode &node)
virtual void	_clearMaps ()
Protected Attributes
string	trainBinaryFilename
string	trainArgs
string	trainInputFilename
string	modelFilename
string	testBinaryFilename
string	testArgs
string	testInputFilename
string	testOutputFilename
MyFeatureNumberMap	_featureNameToNumber
MyFeatureNameMap	_featureNumberToName
MyVectorWeightMap	_vectorWeights
MySeparatorCoefficientMap	_separatorCoefficients
double	_threshold
MyLearnMode	_learnMode
bool	_onboardPrediction

---

Member Function Documentation

void MyOneVersusAllAbstractSVMGainAlgo::run

(

const MyNodeIdList &

nodesToAnnotate

)

[virtual]

This method repeatedly iterates over all the nodes in nodesToAnnotate in the order in which they occur in nodesToAnnotate. It computes the state of each node in this list. The method iterates until the states converge.

Reimplemented from MyOneVersusAllGainAlgo.

void MyOneVersusAllAbstractSVMGainAlgo::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 >.

void MyOneVersusAllAbstractSVMGainAlgo::visualiseCut	(	const BioFunction &	currentFunction,
		MyNodeIdList &	predictedNodes
	)		[virtual]

Layout a graph that highlights the cut seprating nodes annotated with or predicted to be annotated with currentFunction from all the other nodes.

The method lays out the graph induced by the edges in the cut and all the nodes on the "currentFunction" side of the cut.

Reimplemented from MyOneVersusAllGainAlgo.

---

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