PolypeptidePatternMutation (JAGA - Java API for Genetic Algorithms)

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

JAGA Homepage

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

org.jaga.reproduction.proteinLocation
Class PolypeptidePatternMutation

java.lang.Object
  org.jaga.reproduction.Mutation
      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