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## Hierarchy For All Packages

Package Hierarchies:
  baseCode.algorithm, baseCode.algorithm.learning.unsupervised, baseCode.algorithm.learning.unsupervised.cluster, baseCode.bio, baseCode.bio.geneset, baseCode.common, baseCode.dataFilter, baseCode.dataStructure, baseCode.dataStructure.graph, baseCode.dataStructure.matrix, baseCode.dataStructure.tree, baseCode.db, baseCode.graphics.text, baseCode.gui, baseCode.gui.file, baseCode.gui.table, baseCode.io, baseCode.io.reader, baseCode.io.writer, baseCode.math, baseCode.math.distribution, baseCode.math.metaanalysis, baseCode.misc, baseCode.util, baseCode.xml

## Class Hierarchy

- class java.lang.Object
  - class baseCode.dataFilter.AbstractFilter (implements baseCode.dataFilter.Filter)
    - class baseCode.dataFilter.AbstractLevelFilter
      - class baseCode.dataFilter.ItemLevelFilter
      - class baseCode.dataFilter.RowLevelFilter
    - class baseCode.dataFilter.AffymetrixProbeNameFilter (implements baseCode.dataFilter.Filter)
    - class baseCode.dataFilter.RowAbsentFilter (implements baseCode.dataFilter.Filter)
    - class baseCode.dataFilter.RowAffyNameFilter (implements baseCode.dataFilter.Filter)
    - class baseCode.dataFilter.RowMissingFilter (implements baseCode.dataFilter.Filter)
    - class baseCode.dataFilter.RowNameFilter (implements baseCode.dataFilter.Filter)
  - class baseCode.dataStructure.graph.AbstractGraph (implements baseCode.dataStructure.graph.Graph)
    - class baseCode.dataStructure.graph.DirectedGraph
  - class baseCode.dataStructure.matrix.AbstractNamedMatrix (implements baseCode.dataStructure.matrix.NamedMatrix)
    - class baseCode.dataStructure.matrix.AbstractNamedDoubleMatrix
      - class baseCode.dataStructure.matrix.DenseDoubleMatrix2DNamed
      - class baseCode.dataStructure.matrix.SparseDoubleMatrix2DNamed (implements baseCode.dataStructure.matrix.NamedMatrix)
      - class baseCode.dataStructure.matrix.SparseRaggedDoubleMatrix2DNamed
    - class baseCode.dataStructure.matrix.StringMatrix2DNamed
  - class baseCode.io.reader.AbstractNamedMatrixReader
    - class baseCode.io.reader.DoubleMatrixReader
    - class baseCode.io.reader.SparseDoubleMatrixReader
    - class baseCode.io.reader.SparseRaggedDouble2DNamedMatrixReader
    - class baseCode.io.reader.StringMatrixReader
  - class javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
    - class baseCode.gui.table.TableSorter
  - class baseCode.algorithm.Algorithm
    - class baseCode.algorithm.learning.unsupervised.cluster.ClusteringAlgorithm
      - class baseCode.algorithm.learning.unsupervised.cluster.HierarchicalClusterer
    - class baseCode.algorithm.learning.unsupervised.RankProp
  - class baseCode.algorithm.learning.unsupervised.cluster.AverageLinkageDistancer (implements baseCode.algorithm.learning.unsupervised.cluster.Distancer)
  - class baseCode.dataStructure.tree.BinaryTree
  - class baseCode.util.BrowserLauncher
  - class baseCode.io.ByteArrayConverter
  - class baseCode.gui.ColorMap
  - class baseCode.gui.ColorMatrix (implements java.lang.Cloneable)
  - 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.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          - class baseCode.gui.table.JBarGraphCellRenderer (implements javax.swing.table.TableCellRenderer)
          - class baseCode.gui.JLinkLabel (implements java.awt.event.MouseListener)
          - class baseCode.gui.table.JMatrixCellRenderer (implements javax.swing.table.TableCellRenderer)
        - class javax.swing.JPanel (implements javax.accessibility.Accessible)
          - class baseCode.gui.JGradientBar
          - class baseCode.gui.JMatrixDisplay
          - class baseCode.gui.TreePanel (implements javax.swing.event.TreeSelectionListener)
          - class baseCode.gui.WizardStep
        - class javax.swing.table.JTableHeader (implements javax.accessibility.Accessible, javax.swing.event.TableColumnModelListener)
          - class baseCode.gui.table.JVerticalHeaderRenderer (implements javax.swing.table.TableCellRenderer)
      - class java.awt.Window (implements javax.accessibility.Accessible)
        - class java.awt.Dialog
          - class javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - class baseCode.gui.AppDialog
            - class baseCode.gui.Wizard
        - class java.awt.Frame (implements java.awt.MenuContainer)
