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- 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
Overview
Package
Class
Use
Tree
Deprecated
Index
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