statalign.postprocess.plugins.benchmarks
Class Dataset

java.lang.Object
  statalign.postprocess.plugins.benchmarks.Dataset

All Implemented Interfaces:

java.io.Serializable

public class Dataset
extends java.lang.Object
implements java.io.Serializable

See Also:

Serialized Form

Field Summary

int	burnIn
java.util.ArrayList<com.ppfold.algo.FuzzyAlignment>	cumulativeFuzzyAlignment
java.util.ArrayList<com.ppfold.algo.ResultBundle>	cumulativeFuzzyExpResults
java.util.ArrayList<com.ppfold.algo.ResultBundle>	cumulativeFuzzyObsResults
java.io.File	fastaFile
double	fuzzyAlignmentObsEntropyMax
double	fuzzyAlignmentObsEntropyPerc
double	fuzzyAlignmentObsEntropyVal
com.ppfold.algo.AlignmentData	inputAlignment
java.util.ArrayList<java.lang.Double>	logLikelihoods
java.util.ArrayList<com.ppfold.algo.ResultBundle>	matrixFolds
int	mcmcSteps
com.ppfold.algo.AlignmentData	mpdAlignment
double	mpdVsInputSim
int[]	pairedSites
int[]	pairedSitesCombined
int[]	pairedSitesEntropyExp
int[]	pairedSitesEntropyObs
int[]	pairedSitesMatrix
int[]	pairedSitesMPD
int[]	pairedSitesPPfoldProjected
java.util.ArrayList<int[]>	pairedSitesProjectedRnaAlifoldSamples
java.util.ArrayList<int[]>	pairedSitesProjectedSamples
java.lang.String	pairedSitesRefSeq
int[]	pairedSitesRNAalifold
int[]	pairedSitesRNAalifoldMPDProjected
int[]	pairedSitesRNAalifoldRefProjected
int[]	pairedSitesWeighted
java.lang.String	pairedSitesWeightedRefSeq
double	pairsOnlyMPDPosteriorWeighted
double	pairsOnlyReliabilityEntropyObs
double	pairsOnlyReliabilityEntropyObsPosteriorWeighted
double	pairsOnlyReliabilityMPD
double	pairsOnlyReliabilityScoreCombined
double	pairsOnlyReliabilityScoreConsensusEvol
double	pairsOnlyReliabilityScoreRNAalifold
double	pairsOnlyReliabilityScoreSamplingAndAveraging
double	pairsOnlyReliabilityScoreSamplingAndAveragingPosteriorWeighted
double	pairsOnlyReliabilityScoreSamplingAndAveragingWeighted
java.util.ArrayList<java.lang.Double>	posteriors
double	posteriorsAverage
double	ppfoldReliabilityEntropyObs
double	ppfoldReliabilityMPD
double	ppfoldReliabilityScoreCombined
double	ppfoldReliabilityScoreConsensusEvol
double	ppfoldReliabilityScoreRNAalifold
double	ppfoldReliabilityScoreSamplingAndAveraging
double	ppfoldReliabilityScoreSamplingAndAveragingWeighted
java.util.ArrayList<int[]>	projectPairedSitesOnCumulativeMatrix
long	randomSeed
com.ppfold.algo.ResultBundle	resultBundleEntropyExp
com.ppfold.algo.ResultBundle	resultBundleEntropyObs
com.ppfold.algo.ResultBundle	resultBundleMPD
com.ppfold.algo.ResultBundle	resultBundlePPfold
com.ppfold.algo.ResultBundle	resultBundleReference
RNAalifoldResult	rnaAlifoldMPD
RNAalifoldResult	rnaAlifoldRef
java.util.ArrayList<com.ppfold.algo.AlignmentData>	sampledAlignments
java.util.ArrayList<com.ppfold.algo.ResultBundle>	sampledStructures
int	samplingRate
java.lang.String	title

Constructor Summary

Dataset()

Method Summary

static Dataset	loadDatasetResult(java.io.File inFile)
void	saveDatasetResult(java.io.File outFile)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

title

public java.lang.String title

randomSeed

public long randomSeed

burnIn

public int burnIn

mcmcSteps

public int mcmcSteps

samplingRate

public int samplingRate

fastaFile

public java.io.File fastaFile

inputAlignment

public com.ppfold.algo.AlignmentData inputAlignment

mpdAlignment

public com.ppfold.algo.AlignmentData mpdAlignment

posteriors

public java.util.ArrayList<java.lang.Double> posteriors

posteriorsAverage

public double posteriorsAverage

mpdVsInputSim

public double mpdVsInputSim

sampledAlignments

public java.util.ArrayList<com.ppfold.algo.AlignmentData> sampledAlignments

logLikelihoods

public java.util.ArrayList<java.lang.Double> logLikelihoods

sampledStructures

public java.util.ArrayList<com.ppfold.algo.ResultBundle> sampledStructures

pairedSitesProjectedSamples

public java.util.ArrayList<int[]> pairedSitesProjectedSamples

projectPairedSitesOnCumulativeMatrix

public java.util.ArrayList<int[]> projectPairedSitesOnCumulativeMatrix

cumulativeFuzzyAlignment

public java.util.ArrayList<com.ppfold.algo.FuzzyAlignment> cumulativeFuzzyAlignment

