Hierarchy For All Packages

Package Hierarchies:

bioroot, bioroot.antibody, bioroot.oligo, bioroot.parsers, bioroot.plasmid, bioroot.strain, cgar, com.amazon.s3, com.amazon.thirdparty, expr, gata.aligner, gata.geneGlyphs, gata.main, gata.menu, gata.plotter, igb.util, meme, selex, trans.anno, trans.bkgrnd, trans.cel, trans.graphics, trans.main, trans.misc, trans.qc, trans.roc, trans.tpmap, util.amazon, util.apps, util.bio.annotation, util.bio.calc, util.bio.cluster, util.bio.converters, util.bio.digest, util.bio.parsers, util.bio.parsers.gff, util.bio.seq, util.bio.wrappers, util.bio.xamer, util.gen, util.xml

Class Hierarchy

• class java.lang.Object
  • class util.bio.parsers.ADFDataBaseSplitter
  • class trans.graphics.AggregatePlots
  • class util.bio.converters.AlignedBaseCounter
  • class gata.aligner.AlignerPreferences (implements java.io.Serializable)
  • class gata.aligner.Alignment (implements java.lang.Comparable, java.io.Serializable)
  • class util.bio.calc.Alignment
  • class gata.aligner.AlignParams (implements java.io.Serializable)
  • class gata.main.AnnoSpecParams
  • class trans.anno.AnnotateRegions
  • class trans.anno.AnnotateRegionsWithGeneList
  • class gata.geneGlyphs.Annotation
  • class bioroot.antibody.AntibodyPrep
  • class util.apps.ArrayPrinter
  • class trans.cel.AverageACels
  • class trans.misc.AverageDoubles
  • class trans.cel.AveragePCels
  • class com.amazon.s3.AWSAuthConnection
  • class trans.bkgrnd.BackGroundOligo (implements java.io.Serializable)
  • class trans.misc.Bar2Gr
  • class com.amazon.thirdparty.Base64
  • class trans.misc.Bed2Gr
  • class trans.roc.Bin
  • class util.gen.Bin
  • class trans.main.BindingPeak (implements java.io.Serializable)
  • class trans.anno.BindingRegion (implements java.lang.Comparable)
  • class trans.anno.BindingRegionComparator (implements java.util.Comparator)
  • class trans.main.BindingRegionGraphPrinter
  • class trans.anno.BindingRegionsToGff3
  • class trans.anno.BindingRegionsToIntervals
  • class util.bio.wrappers.BL2Seq
  • class util.bio.wrappers.BL2SeqHit
  • class gata.aligner.Blast
  • class util.bio.wrappers.Blast
  • class trans.tpmap.BlastFilterResult
  • class bioroot.BlastMatcher (implements java.lang.Comparable)
  • class util.bio.wrappers.BlastResult
  • class trans.graphics.Box
  • class gata.aligner.BrowseButtonAction (implements java.awt.event.ActionListener)
  • class com.amazon.s3.Bucket
  • class trans.bkgrnd.CalcBkgrndRatios
  • class trans.misc.CalcGCAndTransform
  • class trans.misc.CalcGCRatiosFromIntervals
  • class trans.bkgrnd.CalculateBackgroundStats
  • class trans.cel.CelFileConverter
  • class trans.qc.CelFileQualityControl
  • class trans.qc.CelFileStats
  • class trans.cel.CelLine (implements java.lang.Comparable)
  • class bioroot.CellTypeBean
  • class trans.cel.CelMapper
  • class trans.graphics.CelMasker
  • class trans.cel.CelPHistogram
  • class trans.cel.CelProcessor
  • class trans.cel.ChromosomeIndex
  • class trans.main.ChromSet
  • class util.bio.cluster.Cluster (implements java.io.Serializable)
  • class trans.tpmap.CollapseTPMap
  • class trans.graphics.CombineXYSeries
  • class cgar.CommitFiles
  • class com.amazon.s3.CommonPrefixEntry
  • class trans.cel.ComparatorMultiSetQuantile (implements java.util.Comparator)
  • class trans.cel.ComparatorQuantile (implements java.util.Comparator)
