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T

TAGS_FILTER - Static variable in class classifier.wekaSVM.SMO
The filter to apply to the training data
test - package test
 
Test - Class in test
 
Test(String[]) - Constructor for class test.Test
 
Test_2_Conversion - Class in util.conversions.implementations
 
Test_2_Conversion() - Constructor for class util.conversions.implementations.Test_2_Conversion
 
TEST_Conversion - Class in util.conversions.implementations
 
TEST_Conversion() - Constructor for class util.conversions.implementations.TEST_Conversion
 
TestAttribEval - Class in util.featureSelection.implementations
 
TestAttribEval() - Constructor for class util.featureSelection.implementations.TestAttribEval
 
testClassificationFeatures(FeatureFileContent, FeatureFileContent) - Method in class var.FSCompare
This method tests whether or not two featurefiles are generated by the same amount and types of classificationfeatures.
testData(EmblFileData) - Static method in class util.parsers.embl.EmblUtils
 
testData(GeneTrainingData) - Method in class util.parsers.ExtractTrainingData
 
TestNucleotideDistanceClassificationFeature - Class in util.classificationFeatures.implementations.test
 
TestNucleotideDistanceClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
 
testSimilarLocations(FeatureFileContent, FeatureFileContent) - Method in class var.FSCompare
This method tests the same locations within both contents of featurefiles.
TetraHedronClassificationFeature - Class in util.classificationFeatures.implementations.test
 
TetraHedronClassificationFeature() - Constructor for class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
 
to_genomeview_output(int, Double, int, int, String) - Method in interface classifier.Classifier
Method which produces a string that can be used by the GenomeView program.
to_genomeview_output(int, Double, int, int, String) - Method in class classifier.WekaSVM
Method which produces a string that can be used by the GenomeView program.
to_splice_machine_output(String, int, int, String) - Method in interface classifier.Classifier
Method which produces a string that is similar to that of the Splicemachine program, according to the provided results.
to_splice_machine_output(Double, int, int, String) - Method in interface classifier.Classifier
Method which produces a string that is similar to the output provided by Splicemachine (with the provided results).
to_splice_machine_output(String, int, int, String) - Method in class classifier.WekaSVM
Method which produces a string that is similar to that of the Splicemachine program, according to the provided results.
to_splice_machine_output(Double, int, int, String) - Method in class classifier.WekaSVM
Method which produces a string that is similar to the output provided by Splicemachine (with the provided results).
toForwardStrand(String) - Static method in class util.Util
This method changes the strand of a sequence by both replacing the nucleotides by their complements and by inversing the order of the sequence.
toInverseString(String) - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
 
toleranceParameterTipText() - Method in class classifier.wekaSVM.SMO
Returns the tip text for this property
toNoRangeString() - Method in interface util.classificationFeatures.ClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
 
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
toNoRangeString() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
String representation of the classificationFeature that contains the core elements, and discards the upstream/downstream range elements.
toOppositeStrand(String) - Method in class util.gene.DNAUtil
 
toString() - Method in class classifier.wekaSVM.SMO.BinarySMO
Prints out the classifier.
toString() - Method in class classifier.wekaSVM.SMO
Prints out the classifier.
toString() - Method in class util.classificationFeatures.AttributeDescription
 
toString() - Method in interface util.classificationFeatures.ClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
toString() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
String representation of the classificationFeature
toString() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
toString() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
String representation of the classificationFeature
toString() - Method in class var.experimenter.ChoosePanel
 
toString() - Method in class var.experimenter.RangeOption
 
toStringUnderscore() - Method in interface util.classificationFeatures.ClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.BranchpointClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.CompositionalClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.CompositionalGeneralClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.CompositionalSecondaryStructureClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.PositionalClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.PositionalGeneralClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.RFClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.DeterminantClassificationFeature
 
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.GcContentClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.HydrophilicClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.IntronRetention1ClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.IntronRetention2ClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.IntronRetentionCompareClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.NearestEqualClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.NearSecondaryStructureClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.NonBindingClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.PentaClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.PhysicalPropertiesClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.PositionalSecondaryStructureClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.RF2ClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.SecStructEvalClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.SecStructSimpleClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.TestNucleotideDistanceClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.TetraHedronClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.VarianceClassificationFeature
 
toStringUnderscore() - Method in class util.classificationFeatures.implementations.test.WaveContentClassificationFeature
Returns the string representation of the classificationfeature, but with all possible spaces and tabs replaced by underscores.
trainSigmoid(double[], double[], int, int, Double[]) - Method in class util.results.SigmoidFunction
Computes the sigmoid function for data, and stores the resulting A and B values in a passed Parameter.
turnChecksOff() - Method in class classifier.wekaSVM.SMO
Turns off checks for missing values, etc.
turnChecksOn() - Method in class classifier.wekaSVM.SMO
Turns on checks for missing values, etc.
type - Variable in class util.classificationFeatures.AttributeDescription
 

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