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org.jaga.individualRepresentation.proteinLocation
Class AminoAcidGroup

java.lang.Object
  extended by org.jaga.individualRepresentation.proteinLocation.PolypeptidePatternItem
      extended by org.jaga.individualRepresentation.proteinLocation.AminoAcidGroup

public class AminoAcidGroup
extends PolypeptidePatternItem

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 acids
           
private  int countAliphatic
           
private  int countAromatic
           
private  int countHydrophobic
           
private  int countNegative
           
private  int countPolar
           
private  int countPositive
           
private  int countSmall
           
private  int countTiny
           
 
Constructor Summary
AminoAcidGroup()
           
 
Method Summary
private  void addAcidToStats(AminoAcid aminoAcid)
           
 void addResidue(AminoAcid aminoAcid)
           
 boolean doesntMatch(AminoAcid aminoAcid)
           
 int getMaxRepresentedProperty()
           
 double getPropertyProportion(int property)
           
 AminoAcid getResidue(int index)
           
private  void removeAcidFromStats(AminoAcid aminoAcid)
           
 AminoAcid removeResidue(int index)
           
 int size()
           
 void swapResidue(int index, AminoAcid newAminoAcid)
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

acids

private java.util.ArrayList acids

countSmall

private int countSmall

countHydrophobic

private int countHydrophobic

countPolar

private int countPolar

countPositive

private int countPositive

countNegative

private int countNegative

countTiny

private int countTiny

countAliphatic

private int countAliphatic

countAromatic

private int countAromatic
Constructor Detail

AminoAcidGroup

public AminoAcidGroup()
Method Detail

doesntMatch

public boolean doesntMatch(AminoAcid aminoAcid)
Specified by:
doesntMatch in class PolypeptidePatternItem

getResidue

public AminoAcid getResidue(int index)

swapResidue

public void swapResidue(int index,
                        AminoAcid newAminoAcid)

removeResidue

public AminoAcid removeResidue(int index)

addResidue

public void addResidue(AminoAcid aminoAcid)

size

public int size()

addAcidToStats

private void addAcidToStats(AminoAcid aminoAcid)

removeAcidFromStats

private void removeAcidFromStats(AminoAcid aminoAcid)

getPropertyProportion

public double getPropertyProportion(int property)

getMaxRepresentedProperty

public int getMaxRepresentedProperty()

toString

public java.lang.String toString()
Specified by:
toString in class PolypeptidePatternItem

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