Public Member Functions
	MyGainParams ()
	Constructor.
virtual	~MyGainParams ()
	Destructor.
string	getAnnotationsFile () const
	Return the name of the file containing functional annotations.
bool	getApplyTruePathRuleDownward () const
string	getGOFile () const
	Return the name of the file containing the definition of GO.
vector< string >	getFLNFiles () const
	Return the names of the file containing the functional linkage network.
string	getDataIntegrationType () const
	Return the type of data integration GAIN should perform.
unsigned int	getMaximumGoDepth () const
unsigned int	getMinimumGoDepth () const
unsigned int	getMaximumAnnotatedGenes () const
unsigned int	getMinimumAnnotatedGenes () const
bool	getDoNotReduce () const
	Return true if the FLN should not be reduced.
unsigned int	getNumRounds () const
	Return the number of times to push flow in the FunctionalFlow algorithm.
unsigned int	getNumRuns () const
bool	getAnnotationsAreOriginal () const
	Return whether the annotations in the functional file on the command line are transitively closed.
string	getExperimentName () const
	Return the name of the experiment provided by the --experiment-name command-line argument.
void	setGroupFunctionsMethod (string method)
bool	getGroupFunctionsMethodIsParent () const
bool	getGroupFunctionsMethodIsDepth () const
string	getGroupFunctionsMethod () const
void	setFunctionEdgeProbabilities (const map< BioFunction, MyHistogram > &hists)
	Store the histograms storing mapping edge weights to probabilities for each function.
MyNT	getMinimumConfidence () const
	Return the minimum prediction confidence to consider.
MyNT	getOneVersusNoneSinkSourceArtificialEdgeWeight () const
bool	processCategory (string cat) const
	Return true if and only if cat is a function category that GAIN should process.
string	getOutputDirectory () const
	Return the name of the directory to print results to.
string	getOutputFileName (string name, string dir="") const
const set< string > *	getEvidenceCodesToIgnore () const
	Return pointer to set of evidence codes to ignore.
void	printInvocation ()
bool	getPrintDetailedCVResults () const
	Return true if detailed cross validation results should be printed.
bool	getRunGraphviz () const
	Return true if the user wants to run the Graphviz algorithms.
bool	getPerformSanityCheck () const
string	getVisualiseParamsFile () const
int	getNumPredictionsToPrintPerFunction () const
	Return the number of predictions to be printed for each function.
bool	runAnyOneVersusNoneAlgorithm () const
	Return true if user asked for any one-versus-none algorithm to be executed.
bool	runOneVersusAllAlgorithm (string algorithm) const
bool	runOneVersusNoneAlgorithm (string algorithm) const
string	getPredictionsFile () const
string	getValidationAnnotationsFile () const
	Return the name of the file containing (new) annotations to be used to validate predictions.
string	getLibSVMDirectory () const
	Return the name of the directory containing the libSVM executables.
string	getSVMLightDirectory () const
	Return the name of the directory containing the SVMLight executables.
string	getLibSVMTrainOptions () const
	Return a string containing extra options to be passed to the libSVM training programme.
string	getLibSVMTestOptions () const
	Return a string containing extra options to be passed to the libSVM testing programme.
string	getSVMLightTrainOptions () const
	Return the name of extra options to be passed to the SVMLight training programme.
string	getSVMLightTestOptions () const
	Return the name of extra options to be passed to the SVMLight testing programme.
bool	getComputeTreewidth () const
	Return true if GAIN should compute the treewidth of the FLN.
bool	getWeightEvidenceCodes () const
	Return true if evidence codes should be weighted.
string	getEvidenceCodeWeightsFile () const
	Return the name of the file that contains evidence code weights.
void	setParameters (gengetopt_args_info &gainOptions)
Public Attributes
ofstream	cvStream
ofstream	ecwCVStream
ofstream	detailedCVStream
ofstream	edgeWeightsStream
ofstream	geneUniverseStream
ofstream	groupedCVStream
ofstream	groupedEcwCVStream
ofstream	invocationStream
ofstream	logStream
ofstream	predictionsStream
ofstream	propagationDiagramsStream
ofstream	sanityCheckStream
ofstream	statsStream
map< string, ofstream * >	outputStreams
string	_invocationFile
bool	allowZeroStates
MyNT	gainThreshold
bool	gainThresholdUserInput
bool	gainThresholdRangeUserInput
string	geneExpressionFile
set< string >	ignoredThings
set< string >	ignoredEvidenceCodes
bool	justUseCorrelations
MyGainUpdateType	updateType
bool	useDegree
unsigned int	localRuleDistance
bool	computePvalues
bool	checkPropagation
bool	crossValidate
string	crossValidationFile
bool	leaveOneOutCrossValidate
int	foldCrossValidate
MyGainFoldInfo	foldInfo
MyGainLOOCVInfo	loocvInfo
MyNT	functionFrequency
bool	printAllStates
bool	unclampPositives
bool	unclampNegatives
bool	useStateWeights
bool	visualisePredictions
bool	visualiseCrossValidation
bool	visualiseCut
bool	onlyPredictions
bool	onlyCrossVal
bool	weightEdgeTypesCutoff
string	cutoffsFile
bool	weightEdgeTypesDepth
bool	weightEdgeTypesJaccard
bool	groupEdgeTypes
string	edgeTypeGroupsFile
bool	useCustomRNGSeed
int	customRNGSeed
string	edgeWeightingScheme

