Package pal.substmodel
Class SequenceSimulator
java.lang.Object
pal.substmodel.SequenceSimulator
-
Constructor Summary
ConstructorsConstructorDescriptionSequenceSimulator
(SubstitutionModel model, int sequenceLength, boolean stochasticDistribution) A constructor (with no provided random number generator - a fresh one is created)SequenceSimulator
(SubstitutionModel model, int sequenceLength, MersenneTwisterFast random, boolean stochasticDistribution) A constructor (with no provided random number generator - a fresh one is created) -
Method Summary
Modifier and TypeMethodDescriptionint[]
int[]
getSimulated
(int[] startingSequence, double distance) int[]
void
resetSiteCategoryDistribution
(boolean stochasticDistribution) Reassigns model classes to each site (a site belongs to a particular class/category of the model)void
resetSiteCategoryDistribution
(double[][] posteriorCategoryDistribution) void
resetSiteCategoryDistribution
(double[][] posteriorCategoryDistribution, int[] baseSiteCategories) void
resetSiteCategoryDistribution
(double[][] posteriorCategoryDistribution, SequenceSimulator base) void
resetSiteCategoryDistribution
(double[] categoryDistribution, boolean stochasticDistribution) void
simulate
(int[] startingSequence, double distance, int[] endingSequenceStore)
-
Constructor Details
-
SequenceSimulator
public SequenceSimulator(SubstitutionModel model, int sequenceLength, boolean stochasticDistribution) A constructor (with no provided random number generator - a fresh one is created)- Parameters:
model
- The substitution model used for simulationsequenceLength
- The length of all sequences generated by this simulator
-
SequenceSimulator
public SequenceSimulator(SubstitutionModel model, int sequenceLength, MersenneTwisterFast random, boolean stochasticDistribution) A constructor (with no provided random number generator - a fresh one is created)- Parameters:
model
- The substitution model used for simulationsequenceLength
- The length of all sequences generated by this simulatorrandom
- A random number generator
-
-
Method Details
-
resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(boolean stochasticDistribution) Reassigns model classes to each site (a site belongs to a particular class/category of the model) -
resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[] categoryDistribution, boolean stochasticDistribution) -
resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution) -
getSiteCategoryDistribution
public int[] getSiteCategoryDistribution() -
resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution, SequenceSimulator base) -
resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution, int[] baseSiteCategories) -
simulate
public void simulate(int[] startingSequence, double distance, int[] endingSequenceStore) -
getSimulated
public int[] getSimulated(int[] startingSequence, double distance) -
generateRoot
public int[] generateRoot()
-