Class Hierarchy (NeoBio API)

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## Hierarchy For All Packages

Package Hierarchies:
  neobio.alignment, neobio.gui, neobio.textui

## Class Hierarchy

- class java.lang.Object
  - class neobio.alignment.AlignmentBlock
    - class neobio.alignment.LocalAlignmentBlock
  - class neobio.alignment.CharSequence
  - 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.JInternalFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
          - class neobio.gui.PairwiseAlignmentFrame
      - 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 neobio.gui.AboutDialog
        - class java.awt.Frame (implements java.awt.MenuContainer)
          - class javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            - class neobio.gui.NeoBio
  - class neobio.alignment.Factor
  - class neobio.alignment.FactorSequence
  - class neobio.textui.NeoBio
  - class neobio.alignment.OutMatrix (implements neobio.alignment.Matrix)
  - class neobio.alignment.PairwiseAlignment (implements java.io.Serializable)
  - class neobio.alignment.PairwiseAlignmentAlgorithm
    - class neobio.alignment.CrochemoreLandauZivUkelson
      - class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment
      - class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment
    - class neobio.alignment.NeedlemanWunsch
    - class neobio.alignment.SmithWaterman
  - class neobio.textui.RandomFactorSequenceGenerator
  - class neobio.textui.RandomSequenceGenerator
  - class neobio.alignment.ScoringScheme
    - class neobio.alignment.BasicScoringScheme
    - class neobio.alignment.ScoringMatrix
  - class neobio.alignment.Smawk
  - class java.lang.Throwable (implements java.io.Serializable)
    - class java.lang.Exception
      - class neobio.alignment.IncompatibleScoringSchemeException
      - class neobio.alignment.InvalidScoringMatrixException
      - class neobio.alignment.InvalidSequenceException
  - class neobio.alignment.Trie

## Interface Hierarchy

- interface neobio.alignment.Matrix

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http://neobio.sourceforge.net
NeoBio is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. NeoBio is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with NeoBio; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.