, including all inherited members.
_allFinalStates (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_allInitialStates (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_allowApproximateConvergence (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [protected] |
_annotations (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_currentFunction (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_cutNodes (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_finalEnergies (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [protected] |
_globalNodePermutation (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_globalNodePermutationMap (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [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] |
_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] |
_numProcessedChildren (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_numStatesFixedAtStart (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_numTruePathViolatingAnnotations (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [protected] |
_numTruePathViolatingPredictions (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [protected] |
_params (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_realStateTypes (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_reporter (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_states (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [protected] |
_statesFixedAtStart (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_storeResults(const BioFunction &function) (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [protected] |
_truePathViolatingAnnotations (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [protected] |
_truePathViolatingPredictions (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [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) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [virtual] |
computeState(MyNode &node) | MyOneVersusAllHopfieldGainAlgo | [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() | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [inline, virtual] |
hasConverged(const MyNodeIdList &nodesToAnnotate) | MyOneVersusAllGainAlgo | [virtual] |
initialiseAlgorithm() | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [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) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [virtual] |
maskNodeStates(const MyNodeIdList &nodes) | MyOneVersusAllGainAlgo | [virtual] |
MyAbstractGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL) (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [inline] |
MyOneVersusAllGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL) (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [inline] |
MyOneVersusAllHopfieldGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go=NULL) (defined in MyOneVersusAllHopfieldGainAlgo) | MyOneVersusAllHopfieldGainAlgo | [inline] |
MyOneVersusAllSemiHierarchicalHopfieldGainAlgo(MyGainGraph &g, MyAnnotations &a, MyGainParams &p, Reporter &r, GeneOntology *go) (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [inline] |
pipeline(const BioFunction &function) | MyAbstractGainAlgo< MyGainTriStateType > | [virtual] |
predict(const BioFunction &function) (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [virtual] |
printStatistics(ostream &statsStream) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [virtual] |
removeUnpredictableNodes(const MyNodeIdSet &unpredictableNodes, MyNodeIdList &oldNodes) (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [inline, virtual] |
run(const MyNodeIdList &nodesToAnnotate) | MyOneVersusAllHopfieldGainAlgo | [virtual] |
setCrossValidationList(MyNodeIdList &nodesToAnnotate, const MyNodeIdList &cvList) | MyAbstractGainAlgo< MyGainTriStateType > | [virtual] |
visualiseCrossValidation(const BioFunction ¤tFunction) | MyAbstractGainAlgo< MyGainTriStateType > | [virtual] |
visualiseCut(const BioFunction ¤tFunction, MyNodeIdList &predictedNodes) | MyOneVersusAllGainAlgo | [virtual] |
visualisePredictions(const BioFunction ¤tFunction, MyNodeIdList &nodesToAnnotate) (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [virtual] |
~MyAbstractGainAlgo() (defined in MyAbstractGainAlgo< MyGainTriStateType >) | MyAbstractGainAlgo< MyGainTriStateType > | [inline, virtual] |
~MyOneVersusAllGainAlgo() (defined in MyOneVersusAllGainAlgo) | MyOneVersusAllGainAlgo | [inline, virtual] |
~MyOneVersusAllHopfieldGainAlgo() (defined in MyOneVersusAllHopfieldGainAlgo) | MyOneVersusAllHopfieldGainAlgo | [inline, virtual] |
~MyOneVersusAllSemiHierarchicalHopfieldGainAlgo() (defined in MyOneVersusAllSemiHierarchicalHopfieldGainAlgo) | MyOneVersusAllSemiHierarchicalHopfieldGainAlgo | [inline, virtual] |