jaga.evolve
Class BunchMutator
java.lang.Object
|
+--jaga.evolve.BunchMutator
- All Implemented Interfaces:
- GeneticOperator, java.io.Serializable
- public class BunchMutator
- extends java.lang.Object
- implements GeneticOperator
A BunchMutator can mutate bits in a genotype per bunches. For example:
10000100001000010000
may be mutated to 1000011011100001000 if the bunchsize=alignmentsize=5.
This is useful for simulated high level representation mutations when the
genotype->phenotype mapping is known.
- See Also:
- Serialized Form
Constructor Summary |
BunchMutator(int pbunchSize)
Creates new BunchMutator |
BunchMutator(int pbunchSize,
int pnrBunches)
|
BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize)
|
BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize,
int palignmentOffset)
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BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize,
int palignmentOffset,
int plockedAlignments)
|
BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize,
int palignmentOffset,
int plockedAlignments,
int globalOffset)
Complete constructor for a BunchMutator |
Method Summary |
void |
operate(Selector selector,
Population oldPopulation,
Population newPopulation,
int howMany)
method that adds genotypes to the new population by extracting some
from the old one and manipulating them in some way. |
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
BunchMutator
public BunchMutator(int pbunchSize)
- Creates new BunchMutator
BunchMutator
public BunchMutator(int pbunchSize,
int pnrBunches)
BunchMutator
public BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize)
BunchMutator
public BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize,
int palignmentOffset)
BunchMutator
public BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize,
int palignmentOffset,
int plockedAlignments)
BunchMutator
public BunchMutator(int pbunchSize,
int pnrBunches,
int palignmentSize,
int palignmentOffset,
int plockedAlignments,
int globalOffset)
- Complete constructor for a BunchMutator
- Parameters:
pbunchSize
- the size of the bunches to mutatepnrBunches
- how many bunches to mutatepalignmentSize
- the size of aligned blocks at which to start a bunchpalignmentOffset
- the offset within these blocks at which to start a bunchplockedAlignments
- the number of blocks starting from block 0 which shouldn`t be touched
operate
public void operate(Selector selector,
Population oldPopulation,
Population newPopulation,
int howMany)
- method that adds genotypes to the new population by extracting some
from the old one and manipulating them in some way.
- Specified by:
operate
in interface GeneticOperator
- Parameters:
oldPopulation
- in parameter having all the original genotypesnewPopulation
- in/out parameter where the next generation of genotypes is being builthowMany
- how many new genotypes to add to the new population
toString
public java.lang.String toString()
- Overrides:
toString
in class java.lang.Object