Hierarchy For All Packages

Package Hierarchies:

• com.mastfrog.util.streams,
• umcg.genetica.collections,
• umcg.genetica.collections.intervaltree,
• umcg.genetica.console,
• umcg.genetica.containers,
• umcg.genetica.ensembl,
• umcg.genetica.genomicboundaries,
• umcg.genetica.graphics,
• umcg.genetica.gwas,
• umcg.genetica.io,
• umcg.genetica.io.bed,
• umcg.genetica.io.bedgraph,
• umcg.genetica.io.bin,
• umcg.genetica.io.binInteraction,
• umcg.genetica.io.binInteraction.gene,
• umcg.genetica.io.binInteraction.variant,
• umcg.genetica.io.concurrent,
• umcg.genetica.io.fasta,
• umcg.genetica.io.geofiles,
• umcg.genetica.io.gmt,
• umcg.genetica.io.gtf,
• umcg.genetica.io.gwascatalog,
• umcg.genetica.io.pileup,
• umcg.genetica.io.probemapping,
• umcg.genetica.io.regulomedb,
• umcg.genetica.io.text,
• umcg.genetica.io.text.converters,
• umcg.genetica.io.trityper,
• umcg.genetica.io.trityper.bin,
• umcg.genetica.io.trityper.converters,
• umcg.genetica.io.trityper.probeannotation,
• umcg.genetica.io.trityper.util,
• umcg.genetica.io.ucsc,
• umcg.genetica.legacy,
• umcg.genetica.math,
• umcg.genetica.math.interpolation,
• umcg.genetica.math.matrix,
• umcg.genetica.math.matrix2,
• umcg.genetica.math.stats,
• umcg.genetica.math.stats.concurrent,
• umcg.genetica.methylation,
• umcg.genetica.ncbi.dbsnp,
• umcg.genetica.text,
• umcg.genetica.text.parsing,
• umcg.genetica.util,
• umcg.genetica.variantAnnotator

