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