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org.jaga.individualRepresentation.proteinLocation
Class ProteinGroup

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

public class ProteinGroup
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 groups
           
private  java.lang.String name
           
private  java.util.ArrayList proteins
           
 
Constructor Summary
ProteinGroup()
           
ProteinGroup(java.lang.String name)
           
ProteinGroup(java.lang.String name, ProteinFileParser parser, java.lang.String fileName)
           
 
Method Summary
 void add(Protein prot)
           
 void add(ProteinGroup group)
           
 int align(PolypeptidePattern pattern, int minOverlap)
           
private  int alignInProteins(PolypeptidePattern pattern, int minOverlap)
           
private  int alignInSubgroups(PolypeptidePattern pattern, int minOverlap)
           
private  boolean alignProtein(Protein protein, PolypeptidePattern pattern, int minOverlap)
           
 void flatten()
           
 java.lang.String getName()
           
 Protein getProtein(int index)
           
 void load(ProteinFileParser parser, java.lang.String fileName)
           
 void randomise(RandomGenerator rnd)
           
 void setName(java.lang.String name)
           
 int size()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

proteins

private java.util.ArrayList proteins

groups

private java.util.ArrayList groups

name

private java.lang.String name
Constructor Detail

ProteinGroup

public ProteinGroup()

ProteinGroup

public ProteinGroup(java.lang.String name)

ProteinGroup

public ProteinGroup(java.lang.String name,
                    ProteinFileParser parser,
                    java.lang.String fileName)
Method Detail

add

public void add(Protein prot)

add

public void add(ProteinGroup group)

getProtein

public Protein getProtein(int index)

size

public int size()

flatten

public void flatten()

randomise

public void randomise(RandomGenerator rnd)

align

public int align(PolypeptidePattern pattern,
                 int minOverlap)

alignInProteins

private int alignInProteins(PolypeptidePattern pattern,
                            int minOverlap)

alignProtein

private boolean alignProtein(Protein protein,
                             PolypeptidePattern pattern,
                             int minOverlap)

alignInSubgroups

private int alignInSubgroups(PolypeptidePattern pattern,
                             int minOverlap)

load

public void load(ProteinFileParser parser,
                 java.lang.String fileName)

getName

public java.lang.String getName()

setName

public void setName(java.lang.String name)

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