  • class java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • class java.awt.Container
      • class javax.swing.JComponent (implements java.io.Serializable)
        • class javax.swing.JPanel (implements javax.accessibility.Accessible)
          • class gata.aligner.AlignerInputPanel
          • class gata.plotter.AlignPanel
          • class util.bio.cluster.ClusterDrawPanel
          • class gata.menu.FileInputPanel
          • class gata.geneGlyphs.GlyphPanel
          • class trans.graphics.IntervalDrawPanel
          • class gata.plotter.MultiAlignPanel
          • class trans.graphics.RankedSetDrawPanel
          • class gata.menu.SaveImagePanel (implements java.awt.event.ActionListener)
          • class util.apps.ScatterDrawPanel
          • class trans.graphics.VirtualCelPanel
      • class java.awt.Window (implements javax.accessibility.Accessible)
        • class java.awt.Frame (implements java.awt.MenuContainer)
          • class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • class gata.aligner.AlignerInputForm
            • class trans.qc.ChartFrame
            • class util.bio.cluster.ClusterDrawFrame
            • class gata.plotter.Console
            • class gata.menu.FileInputForm
            • class gata.menu.GATAFrame
            • class trans.graphics.IntervalDrawFrame
            • class trans.graphics.RankedSetDrawFrame
            • class gata.menu.SaveImageForm
            • class util.apps.ScatterDrawFrame
            • class gata.main.SimpleTextWindow
            • class util.gen.TextFrame
            • class gata.main.TextWindow
            • class gata.plotter.ToolsFrame
            • class trans.graphics.VirtualCelFrame
  • class gata.plotter.ConservedSeqs
  • class bioroot.ContactBean
  • class trans.roc.ControlGene
  • class trans.cel.ControlStats (implements java.io.Serializable)
  • class trans.misc.ConvertAgilentData
  • class util.apps.ConvertFasta2GCBoolean
  • class trans.misc.ConvertGeoData
  • class trans.misc.ConvertNimblegenNDF2TPMap
  • class trans.misc.ConvertNimblegenPAIR2Cela
  • class trans.tpmap.ConvertTPMapsToFeatures
  • class trans.cel.ConvertTVSToCelps
  • class trans.qc.CoordinateExtractor1lq
  • class util.bio.annotation.Coordinates (implements java.lang.Comparable)
  • class util.apps.Correlate
  • class trans.misc.CorrelateGrFiles
  • class expr.CorrelationMaps
  • class expr.CorrelationWindow
  • class bioroot.CronArchive
  • class util.gen.CubicSpline
  • class bioroot.DBUtil
  • class bioroot.DeleteMeNow
  • class util.apps.Delme2
  • class gata.aligner.DelmeAligner
  • class trans.qc.DestypeIntensityCalculator
  • class trans.anno.DmelCGNameCoordinatePrinter
  • class util.bio.parsers.gff.DmelRel4Extractor
  • class util.bio.parsers.DrosGeneCollFileParser
  • class util.gen.Email
  • class util.bio.digest.Enzyme (implements java.lang.Comparable)
  • class util.bio.annotation.ExonIntron (implements java.lang.Comparable, java.io.Serializable)
  • class trans.roc.ExonScoreExtractor
  • class util.bio.annotation.ExportIntergenicRegions
  • class trans.main.ExportIntervalData
  • class util.bio.annotation.ExportIntronicRegions
  • class expr.ExpressedGene (implements java.lang.Comparable)
  • class expr.ExpressionScores2CoordinatesViaGFF
  • class util.bio.parsers.gff.ExtractGffFeatures
