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saveModel(SMO, String)
- Method in class classifier.
WekaSVM
This method saves the SMO java-object to a file in the filesystem.
ScriptGenerator
- Class in
var.experimenter
ScriptGenerator()
- Constructor for class var.experimenter.
ScriptGenerator
ScriptOptionAbstractClass
- Class in
var.experimenter
ScriptOptionAbstractClass()
- Constructor for class var.experimenter.
ScriptOptionAbstractClass
ScriptOptionInterface
- Interface in
var.experimenter
SecondaryStructureData
- Class in
util.io
SecondaryStructureData()
- Constructor for class util.io.
SecondaryStructureData
SecondaryStructureData
- Class in
util.secondaryStructure
SecondaryStructureData()
- Constructor for class util.secondaryStructure.
SecondaryStructureData
SecondaryStructureExtraction
- Class in
util.secondaryStructure
This method is primarily used for buiding the secondary structure of non-training files (although it can also be used for this purpose, there are better ways of doing this).
SecondaryStructureExtraction(Logger)
- Constructor for class util.secondaryStructure.
SecondaryStructureExtraction
Constructor of the secondary structure builder class
SeconderyStructureClassificationFeature
- Interface in
util.classificationFeatures
SecStructEvalClassificationFeature
- Class in
util.classificationFeatures.implementations.test
SecStructEvalClassificationFeature()
- Constructor for class util.classificationFeatures.implementations.test.
SecStructEvalClassificationFeature
SecStructEvalClassificationFeatureDrawing
- Class in
util.classificationFeatures.implementations.test
SecStructEvalClassificationFeatureDrawing(SecStructEvalClassificationFeature)
- Constructor for class util.classificationFeatures.implementations.test.
SecStructEvalClassificationFeatureDrawing
SecStructSimpleClassificationFeature
- Class in
util.classificationFeatures.implementations.test
SecStructSimpleClassificationFeature()
- Constructor for class util.classificationFeatures.implementations.test.
SecStructSimpleClassificationFeature
SecStructSimpleClassificationFeatureDrawing
- Class in
util.classificationFeatures.implementations.test
SecStructSimpleClassificationFeatureDrawing(SecStructSimpleClassificationFeature)
- Constructor for class util.classificationFeatures.implementations.test.
SecStructSimpleClassificationFeatureDrawing
seperateData(SortedSet<Integer>, SortedSet<Integer>, File, File, File, File)
- Static method in class util.io.
FileUtils
serialVersionUID
- Static variable in class startup.gui.
OptionsPanel
serialVersionUID
- Static variable in class startup.gui.
SprClassificationActionPanel
serialVersionUID
- Static variable in class startup.gui.
SprClassificationFeaturePanel
serialVersionUID
- Static variable in class startup.gui.
SprOutputEditorWriter
serialVersionUID
- Static variable in class startup.gui.
SprOutputPanel
serialVersionUID
- Static variable in class startup.gui.
SprSplashScreen
serialVersionUID
- Static variable in class startup.gui.
SprWorkflowPanel
serialVersionUID
- Static variable in class startup.gui.
WizardFramework
serialVersionUID
- Static variable in exception util.classificationFeatures.
FeatureExtractionException
serialVersionUID
- Static variable in exception util.classificationFeatures.
IncorrectClassificationFeatureException
serialVersionUID
- Static variable in exception util.
FeatureException
serialVersionUID
- Static variable in class util.featureSelection.implementations.
TestAttribEval
serialVersionUID
- Static variable in class var.experimenter.
ActionPanel
serialVersionUID
- Static variable in class var.experimenter.
ActionsPanel
serialVersionUID
- Static variable in class var.experimenter.
ChoosePanel
serialVersionUID
- Static variable in class var.experimenter.
FixedOption
serialVersionUID
- Static variable in class var.experimenter.
FixedRangeOption
serialVersionUID
- Static variable in class var.experimenter.
OverridePanel
serialVersionUID
- Static variable in class var.experimenter.
