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
  • Constructor Details

  • Method Details

    • setMaxCrossOvers

      public final void setMaxCrossOvers(int maxCrossOvers) throws ChangeVetoException
      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 interface CrossOverFunction
      Parameters:
      maxCrossOvers - the limit on crosses
      Throws:
      ChangeVetoException - if a ChangeListener vetoes this change
    • getMaxCrossOvers

      public final int getMaxCrossOvers()
      Specified by:
      getMaxCrossOvers in interface CrossOverFunction
      Returns:
      the limit on crosses.
    • setCrossOverProbs

      public final void setCrossOverProbs(double[] crossOverProbs) throws ChangeVetoException
      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 the SymbolList is given by crossOverProbs[1]. CrossOverProbs[0] is effectively redundant as the cross would occur before the 1st position in the SymbolList. 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 be DEFAULT_CROSS_PROB
      Specified by:
      setCrossOverProbs in interface CrossOverFunction
      Parameters:
      crossOverProbs - an array of doubles giving the probability of a cross occuring at any place.
      Throws:
      ChangeVetoException
    • getCrossOverProbs

      public final double[] getCrossOverProbs()
      Specified by:
      getCrossOverProbs in interface CrossOverFunction