  • class trans.roc.ExtractNonOverlappingWindows
  • class trans.roc.ExtractSaveSgrScores
  • class trans.roc.ExtractScoresForRoc
  • class bioroot.parsers.ExtractWords
  • class trans.main.FDRVsQValues
  • class trans.main.FDRWindowConverter
  • class bioroot.Feature (implements java.lang.Comparable)
  • class util.bio.parsers.FetchGenomicSequences
  • class util.bio.seq.FetchIndexedSequence
  • class gata.aligner.FileFocusListener (implements java.awt.event.FocusListener)
  • class util.apps.FileJoiner
  • class util.gen.FileSize (implements java.lang.Comparable)
  • class util.apps.FileSplitter
  • class util.apps.FileTrimmer
  • class trans.tpmap.FilterTPMapByRegions
  • class trans.main.FindSubBindingRegions
  • class util.apps.Flash
  • class util.bio.parsers.gff.GadFlyGffExtractor
  • class gata.aligner.GATAligner
  • class gata.main.GATAParams
  • class gata.main.GATAPlotter
  • class gata.main.GATAUtil
  • class trans.misc.GCRatio (implements java.lang.Comparable)
  • class bioroot.GeneBean
  • class util.bio.annotation.GeneGroup (implements java.lang.Comparable, java.io.Serializable)
  • class util.apps.GeneNameCounter
  • class util.bio.annotation.GeneRep (implements java.io.Serializable)
  • class gata.geneGlyphs.GeneRepGlyph
  • class util.bio.annotation.GenericFeature (implements java.lang.Comparable)
  • class gata.geneGlyphs.GenericGlyph
  • class javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • class javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • class bioroot.AccountManagement
      • class bioroot.antibody.AntibodyBase
      • class bioroot.antibody.AntibodyModify
      • class bioroot.antibody.AntibodySpreadSheet
      • class bioroot.antibody.AntibodyViewPreferences
      • class bioroot.Archive
      • class bioroot.CellType
      • class bioroot.Contact
      • class bioroot.Gene
      • class bioroot.Login
      • class bioroot.Logout
      • class bioroot.Marker
      • class bioroot.antibody.NewAntibody
      • class bioroot.oligo.NewOligo
      • class bioroot.plasmid.NewPlasmid
      • class bioroot.strain.NewStrain
      • class bioroot.oligo.OligoBase
      • class bioroot.oligo.OligoModify
      • class bioroot.oligo.OligoSpreadSheet
      • class bioroot.oligo.OligoUpload
      • class bioroot.oligo.OligoViewPreferences
      • class bioroot.Organism
      • class bioroot.plasmid.PlasmidBase
      • class bioroot.plasmid.PlasmidModify
      • class bioroot.plasmid.PlasmidSpreadSheet
      • class bioroot.plasmid.PlasmidUpload
      • class bioroot.plasmid.PlasmidViewPreferences
      • class bioroot.Search
      • class bioroot.strain.StrainBase
      • class bioroot.strain.StrainModify
      • class bioroot.strain.StrainSpreadSheet
      • class bioroot.strain.StrainUpload
      • class bioroot.strain.StrainViewPreferences
      • class bioroot.UserRegistration
  • class util.bio.converters.GenomeFASTASplitter
  • class trans.graphics.GenomicRegion
  • class trans.graphics.GenomicRegionGlyph
  • class trans.anno.Gff2ToBindingRegions
  • class trans.anno.Gff2ToIntervals
  • class util.bio.parsers.gff.Gff3Feature (implements java.lang.Cloneable, java.lang.Comparable)
  • class util.bio.parsers.gff.Gff3Parser
  • class util.bio.parsers.gff.GffFeature
  • class util.bio.parsers.gff.GffParser
  • class trans.roc.Gr