RangeOption
serialVersionUID
- Static variable in class var.experimenter.
RangePanel
serialVersionUID
- Static variable in class var.experimenter.
ScriptOptionAbstractClass
serialVersionUID
- Static variable in class var.
Experimenter
serialVersionUID
- Static variable in class var.experimenter.
VariableRangeExpOption
serialVersionUID
- Static variable in class var.experimenter.
VariableRangeLinearOption
setAcceptorMap(Map<Integer, Instances>)
- Method in class util.results.
PotentialResultsMap
setAcceptorSites(List<Integer>)
- Method in class util.parsers.
GeneData
setAccordingToCheck(boolean, JCheckBox, JPanel)
- Method in class startup.gui.
SprClassificationActionPanel
setAccordingToCheck(boolean, JCheckBox, JPanel)
- Method in class startup.gui.
SprWorkflowPanel
setAccuracy(double)
- Method in class util.results.
CrossValidationResult
setAccuracy2(double)
- Method in class util.results.
CrossValidationResult
setActions(List<ActionPanel>)
- Method in class var.experimenter.
RangePanel
setApproximate_correlation(double)
- Method in class util.results.
CrossValidationResult
setAuc(double)
- Method in class util.results.
CrossValidationResult
setBeUsed(boolean)
- Method in class var.experimenter.
RangeOption
setBoundaries(List<String>)
- Method in class util.parsers.embl.
Embl_CDS_Data
setBoundaries(List<String>)
- Method in class util.parsers.
GeneData
setBuildLogisticModels(boolean)
- Method in class classifier.wekaSVM.
SMO
Set the value of buildLogisticModels.
setButtons()
- Method in class startup.gui.
WizardFramework
setC(double)
- Method in class classifier.wekaSVM.
SMO
Set the value of C.
setCds_data_list(List<Embl_CDS_Data>)
- Method in class util.parsers.embl.
EmblFileData
setCds_length(int)
- Method in class util.parsers.embl.
Embl_CDS_Data
setCdsLength(int)
- Method in class util.parsers.
GeneData
setCfList(List<ClassificationFeature>)
- Method in class var.featureSelection.
FeatureFileContent
setChecksTurnedOff(boolean)
- Method in class classifier.wekaSVM.
SMO
Disables or enables the checks (which could be time-consuming).
setClassification(String)
- Method in class util.results.
ClassificationResult
setClassification_name(String)
- Method in class startup.
ClassificationAction
setClassification_name(String)
- Method in class var.featureSelection.
FeatureFileContent
setClassificationActions(List<ClassificationAction>)
- Method in class startup.
FunSiPWorkflow
setClassificationFeatures(List<ClassificationFeature>)
- Method in class startup.
ClassificationAction
setClassifier_options(String[])
- Method in class startup.
ClassificationAction
setClassifier_type(ClassificationAction.CLASSIFIERS)
- Method in class startup.
ClassificationAction
setClassifier_type(String)
- Method in class startup.
ClassificationAction
setCommand(ClassificationAction.COMMAND)
- Method in class startup.
ClassificationAction
setCommand(String)
- Method in class startup.
ClassificationAction
setCommandLinePath(String)
- Method in class util.secondaryStructure.
CreateSS
setCommandName(String)
- Method in class var.experimenter.
RangeOption
setComment(String)
- Method in class util.
SpliceSite
setComplexityCrossvalidation(boolean)
- Method in class startup.
ClassificationAction
setConversionList(List<Conversion>)
- Method in class startup.
ClassificationAction
setCorrectCDSLength(boolean)
- Method in class util.parsers.embl.
Embl_CDS_Data
setCorrectFilePath(String)
- Static method in class main.
FunSiPJar
Changes the pathname when running from a jar-file (some indicators change for some weird reason).
setCorrectStartCodon(boolean)
- Method in class util.parsers.embl.
Embl_CDS_Data
setCorrectStopCodon(boolean)
- Method in class util.parsers.embl.
