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org.jaga.reproduction.proteinLocation
Class PolypeptidePatternMutation

java.lang.Object
  extended by org.jaga.reproduction.Mutation
      extended by org.jaga.reproduction.proteinLocation.PolypeptidePatternMutation
All Implemented Interfaces:
ReproductionAlgorithm

public class PolypeptidePatternMutation
extends Mutation

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 aminoAcid_cloneChance
           
private  int aminoAcid_deleteChance
           
private  int aminoAcid_generaliseToGroupChance
           
private  int aminoAcid_generaliseToPropertyChance
           
private  int aminoAcid_mutateChance
           
private  int group_addChance
           
private  int group_cloneChance
           
private  int group_deleteChance
           
private  int group_onEmptyDeleteChance
           
private  int group_onEmptyReplaceChance
           
private  int group_onLargeDontActChance
           
private  int group_onLargeReplaceChance
           
private  int group_onLargeSplitChance
           
private  int group_onLargeTriggerLength
           
private  double group_onPropertyReplaceProb
           
private  double group_onPropertyTriggerPercent
           
private  double group_onSingleReplaceProb
           
private  int group_substractChance
           
private  int group_swapChance
           
private  int property_cloneChance
           
private  int property_deleteChance
           
private  int property_expandChance
           
private  int property_expandGroupSize
           
private  int property_expandSamePropCount
           
private  int property_mutateChance
           
private  SubstitutionScoringMatrix scoringMatrix
           
private  int singleGap_cloneChance
           
private  int singleGap_deleteChance
           
private  int singleGap_expandChance
           
private  int singleGap_expandGroupSize
           
private  int singleGap_mutateChance
           
 
Constructor Summary
PolypeptidePatternMutation()
           
PolypeptidePatternMutation(double mutProb)
           
 
Method Summary
 int getAminoAcid_cloneChance()
           
 int getAminoAcid_deleteChance()
           
 int getAminoAcid_generaliseToGroupChance()
           
 int getAminoAcid_generaliseToPropertyChance()
           
 int getAminoAcid_mutateChance()
           
 java.lang.Class getApplicableClass()
          Returns the class of individuals handled by this reproduction algorithm.
 int getGroup_addChance()
           
 int getGroup_cloneChance()
           
 int getGroup_deleteChance()
           
 int getGroup_onEmptyDeleteChance()
           
 int getGroup_onEmptyReplaceChance()
           
 int getGroup_onLargeDontActChance()
           
 int getGroup_onLargeReplaceChance()
           
 int getGroup_onLargeSplitChance()
           
 int getGroup_onLargeTriggerLength()
           
 double getGroup_onPropertyReplaceProb()
           
 double getGroup_onPropertyTriggerPercent()
           
 double getGroup_onSingleReplaceProb()
           
 int getGroup_substractChance()
           
 int getGroup_swapChance()
           
 int getProperty_cloneChance()
           
 int getProperty_deleteChance()
           
 int getProperty_expandChance()
           
 int getProperty_expandGroupSize()
           
 int getProperty_expandSamePropCount()
           
 int getProperty_mutateChance()
           
 SubstitutionScoringMatrix getScoringMatrix()
           
 int getSingleGap_cloneChance()
           
 int getSingleGap_deleteChance()
           
 int getSingleGap_expandChance()
           
 int getSingleGap_expandGroupSize()
           
 int getSingleGap_mutateChance()
           
private  PolypeptidePatternItem[] mutateItem(AminoAcid aAcid, GAParameterSet params)
           
private  PolypeptidePatternItem[] mutateItem(AminoAcidGroup group, GAParameterSet params)
           
private  PolypeptidePatternItem[] mutateItem(AminoAcidProperty property, GAParameterSet params)
           
private  PolypeptidePatternItem[] mutateItem(SingleGap gap, GAParameterSet params)
           
private  PolypeptidePatternItem[] mutatePatternItem(PolypeptidePatternItem item, GAParameterSet params)
           