  • class trans.misc.Gr2Bar
  • class trans.graphics.Graph
  • class trans.roc.GrComparator (implements java.util.Comparator)
  • class trans.misc.GrGraph
  • class util.bio.cluster.HierarchicalClustering
  • class util.gen.Histogram
  • class igb.util.HistogramSgrOrGrFile
  • class util.apps.HouseBean
  • class util.gen.HTML
  • class bioroot.IdNameMatch
  • class util.bio.seq.IndexedSequence (implements java.lang.Comparable)
  • class util.bio.seq.IndexFastas
  • class util.bio.seq.IndexRegions
  • class trans.misc.InefficientPseudoMedian
  • class java.io.InputStream
    • class java.io.FilterInputStream
      • class com.amazon.thirdparty.Base64.InputStream
  • class trans.tpmap.IntensityFeature (implements java.lang.Comparable, java.io.Serializable)
  • class trans.main.IntensityPrinter
  • class trans.anno.IntersectBindingPeaks
  • class trans.anno.IntersectKeyWithRegions
  • class util.apps.IntersectLists
  • class trans.anno.IntersectRegions
  • class trans.main.Interval (implements java.lang.Comparable, java.io.Serializable)
  • class trans.main.IntervalComparator (implements java.util.Comparator)
  • class trans.main.IntervalFilter
  • class trans.main.IntervalGFFPrinter
  • class trans.main.IntervalGraphPrinter
  • class trans.main.IntervalMaker
  • class trans.graphics.IntervalPlotter
  • class trans.main.IntervalReportPrinter
  • class util.gen.IO
  • class util.gen.Job
  • class util.apps.JQSub
  • class bioroot.LabGroup
  • class util.gen.LinearRegression
  • class com.amazon.s3.ListEntry
  • class trans.main.LoadChipSetIntervalOligoInfo
  • class trans.bkgrnd.LoadedOligo (implements java.lang.Comparable)
  • class trans.main.LoadIntervalOligoInfo
  • class gata.aligner.LocalAlignment (implements java.io.Serializable)
  • class bioroot.LoginBean
  • class util.bio.seq.LowerCase2Xs
  • class trans.main.MakeAllWindows
  • class util.apps.MakeBioTools
  • class trans.cel.MakeChromosomeSets
  • class trans.bkgrnd.MapControlIntensities
  • class trans.tpmap.MapFeature (implements java.lang.Comparable, java.io.Serializable)
  • class trans.tpmap.MapSplitter
  • class bioroot.MarkerBean
  • class util.gen.MD5Crypt
  • class meme.MemeMotif
  • class meme.MemeParser
  • class meme.MemeR
  • class meme.MemeResults
  • class trans.anno.MergeRegions
  • class trans.main.MergeWindowArrays
  • class java.security.MessageDigestSpi
    • class java.security.MessageDigest
      • class util.gen.MD5 (implements java.lang.Cloneable)
  • class trans.roc.MethodTester
  • class util.gen.Misc
  • class meme.MotifHit (implements java.lang.Comparable)
  • class meme.MotifScanner
  • class meme.MotifSearchResult (implements java.lang.Comparable)
  • class util.bio.parsers.MultiFastaParser
  • class trans.cel.MultiSetQuantile (implements java.io.Serializable)
  • class trans.main.MultiSGRPrinter
  • class trans.main.MultiWindowIntervalMaker
  • class trans.tpmap.MummerMapper
  • class util.bio.digest.NEBParser
  • class util.bio.calc.NucleicAcid
  • class util.gen.Num
  • class trans.main.Oligo (implements java.io.Serializable)
  • class trans.tpmap.OligoFlipper
  • class trans.main.OligoIntensityPrinter
  • class bioroot.plasmid.OligoMatch
  • class bioroot.oligo.OligoUploadBean
  • class bioroot.OrganismBean
  • class bioroot.Organization
  • class java.io.OutputStream
    • class java.io.FilterOutputStream