Class Hierarchy

• java.lang.Object
  • umcg.genetica.math.stats.AndersonDarling
  • umcg.genetica.methylation.AssociatingPcasWithAnnotation
  • umcg.genetica.math.stats.AUC
  • umcg.genetica.io.trityper.util.BaseAnnot
  • umcg.genetica.io.trityper.converters.BeagleImputedToTriTyper
  • umcg.genetica.io.bed.BedEntry (implements umcg.genetica.variantAnnotator.GenomicRange)
  • umcg.genetica.io.bed.BedFile (implements java.lang.Iterable<T>)
  • umcg.genetica.io.bedgraph.BedGraphEntry (implements umcg.genetica.variantAnnotator.GenomicRange)
  • umcg.genetica.io.bedgraph.BedGraphFile (implements java.lang.Iterable<T>)
  • umcg.genetica.io.bin.BinaryFile
  • umcg.genetica.io.trityper.bin.BinaryGZipFloatMatrix
  • umcg.genetica.io.binInteraction.BinaryInteractionCohort
  • umcg.genetica.io.binInteraction.BinaryInteractionCovariateIterator (implements java.util.Iterator<E>)
  • umcg.genetica.io.binInteraction.BinaryInteractionFile (implements java.io.Closeable)
  • umcg.genetica.io.binInteraction.BinaryInteractionFileConstructorBuilder
  • umcg.genetica.io.binInteraction.BinaryInteractionFileCreator
  • umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneAbstract (implements umcg.genetica.io.binInteraction.gene.BinaryInteractionGene)
    • umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneCreator
    • umcg.genetica.io.binInteraction.gene.BinaryInteractionGeneStatic
  • umcg.genetica.io.binInteraction.BinaryInteractionQtlZscores
  • umcg.genetica.io.binInteraction.BinaryInteractionQueryResult
  • umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantAbstract (implements umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant)
    • umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantCreator
    • umcg.genetica.io.binInteraction.variant.BinaryInteractionVariantStatic
  • umcg.genetica.io.binInteraction.BinaryInteractionZscores
  • umcg.genetica.io.trityper.bin.BinaryResultDataset
  • umcg.genetica.io.trityper.bin.BinaryResultProbe
  • umcg.genetica.io.trityper.bin.BinaryResultProbeSummary
  • umcg.genetica.io.trityper.bin.BinaryResultSNP
  • umcg.genetica.io.trityper.bin.BinaryResultSNPSummary
  • umcg.genetica.math.stats.Binning
  • umcg.genetica.io.trityper.BufferedSNPLoader
  • umcg.genetica.util.CheckAssocationMultipleGeneProbes
  • umcg.genetica.methylation.CheckMatrixForValidBetaValues
  • umcg.genetica.math.stats.ChiSquare
  • umcg.genetica.io.trityper.util.ChrAnnotation
  • umcg.genetica.containers.Chromosome
  • umcg.genetica.collections.ChrPosMap<E> (implements java.lang.Iterable<T>)
  • umcg.genetica.collections.ChrPosTreeMap<E> (implements java.lang.Iterable<T>)
  • umcg.genetica.io.trityper.util.CompareAllelicDirections
  • umcg.genetica.math.stats.concurrent.ConcurrentCorrelation
  • umcg.genetica.math.stats.concurrent.ConcurrentCorrelationTask (implements java.util.concurrent.Callable<V>)
  • umcg.genetica.math.stats.concurrent.ConcurrentCovariation
  • umcg.genetica.math.stats.concurrent.ConcurrentCovariationTask (implements java.util.concurrent.Callable<V>)
  • umcg.genetica.console.ConsoleGUIElems
  • umcg.genetica.methylation.ConvertBetaAndMvalues
  • umcg.genetica.io.trityper.ConvertDoubleMatrixDataToTriTyper
  • umcg.genetica.methylation.ConverteUandMTo
  • umcg.genetica.math.stats.Correlation
  • umcg.genetica.math.interpolation.CubicSpline
  • umcg.genetica.methylation.DeepCopy
  • umcg.genetica.text.parsing.Demographics
  • umcg.genetica.gwas.Dependifier
  • umcg.genetica.math.stats.Descriptives
  • umcg.genetica.io.trityper.util.DetermineLD
  • umcg.genetica.math.matrix2.DoubleMatrixDataset<R,C>
  • umcg.genetica.math.matrix.DoubleMatrixDatasetAC<T,U>
    • umcg.genetica.math.matrix.DoubleMatrixDataset<T,U>
    • umcg.genetica.math.matrix.DoubleMatrixDatasetRA<T,U>
  • umcg.genetica.io.concurrent.DoubleParseTask (implements java.util.concurrent.Callable<V>)
  • umcg.genetica.io.trityper.EQTL (implements java.lang.Comparable<T>)
  • umcg.genetica.containers.Exon
  • umcg.genetica.legacy.ExpressionDataset
  • umcg.genetica.math.stats.FDRUtils
  • umcg.genetica.ensembl.Features
  • umcg.genetica.io.trityper.converters.FinalReportToTriTyper
  • umcg.genetica.math.stats.FisherExactTest
  • umcg.genetica.math.Fmath
  • umcg.genetica.graphics.ForestPlot
  • umcg.genetica.containers.Gene
  • umcg.genetica.genomicboundaries.GenomicBoundaries<V> (implements java.lang.Iterable<T>)
  • umcg.genetica.genomicboundaries.GenomicBoundariesIterator<V> (implements java.util.Iterator<E>)
  • umcg.genetica.genomicboundaries.GenomicBoundariesSimple
  • umcg.genetica.genomicboundaries.GenomicBoundary<V> (implements java.lang.Comparable<T>)
  • umcg.genetica.io.gtf.GffAttributeFilter
  • umcg.genetica.io.gtf.GffElement (implements umcg.genetica.variantAnnotator.GenomicRange)
  • umcg.genetica.io.gtf.GffElementIterator (implements java.util.Iterator<E>)
  • umcg.genetica.io.gmt.GMTFile
  • umcg.genetica.math.Goniometry
  • umcg.genetica.io.Gpio
  • umcg.genetica.io.gtf.GtfReader (implements umcg.genetica.io.gtf.GffReaderInterface)
  • umcg.genetica.io.gwascatalog.GWASCatalog
  • umcg.genetica.io.gwascatalog.GWASLocus
  • umcg.genetica.io.gwascatalog.GWASPublication
  • umcg.genetica.io.gwascatalog.GWASSNP
  • umcg.genetica.io.gwascatalog.GWASTrait
  • umcg.genetica.graphics.Heatmap
  • umcg.genetica.math.stats.Heterogeneity
  • umcg.genetica.math.stats.HWE
  • umcg.genetica.io.trityper.converters.ImputeImputedToTriTyperV2
  • umcg.genetica.gwas.Independifier
  • umcg.genetica.util.InplaceArrayQuickSort
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • com.mastfrog.util.streams.HashingInputStream
  • umcg.genetica.collections.intervaltree.IntervalTree<E>
  • umcg.genetica.io.trityper.converters.InversionCallsToTriTyper