          - class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - class baseCode.gui.JWebBrowser (implements java.awt.event.ActionListener, javax.swing.event.HyperlinkListener)
  - class baseCode.math.Constants
  - class baseCode.math.CorrelationStats
  - class cern.jet.stat.Descriptive
    - class baseCode.math.DescriptiveWithMissing
  - class baseCode.math.distribution.Dirichlet
  - class baseCode.math.Distance
  - class baseCode.algorithm.learning.unsupervised.cluster.DistanceFactory
  - class baseCode.dataStructure.matrix.DoubleMatrix2DNamedFactory
  - class javax.swing.filechooser.FileFilter
    - class baseCode.gui.file.DataFileFilter
    - class baseCode.gui.file.ImageFileFilter
    - class baseCode.gui.file.XMLFileFilter
  - class baseCode.util.FileTools
  - class baseCode.bio.geneset.GeneAnnotations
  - class baseCode.bio.geneset.GeneSetMapTools
  - class baseCode.bio.geneset.GONames
  - class baseCode.xml.GOParser
  - class baseCode.bio.GOTermList
  - class baseCode.bio.GOTermProbability
  - class baseCode.misc.GroupMap
  - class baseCode.gui.GuiUtil
  - class baseCode.db.Handle
  - class baseCode.io.writer.HistogramWriter
  - class baseCode.math.KSTest
  - class baseCode.io.reader.MapReader
  - class baseCode.math.MatrixRowStats
  - class baseCode.math.MatrixStats
  - class baseCode.math.metaanalysis.MetaAnalysis
    - class baseCode.math.metaanalysis.CorrelationEffectMetaAnalysis
    - class baseCode.math.metaanalysis.MeanDifferenceMetaAnalysis
  - class baseCode.math.MultipleTestCorrection
  - class baseCode.math.distribution.NormalProbabilityComputer (implements baseCode.math.distribution.ProbabilityComputer)
  - class baseCode.dataStructure.OntologyEntry
    - class baseCode.bio.GOEntry
  - class cern.colt.PersistentObject (implements java.lang.Cloneable, java.io.Serializable)
    - class cern.colt.matrix.impl.AbstractMatrix
      - class cern.colt.matrix.impl.AbstractMatrix1D
        - class cern.colt.matrix.DoubleMatrix1D
          - class cern.colt.matrix.impl.DenseDoubleMatrix1D
            - class baseCode.dataStructure.matrix.DenseDoubleMatrix1D
          - class baseCode.dataStructure.matrix.RCDoubleMatrix1D
  - class baseCode.dataStructure.Point
    - class baseCode.dataStructure.Link
  - class baseCode.dataStructure.Queue
  - class baseCode.math.RandomChooser
  - class baseCode.math.Rank
  - class baseCode.algorithm.Ranker
  - class baseCode.util.RegressionTesting
  - class baseCode.math.ROC
  - class baseCode.math.SpecFunc
  - class baseCode.dataStructure.Stack
  - class baseCode.math.Stats
  - class baseCode.util.StatusDebugLogger (implements baseCode.util.StatusViewer)
  - class baseCode.gui.StatusJlabel (implements baseCode.util.StatusViewer)
  - class baseCode.util.StatusStderr (implements baseCode.util.StatusViewer)
  - class baseCode.io.StringConverter
  - class baseCode.dataStructure.tree.Tree
  - class baseCode.math.distribution.UniformDensityComputer (implements baseCode.math.distribution.DensityGenerator)
  - class baseCode.math.distribution.UniformProbabilityComputer (implements baseCode.math.distribution.ProbabilityComputer)
  - class baseCode.graphics.text.Util
  - class baseCode.common.Visitable (implements java.lang.Comparable)
    - class baseCode.dataStructure.graph.AbstractGraphNode (implements baseCode.dataStructure.graph.GraphNode)
      - class baseCode.dataStructure.graph.DirectedGraphNode (implements java.lang.Comparable)
      - class baseCode.dataStructure.graph.UndirectedGraphNode
    - class baseCode.dataStructure.tree.BinaryTreeNode
    - class baseCode.common.Distanceable
      - class baseCode.algorithm.learning.unsupervised.cluster.Cluster
    - class baseCode.dataStructure.tree.TreeNode
  - class baseCode.math.distribution.Wishart

## Interface Hierarchy

- interface baseCode.math.distribution.DensityGenerator
- interface baseCode.algorithm.learning.unsupervised.cluster.Distancer
- interface baseCode.dataFilter.Filter
- interface baseCode.dataStructure.graph.Graph
- interface baseCode.dataStructure.graph.GraphNode
- interface baseCode.dataStructure.matrix.NamedMatrix
- interface baseCode.math.distribution.ProbabilityComputer
- interface baseCode.algorithm.learning.unsupervised.cluster.Similarity
- interface baseCode.util.StatusViewer

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