pal.substmodel
Class SequenceSimulator
java.lang.Object
pal.substmodel.SequenceSimulator
public class SequenceSimulator
- extends java.lang.Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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()