Member Function Documentation

bool MyGainParams::getApplyTruePathRuleDownward ( ) const [inline]

Return true iff the GO true path rule should be applied downward to the annotations.

bool MyGainParams::getDoNotReduce ( ) const [inline]

Return true if the FLN should not be reduced.

"Reduction" of an FLN is the operation of deleting all connected components that do not contain both positive and negative examples. This operation does not make sense for one-versus-none algorithms, which do not have any negative examples. Hence, this method returns false if even one algorithm is invoked on the command line with the --one-versus-none option.

unsigned int MyGainParams::getMaximumAnnotatedGenes ( ) const [inline]

Return the maximum number of annotated genes for which GAIN should analyse (make predictions or perform cross validation for) a GO function.

unsigned int MyGainParams::getMaximumGoDepth ( ) const [inline]

Return the maximum depth at which GAIN should analyse (make predictions or perform cross validation for) a GO function.

unsigned int MyGainParams::getMinimumAnnotatedGenes ( ) const [inline]

Return the minimum number of annotated genes for which GAIN should analyse (make predictions or perform cross validation for) a GO function.

unsigned int MyGainParams::getMinimumGoDepth ( ) const [inline]

Return the minimum depth at which GAIN should analyse (make predictions or perform cross validation for) a GO function.

unsigned int MyGainParams::getNumRuns ( ) const [inline]

Return the number of times to run the algorithm (semi-hierarchical Hopfield or hierarchical Hopfield).

MyNT MyGainParams::getOneVersusNoneSinkSourceArtificialEdgeWeight ( ) const [inline]

Return the value passed as the command-line argument ovn-sinksource-edge-weight.

bool MyGainParams::getPerformSanityCheck ( ) const [inline]

Return true if the user wants to perform a sanity check, e.g., whether gene ids in gene expression data match the ones in the functional annotations file.

string MyGainParams::getPredictionsFile ( ) const [inline]

Return the name of the file containing predictions made by GAIN during an earlier run or by another algorithm.

string MyGainParams::getVisualiseParamsFile ( ) const [inline]

Return the name of the file specifying how nodes and edges should look in propagation diagrams.

void MyGainParams::printInvocation ( )

Print details about the invocation in a two-column format.

Each row contains the name of a parameter and its value.

bool MyGainParams::processCategory ( string cat ) const [inline]

Return true if and only if cat is a function category that GAIN should process.

Parameters:

cat	A string representing a biological function category, e.g., "biological process" or "p".

If the user did not specify any function categories in the command line, the method always returns true.

bool MyGainParams::runOneVersusAllAlgorithm ( string algorithm ) const

Return true if user asked for algorithm to be executed.

Parameters:

[in] algorithm The name of a one-versus-all algorithm, e.g., "Hopfield" or "sinksource".

bool MyGainParams::runOneVersusNoneAlgorithm ( string algorithm ) const

Return true if user asked for algorithm to be executed.

Parameters:

[in] algorithm The name of a one-versus-none algorithm, e.g., "functional-flow"

void MyGainParams::setParameters ( gengetopt_args_info & gainOptions )

Set all parameters based on the command line.

Parameters:

gainOptions an instance of gengetopt_args_info, created by a call to cmdline_parser.

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

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

Public Member Functions

Public Attributes

Member Function Documentation