Package org.biojavax.ga.functions
Class AbstractCrossOverFunction
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojavax.ga.functions.AbstractCrossOverFunction
- All Implemented Interfaces:
Changeable
,CrossOverFunction
- Direct Known Subclasses:
OrderCrossover
,SimpleCrossOverFunction
public abstract class AbstractCrossOverFunction
extends AbstractChangeable
implements CrossOverFunction
Abstract implementation of
CrossOverFunction
. All custom
implementations should inherit from here.- Since:
- 1.5
- Version:
- 1.0
- Author:
- Mark Schreiber
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Nested Class Summary
Nested classes/interfaces inherited from interface org.biojavax.ga.functions.CrossOverFunction
CrossOverFunction.NoCross
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Field Summary
Fields inherited from interface org.biojavax.ga.functions.CrossOverFunction
CROSS_PROB, DEFAULT_CROSS_PROB, DEFAULT_MAX_CROSS, MAX_CROSSES, NO_CROSS
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfinal double[]
final int
final void
setCrossOverProbs
(double[] crossOverProbs) Sets the probability of crossing at each base.final void
setMaxCrossOvers
(int maxCrossOvers) Sets an upper limit on the number of crosses.Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojavax.ga.functions.CrossOverFunction
performCrossOver
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Constructor Details
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AbstractCrossOverFunction
protected AbstractCrossOverFunction()
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Method Details
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setMaxCrossOvers
Description copied from interface:CrossOverFunction
Sets an upper limit on the number of crosses. Its up to the implementation to decide what to do when the limit is reached although a good convention would be to keep only the first N crosses from the left end (5' end) of the sequence. By convention the default upper limit is DEFAULT_MAX_CROSS (eg infinite). This value should be used as the default by all implementations.- Specified by:
setMaxCrossOvers
in interfaceCrossOverFunction
- Parameters:
maxCrossOvers
- the limit on crosses- Throws:
ChangeVetoException
- if a ChangeListener vetoes this change
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getMaxCrossOvers
- Specified by:
getMaxCrossOvers
in interfaceCrossOverFunction
- Returns:
- the limit on crosses.
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setCrossOverProbs
Description copied from interface:CrossOverFunction
Sets the probability of crossing at each base. Each position in the array corresponds to a position in the sequences to be crossed. The probability of a cross occuring after position 1 in theSymbolList
is given bycrossOverProbs[1]
.CrossOverProbs[0]
is effectively redundant as the cross would occur before the 1st position in theSymbolList
. By convention if the array is shorter than the SymbolList it is being applied to then the last value in the array will be applied to every subsequent residue. The default value in all implementations should beDEFAULT_CROSS_PROB
- Specified by:
setCrossOverProbs
in interfaceCrossOverFunction
- Parameters:
crossOverProbs
- an array of doubles giving the probability of a cross occuring at any place.- Throws:
ChangeVetoException
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getCrossOverProbs
- Specified by:
getCrossOverProbs
in interfaceCrossOverFunction
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