Embl_CDS_Data
setCorrectTest(boolean)
- Method in class util.parsers.
GeneTestResult
setCorrelation_coefficient(double)
- Method in class util.results.
CrossValidationResult
setCrossvalidation_fold(int)
- Method in class startup.
ClassificationAction
setCrossValidationTabFile(File)
- Method in class startup.
ClassificationAction
setDefinedBasePairs(int)
- Method in class util.parsers.embl.
EmblFileData
setDefinedBP(int)
- Method in class util.parsers.
GeneTrainingData
setDimensions(Dimension, Component)
- Method in class startup.gui.
WizardFramework
setDistance(double)
- Method in class util.results.
ClassificationResult
setDistances(double[])
- Method in class util.results.
CrossValidationResult
Sets the distancesto the hyperplane for all training examples
setDonor(boolean)
- Method in class util.results.
ClassificationResult
setDonorMap(Map<Integer, Instances>)
- Method in class util.results.
PotentialResultsMap
setDonorSites(List<Integer>)
- Method in class util.parsers.
GeneData
setDouble_arg_1(double)
- Method in class var.experimenter.
RangeOption
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.
CompositionalClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.
CompositionalGeneralClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.
PositionalClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.
PositionalGeneralClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
GcContentClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
HydrophilicClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
NearestEqualClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
PhysicalPropertiesClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
TestNucleotideDistanceClassificationFeature
setDownstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
WaveContentClassificationFeature
setEnergies(List<Double>)
- Method in class util.io.
SecondaryStructureData
setEnergies(List<Double>)
- Method in class util.secondaryStructure.
SecondaryStructureData
setEpsilon(double)
- Method in class classifier.wekaSVM.
SMO
Set the value of epsilon.
setError_rate(double)
- Method in class util.results.
CrossValidationResult
setExplicitFiles(File[])
- Method in class startup.
FunSiPWorkflow
This method is used when additional fastafiles that need to be evaluated are provided on the commandline by the user.
setExtended_structure(boolean)
- Method in class util.secondaryStructure.
SecondaryStructureData
setExtra_energies(List<Double>)
- Method in class util.secondaryStructure.
SecondaryStructureData
setExtra_structures(List<String>)
- Method in class util.secondaryStructure.
SecondaryStructureData
setExtraInfo(List<String>)
- Method in class util.io.
CrossValidationOutput
setExtraInfoLabel(String)
- Method in class util.io.
CrossValidationOutput
setF1_measure(double)
- Method in class util.results.
CrossValidationResult
setFalseNegatives(int)
- Method in class util.results.
CrossValidationResult
Sets the amount of false negatives of the crossvalidation
setFalsePositives(int)
- Method in class util.results.
CrossValidationResult
Sets the amount of false positives
setFeature_selection_input_file(String)
- Method in class util.featureSelection.
FeatureSelectionStub
setFeature_selection_output_file(String)
- Method in class util.featureSelection.
FeatureSelectionStub
setFeature_selection_purpose(FeatureSelectionStub.FEATURE_SELECTION_PURPOSE)
- Method in class util.featureSelection.
FeatureSelectionStub
setFeature_selection_purpose(String)
- Method in class util.featureSelection.
FeatureSelectionStub
setFeature_selection_type(FeatureSelectionStub.FEATURE_SELECTION_TYPE)
- Method in class util.featureSelection.
FeatureSelectionStub
setFeature_selection_type(String)
- Method in class util.featureSelection.
FeatureSelectionStub
setFeatures_output_file(String)
- Method in class startup.
ClassificationAction
setFeatureSelection(FeatureSelectionStub)
- Method in class startup.
ClassificationAction
setFileEnabled(boolean)
- Method in class startup.gui.
SprOutputPanel
setFileName(String)
- Method in class startup.
FunSiPWorkflow
setFileName(String)
- Method in class util.parsers.embl.
EmblFileData
setFileName(String)
- Method in class util.parsers.
GeneTrainingData
setFileName(String)
- Method in class util.
