de.jstacs.parameters
Interface GalaxyConvertible
- All Known Implementing Classes:
- AbsoluteValueCondition.AbsoluteValueConditionParameterSet, AbstractBurnInTestParameterSet, AbstractPerformanceMeasure, AbstractSelectionParameter, AbstractTerminationCondition.AbstractTerminationConditionParameterSet, Alphabet.AlphabetParameterSet, AlphabetContainer.AbstractAlphabetContainerParameterSet, AlphabetContainerParameterSet, AlphabetContainerParameterSet.AlphabetArrayParameterSet, AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet, ArrayParameterSet, AucPR, AucROC, BaumWelchParameterSet, BayesianNetworkDiffSMParameterSet, BayesianNetworkTrainSMParameterSet, BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet, BTMutualInformation.BTMutualInformationParameterSet, ClassificationRate, ClassifierAssessmentAssessParameterSet, CombinedCondition.CombinedConditionParameterSet, ConfusionMatrix, ContinuousAlphabet.ContinuousAlphabetParameterSet, DGTrainSMParameterSet, DiscreteAlphabet.DiscreteAlphabetParameterSet, DNAAlphabet.DNAAlphabetParameterSet, DNAAlphabetContainer.DNAAlphabetContainerParameterSet, EnumParameter, ExpandableParameterSet, FalsePositiveRateForFixedSensitivity, FileParameter, FSDAGModelForGibbsSamplingParameterSet, FSDAGTrainSMParameterSet, GenDisMixClassifierParameterSet, GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet, HMMTrainingParameterSet, HomMMParameterSet, HomogeneousTrainSMParameterSet, IDGTrainSMParameterSet, InhomogeneousMarkov.InhomogeneousMarkovParameterSet, InstanceParameterSet, IterationCondition.IterationConditionParameterSet, KFoldCrossValidationAssessParameterSet, MaxHMMTrainingParameterSet, MaximumCorrelationCoefficient, MaximumFMeasure, MaximumNumericalTwoClassMeasure, Measure.MeasureParameterSet, 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, TwoClassAbstractPerformanceMeasure, VarianceRatioBurnInTestParameterSet, ViterbiParameterSet
public interface GalaxyConvertible
Interface for Parameter
s 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 ParameterSet
s that contain
the parameters for a specific application.
- Author:
- Jan Grau
toGalaxy
void toGalaxy(String namePrefix,
String configPrefix,
int depth,
StringBuffer descBuffer,
StringBuffer configBuffer)
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 configuation
is also used to parse user-supplied values returned by Galaxy.
- Parameters:
namePrefix
- the prefix of the variable name used in GalaxyconfigPrefix
- the prefix for conditionalsdepth
- the depth in the parameter hierarchy, used for graphical representation of nestingdescBuffer
- the buffer for the parameter descriptionconfigBuffer
- the buffer for the configuration line
- 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)
and sets the values of the Parameter
or ParameterSet
accordingly.
- Parameters:
namePrefix
- the prefix of the variable namecommand
- the command string
- Throws:
Exception
- if the command string could not be parsed