 Individual[] reproduce(Individual[] parents, GAParameterSet params)
          Reproduces the specified individuals.
 Individual reproduce(Individual parent, GAParameterSet params)
           
 void setAminoAcid_cloneChance(int aminoAcid_cloneChance)
           
 void setAminoAcid_deleteChance(int aminoAcid_deleteChance)
           
 void setAminoAcid_generaliseToGroupChance(int aminoAcid_generaliseToGroupChance)
           
 void setAminoAcid_generaliseToPropertyChance(int aminoAcid_generaliseToPropertyChance)
           
 void setAminoAcid_mutateChance(int aminoAcid_mutateChance)
           
 void setGroup_addChance(int group_addChance)
           
 void setGroup_cloneChance(int group_cloneChance)
           
 void setGroup_deleteChance(int group_deleteChance)
           
 void setGroup_onEmptyDeleteChance(int group_onEmptyDeleteChance)
           
 void setGroup_onEmptyReplaceChance(int group_onEmptyReplaceChance)
           
 void setGroup_onLargeDontActChance(int group_onLargeDontActChance)
           
 void setGroup_onLargeReplaceChance(int group_onLargeReplaceChance)
           
 void setGroup_onLargeSplitChance(int group_onLargeSplitChance)
           
 void setGroup_onLargeTriggerLength(int group_onLargeTriggerLength)
           
 void setGroup_onPropertyReplaceProb(double group_onPropertyReplaceProb)
           
 void setGroup_onPropertyTriggerPercent(double group_onPropertyTriggerPercent)
           
 void setGroup_onSingleReplaceProb(double group_onSingleReplaceProb)
           
 void setGroup_substractChance(int group_substractChance)
           
 void setGroup_swapChance(int group_swapChance)
           
 void setProperty_cloneChance(int property_cloneChance)
           
 void setProperty_deleteChance(int property_deleteChance)
           
 void setProperty_expandChance(int property_expandChance)
           
 void setProperty_expandGroupSize(int property_expandGroupSize)
           
 void setProperty_expandSamePropCount(int property_expandSamePropCount)
           
 void setProperty_mutateChance(int property_mutateChance)
           
 void setScoringMatrix(SubstitutionScoringMatrix scoringMatrix)
           
 void setSingleGap_cloneChance(int singleGap_cloneChance)
           
 void setSingleGap_deleteChance(int singleGap_deleteChance)
           
 void setSingleGap_expandChance(int singleGap_expandChance)
           
 void setSingleGap_expandGroupSize(int singleGap_expandGroupSize)
           
 void setSingleGap_mutateChance(int singleGap_mutateChance)
           
 
Methods inherited from class org.jaga.reproduction.Mutation
getMutationProbability, getRequiredNumberOfParents, setMutationProbability
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

scoringMatrix

private SubstitutionScoringMatrix scoringMatrix

aminoAcid_deleteChance

private int aminoAcid_deleteChance

aminoAcid_cloneChance

private int aminoAcid_cloneChance

aminoAcid_mutateChance

private int aminoAcid_mutateChance

aminoAcid_generaliseToPropertyChance

private int aminoAcid_generaliseToPropertyChance

aminoAcid_generaliseToGroupChance

private int aminoAcid_generaliseToGroupChance

group_substractChance

private int group_substractChance

group_addChance

private int group_addChance

group_swapChance

private int group_swapChance

group_deleteChance

private int group_deleteChance

group_cloneChance

private int group_cloneChance

group_onEmptyDeleteChance

private int group_onEmptyDeleteChance

group_onEmptyReplaceChance

private int group_onEmptyReplaceChance

group_onSingleReplaceProb

private double group_onSingleReplaceProb

group_onPropertyTriggerPercent

private double group_onPropertyTriggerPercent

group_onPropertyReplaceProb

private double group_onPropertyReplaceProb

group_onLargeTriggerLength

private int group_onLargeTriggerLength

group_onLargeSplitChance

private int group_onLargeSplitChance

group_onLargeReplaceChance

private int group_onLargeReplaceChance

group_onLargeDontActChance

private int group_onLargeDontActChance

property_deleteChance

private int property_deleteChance

property_cloneChance

private int property_cloneChance

property_mutateChance

private int property_mutateChance

property_expandChance

private int property_expandChance

property_expandGroupSize

private int property_expandGroupSize

property_expandSamePropCount

private int property_expandSamePropCount

singleGap_deleteChance

private int singleGap_deleteChance

singleGap_cloneChance

private int singleGap_cloneChance

singleGap_mutateChance

private int singleGap_mutateChance

singleGap_expandChance

private int singleGap_expandChance

singleGap_expandGroupSize

private int singleGap_expandGroupSize
Constructor Detail

PolypeptidePatternMutation

public PolypeptidePatternMutation()