  • umcg.genetica.math.stats.KolmogorovSmirnov
  • umcg.genetica.io.fasta.LargeByteArray
  • umcg.genetica.math.stats.Log2Transform
  • umcg.genetica.io.trityper.converters.MachImputedToTriTyper
  • umcg.genetica.io.trityper.converters.MachImputedTransposedDosageToTriTyper
  • umcg.genetica.math.matrix.MatrixHandling
  • umcg.genetica.math.matrix2.MatrixHandling
  • umcg.genetica.math.matrix.MatrixTools
  • umcg.genetica.math.matrix2.MatrixTools
  • umcg.genetica.math.matrix.MergeDoubleMatrices
  • umcg.genetica.math.matrix2.MergeDoubleMatrices
  • umcg.genetica.methylation.MethylationAssociatoingAnnotationWithValues
  • umcg.genetica.io.trityper.converters.MinimacImputedToTriTyper
  • umcg.genetica.util.MultiThreadedInPlaceQuickSort
  • umcg.genetica.io.text.converters.NetworkConverter
  • umcg.genetica.math.stats.Normalization
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.FilterOutputStream
      • com.mastfrog.util.streams.HashingOutputStream
  • umcg.genetica.containers.Pair<L,R> (implements java.lang.Comparable<T>)
  • umcg.genetica.io.geofiles.ParseSoftFile
  • umcg.genetica.methylation.ParseTcgaMethylationFile
  • umcg.genetica.io.geofiles.ParseTextTable
  • umcg.genetica.math.PCA
  • umcg.genetica.io.trityper.converters.PedAndMapToTriTyper
  • umcg.genetica.collections.intervaltree.PerChrIntervalTree<E>
  • umcg.genetica.io.pileup.PileupEntry
  • umcg.genetica.io.pileup.PileupFile (implements java.lang.Iterable<T>)
  • umcg.genetica.io.pileup.PileupToVcf
  • umcg.genetica.util.Primitives
  • umcg.genetica.io.trityper.ProbeAnnotation
  • umcg.genetica.io.trityper.probeannotation.ProbeAnnotation
  • umcg.genetica.io.trityper.probeannotation.ProbeTranslation
  • umcg.genetica.console.ProgressBar
  • umcg.genetica.math.stats.QuantileNormalization
  • umcg.genetica.math.stats.QValues
  • umcg.genetica.io.bin.RandomAccessFile (implements java.io.DataInput, java.io.DataOutput)
  • umcg.genetica.collections.intervaltree.RangeEndReverseComparator (implements java.util.Comparator<T>)
  • umcg.genetica.collections.intervaltree.RangeStartComparator (implements java.util.Comparator<T>)
  • umcg.genetica.util.RankArray
  • umcg.genetica.util.RankDoubleArray
  • umcg.genetica.util.RankIntArray
  • umcg.genetica.io.probemapping.reading
  • umcg.genetica.io.fasta.ReferenceGenomeFasta
  • umcg.genetica.math.stats.Regression
    • umcg.genetica.math.stats.TwoStepLeastSquares
  • umcg.genetica.io.regulomedb.RegulomeDbEntry
  • umcg.genetica.io.regulomedb.RegulomeDbFile (implements java.lang.Iterable<T>)
  • umcg.genetica.io.regulomedb.RegulomeDbFiles (implements java.lang.Iterable<T>)
  • umcg.genetica.io.regulomedb.RegulomeDbIterator (implements java.util.Iterator<E>)
  • umcg.genetica.io.regulomedb.RegulomeDbSupportingData
  • umcg.genetica.util.RunTimer
  • umcg.genetica.graphics.ScatterPlot
  • umcg.genetica.util.SmoothSort
  • umcg.genetica.io.trityper.SNP
  • umcg.genetica.ncbi.dbsnp.SNPAnnotation (implements java.io.Serializable)
  • umcg.genetica.io.trityper.SNPLoader
  • umcg.genetica.methylation.SoftfileAnnotation
  • umcg.genetica.containers.SortableSNP (implements java.lang.Comparable<T>)
  • umcg.genetica.containers.StringDoubleObject
  • umcg.genetica.containers.StringIntegerObject
  • umcg.genetica.collections.intervaltree.StringRange (implements umcg.genetica.collections.intervaltree.Range)
  • umcg.genetica.text.Strings
  • umcg.genetica.math.matrix.SymmetricByteDistanceMatrix
  • umcg.genetica.math.matrix.SymmetricShortDistanceMatrix
  • umcg.genetica.io.gtf.TestGffIntervalTree
  • umcg.genetica.io.text.TextFile (implements java.lang.Iterable<T>)
    • umcg.genetica.io.ucsc.PeakFile
    • umcg.genetica.io.trityper.QTLTextFile
    • umcg.genetica.io.ucsc.WigFile
  • umcg.genetica.math.stats.TheilSen
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • umcg.genetica.io.binInteraction.BinaryInteractionFileException
      • umcg.genetica.io.pileup.PileupParseException
  • umcg.genetica.containers.Transcript
  • umcg.genetica.containers.Triple<L,M,R>
  • umcg.genetica.io.trityper.util.TriTyperConcatDatasets
  • umcg.genetica.io.trityper.TriTyperExpressionData
  • umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDataset (implements java.lang.Comparable<T>)
  • umcg.genetica.io.trityper.TriTyperGeneticalGenomicsDatasetSettings
  • umcg.genetica.io.trityper.TriTyperGenotypeData
  • umcg.genetica.io.trityper.util.TriTyperGenotypeDataMerger
  • umcg.genetica.io.trityper.converters.TriTyperReferenceConcordantPedAndMapExporter
  • umcg.genetica.io.trityper.TriTyperSNPMappings
  • umcg.genetica.io.trityper.converters.TriTyperToDosageConverter
  • umcg.genetica.io.trityper.converters.TriTyperToMachImputedTransposed
  • umcg.genetica.io.trityper.converters.TriTyperToPedAndMapConverter
  • umcg.genetica.io.trityper.converters.TriTyperToPlinkDosage
  • umcg.genetica.io.trityper.converters.TriTyperToTabSeparated
  • umcg.genetica.io.trityper.converters.TriTyperToVCF
  • umcg.genetica.math.stats.TTest
  • umcg.genetica.io.ucsc.UCSCDataObject (implements java.lang.Comparable<T>)
  • umcg.genetica.io.ucsc.UCSCTrack (implements java.lang.Comparable<T>)
  • umcg.genetica.variantAnnotator.VariantAnnotator<E>
  • umcg.genetica.io.trityper.converters.VCFToTriTyper
  • umcg.genetica.util.VectorSorter
    • umcg.genetica.util.StringDoubleObjectSorterSortOnDouble
    • umcg.genetica.util.StringIntegerObjectSorterSortOnInteger
  • umcg.genetica.graphics.VennDiagram
  • umcg.genetica.graphics.ViolinBoxPlot
  • umcg.genetica.io.trityper.WGAFileMatrixGenotype
  • umcg.genetica.io.trityper.WGAFileMatrixImputedDosage
  • umcg.genetica.io.trityper.WGAFileMatrixRawData
  • umcg.genetica.math.stats.WilcoxonMannWhitney
  • umcg.genetica.math.stats.ZScores

