Hierarchy For All Packages

Package Hierarchies:

nix.affy.anno, nix.affy.bkgrnd, nix.affy.bpmap, nix.affy.graphics, nix.affy.main, nix.affy.misc, nix.affy.roc, nix.bdtnp.bid, nix.gata.aligner, nix.gata.geneGlyphs, nix.gata.main, nix.gata.menu, nix.gata.plotter, nix.meme, nix.selex, nix.util.apps, nix.util.bio.annotation, nix.util.bio.calc, nix.util.bio.converters, nix.util.bio.digest, nix.util.bio.parsers, nix.util.bio.parsers.gff, nix.util.bio.seq, nix.util.bio.wrappers, nix.util.bio.xamer, nix.util.gen, nix.xml

Class Hierarchy

• class java.lang.Object
  • class nix.util.bio.converters.AlignedBaseCounter
  • class nix.gata.aligner.AlignerPreferences (implements java.io.Serializable)
  • class nix.gata.aligner.Alignment (implements java.lang.Comparable, java.io.Serializable)
  • class nix.util.bio.calc.Alignment
  • class nix.gata.aligner.AlignParams (implements java.io.Serializable)
  • class nix.gata.main.AnnoSpecParams
  • class nix.affy.anno.AnnotateRegions
  • class nix.affy.anno.AnnotateRegionsWithGeneList
  • class nix.gata.geneGlyphs.Annotation
  • class nix.util.apps.ArrayPrinter
  • class nix.affy.misc.AverageDoubles
  • class nix.affy.bkgrnd.BackGroundOligo (implements java.io.Serializable)
  • class nix.bdtnp.bid.BIDBean
    • class nix.bdtnp.bid.ConstructBean
    • class nix.bdtnp.bid.EmbryoBean
    • class nix.bdtnp.bid.EmbryoPreparationBean
    • class nix.bdtnp.bid.FluorBean
    • class nix.bdtnp.bid.HybridizationBean
    • class nix.bdtnp.bid.ImageStackBean
    • class nix.bdtnp.bid.MoleculeBean
    • class nix.bdtnp.bid.NuclearCloudBean
    • class nix.bdtnp.bid.ProbeBean
    • class nix.bdtnp.bid.SecondaryAntibodyBean
    • class nix.bdtnp.bid.SlideBean
    • class nix.bdtnp.bid.StainBean
    • class nix.bdtnp.bid.VectorBean
  • class nix.bdtnp.bid.BIDUtil
  • class nix.affy.roc.Bin
  • class nix.affy.main.BindingPeak (implements java.io.Serializable)
  • class nix.affy.anno.BindingRegion (implements java.lang.Comparable)
  • class nix.affy.main.BindingRegionGraphPrinter
  • class nix.affy.anno.BindingRegionsToGff3
  • class nix.affy.anno.BindingRegionsToIntervals
  • class nix.util.bio.wrappers.BL2Seq
  • class nix.util.bio.wrappers.BL2SeqHit
  • class nix.util.bio.wrappers.Blast
  • class nix.gata.aligner.Blast
  • class nix.affy.bpmap.BlastFilterResult
  • class nix.util.bio.wrappers.BlastResult
  • class nix.affy.graphics.Box
  • class nix.affy.bpmap.BPMapDuplicateFilter
  • class nix.affy.bpmap.BPMapFeature (implements java.io.Serializable)
  • class nix.affy.bpmap.BPMapLine (implements java.lang.Comparable)
  • class nix.affy.bpmap.BPMapOligoBlastFilter
  • class nix.affy.bpmap.BPMapProcessor
  • class nix.affy.bpmap.BPMapSort
  • class nix.affy.bpmap.BPMapStripHighLowGC
  • class nix.bdtnp.bid.BrowseBean
  • class nix.gata.aligner.BrowseButtonAction (implements java.awt.event.ActionListener)
  • class nix.affy.bkgrnd.CalcBkgrndRatios
  • class nix.affy.misc.CalcGCAndTransform
  • class nix.affy.misc.CalcGCRatiosFromIntervals
  • class nix.affy.bkgrnd.CalculateBackgroundStats
  • class nix.affy.main.CelMapper
  • class nix.affy.graphics.CelMasker
  • class nix.affy.main.CelProcessor
  • class nix.affy.bpmap.CollapseBPMap
  • 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 nix.gata.aligner.AlignerInputPanel
          • class nix.gata.plotter.AlignPanel
          • class nix.affy.graphics.DrawPanel
          • class nix.gata.menu.FileInputPanel
          • class nix.gata.geneGlyphs.GlyphPanel
          • class nix.gata.plotter.MultiAlignPanel
          • class nix.gata.menu.SaveImagePanel (implements java.awt.event.ActionListener)
          • class nix.util.apps.ScatterDrawPanel
          • class nix.affy.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 nix.gata.aligner.AlignerInputForm
            • class nix.gata.plotter.Console
            • class nix.affy.graphics.DrawFrame
            • class nix.gata.menu.FileInputForm
            • class nix.gata.menu.GATAFrame
