A B C D E F G H I J L M N O P R S T U V W X

G

G - Static variable in class contextFold.rna.RNA
 
get(int) - Method in class contextFold.rna.RNA
 
getAlphabetSize() - Method in class contextFold.features.Context
 
getAnnotationVal(String) - Method in class contextFold.rna.RNA
 
getCardinality() - Method in class contextFold.features.Context
 
getCardinality() - Method in class contextFold.features.FeatureExtractor
 
getCardinality() - Method in class contextFold.features.FeatureTemplate
 
getCombinedElements(int[]) - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getCombinedElements(int[]) - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getEffectiveCardinality() - Method in class contextFold.features.DoublePosContext
 
getEffectiveCardinality() - Method in class contextFold.features.FeatureExtractor
 
getEffectiveCardinality() - Method in class contextFold.features.SinglePosContext
 
getElementFeaturs(RNA, int, int) - Method in class contextFold.features.FeatureManager
 
getElementName(int) - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getElementName(int) - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getElementScore(RNA, int, int) - Method in class contextFold.features.FeatureManager
 
getElementScorer(RNA) - Method in class contextFold.features.FeatureManager
 
getElementWeightedFeaturs(RNA, int, int) - Method in class contextFold.features.FeatureManager
 
getFeature(byte[], int) - Method in class contextFold.features.BinnedLengthFeatureExtractor
 
getFeature(byte[], int) - Method in class contextFold.features.DoublePosContext
 
getFeature(int) - Method in class contextFold.features.FeatureExtractor
 
getFeature(byte[], int) - Method in class contextFold.features.FeatureExtractor
 
getFeature(byte[], int) - Method in class contextFold.features.SinglePosContext
 
getFeature(byte[]) - Static method in class contextFold.features.WordFeatureCalculator
 
getFeature(byte[], int) - Static method in class contextFold.features.WordFeatureCalculator
 
getFeatureExtractor() - Method in class contextFold.features.FeatureTemplate
 
getFeatureName(int) - Method in class contextFold.features.DoublePosContext
 
getFeatureName(int) - Method in class contextFold.features.FeatureExtractor
 
getFeatureName(int) - Method in class contextFold.features.FeatureTemplate
 
getFeatureName(int) - Method in class contextFold.features.SinglePosContext
 
getFeatures() - Method in class contextFold.features.FeatureExtractor
 
getFeatures() - Method in class contextFold.scoring.StructreElementsScorerImpl
 
getFeaturesMap(ContextFeatureExtractor) - Method in class contextFold.features.ContextFeatureExtractor
 
getFeaturesMap(ContextFeatureExtractor) - Method in class contextFold.features.DoublePosContext
 
getFeaturesMap(ContextFeatureExtractor) - Method in class contextFold.features.SinglePosContext
 
getFeatureWeight(int) - Method in class contextFold.features.AbstractFeatureVector
 
getFeatureWeight(int) - Method in class contextFold.features.DenseFeatureVector
 
getFeatureWeight(int) - Method in class contextFold.features.SparseFeatureVector
 
getFeatureWeights() - Method in class contextFold.features.FeatureManager
 
getFirstBasepairType() - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getFirstBasepairType() - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getFirstBaseType() - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getFirstBaseType() - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getFirstLengthType() - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getFirstLengthType() - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getFirstPosContext() - Method in class contextFold.features.DoublePosContext
 
getFirstVectorIx() - Method in class contextFold.features.FeatureTemplate
 
getFold(String, int) - Static method in class contextFold.rna.RNA
Returns the index paring described by a dot-bracket string.
getFold(String) - Static method in class contextFold.rna.RNA
 
getFold(String, Pattern, Pattern) - Static method in class contextFold.rna.RNA
Returns the index paring described by a dot-bracket string.
getFoldNo(int) - Method in class contextFold.rna.RNA
 