PolypeptidePatternMutation

public PolypeptidePatternMutation(double mutProb)
Method Detail

getApplicableClass

public java.lang.Class getApplicableClass()
Description copied from interface: ReproductionAlgorithm
Returns the class of individuals handled by this reproduction algorithm.

Specified by:
getApplicableClass in interface ReproductionAlgorithm
Specified by:
getApplicableClass in class Mutation
Returns:
The required type of the array-members in the parameter parents to the method ReproductionAlgorithm.reproduce.

mutateItem

private PolypeptidePatternItem[] mutateItem(AminoAcid aAcid,
                                            GAParameterSet params)

mutateItem

private PolypeptidePatternItem[] mutateItem(AminoAcidGroup group,
                                            GAParameterSet params)

mutateItem

private PolypeptidePatternItem[] mutateItem(AminoAcidProperty property,
                                            GAParameterSet params)

mutateItem

private PolypeptidePatternItem[] mutateItem(SingleGap gap,
                                            GAParameterSet params)

mutatePatternItem

private PolypeptidePatternItem[] mutatePatternItem(PolypeptidePatternItem item,
                                                   GAParameterSet params)

reproduce

public Individual reproduce(Individual parent,
                            GAParameterSet params)

reproduce

public Individual[] reproduce(Individual[] parents,
                              GAParameterSet params)
Description copied from interface: ReproductionAlgorithm
Reproduces the specified individuals.

Specified by:
reproduce in interface ReproductionAlgorithm
Specified by:
reproduce in class Mutation
Parameters:
parents - The individuals to reproduce. The type of objects in this array must be the class returned by getApplicableClass. The number of objects in this array must be the same as returned by getRequiredNumberOfParents.
params - Experiment parameters.
Returns:
The children - i.e. the result of the reproduction of parents.

getAminoAcid_cloneChance

public int getAminoAcid_cloneChance()

setAminoAcid_cloneChance

public void setAminoAcid_cloneChance(int aminoAcid_cloneChance)

getAminoAcid_deleteChance

public int getAminoAcid_deleteChance()

setAminoAcid_deleteChance

public void setAminoAcid_deleteChance(int aminoAcid_deleteChance)

getAminoAcid_generaliseToGroupChance

public int getAminoAcid_generaliseToGroupChance()

setAminoAcid_generaliseToGroupChance

public void setAminoAcid_generaliseToGroupChance(int aminoAcid_generaliseToGroupChance)

getAminoAcid_generaliseToPropertyChance

public int getAminoAcid_generaliseToPropertyChance()

setAminoAcid_generaliseToPropertyChance

public void setAminoAcid_generaliseToPropertyChance(int aminoAcid_generaliseToPropertyChance)

getAminoAcid_mutateChance

public int getAminoAcid_mutateChance()

setAminoAcid_mutateChance

public void setAminoAcid_mutateChance(int aminoAcid_mutateChance)

getGroup_addChance

public int getGroup_addChance()

setGroup_addChance

public void setGroup_addChance(int group_addChance)

getGroup_cloneChance

public int getGroup_cloneChance()

setGroup_cloneChance

public void setGroup_cloneChance(int group_cloneChance)

getGroup_deleteChance

public int getGroup_deleteChance()

setGroup_deleteChance

public void setGroup_deleteChance(int group_deleteChance)

getGroup_onEmptyDeleteChance

public int getGroup_onEmptyDeleteChance()

setGroup_onEmptyDeleteChance

public void setGroup_onEmptyDeleteChance(int group_onEmptyDeleteChance)