      • class com.amazon.thirdparty.Base64.OutputStream
  • class trans.main.OverlapCounter
  • class trans.main.OverlappingWindowScoreExtractor
  • class com.amazon.s3.Owner
  • class trans.roc.ParseBarsForParticularRegions
  • class util.apps.ParseMLSHTML
  • class trans.roc.ParsePatternedWindows
  • class trans.qc.Parser1lq
  • class trans.roc.ParseSgrsForParticularRegions
  • class trans.roc.ParseSgrsForParticularScores
  • class util.xml.ParseXMLFile
  • class util.gen.Passwords
  • class bioroot.PatternMatch
  • class trans.main.PeakPicker
  • class bioroot.plasmid.PlasmidUploadBean
  • class trans.graphics.PlotFloatArrays
  • class gata.main.PlotterPreferences (implements java.io.Serializable)
  • class trans.roc.Positive
  • class trans.roc.PositiveComparator (implements java.util.Comparator)
  • class trans.main.PosRegion (implements java.lang.Comparable)
  • class util.bio.converters.PossumToGFF
  • class bioroot.Preference
    • class bioroot.strain.StrainPreference
  • class trans.misc.PrependColumn
  • class util.bio.wrappers.Primer3Pick
  • class util.bio.wrappers.Primer3Wrapper
  • class util.apps.PrintSelectColumns
  • class trans.roc.PWMScoreWindows
  • class util.bio.parsers.QualityFileParser
  • class trans.cel.Quantile
  • class trans.cel.QuantileNormalization
  • class com.amazon.s3.QueryStringAuthGenerator
  • class trans.main.RandomizeLabels
  • class trans.anno.RandomRegions
  • class util.gen.RankedFloatArray
  • class trans.graphics.RankedSetAnalysis
  • class util.gen.RankSample
  • class util.gen.RankSampleIndexComparator (implements java.util.Comparator)
  • class util.gen.RankSampleValueComparator (implements java.util.Comparator)
  • class util.gen.ReadZip
  • class bioroot.ReagentBean (implements java.lang.Comparable)
    • class bioroot.antibody.AntibodyBean
    • class bioroot.oligo.OligoBean
    • class bioroot.plasmid.PlasmidBean
    • class bioroot.strain.StrainBean
  • class util.bio.digest.REDigest
  • class trans.anno.Region (implements java.io.Serializable)
  • class trans.anno.RegionComparator (implements java.util.Comparator)
  • class trans.misc.Regions2Intervals
  • class util.apps.RenameRWSResults
  • class bioroot.parsers.RenameWords
  • class util.bio.converters.RepeatMaskerToGFF
  • class trans.main.ReplaceWindowScores
  • class com.amazon.s3.Response
    • class com.amazon.s3.GetResponse
    • class com.amazon.s3.ListAllMyBucketsResponse
    • class com.amazon.s3.ListBucketResponse
  • class trans.roc.RocWindow (implements java.lang.Comparable, java.io.Serializable)
  • class trans.roc.RocWindowScanner
  • class trans.cel.RotateCelFile
  • class util.amazon.S3CodeSamples
  • class util.amazon.S3Manager
  • class com.amazon.s3.S3Object
  • class trans.main.SamChromosomeData
  • class gata.geneGlyphs.ScaleBar
  • class trans.main.ScanChip
  • class trans.main.ScanChromosomes
  • class trans.main.ScanGenes
  • class util.apps.ScatterPlot
  • class util.apps.ScoreChromosomes
  • class trans.main.ScoredGene (implements java.lang.Comparable)
  • class trans.misc.ScoredRegionsFormatFixer
  • class trans.main.ScoreIntervals
  • class util.apps.ScoreSequences
  • class bioroot.SearchBean
  • class bioroot.SearchHit (implements java.lang.Comparable)
  • class selex.SelexParams
  • class selex.SelexSeqParser
  • class util.bio.seq.Seq
