MyOneVersusAllAbstractSVMGainAlgo Member List

This is the complete list of members for MyOneVersusAllAbstractSVMGainAlgo, including all inherited members.

_addComment(ostream &ostr, MyNode &node)=0 (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, pure virtual]
_allowApproximateConvergence (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_annotations (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_calculateSVMResult(MyNode &node) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_clearMaps() (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_createSVMOutputLine(ostream &ostr, MyGainTriStateType state, MyNode &node, bool includeHypothetical) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_createTestInputFile(const MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_createTrainInputFile(const MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_currentFunction (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_cutNodes (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_featureNameToNumber (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
_featureNumberToName (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
_finalEnergies (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_go (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_graph (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_initialEnergies (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_initialStateTypes (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_learnMode (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
_nodesByInitialStateType (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_nodesByRealStateType (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_numIterations (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_numOperations (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_numTruePathViolatingAnnotations (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_numTruePathViolatingPredictions (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_onboardPrediction (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
_params (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_predict(const MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_readModelFile()=0 (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, pure virtual]
_readTestOutputFile(const MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_realStateTypes (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_reporter (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_separatorCoefficients (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
_states (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[protected]
_threshold (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
_train(const MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected, virtual]
_truePathViolatingAnnotations (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_truePathViolatingPredictions (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[protected]
_vectorWeights (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
computeCrossValidationResults(const BioFunction &function, const MyNodeIdList &cvNodes)	MyOneVersusAllGainAlgo	[virtual]
computeCut(MyNodeIdList &nodesToAnnotate, MyNodeIdSet &cutNodes)	MyOneVersusAllGainAlgo	[virtual]
computeEnergy(const MyNodeIdList &nodesToAnnotate)	MyOneVersusAllGainAlgo	[virtual]
computePredictionConfidences(const BioFunction &function, MyNodeIdList &nodesToAnnotate, MyNodeIdList &predictedNodes) (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[virtual]
computePredictions(const BioFunction &function, const MyNodeIdList &nodesToAnnotate, MyNodeIdList &predictedNodes)	MyOneVersusAllGainAlgo	[virtual]
computeState(MyNode &node)	MyOneVersusAllGainAlgo	[virtual]
constructCrossValidationLists(vector< MyNodeIdList > &cvLists)	MyOneVersusAllGainAlgo	[virtual]
crossValidate(const BioFunction &function) (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[virtual]
evaluatePredictions(MyAnnotations &newAnnotations)	MyAbstractGainAlgo< MyGainTriStateType >	[virtual]
getName()	MyOneVersusAllGainAlgo	[inline, virtual]
hasConverged(const MyNodeIdList &nodesToAnnotate)	MyOneVersusAllGainAlgo	[virtual]
initialiseAlgorithm()	MyReallyAbstractGainAlgo	[inline, virtual]
initialiseEdgeWeights(const BioFunction &function) (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[inline, virtual]
initialiseEdgeWeightsCutoff(const BioFunction &function) (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[virtual]
initialiseEdgeWeightsDepth(const BioFunction &function) (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[virtual]
initialiseNodeStates(const BioFunction &function, MyNodeIdList &nodesToAnnotate)	MyOneVersusAllGainAlgo	[virtual]
maskNodeStates(const MyNodeIdList &nodes)	MyOneVersusAllGainAlgo	[virtual]
modelFilename (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
MyAbstractGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL) (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[inline]
MyOneVersusAllAbstractSVMGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo
MyOneVersusAllGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL) (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[inline]
pipeline(const BioFunction &function)	MyAbstractGainAlgo< MyGainTriStateType >	[virtual]
predict(const BioFunction &function) (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[virtual]
printStatistics(ostream &statsStream)	MyOneVersusAllGainAlgo	[virtual]
removeUnpredictableNodes(const MyNodeIdSet &unpredictableNodes, MyNodeIdList &oldNodes) (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[inline, virtual]
run(const MyNodeIdList &nodesToAnnotate)	MyOneVersusAllAbstractSVMGainAlgo	[virtual]
setCrossValidationList(MyNodeIdList &nodesToAnnotate, const MyNodeIdList &cvList)	MyOneVersusAllAbstractSVMGainAlgo	[virtual]
testArgs (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
testBinaryFilename (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
testInputFilename (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
testOutputFilename (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
trainArgs (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
trainBinaryFilename (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
trainInputFilename (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[protected]
visualiseCrossValidation(const BioFunction &currentFunction)	MyAbstractGainAlgo< MyGainTriStateType >	[virtual]
visualiseCut(const BioFunction &currentFunction, MyNodeIdList &predictedNodes)	MyOneVersusAllAbstractSVMGainAlgo	[virtual]
visualiseCVTemp(const BioFunction &currentFunction, MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllAbstractSVMGainAlgo)	MyOneVersusAllAbstractSVMGainAlgo	[virtual]
visualisePredictions(const BioFunction &currentFunction, MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[virtual]
~MyAbstractGainAlgo() (defined in MyAbstractGainAlgo< MyGainTriStateType >)	MyAbstractGainAlgo< MyGainTriStateType >	[inline, virtual]
~MyOneVersusAllGainAlgo() (defined in MyOneVersusAllGainAlgo)	MyOneVersusAllGainAlgo	[inline, virtual]