org.jaga.individualRepresentation.proteinLocation
Class ProteinLocationClassifierFactory

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

All Implemented Interfaces:

IndividualsFactory

public class ProteinLocationClassifierFactory

extends java.lang.Object

implements IndividualsFactory

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 int	aminoAcidChance
private java.lang.String	classifierName
private int	groupChance
private int	maxGroupLength
private int	maxPatternLength
private int	propertyChance
private int	singleGapChance

Constructor Summary

ProteinLocationClassifierFactory()

ProteinLocationClassifierFactory(int maxPatternLength, int aminoAcidChance, int groupChance, int propertyChance, int singleGapChance, int maxGroupLength, java.lang.String classifierName)

Method Summary

Individual	createDefaultIndividual(GAParameterSet params) Creates a new default individual.
Individual	createRandomIndividual(GAParameterSet params) Creates a random individual according to this factory's current internal settings and expariment paramanters.
PolypeptidePattern	createRandomPattern(GAParameterSet params)
PolypeptidePattern	createRandomPattern(int length, GAParameterSet params)
PolypeptidePatternItem	createRandomPatternItem(GAParameterSet params)
Individual	createSpecificIndividual(java.lang.Object init, GAParameterSet params) Creates a new individual and initialises it to the specified value(s).
Individual	createSpecificIndividual(PolypeptidePattern init, GAParameterSet params)
Individual	createSpecificIndividual(ProteinLocationClassifier init, GAParameterSet params)
Individual	createSpecificIndividual(java.lang.String init, GAParameterSet params)
int	getAminoAcidChance()
java.lang.String	getClassifierName()
int	getGroupChance()
int	getMaxGroupLength()
int	getMaxPatternLength()
int	getPropertyChance()
int	getSingleGapChance()
void	setAminoAcidChance(int aminoAcidChance)
void	setClassifierName(java.lang.String classifierName)
void	setGroupChance(int groupChance)
void	setMaxGroupLength(int maxGroupLength)
void	setMaxPatternLength(int maxPatternLength)
void	setPropertyChance(int propertyChance)
void	setSingleGapChance(int singleGapChance)

Methods inherited from class java.lang.Object

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

Field Detail

maxPatternLength

private int maxPatternLength

aminoAcidChance

private int aminoAcidChance

groupChance

private int groupChance

propertyChance

private int propertyChance

singleGapChance

private int singleGapChance

maxGroupLength

private int maxGroupLength

classifierName

private java.lang.String classifierName

Constructor Detail

ProteinLocationClassifierFactory

public ProteinLocationClassifierFactory()

ProteinLocationClassifierFactory

public ProteinLocationClassifierFactory(int maxPatternLength,
                                        int aminoAcidChance,
                                        int groupChance,
                                        int propertyChance,
                                        int singleGapChance,
                                        int maxGroupLength,
                                        java.lang.String classifierName)

Method Detail

createRandomPattern

public PolypeptidePattern createRandomPattern(GAParameterSet params)

createRandomPattern

public PolypeptidePattern createRandomPattern(int length,
                                              GAParameterSet params)

createRandomPatternItem

public PolypeptidePatternItem createRandomPatternItem(GAParameterSet params)

createDefaultIndividual

public Individual createDefaultIndividual(GAParameterSet params)

Description copied from interface: IndividualsFactory

Creates a new default individual. For same factory settings, this method must always return the same individual (a new instance holding the same values), which is considered the defaut individual for those settings.

Specified by:

createDefaultIndividual in interface IndividualsFactory

Parameters:

params - Experiment parameters.

Returns:

A new instance of the dafault individual for this factory's current settings.

createRandomIndividual

public Individual createRandomIndividual(GAParameterSet params)

Description copied from interface: IndividualsFactory

Creates a random individual according to this factory's current internal settings and expariment paramanters.

Specified by:

createRandomIndividual in interface IndividualsFactory

Parameters:

params - Experiment parameters.

Returns:

A new instanc eof a randomly created individual.

createSpecificIndividual

public Individual createSpecificIndividual(java.lang.Object init,
                                           GAParameterSet params)

Description copied from interface: IndividualsFactory

Creates a new individual and initialises it to the specified value(s). The parameter init can hold any value(s) which this factory knows to interprete.
In particular, a factory should be able to handle Individual-objects of the same type as produced by the factory. If such an Individual-object is passed as the init-value, a deep copy of the individual should be created and returned by this method.
Any other type is permited for the init-value, but the value should not be null. This method should create a new individual and initialise it with the value(s) packed encoded in init.

Specified by:

createSpecificIndividual in interface IndividualsFactory

Parameters:

init - Initialisation value(s) for a new individual.

params - Experiment parameters.

Returns:

A new instance of an individual produced by this factory, initialised to the value(s) specified in init.

createSpecificIndividual

public Individual createSpecificIndividual(ProteinLocationClassifier init,
                                           GAParameterSet params)

createSpecificIndividual

public Individual createSpecificIndividual(PolypeptidePattern init,
                                           GAParameterSet params)

createSpecificIndividual

public Individual createSpecificIndividual(java.lang.String init,
                                           GAParameterSet params)

getAminoAcidChance

public int getAminoAcidChance()

setAminoAcidChance

public void setAminoAcidChance(int aminoAcidChance)

getGroupChance

public int getGroupChance()

setGroupChance

public void setGroupChance(int groupChance)

getMaxGroupLength

public int getMaxGroupLength()

setMaxGroupLength

public void setMaxGroupLength(int maxGroupLength)

getMaxPatternLength

public int getMaxPatternLength()

setMaxPatternLength

public void setMaxPatternLength(int maxPatternLength)

getPropertyChance

public int getPropertyChance()

setPropertyChance

public void setPropertyChance(int propertyChance)

getSingleGapChance

public int getSingleGapChance()

setSingleGapChance

public void setSingleGapChance(int singleGapChance)

getClassifierName

public java.lang.String getClassifierName()

setClassifierName

public void setClassifierName(java.lang.String classifierName)