RocCurveData
setFileName(String)
- Method in class util.
SVMUtil
setFileName(String)
- Method in class var.featureSelection.
FeatureFileContent
setFilter(List<Integer>)
- Method in class util.featureSelection.
FeatureSelectionStub
setFilterType(SelectedTag)
- Method in class classifier.wekaSVM.
SMO
Sets how the training data will be transformed.
setForwardStrand(boolean)
- Method in class util.parsers.
GeneData
setFp5_measure(double)
- Method in class util.results.
CrossValidationResult
setFp_rate(double)
- Method in class util.results.
CrossValidationResult
setFullTypes(String[])
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
setFullTypes(String[])
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
setFullTypes(String[])
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
setFullTypes(String[])
- Method in interface util.classificationFeatures.
SeconderyStructureClassificationFeature
setGeneData(List<GeneData>)
- Method in class util.parsers.
GeneTrainingData
setIdentifier(int)
- Method in class util.
RocCurveData
setIdentifier(int)
- Method in class var.experimenter.
RangeOption
setInputMergeFiles(List<List<String>>)
- Method in class startup.
FunSiPWorkflow
setInstances(Instances)
- Method in class util.
SVMUtil
setInteger_arg_1(int)
- Method in class var.experimenter.
RangeOption
setInteger_arg_2(int)
- Method in class var.experimenter.
RangeOption
setKernel(Kernel)
- Method in class classifier.wekaSVM.
SMO.BinarySMO
sets the kernel to use
setKernel(Kernel)
- Method in class classifier.wekaSVM.
SMO
sets the kernel to use
setKeyName(String)
- Method in class var.experimenter.
RangeOption
setLabels(double[])
- Method in class util.results.
CrossValidationResult
Sets the labels (1/-1 for positive/negative) for all the training examples.
setLength(int)
- Method in class util.classificationFeatures.implementations.
CompositionalClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.
CompositionalGeneralClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.
PositionalClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.
PositionalGeneralClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
GcContentClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
HydrophilicClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
NearestEqualClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
PhysicalPropertiesClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
TestNucleotideDistanceClassificationFeature
setLength(int)
- Method in class util.classificationFeatures.implementations.test.
WaveContentClassificationFeature
setLocation_in_forward(List<Integer>)
- Method in class util.
DualLocationList
setLocation_in_local(List<Integer>)
- Method in class util.
DualLocationList
setLocations(String)
- Method in class util.io.
ModelDataParser.ModelData
setMainPanel()
- Method in class startup.gui.
WizardFramework
setMax(int)
- Method in class util.results.
ExtractionResult
setMaximum_crossvalidation(int)
- Method in class startup.
ClassificationAction
setMaxNumFeatures(int)
- Method in class util.featureSelection.
FeatureSelectionStub
setMeanSquaredError(double)
- Method in class util.results.
CrossValidationResult
setMergeResults(boolean)
- Method in class startup.
FunSiPWorkflow
setModel_file(String)
- Method in class startup.
ClassificationAction
setModelFile(String)
- Method in interface classifier.
Classifier
Changes the model for the classifier by changing the name of the modelfile.
setModelFile(String)
- Method in class classifier.
WekaSVM
Changes the model for the classifier by changing the name of the modelfile.
setName(String)
- Method in class startup.
ClassificationAction
setName(String)
- Method in class util.
FastaFileData
setName(String)
- Method in class util.
FileInfo
setName(String)
- Method in class util.parsers.embl.
Embl_CDS_Data
setName(String)
- Method in class util.results.
PotentialResultsMap
setName(String)
- Method in class var.experimenter.
ActionPanel
setName(String)
- Method in class var.experimenter.
RangeOption
setNegative_training_amount(int)
- Method in class startup.
ClassificationAction
setNegative_training_file(String)
- Method in class startup.
ClassificationAction
setNegative_training_file_secstruct(String)
- Method in class startup.
ClassificationAction
setNewConfiguration(String)
- Method in class main.