            • class nix.gata.menu.SaveImageForm
            • class nix.util.apps.ScatterDrawFrame
            • class nix.gata.main.SimpleTextWindow
            • class nix.util.gen.TextFrame
            • class nix.gata.main.TextWindow
            • class nix.gata.plotter.ToolsFrame
            • class nix.affy.graphics.VirtualCelFrame
  • class nix.gata.plotter.ConservedSeqs
  • class org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
    • class nix.xml.Sink (implements org.xml.sax.ContentHandler)
  • class nix.bdtnp.bid.Delme
  • class nix.gata.aligner.DelmeAligner
  • class nix.affy.anno.DmelCGNameCoordinatePrinter
  • class nix.util.bio.parsers.gff.DmelRel4Extractor
  • class nix.xml.DOMEcho
  • class nix.util.bio.parsers.DrosGeneCollFileParser
  • class nix.util.gen.Email
  • class nix.util.bio.digest.Enzyme (implements java.lang.Comparable)
  • class nix.util.bio.annotation.Exon (implements java.lang.Comparable, java.io.Serializable)
  • class nix.affy.roc.ExtractNonOverlappingWindows
  • class nix.affy.roc.ExtractScoresForRoc
  • class nix.gata.aligner.FileFocusListener (implements java.awt.event.FocusListener)
  • class nix.util.apps.FileJoiner
  • class nix.util.apps.FileSplitter
  • class nix.util.apps.FileTrimmer
  • class nix.affy.main.FindSubBindingRegions
  • class nix.util.bio.parsers.gff.GadFlyGffExtractor
  • class nix.gata.aligner.GATAligner
  • class nix.gata.main.GATAParams
  • class nix.gata.main.GATAPlotter
  • class nix.gata.main.GATAUtil
  • class nix.affy.misc.GCRatio (implements java.lang.Comparable)
  • class nix.util.bio.annotation.GeneGroup (implements java.lang.Comparable, java.io.Serializable)
  • class nix.util.apps.GeneNameCounter
  • class nix.util.bio.annotation.GeneRep (implements java.io.Serializable)
  • class nix.gata.geneGlyphs.GeneRepGlyph
  • class nix.util.bio.annotation.GenericFeature (implements java.lang.Comparable)
  • class nix.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 nix.bdtnp.bid.Browse
      • class nix.bdtnp.bid.CascadingImageStackReport
      • class nix.bdtnp.bid.CascadingStainReport
      • class nix.bdtnp.bid.Construct
      • class nix.bdtnp.bid.Embryo
      • class nix.bdtnp.bid.EmbryoPreparation
      • class nix.bdtnp.bid.Fluor
      • class nix.bdtnp.bid.Hybridization
      • class nix.bdtnp.bid.ImageStack
      • class nix.bdtnp.bid.Login
      • class nix.bdtnp.bid.Logout
      • class nix.bdtnp.bid.Molecule
      • class nix.bdtnp.bid.NuclearCloud
      • class nix.bdtnp.bid.Probe
      • class nix.bdtnp.bid.SecondaryAntibody
      • class nix.bdtnp.bid.Slide
      • class nix.bdtnp.bid.Stain
      • class nix.bdtnp.bid.User
      • class nix.bdtnp.bid.Vector
  • class nix.util.bio.converters.GenomeFASTASplitter
  • class nix.affy.anno.Gff2ToBindingRegions
  • class nix.affy.anno.Gff2ToIntervals
  • class nix.util.bio.parsers.gff.Gff3Feature (implements java.lang.Cloneable, java.lang.Comparable)
  • class nix.util.bio.parsers.gff.Gff3Parser
  • class nix.util.bio.parsers.gff.GffFeature
  • class nix.util.bio.parsers.gff.GffParser
  • class nix.affy.graphics.Graph
  • class nix.util.gen.Histogram
  • class nix.util.gen.HTML
  • class nix.affy.main.IntensityPrinter
  • class nix.affy.anno.IntersectBindingPeaks
  • class nix.affy.anno.IntersectBindingRegions
  • class nix.affy.anno.IntersectIntervalsWithRegions
  • class nix.util.apps.IntersectLists
  • class nix.affy.main.Interval (implements java.lang.Comparable, java.io.Serializable)
  • class nix.affy.main.IntervalFilter
  • class nix.affy.main.IntervalGFFPrinter
  • class nix.affy.main.IntervalGraphPrinter
  • class nix.affy.main.IntervalMaker
  • class nix.affy.graphics.IntervalPlotter
  • class nix.affy.main.IntervalReportPrinter
  • class nix.util.gen.IO
  • class nix.util.gen.JQsub
  • class nix.affy.bkgrnd.LoadedOligo (implements java.lang.Comparable)
  • class nix.affy.main.LoadIntervalOligoInfo
  • class nix.gata.aligner.LocalAlignment (implements java.io.Serializable)