Interface Hierarchy

• umcg.genetica.io.binInteraction.gene.BinaryInteractionGene
• umcg.genetica.io.binInteraction.variant.BinaryInteractionVariant
• java.lang.Iterable<T>
  • umcg.genetica.io.gtf.GffReaderInterface
• umcg.genetica.collections.intervaltree.Range
  • umcg.genetica.variantAnnotator.GenomicRange

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • umcg.genetica.util.RunTimer.Granularity
    • umcg.genetica.io.ucsc.WigFile.STEPMODE
    • umcg.genetica.io.ucsc.UCSCDataObject.SORTBY
    • umcg.genetica.io.ucsc.PeakFile.PEAKFORMAT
    • umcg.genetica.graphics.ViolinBoxPlot.Output
    • umcg.genetica.graphics.ScatterPlot.OUTPUTFORMAT
    • umcg.genetica.graphics.Heatmap.Output
    • umcg.genetica.graphics.ForestPlot.Output
    • umcg.genetica.math.matrix.DoubleMatrixDatasetAC.LoadLabels
    • umcg.genetica.math.stats.QValues.SMOOTHER
    • umcg.genetica.math.stats.FDRUtils.CloneArrays
    • umcg.genetica.math.stats.FDRUtils.SortArrays
    • umcg.genetica.math.stats.FDRUtils.AbsoluteValues
    • umcg.genetica.math.stats.AndersonDarling.IS_DATA_NORMALIZED
    • umcg.genetica.containers.Pair.SORTBY
    • umcg.genetica.containers.SortableSNP.SORTBY