FunSiPGui
Sets a new configuration file as standard loaded configuration file.
setNumExons(int)
- Method in class util.parsers.embl.
Embl_CDS_Data
setNumExons(int)
- Method in class util.parsers.
GeneData
setNumFolds(int)
- Method in class classifier.wekaSVM.
SMO
Set the value of numFolds.
setOf(SprOutputPanel.OUTPUT_FILTER)
- Method in class startup.gui.
SprOutputPanel
setOptimizer(boolean)
- Method in class startup.
FunSiPWorkflow
setOptimizer_steps(int, int, int)
- Method in class startup.
FunSiPWorkflow
setOptions(ClassifierOptions)
- Method in interface classifier.
Classifier
Changes the various options of this classifier.
setOptions(ClassifierOptions)
- Method in class classifier.
WekaSVM
Changes the various options of this classifier.
setOptions(String[])
- Method in class classifier.wekaSVM.
SMO
Parses a given list of options.
setOptions()
- Method in class startup.gui.
OptionsPanel
setOptions(String[])
- Method in interface util.conversions.
Conversion
This method sets the possible options for this conversion.
setOptions(String[])
- Method in class util.conversions.implementations.
DNA_AA_Conversion
This method sets the possible options for this conversion.
setOptions(String[])
- Method in class util.conversions.implementations.
DNA_MK_Conversion
setOptions(String[])
- Method in class util.conversions.implementations.
DNA_RY_Conversion
setOptions(String[])
- Method in class util.conversions.implementations.
DNA_SW_Conversion
setOptions(String[])
- Method in class util.conversions.implementations.
FibonacciSwitchConversion
This method sets the possible options for this conversion.
setOptions(String[])
- Method in class util.conversions.implementations.
Test_2_Conversion
This method sets the possible options for this conversion.
setOptions(String[])
- Method in class util.conversions.implementations.
TEST_Conversion
setOutput(SprOutputPanel.OUTPUT)
- Method in class startup.gui.
SprOutputPanel
setOutput_fixed_alpha(Double)
- Method in class startup.
ClassificationAction
setOutput_fixed_beta(Double)
- Method in class startup.
ClassificationAction
setOutputdirectory(String)
- Method in class startup.
ClassificationAction
setOutputMergeFile(List<String>)
- Method in class startup.
FunSiPWorkflow
setParameters(String[])
- Method in interface classifier.
ClassifierOptions
Sets classifier parameters by parsing them from an array of strings.
setParameters(String[])
- Method in class classifier.
SVMOptions
Sets classifier parameters by parsing them from an array of strings.
setParameters(String[])
- Method in interface util.classificationFeatures.
ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
BranchpointClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
CompositionalClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
CompositionalGeneralClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
PositionalClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
PositionalGeneralClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.
RFClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
DeterminantClassificationFeature
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
GcContentClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
HydrophilicClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
IntronRetention1ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
IntronRetention2ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
IntronRetentionCompareClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
NearestEqualClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
NonBindingClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
PentaClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
PhysicalPropertiesClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
RF2ClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
SecStructEvalClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
SecStructSimpleClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
TestNucleotideDistanceClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
TetraHedronClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
VarianceClassificationFeature
setParameters(String[])
- Method in class util.classificationFeatures.implementations.test.
WaveContentClassificationFeature
This method sets the necessary parameters for the classificationfeature.
setPattern(String)
- Method in class startup.
ClassificationAction
setPattern_classification_location(int)
- Method in class startup.
ClassificationAction
setPattern_classification_output_f(int)
- Method in class startup.
ClassificationAction
setPattern_classification_output_r(int)
- Method in class startup.
ClassificationAction
setPattern_regexp(boolean)
- Method in class startup.
ClassificationAction
setPosition(int)
- Method in class util.featureSelection.
ValPosCombination
setPositive_training_amount(int)
- Method in class startup.
ClassificationAction
setPositive_training_file(String)
- Method in class startup.
