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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
Overview
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