Uses of Class
contextFold.rna.RNA

Packages that use RNA
contextFold.app Contains java-executable programs that perform the main functionalities of the contextFold package. 
contextFold.features Contains scoring model's parameterization related functionalities. 
contextFold.learn Contains weight learning related functionalities. 
contextFold.rna Contains RNA representation related utilities. 
contextFold.rnaFolding Contains RNA secondary structure prediction related utilities. 
contextFold.scoring Contains RNA secondary structure scoring and similarity computation related utilities. 
 

Uses of RNA in contextFold.app
 

Method parameters in contextFold.app with type arguments of type RNA
static void Predict.predictAll(FeatureManager featureManager, java.lang.String outputPath, java.util.List<RNA> rnas)
           
static void Predict.predictAll(FeatureManager featureManager, java.lang.String output, java.util.List<RNA> rnas, java.lang.String echoStr)
           
 

Uses of RNA in contextFold.features
 

Methods in contextFold.features with parameters of type RNA
 AbstractFeatureVector FeatureManager.getElementFeaturs(RNA rna, int elementType, int val1)
           
 float FeatureManager.getElementScore(RNA rna, int elementType, int val)
           
 StructreElementsScorer FeatureManager.getElementScorer(RNA rna)
           
 AbstractFeatureVector FeatureManager.getElementWeightedFeaturs(RNA rna, int elementType, int val1)
           
 

Uses of RNA in contextFold.learn
 

Methods in contextFold.learn with parameters of type RNA
 void Learn.costSensitivePAUpdate(RNA rna, int[] guessFold, int[] goldFold, float lt)
           
 void Learn.updateKbest(int[][] guessFolds, int[] goldFold, float[] margins, int iter, int seqnum, int seqlen, RNA rna)
           
 

Method parameters in contextFold.learn with type arguments of type RNA
 float Learn.doIter(int iter, java.util.List<RNA> rnas, int averageEvery, int niters)
           
 void Learn.learn(int iters, java.util.List<RNA> rnas, java.lang.String weightsOutputFile, int averageEvery, boolean shuffle, float requiredImproveFactor, int maxNoImprovements, boolean keepIterationWeights)
           
 

Uses of RNA in contextFold.rna
 

Methods in contextFold.rna that return RNA
static RNA RNA.randomRNA(int length)
           
 

Methods in contextFold.rna that return types with arguments of type RNA
 java.util.List<RNA> RNA_Filter.filter(java.util.Collection<RNA> rnas)
           
 java.util.List<RNA> RNA_Filter.filter(java.util.Collection<RNA> rnas, int keep, boolean shuffle)
           
 java.util.List<RNA> RNA_Filter.getLastFiltered()
           
 java.util.List<RNA> RNAStrandReader.readList(java.lang.CharSequence list)
           
abstract  java.util.List<RNA> RNAListReader.readList(java.lang.CharSequence list)
           
 java.util.List<RNA> OneLineReader.readList(java.lang.CharSequence list)
           
 java.util.List<RNA> RNAListReader.readList(java.io.File f)
           
 

Methods in contextFold.rna with parameters of type RNA
abstract  boolean RNA_Filter.filter(RNA rna)
           
 boolean AnnotationFilter.filter(RNA rna)
           
 void RNAWriter.write(RNA rna)
           
 

Method parameters in contextFold.rna with type arguments of type RNA
 java.util.List<RNA> RNA_Filter.filter(java.util.Collection<RNA> rnas)
           
 java.util.List<RNA> RNA_Filter.filter(java.util.Collection<RNA> rnas, int keep, boolean shuffle)
           
static void RNA.filter(java.util.List<RNA> rnas, int maxLength)
           
static void RNA.filter(java.util.List<RNA> rnas, java.lang.String annotationFilter)
           
static java.lang.String RNA.RNAListStatistics(java.util.List<RNA> rnas)
           
 void RNAWriter.writeAll(java.util.List<RNA> rnas)
           
 

Uses of RNA in contextFold.rnaFolding
 

Methods in contextFold.rnaFolding that return RNA
 RNA Folder.tagOne(java.lang.String sequence)
          Deprecated. 
 RNA Fold.tagOne(java.lang.String sequence)
           
 

Methods in contextFold.rnaFolding that return types with arguments of type RNA
 java.util.List<RNA> Folder.tagMany(java.lang.String listInput)
           
 java.util.List<RNA> Fold.tagMany(java.lang.String sequences)
           
 

Uses of RNA in contextFold.scoring
 

Methods in contextFold.scoring that return RNA
 RNA StructreElementsScorerImpl.getRna()
           
 RNA StructreElementsScorer.getRna()
           
 

Methods in contextFold.scoring with parameters of type RNA
 void FoldEvaluatorImpl.differenceFeatureVector(int[] guessFold, int[] goldFold, AbstractFeatureVector diffVector, RNA rna)
           
 void FoldEvaluator.differenceFeatureVector(int[] guessFold, int[] goldFold, AbstractFeatureVector result, RNA rna)
          Computes the feature difference between two foldings.
 AbstractFeatureVector FoldEvaluatorImpl.differenceFeatureVector(int[] guessFold, int[] goldFold, RNA rna)
           
 AbstractFeatureVector FoldEvaluator.differenceFeatureVector(int[] guessFold, int[] goldFold, RNA rna)
           
 float FoldEvaluatorImpl.scoreFold(RNA rna, int[] fold)
           
 float FoldEvaluator.scoreFold(RNA rna, int[] fold)
          Computes the score of a given sequence-folding pair.
 void StructreElementsScorerImpl.setManagerAndRNA(FeatureManager manager, RNA rna)
           
 

Method parameters in contextFold.scoring with type arguments of type RNA
static void PredictionQuality.predictionStatistics(java.util.List<RNA> rnas, int binSize)
           
static void PredictionQuality.predictionStatistics(java.util.List<RNA> rnas, int binSize, boolean verbose)