  • class selex.SeqFiles
  • class selex.SeqRead
  • class gata.aligner.Seqs
  • class trans.main.SetNumberIntervalMaker
  • class trans.roc.Sgr (implements java.io.Serializable)
  • class trans.misc.Sgr2Bar
  • class trans.roc.SgrBacCounter
  • class trans.misc.SgrComparator (implements java.util.Comparator)
  • class util.bio.wrappers.SimpleBlast
  • class gata.plotter.Sliders
  • class bioroot.Spammer
  • class util.gen.SpearmanCorrelation
  • class trans.cel.SplineScalar
  • class trans.main.SplitWindowArraysByChromosome
  • class util.gen.SQL
  • class util.bio.annotation.StartEnd (implements java.lang.Comparable, java.io.Serializable)
  • class gata.plotter.StartStop (implements java.lang.Comparable)
  • class trans.tpmap.Stat1lq
  • class trans.qc.StatFlag
  • class trans.cel.StatIntensityFeatureArray
  • class trans.tpmap.StatTPMap
  • class trans.tpmap.StatTPMapControlSeqs
  • class bioroot.strain.StrainUploadBean
  • class selex.SubSeq
  • class util.apps.SubtractOneFromLastColumn
  • class trans.main.SubWindow (implements java.io.Serializable)
  • class util.gen.Swing
  • class util.bio.parsers.SynonymTables
  • class trans.main.T2
  • class trans.main.T2Parameter
  • class bioroot.TableHeading (implements java.lang.Comparable)
  • class util.apps.TASSignalChromFileSplitter
  • class trans.main.TestScanChip
  • class util.apps.TextParser
  • class trans.misc.TextPValOrSig2Gr
  • class java.lang.Thread (implements java.lang.Runnable)
    • class gata.aligner.AlignerThread
  • class trans.tpmap.TPMapDensityReducer
  • class trans.tpmap.TPMapDuplicateFilter
  • class trans.tpmap.TPMapFeature (implements java.io.Serializable)
  • class trans.tpmap.TPMapLine (implements java.lang.Comparable)
  • class trans.tpmap.TPMapOligoBlastFilter
  • class trans.tpmap.TPMapProcessor
  • class trans.tpmap.TPMapSort
  • class trans.tpmap.TPMapStripHighLowGC
  • class util.bio.annotation.Transcript (implements java.io.Serializable)
  • class trans.misc.TransformRatios
  • class util.bio.annotation.TransGroup (implements java.io.Serializable)
  • class gata.geneGlyphs.TransGrpGlyph
  • class util.bio.annotation.Translation (implements java.io.Serializable)
  • class util.bio.parsers.UCSCGeneLine
  • class util.bio.parsers.UCSCGeneLineComparator (implements java.util.Comparator)
  • class util.bio.parsers.UCSCGeneModelTableReader
  • class bioroot.antibody.UseDilution
  • class bioroot.UserBean
  • class bioroot.UserRegistrationBean
  • class bioroot.Util
  • class trans.misc.Util
  • class meme.UtilMeme
  • class com.amazon.s3.Utils
  • class selex.UtilSelex
  • class trans.graphics.VirtualCel
  • class trans.main.WilcoxonRankSumTest
  • class trans.main.WilcoxonSample (implements java.lang.Comparable)
  • class trans.main.WilcoxonSamplePair (implements java.lang.Comparable)
  • class trans.main.WilcoxonSignedRankTest
  • class trans.main.Window (implements java.lang.Comparable, java.io.Serializable)
  • class trans.main.WindowBlockMaker
  • class trans.main.WindowBlockMakerTwoColor
  • class trans.main.WindowComparator (implements java.util.Comparator)
  • class trans.misc.WindowHistogram
  • class trans.tpmap.WindowMaker
  • class igb.util.Windows2HeatMapSgr
  • class util.apps.WindowScoreSmoother
  • class util.bio.xamer.Xamer
  • class util.bio.xamer.XamerCounter
  • class util.gen.XML