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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
Overview
Package
Class
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Tree
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Index
Help
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