org.jaga.individualRepresentation.proteinLocation
Class AminoAcidGroup

java.lang.Object
  org.jaga.individualRepresentation.proteinLocation.PolypeptidePatternItem
      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