ClassificationAction
setPositive_training_file_secstruct(String)
- Method in class startup.
ClassificationAction
setPredictionOutputFiles(String[])
- Method in class startup.
ClassificationAction
setPurpose(String)
- Method in class util.io.
ModelDataParser.ModelData
setRandomSeed(int)
- Method in class classifier.wekaSVM.
SMO
Set the value of randomSeed.
setRangeOptions(List<RangeOption>)
- Method in class var.experimenter.
ActionPanel
setReducedTypes(String[])
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
setReducedTypes(String[])
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
setReducedTypes(String[])
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
setReducedTypes(String[])
- Method in interface util.classificationFeatures.
SeconderyStructureClassificationFeature
setResult(Map<String, Integer>)
- Method in class util.results.
ExtractionResult
setReverse(boolean)
- Method in class util.parsers.embl.
Embl_CDS_Data
setRoc_fp_rate(double[])
- Method in class util.results.
CrossValidationResult
setRoc_tp_rate(double[])
- Method in class util.results.
CrossValidationResult
setRuntimeFunSiP(FunSiPGui)
- Method in class startup.gui.
SprOutputEditorWriter
setSelect_arg_1(List<String>)
- Method in class var.experimenter.
RangeOption
setSelect_arg_2(List<String>)
- Method in class var.experimenter.
RangeOption
setSensitivity(double)
- Method in class util.results.
CrossValidationResult
setSeqName(String)
- Method in class util.results.
ClassificationResult
setSequence(String)
- Method in class util.
FastaFileData
setSequence(String)
- Method in class util.
FileInfo
setSequence(String)
- Method in class util.parsers.embl.
EmblFileData
setSequence(String)
- Method in class util.parsers.
GeneTrainingData
setSequences(List<String>)
- Method in class util.secondaryStructure.
SecondaryStructureData
setSigmoid_A(double)
- Method in interface classifier.
Classifier
Changes the sigmoid variable A (see documentation about restructuring the output by use of sigmoid curves)
setSigmoid_A(double)
- Method in class classifier.
WekaSVM
Changes the sigmoid variable A (see documentation about restructuring the output by use of sigmoid curves)
setSigmoid_B(double)
- Method in interface classifier.
Classifier
Changes the sigmoid variable B (see documentation about restructuring the output by use of sigmoid curves)
setSigmoid_B(double)
- Method in class classifier.
WekaSVM
Changes the sigmoid variable B (see documentation about restructuring the output by use of sigmoid curves)
setSmo(SMO)
- Method in class util.
SVMUtil
setSpecies(String)
- Method in class util.io.
ModelDataParser.ModelData
setSpecificity(double)
- Method in class util.results.
CrossValidationResult
setSplicesite(int)
- Method in class util.results.
ClassificationResult
setSplicesites(List<SpliceSite>)
- Method in class util.
FileInfo
setSplicesites(List<Integer>)
- Method in class util.parsers.embl.
Embl_CDS_Data
setSplicesites(List<Integer>)
- Method in class util.parsers.
GeneData
setSpliceVariant(String)
- Method in class util.
FileInfo
setSprOutput(FunSiP, SprOutputPanel)
- Method in class main.
FunSiPGui
Changes the output of the supplied FunSiP program, according to the content of the output panel.
setSquaredCorrelationCoefficient(double)
- Method in class util.results.
CrossValidationResult
setStart(Integer)
- Method in class util.
SpliceSite
setStartCodon(String)
- Method in class util.parsers.embl.
Embl_CDS_Data
setStartCodon(String)
- Method in class util.parsers.
GeneData
setStop(Integer)
- Method in class util.
SpliceSite
setStopCodon(String)
- Method in class util.parsers.embl.
Embl_CDS_Data
setStopCodon(String)
- Method in class util.parsers.
GeneData
setStrand(ClassificationAction.STRAND)
- Method in class startup.
ClassificationAction
setStrand(String)
- Method in class startup.
ClassificationAction
setStrand(char)
- Method in class util.
