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org.jaga.individualRepresentation.proteinLocation
Class PolypeptidePattern

java.lang.Object
  extended by org.jaga.individualRepresentation.proteinLocation.PolypeptidePattern

public class PolypeptidePattern
extends java.lang.Object

TODO: Complete these comments.

Project: JAGA - Java API for Genetic Algorithms.

Company: University College London and JAGA.Org (http://www.jaga.org).

Copyright: (c) 2004 by G. Paperin.
This program 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, ONLY if you include a note of the original author(s) in any redistributed/modified copy.
This program 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 this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA or see http://www.gnu.org/licenses/gpl.html

Version:
JAGA public release 1.0 beta
Author:
Greg Paperin (greg@jaga.org)

Field Summary
private  java.util.ArrayList items
           
 
Constructor Summary
PolypeptidePattern()
           
 
Method Summary
 void clearAllItems()
           
 PolypeptidePatternItem getItem(int index)
           
 int getLength()
           
 void insertItem(int index, PolypeptidePatternItem item)
           
 void insertItem(PolypeptidePatternItem item)
           
 boolean matches(Protein prot, int fromLocation)
           
 boolean matchesPerformanceHack(AminoAcid[] sequence, int fromLocation)
           
 void removeItem(int index)
           
 void replaceItem(int index, PolypeptidePatternItem item)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

items

private java.util.ArrayList items
Constructor Detail

PolypeptidePattern

public PolypeptidePattern()
Method Detail

clearAllItems

public void clearAllItems()

getLength

public int getLength()

getItem

public PolypeptidePatternItem getItem(int index)

removeItem

public void removeItem(int index)

replaceItem

public void replaceItem(int index,
                        PolypeptidePatternItem item)

insertItem

public void insertItem(int index,
                       PolypeptidePatternItem item)

insertItem

public void insertItem(PolypeptidePatternItem item)

matches

public boolean matches(Protein prot,
                       int fromLocation)

matchesPerformanceHack

public boolean matchesPerformanceHack(AminoAcid[] sequence,
                                      int fromLocation)

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

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