  • class nix.affy.bkgrnd.MapControlIntensities
  • class nix.affy.bpmap.MapSplitter
  • class nix.util.gen.MD5Crypt
  • class nix.meme.MemeMotif
  • class nix.meme.MemeParser
  • class nix.meme.MemeR
  • class nix.meme.MemeResults
  • class java.security.MessageDigestSpi
    • class java.security.MessageDigest
      • class nix.util.gen.MD5 (implements java.lang.Cloneable)
  • class nix.util.gen.Misc
  • class nix.meme.MotifHit (implements java.lang.Comparable)
  • class nix.meme.MotifScanner
  • class nix.meme.MotifSearchResult (implements java.lang.Comparable)
  • class nix.util.bio.parsers.MultiFastaParser
  • class nix.affy.bpmap.MummerFilter
  • class nix.util.bio.digest.NEBParser
  • class nix.util.bio.calc.NucleicAcid
  • class nix.util.gen.Num
  • class nix.affy.main.Oligo (implements java.io.Serializable)
  • class nix.affy.main.OligoIntensityPrinter
  • class nix.affy.main.OverlapCounter
  • class nix.affy.roc.ParsePatternedWindows
  • class nix.affy.roc.ParseSgrsForParticularRegions
  • class nix.util.gen.Passwords
  • class nix.bdtnp.bid.PatternMatch
  • class nix.affy.main.PeakPicker
  • class nix.gata.main.PlotterPreferences (implements java.io.Serializable)
  • class nix.affy.main.PMMMTransformer
  • class nix.affy.roc.Positive
  • class nix.affy.main.PosRegion (implements java.lang.Comparable)
  • class nix.util.bio.converters.PossumToGFF
  • class nix.affy.roc.PWMScoreWindows
  • class nix.util.bio.parsers.QualityFileParser
  • class nix.affy.main.Quantile (implements java.lang.Comparable)
  • class nix.affy.main.QuantileNormalization
  • class nix.affy.main.RatioTest
  • class nix.util.bio.digest.REDigest
  • class nix.affy.anno.Region
  • class nix.util.bio.converters.RepeatMaskerToGFF
  • class nix.affy.roc.RocWindow (implements java.lang.Comparable, java.io.Serializable)
  • class nix.gata.geneGlyphs.ScaleBar
  • class nix.util.apps.ScatterPlot
  • class nix.util.apps.ScoreChromosomes
  • class nix.affy.main.ScoreIntervals
  • class nix.util.apps.ScoreSequences
  • class nix.selex.SelexParams
  • class nix.selex.SelexSeqParser
  • class nix.util.bio.seq.Seq
  • class nix.selex.SeqFiles
  • class nix.selex.SeqRead
  • class nix.gata.aligner.Seqs
  • class nix.affy.roc.Sgr
  • class nix.affy.roc.SgrBacCounter
  • class nix.util.bio.wrappers.SimpleBlast
  • class nix.affy.main.SkepticalSumIntensityTest
  • class nix.gata.plotter.Sliders
  • class nix.util.gen.SQL
  • class nix.util.bio.annotation.StartEnd (implements java.lang.Comparable, java.io.Serializable)
  • class nix.gata.plotter.StartStop (implements java.lang.Comparable)
  • class nix.affy.bpmap.StatBPMap
  • class nix.selex.SubSeq
  • class nix.affy.main.SubWindow (implements java.io.Serializable)
  • class nix.affy.main.SumIntensityTest
  • class nix.util.gen.Swing
  • class nix.bdtnp.bid.Table
  • class nix.affy.misc.TestDelMe
  • class nix.util.apps.TextParser
  • class java.lang.Thread (implements java.lang.Runnable)
    • class nix.gata.aligner.AlignerThread
  • class nix.util.bio.annotation.Transcript (implements java.io.Serializable)
  • class nix.affy.misc.TransformRatios
  • class nix.util.bio.annotation.TransGroup (implements java.io.Serializable)
  • class nix.gata.geneGlyphs.TransGrpGlyph
  • class nix.util.bio.annotation.Translation (implements java.io.Serializable)
  • class nix.bdtnp.bid.UserBean
  • class nix.meme.UtilMeme
  • class nix.selex.UtilSelex
  • class nix.affy.graphics.VirtualCel
  • class nix.affy.main.WilcoxonRankSumTest
  • class nix.affy.main.WilcoxonSample (implements java.lang.Comparable)
  • class nix.affy.main.WilcoxonSamplePair (implements java.lang.Comparable)
  • class nix.affy.main.WilcoxonSignedRankTest
  • class nix.affy.main.Window (implements java.lang.Comparable, java.io.Serializable)
  • class nix.affy.bpmap.WindowMaker
  • class nix.affy.main.WindowScanner
  • class nix.util.bio.xamer.Xamer
  • class nix.util.bio.xamer.XamerCounter
  • class nix.util.gen.XML
  • class nix.xml.XMLAnalyzer