FileInfo
setString_arg_1(String)
- Method in class var.experimenter.
RangeOption
setStructures(List<String>)
- Method in class util.io.
SecondaryStructureData
setStructures(List<String>)
- Method in class util.secondaryStructure.
SecondaryStructureData
setSvmType(ClassificationAction.CLASSIFIERS)
- Method in class util.
SVMUtil
setTarget(FeatureRecognition.TARGET)
- Method in class startup.features.
FeatureRecognition
setTestFile(File)
- Method in class util.io.
CrossValidationData
setTestfiles(String[])
- Method in class startup.
ClassificationAction
setTestfiles_filetype(ClassificationAction.FILE_TYPE)
- Method in class startup.
ClassificationAction
setTestfiles_filetype(String)
- Method in class startup.
ClassificationAction
setThreading(String)
- Method in class startup.
FunSiPWorkflow
setToleranceParameter(double)
- Method in class classifier.wekaSVM.
SMO
Set the value of tolerance parameter.
setTotalNegatives(int)
- Method in class util.results.
CrossValidationResult
Sets the total amount of negatives
setTotalPositives(int)
- Method in class util.results.
CrossValidationResult
Sets the total amount of positives
setTraining_functional_site_position(int)
- Method in class startup.
ClassificationAction
setTrainingFile(File)
- Method in class util.io.
CrossValidationData
setTrueNegatives(int)
- Method in class util.results.
CrossValidationResult
Sets the amount of true negatives
setTruePositives(int)
- Method in class util.results.
CrossValidationResult
Sets the amount of true positives
setType(RangeOption.TYPE)
- Method in class var.experimenter.
RangeOption
setUpDownRanges(int, int)
- Method in interface util.classificationFeatures.
ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
BranchpointClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
CompositionalClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
CompositionalGeneralClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
PositionalClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
PositionalGeneralClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.
RFClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
DeterminantClassificationFeature
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
GcContentClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
HydrophilicClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
IntronRetention1ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
IntronRetention2ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
IntronRetentionCompareClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
NearestEqualClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
NonBindingClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
PentaClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
PhysicalPropertiesClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
RF2ClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
SecStructEvalClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
SecStructSimpleClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
TestNucleotideDistanceClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
TetraHedronClassificationFeature
This method sets the new upstream and downstream ranges
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
VarianceClassificationFeature
setUpDownRanges(int, int)
- Method in class util.classificationFeatures.implementations.test.
WaveContentClassificationFeature
This method sets the new upstream and downstream ranges
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.
CompositionalClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.
CompositionalGeneralClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.
CompositionalSecondaryStructureClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.
PositionalClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.
PositionalGeneralClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
GcContentClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
HydrophilicClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
NearestEqualClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
NearSecondaryStructureClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
PhysicalPropertiesClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
PositionalSecondaryStructureClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
TestNucleotideDistanceClassificationFeature
setUpstream_range(int)
- Method in class util.classificationFeatures.implementations.test.
WaveContentClassificationFeature
setValue(double)
- Method in class util.featureSelection.
ValPosCombination
setVisible(boolean)
- Method in class var.experimenter.
RangeOption
setVpcList(List<ValPosCombination>)
- Method in class var.featureSelection.
FeatureFileContent
SigmoidFunction
- Class in
util.results
Class that computes the alfa and beta values for a sigmoid function.
SigmoidFunction()
- Constructor for class util.results.
SigmoidFunction
SimpleExperimenter
- Class in
var
SimpleExperimenter(String[])
- Constructor for class var.
SimpleExperimenter
SINGLE_DOUBLE_OPTION
- Static variable in class var.experimenter.
ConfigurationFileReader
SINGLE_INTEGER_OPTION
- Static variable in class var.experimenter.
ConfigurationFileReader
SINGLE_SELECT_OPTION
- Static variable in class var.experimenter.
ConfigurationFileReader
SINGLE_STRING_OPTION
- Static variable in class var.experimenter.
