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Packages that use RNA | |
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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 |
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Method parameters in contextFold.app with type arguments of type RNA | |
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static void |
Predict.predictAll(FeatureManager featureManager,
java.lang.String outputPath,
java.util.List<RNA> rnas)
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static void |
Predict.predictAll(FeatureManager featureManager,
java.lang.String output,
java.util.List<RNA> rnas,
java.lang.String echoStr)
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Uses of RNA in contextFold.features |
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Methods in contextFold.features with parameters of type RNA | |
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AbstractFeatureVector |
FeatureManager.getElementFeaturs(RNA rna,
int elementType,
int val1)
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float |
FeatureManager.getElementScore(RNA rna,
int elementType,
int val)
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StructreElementsScorer |
FeatureManager.getElementScorer(RNA rna)
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AbstractFeatureVector |
FeatureManager.getElementWeightedFeaturs(RNA rna,
int elementType,
int val1)
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Uses of RNA in contextFold.learn |
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Methods in contextFold.learn with parameters of type RNA | |
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void |
Learn.costSensitivePAUpdate(RNA rna,
int[] guessFold,
int[] goldFold,
float lt)
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void |
Learn.updateKbest(int[][] guessFolds,
int[] goldFold,
float[] margins,
int iter,
int seqnum,
int seqlen,
RNA rna)
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Method parameters in contextFold.learn with type arguments of type RNA | |
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float |
Learn.doIter(int iter,
java.util.List<RNA> rnas,
int averageEvery,
int niters)
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void |
Learn.learn(int iters,
java.util.List<RNA> rnas,
java.lang.String weightsOutputFile,
int averageEvery,
boolean shuffle,
float requiredImproveFactor,
int maxNoImprovements,
boolean keepIterationWeights)
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Uses of RNA in contextFold.rna |
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Methods in contextFold.rna that return RNA | |
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static RNA |
RNA.randomRNA(int length)
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Methods in contextFold.rna that return types with arguments of type RNA | |
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java.util.List<RNA> |
RNA_Filter.filter(java.util.Collection<RNA> rnas)
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java.util.List<RNA> |
RNA_Filter.filter(java.util.Collection<RNA> rnas,
int keep,
boolean shuffle)
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java.util.List<RNA> |
RNA_Filter.getLastFiltered()
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java.util.List<RNA> |
RNAStrandReader.readList(java.lang.CharSequence list)
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abstract java.util.List<RNA> |
RNAListReader.readList(java.lang.CharSequence list)
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java.util.List<RNA> |
OneLineReader.readList(java.lang.CharSequence list)
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java.util.List<RNA> |
RNAListReader.readList(java.io.File f)
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Methods in contextFold.rna with parameters of type RNA | |
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abstract boolean |
RNA_Filter.filter(RNA rna)
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boolean |
AnnotationFilter.filter(RNA rna)
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void |
RNAWriter.write(RNA rna)
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Method parameters in contextFold.rna with type arguments of type RNA | |
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java.util.List<RNA> |
RNA_Filter.filter(java.util.Collection<RNA> rnas)
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java.util.List<RNA> |
RNA_Filter.filter(java.util.Collection<RNA> rnas,
int keep,
boolean shuffle)
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static void |
RNA.filter(java.util.List<RNA> rnas,
int maxLength)
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static void |
RNA.filter(java.util.List<RNA> rnas,
java.lang.String annotationFilter)
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static java.lang.String |
RNA.RNAListStatistics(java.util.List<RNA> rnas)
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void |
RNAWriter.writeAll(java.util.List<RNA> rnas)
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Uses of RNA in contextFold.rnaFolding |
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Methods in contextFold.rnaFolding that return RNA | |
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RNA |
Folder.tagOne(java.lang.String sequence)
Deprecated. |
RNA |
Fold.tagOne(java.lang.String sequence)
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Methods in contextFold.rnaFolding that return types with arguments of type RNA | |
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java.util.List<RNA> |
Folder.tagMany(java.lang.String listInput)
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java.util.List<RNA> |
Fold.tagMany(java.lang.String sequences)
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Uses of RNA in contextFold.scoring |
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Methods in contextFold.scoring that return RNA | |
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RNA |
StructreElementsScorerImpl.getRna()
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RNA |
StructreElementsScorer.getRna()
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Methods in contextFold.scoring with parameters of type RNA | |
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void |
FoldEvaluatorImpl.differenceFeatureVector(int[] guessFold,
int[] goldFold,
AbstractFeatureVector diffVector,
RNA rna)
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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)
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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)
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Method parameters in contextFold.scoring with type arguments of type RNA | |
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static void |
PredictionQuality.predictionStatistics(java.util.List<RNA> rnas,
int binSize)
|
static void |
PredictionQuality.predictionStatistics(java.util.List<RNA> rnas,
int binSize,
boolean verbose)
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