getGroup_onEmptyReplaceChance

public int getGroup_onEmptyReplaceChance()

setGroup_onEmptyReplaceChance

public void setGroup_onEmptyReplaceChance(int group_onEmptyReplaceChance)

getGroup_onLargeDontActChance

public int getGroup_onLargeDontActChance()

setGroup_onLargeDontActChance

public void setGroup_onLargeDontActChance(int group_onLargeDontActChance)

getGroup_onLargeReplaceChance

public int getGroup_onLargeReplaceChance()

setGroup_onLargeReplaceChance

public void setGroup_onLargeReplaceChance(int group_onLargeReplaceChance)

getGroup_onLargeSplitChance

public int getGroup_onLargeSplitChance()

setGroup_onLargeSplitChance

public void setGroup_onLargeSplitChance(int group_onLargeSplitChance)

getGroup_onLargeTriggerLength

public int getGroup_onLargeTriggerLength()

setGroup_onLargeTriggerLength

public void setGroup_onLargeTriggerLength(int group_onLargeTriggerLength)

getGroup_onPropertyReplaceProb

public double getGroup_onPropertyReplaceProb()

setGroup_onPropertyReplaceProb

public void setGroup_onPropertyReplaceProb(double group_onPropertyReplaceProb)

getGroup_onPropertyTriggerPercent

public double getGroup_onPropertyTriggerPercent()

setGroup_onPropertyTriggerPercent

public void setGroup_onPropertyTriggerPercent(double group_onPropertyTriggerPercent)

getGroup_onSingleReplaceProb

public double getGroup_onSingleReplaceProb()

setGroup_onSingleReplaceProb

public void setGroup_onSingleReplaceProb(double group_onSingleReplaceProb)

getGroup_substractChance

public int getGroup_substractChance()

setGroup_substractChance

public void setGroup_substractChance(int group_substractChance)

getGroup_swapChance

public int getGroup_swapChance()

setGroup_swapChance

public void setGroup_swapChance(int group_swapChance)

getProperty_cloneChance

public int getProperty_cloneChance()

setProperty_cloneChance

public void setProperty_cloneChance(int property_cloneChance)

getProperty_deleteChance

public int getProperty_deleteChance()

setProperty_deleteChance

public void setProperty_deleteChance(int property_deleteChance)

getProperty_expandChance

public int getProperty_expandChance()

setProperty_expandChance

public void setProperty_expandChance(int property_expandChance)

getProperty_expandGroupSize

public int getProperty_expandGroupSize()

setProperty_expandGroupSize

public void setProperty_expandGroupSize(int property_expandGroupSize)

getProperty_expandSamePropCount

public int getProperty_expandSamePropCount()

setProperty_expandSamePropCount

public void setProperty_expandSamePropCount(int property_expandSamePropCount)

getProperty_mutateChance

public int getProperty_mutateChance()

setProperty_mutateChance

public void setProperty_mutateChance(int property_mutateChance)

getScoringMatrix

public SubstitutionScoringMatrix getScoringMatrix()

setScoringMatrix

public void setScoringMatrix(SubstitutionScoringMatrix scoringMatrix)

getSingleGap_cloneChance

public int getSingleGap_cloneChance()

setSingleGap_cloneChance

public void setSingleGap_cloneChance(int singleGap_cloneChance)

getSingleGap_deleteChance

public int getSingleGap_deleteChance()

setSingleGap_deleteChance

public void setSingleGap_deleteChance(int singleGap_deleteChance)

getSingleGap_expandChance

public int getSingleGap_expandChance()

setSingleGap_expandChance

public void setSingleGap_expandChance(int singleGap_expandChance)

getSingleGap_expandGroupSize

public int getSingleGap_expandGroupSize()

setSingleGap_expandGroupSize

public void setSingleGap_expandGroupSize(int singleGap_expandGroupSize)

getSingleGap_mutateChance

public int getSingleGap_mutateChance()

setSingleGap_mutateChance

public void setSingleGap_mutateChance(int singleGap_mutateChance)

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