org.jaga.individualRepresentation.proteinLocation
Class AminoAcidFactory

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

public class AminoAcidFactory

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 static AminoAcid[]	aliphaticAminoAcids
private static AminoAcid[]	allAminoAcids
private static java.util.HashMap	aminoAcids
private static AminoAcid[]	aromaticAminoAcids
private static AminoAcid[]	hydrophobicAminoAcids
private static AminoAcid[]	negativeAminoAcids
private static AminoAcid[]	polarAminoAcids
private static AminoAcid[]	positiveAminoAcids
private static AminoAcid[]	smallAminoAcids
private static AminoAcid[]	tinyAminoAcids

Constructor Summary

AminoAcidFactory()

Method Summary

private static AminoAcid	getRandomAcid(AminoAcid[] list, RandomGenerator rnd)
static AminoAcid	getRandomResidue(GAParameterSet params)
static AminoAcid	getRandomResidueByProperty(int property, GAParameterSet params)
static AminoAcid	getResidueByCode(java.lang.String code)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

aminoAcids

private static java.util.HashMap aminoAcids

allAminoAcids

private static AminoAcid[] allAminoAcids

smallAminoAcids

private static AminoAcid[] smallAminoAcids

hydrophobicAminoAcids

private static AminoAcid[] hydrophobicAminoAcids

polarAminoAcids

private static AminoAcid[] polarAminoAcids

positiveAminoAcids

private static AminoAcid[] positiveAminoAcids

negativeAminoAcids

private static AminoAcid[] negativeAminoAcids

tinyAminoAcids

private static AminoAcid[] tinyAminoAcids

aliphaticAminoAcids

private static AminoAcid[] aliphaticAminoAcids

aromaticAminoAcids

private static AminoAcid[] aromaticAminoAcids

Constructor Detail

AminoAcidFactory

public AminoAcidFactory()

Method Detail

getResidueByCode

public static AminoAcid getResidueByCode(java.lang.String code)

getRandomResidueByProperty

public static AminoAcid getRandomResidueByProperty(int property,
                                                   GAParameterSet params)

getRandomResidue

public static AminoAcid getRandomResidue(GAParameterSet params)

getRandomAcid

private static AminoAcid getRandomAcid(AminoAcid[] list,
                                       RandomGenerator rnd)