Uses of Interface
util.conversions.Conversion

Packages that use Conversion
startup   
util.classificationFeatures   
util.classificationFeatures.implementations   
util.classificationFeatures.implementations.test   
util.conversions   
util.conversions.implementations   
 

Uses of Conversion in startup
 

Methods in startup that return types with arguments of type Conversion
 java.util.List<Conversion> ClassificationAction.getConversionList()
           
 

Methods in startup with parameters of type Conversion
 void ClassificationAction.addConversion(Conversion c)
           
 

Method parameters in startup with type arguments of type Conversion
 void ClassificationAction.setConversionList(java.util.List<Conversion> conversionList)
           
 

Uses of Conversion in util.classificationFeatures
 

Methods in util.classificationFeatures that return Conversion
 Conversion ClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 

Method parameters in util.classificationFeatures with type arguments of type Conversion
 java.util.List<java.lang.Double> ClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 

Uses of Conversion in util.classificationFeatures.implementations
 

Methods in util.classificationFeatures.implementations that return Conversion
 Conversion RFClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion PositionalGeneralClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion PositionalClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion CompositionalSecondaryStructureClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion CompositionalGeneralClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion CompositionalClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion BranchpointClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 

Method parameters in util.classificationFeatures.implementations with type arguments of type Conversion
 java.util.List<java.lang.Double> RFClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> PositionalGeneralClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> PositionalClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> CompositionalSecondaryStructureClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> CompositionalGeneralClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> CompositionalClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> BranchpointClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 

Uses of Conversion in util.classificationFeatures.implementations.test
 

Methods in util.classificationFeatures.implementations.test that return Conversion
 Conversion WaveContentClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion VarianceClassificationFeature.getConversion()
           
 Conversion TetraHedronClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion TestNucleotideDistanceClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion SecStructSimpleClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion SecStructEvalClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion RF2ClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion PositionalSecondaryStructureClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion PhysicalPropertiesClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion PentaClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion NonBindingClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion NearSecondaryStructureClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion NearestEqualClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion IntronRetentionCompareClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion IntronRetention2ClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion IntronRetention1ClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion HydrophilicClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion GcContentClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 Conversion DeterminantClassificationFeature.getConversion()
          This method asks the classificationfeature for its conversion-type.
 

Method parameters in util.classificationFeatures.implementations.test with type arguments of type Conversion
 java.util.List<java.lang.Double> WaveContentClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> VarianceClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> TetraHedronClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> TestNucleotideDistanceClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> SecStructSimpleClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> SecStructEvalClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> RF2ClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> PositionalSecondaryStructureClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> PhysicalPropertiesClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> PentaClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> NonBindingClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> NearSecondaryStructureClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> NearestEqualClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> IntronRetentionCompareClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> IntronRetention2ClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> IntronRetention1ClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> HydrophilicClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> GcContentClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> DeterminantClassificationFeature.extractFeatures(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 java.util.List<java.lang.Double> PhysicalPropertiesClassificationFeature.extractFeatures2(java.lang.String[] sequences, int splicesite, java.lang.String[] types, java.util.List<Conversion> conversions, java.lang.String[] conversion_sequences)
          This method extracts the features from a sequence (relative to the splicesite) and returns those features in a list of double-values (standardized on double values because of its generic but still small-sized nature).
 

Uses of Conversion in util.conversions
 

Methods in util.conversions that return Conversion
static Conversion ConversionUtils.parseConversionFromString(java.lang.String[] split)
          This method constructs the actual conversion and translation objects.
static Conversion ConversionUtils.parseConversionFromString2(java.lang.String s)
          This method constructs the actual conversion and translation objects.
static Conversion ConversionUtils.parseConversionFromStringJar(java.lang.String[] split)
           
static Conversion ConversionUtils.parseConversionFromStringNonJar(java.lang.String[] split)
          This method constructs the actual conversion and translation objects.
 

Uses of Conversion in util.conversions.implementations
 

Classes in util.conversions.implementations that implement Conversion
 class DNA_AA_Conversion
           
 class DNA_MK_Conversion
           
 class DNA_RY_Conversion
           
 class DNA_SW_Conversion
           
 class FibonacciSwitchConversion
           
 class Test_2_Conversion
           
 class TEST_Conversion