MyGainParams Member List

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

_invocationFile (defined in MyGainParams)	MyGainParams
allowZeroStates (defined in MyGainParams)	MyGainParams
checkPropagation (defined in MyGainParams)	MyGainParams
computePvalues (defined in MyGainParams)	MyGainParams
crossValidate (defined in MyGainParams)	MyGainParams
crossValidationFile (defined in MyGainParams)	MyGainParams
customRNGSeed (defined in MyGainParams)	MyGainParams
cutoffsFile (defined in MyGainParams)	MyGainParams
cvStream (defined in MyGainParams)	MyGainParams
detailedCVStream (defined in MyGainParams)	MyGainParams
ecwCVStream (defined in MyGainParams)	MyGainParams
edgeTypeGroupsFile (defined in MyGainParams)	MyGainParams
edgeWeightingScheme (defined in MyGainParams)	MyGainParams
edgeWeightsStream (defined in MyGainParams)	MyGainParams
foldCrossValidate (defined in MyGainParams)	MyGainParams
foldInfo (defined in MyGainParams)	MyGainParams
functionFrequency (defined in MyGainParams)	MyGainParams
gainThreshold (defined in MyGainParams)	MyGainParams
gainThresholdRangeUserInput (defined in MyGainParams)	MyGainParams
gainThresholdUserInput (defined in MyGainParams)	MyGainParams
geneExpressionFile (defined in MyGainParams)	MyGainParams
geneUniverseStream (defined in MyGainParams)	MyGainParams
getAnnotationsAreOriginal() const	MyGainParams	[inline]
getAnnotationsFile() const	MyGainParams	[inline]
getApplyTruePathRuleDownward() const	MyGainParams	[inline]
getComputeTreewidth() const	MyGainParams	[inline]
getDataIntegrationType() const	MyGainParams	[inline]
getDoNotReduce() const	MyGainParams	[inline]
getEvidenceCodesToIgnore() const	MyGainParams	[inline]
getEvidenceCodeWeightsFile() const	MyGainParams	[inline]
getExperimentName() const	MyGainParams	[inline]
getFLNFiles() const	MyGainParams	[inline]
getGOFile() const	MyGainParams	[inline]
getGroupFunctionsMethod() const (defined in MyGainParams)	MyGainParams	[inline]
getGroupFunctionsMethodIsDepth() const (defined in MyGainParams)	MyGainParams	[inline]
getGroupFunctionsMethodIsParent() const (defined in MyGainParams)	MyGainParams	[inline]
getLibSVMDirectory() const	MyGainParams	[inline]
getLibSVMTestOptions() const	MyGainParams	[inline]
getLibSVMTrainOptions() const	MyGainParams	[inline]
getMaximumAnnotatedGenes() const	MyGainParams	[inline]
getMaximumGoDepth() const	MyGainParams	[inline]
getMinimumAnnotatedGenes() const	MyGainParams	[inline]
getMinimumConfidence() const	MyGainParams	[inline]
getMinimumGoDepth() const	MyGainParams	[inline]
getNumPredictionsToPrintPerFunction() const	MyGainParams	[inline]
getNumRounds() const	MyGainParams	[inline]
getNumRuns() const	MyGainParams	[inline]
getOneVersusNoneSinkSourceArtificialEdgeWeight() const	MyGainParams	[inline]
getOutputDirectory() const	MyGainParams	[inline]
getOutputFileName(string name, string dir="") const (defined in MyGainParams)	MyGainParams
getPerformSanityCheck() const	MyGainParams	[inline]
getPredictionsFile() const	MyGainParams	[inline]
getPrintDetailedCVResults() const	MyGainParams	[inline]
getRunGraphviz() const	MyGainParams	[inline]
getSVMLightDirectory() const	MyGainParams	[inline]
getSVMLightTestOptions() const	MyGainParams	[inline]
getSVMLightTrainOptions() const	MyGainParams	[inline]
getValidationAnnotationsFile() const	MyGainParams	[inline]
getVisualiseParamsFile() const	MyGainParams	[inline]
getWeightEvidenceCodes() const	MyGainParams	[inline]
groupedCVStream (defined in MyGainParams)	MyGainParams
groupedEcwCVStream (defined in MyGainParams)	MyGainParams
groupEdgeTypes (defined in MyGainParams)	MyGainParams
ignoredEvidenceCodes (defined in MyGainParams)	MyGainParams
ignoredThings (defined in MyGainParams)	MyGainParams
invocationStream (defined in MyGainParams)	MyGainParams
justUseCorrelations (defined in MyGainParams)	MyGainParams
leaveOneOutCrossValidate (defined in MyGainParams)	MyGainParams
localRuleDistance (defined in MyGainParams)	MyGainParams
logStream (defined in MyGainParams)	MyGainParams
loocvInfo (defined in MyGainParams)	MyGainParams
MyGainParams()	MyGainParams
onlyCrossVal (defined in MyGainParams)	MyGainParams
onlyPredictions (defined in MyGainParams)	MyGainParams
outputStreams (defined in MyGainParams)	MyGainParams
predictionsStream (defined in MyGainParams)	MyGainParams
printAllStates (defined in MyGainParams)	MyGainParams
printInvocation()	MyGainParams
processCategory(string cat) const	MyGainParams	[inline]
propagationDiagramsStream (defined in MyGainParams)	MyGainParams
runAnyOneVersusNoneAlgorithm() const	MyGainParams
runOneVersusAllAlgorithm(string algorithm) const	MyGainParams
runOneVersusNoneAlgorithm(string algorithm) const	MyGainParams
sanityCheckStream (defined in MyGainParams)	MyGainParams
setFunctionEdgeProbabilities(const map< BioFunction, MyHistogram > &hists)	MyGainParams	[inline]
setGroupFunctionsMethod(string method) (defined in MyGainParams)	MyGainParams	[inline]
setParameters(gengetopt_args_info &gainOptions)	MyGainParams
statsStream (defined in MyGainParams)	MyGainParams
unclampNegatives (defined in MyGainParams)	MyGainParams
unclampPositives (defined in MyGainParams)	MyGainParams
updateType (defined in MyGainParams)	MyGainParams
useCustomRNGSeed (defined in MyGainParams)	MyGainParams
useDegree (defined in MyGainParams)	MyGainParams
useStateWeights (defined in MyGainParams)	MyGainParams
visualiseCrossValidation (defined in MyGainParams)	MyGainParams
visualiseCut (defined in MyGainParams)	MyGainParams
visualisePredictions (defined in MyGainParams)	MyGainParams
weightEdgeTypesCutoff (defined in MyGainParams)	MyGainParams
weightEdgeTypesDepth (defined in MyGainParams)	MyGainParams
weightEdgeTypesJaccard (defined in MyGainParams)	MyGainParams
~MyGainParams()	MyGainParams	[inline, virtual]