ConfigurationFileReader
SLEEP_TIME
- Static variable in class startup.cluster.
ClusterClassificationAction
The time a node waits between anouncing its finish (milliseconds).
SMO
- Class in
classifier.wekaSVM
Implements John Platt's sequential minimal optimization algorithm for training a support vector classifier.
SMO()
- Constructor for class classifier.wekaSVM.
SMO
SMO.BinarySMO
- Class in
classifier.wekaSVM
Class for building a binary support vector machine.
SMO.BinarySMO()
- Constructor for class classifier.wekaSVM.
SMO.BinarySMO
SMOSizeDataExtractor
- Class in
util
SMOSizeDataExtractor(String, String, int, int, boolean)
- Constructor for class util.
SMOSizeDataExtractor
sort(int[], char[])
- Method in class util.conversions.implementations.
TEST_Conversion
SortingAlgorithms
- Class in
util
SortingAlgorithms()
- Constructor for class util.
SortingAlgorithms
sortScores(List<FunSiPWorkflow.OptimizationScore>)
- Method in class startup.
FunSiPWorkflow
Dummy bubblesort algorithm (normally list only consists of 2-10 items) for the OptimizationScore type.
sparseIndices()
- Method in class classifier.wekaSVM.
SMO
Returns the indices in sparse format.
sparseWeights()
- Method in class classifier.wekaSVM.
SMO
Returns the weights in sparse format.
SPLASH_SCREEN_IMAGE
- Static variable in class startup.gui.
SprSplashScreen
SpliceFileInfo
- Class in
util
SpliceFileInfo(int)
- Constructor for class util.
SpliceFileInfo
SPLICESITE
- Static variable in class util.parsers.
ExtractTrainingData
SpliceSite
- Class in
util
SpliceSite()
- Constructor for class util.
SpliceSite
splitFiles()
- Method in class util.
SpliceFileInfo
splitFiles2()
- Method in class util.
SpliceFileInfo
SprClassificationActionPanel
- Class in
startup.gui
SprClassificationActionPanel(ClassificationAction)
- Constructor for class startup.gui.
SprClassificationActionPanel
SprClassificationFeaturePanel
- Class in
startup.gui
SprClassificationFeaturePanel(ClassificationAction, Dimension)
- Constructor for class startup.gui.
SprClassificationFeaturePanel
SprOutputEditorWriter
- Class in
startup.gui
SprOutputEditorWriter()
- Constructor for class startup.gui.
SprOutputEditorWriter
SprOutputPanel
- Class in
startup.gui
SprOutputPanel()
- Constructor for class startup.gui.
SprOutputPanel
SprOutputPanel.OUTPUT
- Enum in
startup.gui
SprOutputPanel.OUTPUT_FILTER
- Enum in
startup.gui
SprSplashScreen
- Class in
startup.gui
SprSplashScreen()
- Constructor for class startup.gui.
SprSplashScreen
SprWorkflowPanel
- Class in
startup.gui
SprWorkflowPanel(FunSiPWorkflow)
- Constructor for class startup.gui.
SprWorkflowPanel
start_classification()
- Method in class startup.
ClassificationAction
This method starts the actual dataflow within the classification action.
startup
- package startup
startup.cluster
- package startup.cluster
startup.features
- package startup.features
startup.gui
- package startup.gui
svm_complexity
- Variable in class util.
Options
SVMOptions
- Class in
classifier
Class defining various classifier options that are specific to Support vector machines.
SVMOptions()
- Constructor for class classifier.
SVMOptions
SVMOptions.KERNEL_TYPE
- Enum in
classifier
The different kernel functions.
SVMOutput(int, Instance)
- Method in class classifier.wekaSVM.
SMO.BinarySMO
Computes SVM output for given instance.
SVMUtil
- Class in
util
SVMUtil()
- Constructor for class util.
SVMUtil
SVMUtil(SMO, Instances)
- Constructor for class util.
SVMUtil
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