getFolds(StructreElementsScorer) - Method in class contextFold.learn.Learn
 
getGoldBasepairNum() - Method in class contextFold.scoring.PredictionQuality
 
getGuessBasepairNum() - Method in class contextFold.scoring.PredictionQuality
 
getId() - Method in class contextFold.features.Context
 
getIdCounter() - Static method in class contextFold.features.Context
 
getLastBasepairType() - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getLastBasepairType() - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getLastBaseType() - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getLastBaseType() - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getLastFiltered() - Method in class contextFold.rna.RNA_Filter
 
getLastLengthType() - Method in interface contextFold.rnaFolding.StructureRecognizer
 
getLastLengthType() - Method in class contextFold.rnaFolding.StructureRecognizerImpl
 
getLength() - Method in class contextFold.features.Context
 
getLength() - Method in class contextFold.features.ContextFeatureExtractor
 
getLocalFeature(byte[], int) - Method in class contextFold.features.Context
 
getLocalFeature(byte[]) - Method in class contextFold.features.Context
 
getLocalFeatures(byte[], int[]) - Method in class contextFold.features.Context
 
getLocalFeatures(byte[]) - Method in class contextFold.features.Context
 
getMan() - Method in class contextFold.common.CmdArgumentsHandler
 
getName() - Method in class contextFold.features.FeatureTemplate
 
getNonCrossingFold(String) - Static method in class contextFold.rna.RNA
 
getNonZeroFeatures() - Method in class contextFold.features.AbstractFeatureVector
 
getNonZeroFeatures() - Method in class contextFold.features.DenseFeatureVector
 
getNonZeroFeatures() - Method in class contextFold.features.SparseFeatureVector
 
getOffsets() - Method in class contextFold.features.Context
 
getOffsets() - Method in class contextFold.features.SinglePosContext
 
getPossibleRplacement(char) - Static method in class contextFold.rna.RNA
 
getPseudoFold(String) - Static method in class contextFold.rna.RNA
 
getReverseArray() - Method in class contextFold.features.Context
 
getReversedContext() - Method in class contextFold.features.ContextFeatureExtractor
 
getRna() - Method in interface contextFold.scoring.StructreElementsScorer
 
getRna() - Method in class contextFold.scoring.StructreElementsScorerImpl
 
getScores() - Method in class contextFold.scoring.StructreElementsScorerImpl
 
getSecondPosContext() - Method in class contextFold.features.DoublePosContext
 
getSeqLength() - Method in class contextFold.scoring.PredictionQuality
 
getStringFold() - Method in class contextFold.rna.RNA
 
getStringFold(int) - Method in class contextFold.rna.RNA
 
getStringSequence() - Method in class contextFold.rna.RNA
 
getSuperContext(int[], int[]) - Static method in class contextFold.features.Context
 
getSuperContext(ContextFeatureExtractor) - Method in class contextFold.features.ContextFeatureExtractor
 
getSuperContext(ContextFeatureExtractor) - Method in class contextFold.features.DoublePosContext
 
getSuperContext(SinglePosContext) - Method in class contextFold.features.SinglePosContext
 
getSuperContext(ContextFeatureExtractor) - Method in class contextFold.features.SinglePosContext
 
getTruePositiveNum() - Method in class contextFold.scoring.PredictionQuality
 
getUpdateTime() - Method in class contextFold.features.DenseFeatureVector
 
getValue(int[]) - Method in class contextFold.features.LogLengthValueFeature
 
getValue(int) - Method in class contextFold.features.ValueCalculator
 
getValue(int[]) - Method in interface contextFold.features.ValueFeature
 
getValueCalculator() - Method in class contextFold.features.FeatureTemplate
 
getValueName(int) - Method in class contextFold.features.ValueCalculator
 
getWord(int, int, byte[]) - Static method in class contextFold.features.WordFeatureCalculator
 
getWordStr(int, int, int) - Static method in class contextFold.features.WordFeatureCalculator
 
goldFold() - Method in class contextFold.rna.RNA
 

A B C D E F G H I J L M N O P R S T U V W X