de.jstacs.parameters

Interface GalaxyConvertible

All Known Implementing Classes:

AbsoluteValueCondition.AbsoluteValueConditionParameterSet, AbstractBurnInTestParameterSet, AbstractNumericalTwoClassPerformanceMeasure, AbstractPerformanceMeasure, AbstractPerformanceMeasureParameterSet, AbstractSelectionParameter, AbstractTerminationCondition.AbstractTerminationConditionParameterSet, AbstractTwoClassPerformanceMeasure, Alphabet.AlphabetParameterSet, AlphabetContainer.AbstractAlphabetContainerParameterSet, AlphabetContainerParameterSet, AlphabetContainerParameterSet.AlphabetArrayParameterSet, AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet, ArrayParameterSet, AucPR, AucROC, BaumWelchParameterSet, BayesianNetworkDiffSMParameterSet, BayesianNetworkTrainSMParameterSet, BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet, BTMutualInformation.BTMutualInformationParameterSet, ClassificationRate, ClassifierAssessmentAssessParameterSet, CombinedCondition.CombinedConditionParameterSet, ConfusionMatrix, ConstraintParameterSet, ContinuousAlphabet.ContinuousAlphabetParameterSet, CorrelationCoefficient, DataColumnParameter, DGTrainSMParameterSet, DiscreteAlphabet.DiscreteAlphabetParameterSet, DNAAlphabet.DNAAlphabetParameterSet, DNAAlphabetContainer.DNAAlphabetContainerParameterSet, EnumParameter, ExpandableParameterSet, FalsePositiveRateForFixedSensitivity, FileParameter, FSDAGModelForGibbsSamplingParameterSet, FSDAGTrainSMParameterSet, FSMEMParameterSet, GenDisMixClassifierParameterSet, GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet, HMMTrainingParameterSet, HomMMParameterSet, HomogeneousTrainSMParameterSet, IDGTrainSMParameterSet, InhomogeneousMarkov.InhomogeneousMarkovParameterSet, InstanceParameterSet, IterationCondition.IterationConditionParameterSet, KFoldCrossValidationAssessParameterSet, MaxHMMTrainingParameterSet, MaximumCorrelationCoefficient, MaximumFMeasure, MaximumNumericalTwoClassMeasure, Measure.MeasureParameterSet, MEManagerParameterSet, MultilineSimpleParameter, MultipleIterationsCondition.MultipleIterationsConditionParameterSet, MultiSelectionParameter, MultiThreadedTrainingParameterSet, NumberValidator, NumericalHMMTrainingParameterSet, NumericalPerformanceMeasureParameterSet, ParameterSet, ParameterSetContainer, PerformanceMeasureParameterSet, PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet, PMMMutualInformation.PMMMutualInformationParameterSet, PositivePredictiveValueForFixedSensitivity, PRCurve, ProteinAlphabet.ProteinAlphabetParameterSet, RangeParameter, RepeatedHoldOutAssessParameterSet, RepeatedSubSamplingAssessParameterSet, ROCCurve, Sampled_RepeatedHoldOutAssessParameterSet, SamplingGenDisMixClassifierParameterSet, SamplingHMMTrainingParameterSet, SamplingScoreBasedClassifierParameterSet, ScoreClassifierParameterSet, SelectionParameter, SensitivityForFixedSpecificity, SequenceScoringParameterSet, SimpleParameter, SimpleParameterSet, SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet, SmallGradientConditon.SmallGradientConditonParameterSet, SmallStepCondition.SmallStepConditionParameterSet, TimeCondition.TimeConditionParameterSet, VarianceRatioBurnInTestParameterSet, ViterbiParameterSet

public interface GalaxyConvertible

Interface for Parameters that can be converted to and extracted from Galaxy representations. The methods of this interface are used in the GalaxyAdaptor to create Galaxy representation, i.e., config-files, from ParameterSets that contain the parameters for a specific application.

Author:

Jan Grau

Method Summary

Methods

Modifier and Type	Method and Description
void	fromGalaxy(String namePrefix, StringBuffer command) Parses the contents of command in the format defined by configBuffer of toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and sets the values of the Parameter or ParameterSet accordingly.
void	toGalaxy(String namePrefix, String configPrefix, int depth, StringBuffer descBuffer, StringBuffer configBuffer, boolean addLine) Creates an Galaxy XML-representation of the parameters and appends it to descBuffer and variable configuration and appends it to configBuffer.

Method Detail

toGalaxy

void toGalaxy(String namePrefix,
            String configPrefix,
            int depth,
            StringBuffer descBuffer,
            StringBuffer configBuffer,
            boolean addLine)
              throws Exception

Creates an Galaxy XML-representation of the parameters and appends it to descBuffer and variable configuration and appends it to configBuffer. The variable configuration is also used to parse user-supplied values returned by Galaxy.

Parameters:

namePrefix - the prefix of the variable name used in Galaxy

configPrefix - the prefix for conditionals

depth - the depth in the parameter hierarchy, used for graphical representation of nesting

descBuffer - the buffer for the parameter description

configBuffer - the buffer for the configuration line

addLine - if true, a line is added before the title of a parameter

Throws:

Exception - if the conversion fails

fromGalaxy

void fromGalaxy(String namePrefix,
              StringBuffer command)
                throws Exception

Parses the contents of command in the format defined by configBuffer of toGalaxy(String, String, int, StringBuffer, StringBuffer, boolean) and sets the values of the Parameter or ParameterSet accordingly.

Parameters:

namePrefix - the prefix of the variable name

command - the command string

Throws:

Exception - if the command string could not be parsed