com.milaboratory.core.mutations.generator

Class GenericNucleotideMutationModel

java.lang.Object

com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel

All Implemented Interfaces:

NucleotideMutationModel, Serializable

public final class GenericNucleotideMutationModel
extends Object
implements NucleotideMutationModel, Serializable

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
GenericNucleotideMutationModel(SubstitutionModel substitutionModel, double deletionProbability, double insertionProbability)
GenericNucleotideMutationModel(SubstitutionModel substitutionModel, double deletionProbability, double insertionProbability, long seed)

Method Summary

Methods

Modifier and Type	Method and Description
NucleotideMutationModel	clone() Clones only parameters, the state is generated randomly.
int	generateMutation(int position, int inputLetter)
GenericNucleotideMutationModel	multiplyProbabilities(double factor)
void	reseed(long seed)

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenericNucleotideMutationModel

public GenericNucleotideMutationModel(SubstitutionModel substitutionModel,
                              double deletionProbability,
                              double insertionProbability)

GenericNucleotideMutationModel

public GenericNucleotideMutationModel(SubstitutionModel substitutionModel,
                              double deletionProbability,
                              double insertionProbability,
                              long seed)

Method Detail

generateMutation

public int generateMutation(int position,
                   int inputLetter)

Specified by:

generateMutation in interface NucleotideMutationModel

multiplyProbabilities

public GenericNucleotideMutationModel multiplyProbabilities(double factor)

Specified by:

multiplyProbabilities in interface NucleotideMutationModel

reseed

public void reseed(long seed)

Specified by:

reseed in interface NucleotideMutationModel

clone

public NucleotideMutationModel clone()

Description copied from interface: NucleotideMutationModel

Clones only parameters, the state is generated randomly. Use NucleotideMutationModel.reseed(long) to obtain the same sequence of mutations.

Specified by:

clone in interface NucleotideMutationModel

Overrides:

clone in class Object

Returns:

copy of this mutation model