cumulativeFuzzyExpResults

public java.util.ArrayList<com.ppfold.algo.ResultBundle> cumulativeFuzzyExpResults

cumulativeFuzzyObsResults

public java.util.ArrayList<com.ppfold.algo.ResultBundle> cumulativeFuzzyObsResults

resultBundleReference

public com.ppfold.algo.ResultBundle resultBundleReference

resultBundleMPD

public com.ppfold.algo.ResultBundle resultBundleMPD

resultBundleEntropyExp

public com.ppfold.algo.ResultBundle resultBundleEntropyExp

resultBundleEntropyObs

public com.ppfold.algo.ResultBundle resultBundleEntropyObs

resultBundlePPfold

public com.ppfold.algo.ResultBundle resultBundlePPfold

fuzzyAlignmentObsEntropyVal

public double fuzzyAlignmentObsEntropyVal

fuzzyAlignmentObsEntropyPerc

public double fuzzyAlignmentObsEntropyPerc

fuzzyAlignmentObsEntropyMax

public double fuzzyAlignmentObsEntropyMax

ppfoldReliabilityEntropyObs

public double ppfoldReliabilityEntropyObs

pairsOnlyReliabilityEntropyObs

public double pairsOnlyReliabilityEntropyObs

pairsOnlyReliabilityEntropyObsPosteriorWeighted

public double pairsOnlyReliabilityEntropyObsPosteriorWeighted

ppfoldReliabilityScoreSamplingAndAveraging

public double ppfoldReliabilityScoreSamplingAndAveraging

ppfoldReliabilityScoreSamplingAndAveragingWeighted

public double ppfoldReliabilityScoreSamplingAndAveragingWeighted

pairsOnlyReliabilityScoreSamplingAndAveragingPosteriorWeighted

public double pairsOnlyReliabilityScoreSamplingAndAveragingPosteriorWeighted

ppfoldReliabilityMPD

public double ppfoldReliabilityMPD

pairsOnlyReliabilityScoreSamplingAndAveraging

public double pairsOnlyReliabilityScoreSamplingAndAveraging

pairsOnlyReliabilityScoreSamplingAndAveragingWeighted

public double pairsOnlyReliabilityScoreSamplingAndAveragingWeighted

pairsOnlyReliabilityMPD

public double pairsOnlyReliabilityMPD

pairsOnlyMPDPosteriorWeighted

public double pairsOnlyMPDPosteriorWeighted

pairedSites

public int[] pairedSites

pairedSitesWeighted

public int[] pairedSitesWeighted

pairedSitesMPD

public int[] pairedSitesMPD

pairedSitesPPfoldProjected

public int[] pairedSitesPPfoldProjected

pairedSitesRefSeq

public java.lang.String pairedSitesRefSeq

pairedSitesWeightedRefSeq

public java.lang.String pairedSitesWeightedRefSeq

pairedSitesEntropyExp

public int[] pairedSitesEntropyExp

pairedSitesEntropyObs

public int[] pairedSitesEntropyObs

pairedSitesProjectedRnaAlifoldSamples

public java.util.ArrayList<int[]> pairedSitesProjectedRnaAlifoldSamples

pairedSitesRNAalifold

public int[] pairedSitesRNAalifold

ppfoldReliabilityScoreRNAalifold

public double ppfoldReliabilityScoreRNAalifold

pairsOnlyReliabilityScoreRNAalifold

public double pairsOnlyReliabilityScoreRNAalifold

rnaAlifoldMPD

public RNAalifoldResult rnaAlifoldMPD

rnaAlifoldRef

public RNAalifoldResult rnaAlifoldRef

pairedSitesRNAalifoldMPDProjected

public int[] pairedSitesRNAalifoldMPDProjected

pairedSitesRNAalifoldRefProjected

public int[] pairedSitesRNAalifoldRefProjected

pairedSitesCombined

public int[] pairedSitesCombined

ppfoldReliabilityScoreCombined

public double ppfoldReliabilityScoreCombined

pairsOnlyReliabilityScoreCombined

public double pairsOnlyReliabilityScoreCombined

matrixFolds

public java.util.ArrayList<com.ppfold.algo.ResultBundle> matrixFolds

pairedSitesMatrix

public int[] pairedSitesMatrix

ppfoldReliabilityScoreConsensusEvol

public double ppfoldReliabilityScoreConsensusEvol

pairsOnlyReliabilityScoreConsensusEvol

public double pairsOnlyReliabilityScoreConsensusEvol

Constructor Detail

Dataset

public Dataset()

Method Detail

saveDatasetResult

public void saveDatasetResult(java.io.File outFile)

loadDatasetResult

public static Dataset loadDatasetResult(java.io.File inFile)