Package pal.substmodel
Class SequenceSimulator
- java.lang.Object
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- pal.substmodel.SequenceSimulator
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public class SequenceSimulator extends java.lang.Object
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Constructor Summary
Constructors Constructor Description SequenceSimulator(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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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)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)
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Constructor Detail
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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
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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
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Method Detail
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resetSiteCategoryDistribution
public 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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resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[] categoryDistribution, boolean stochasticDistribution)
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resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution)
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getSiteCategoryDistribution
public int[] getSiteCategoryDistribution()
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resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution, SequenceSimulator base)
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resetSiteCategoryDistribution
public void resetSiteCategoryDistribution(double[][] posteriorCategoryDistribution, int[] baseSiteCategories)
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simulate
public void simulate(int[] startingSequence, double distance, int[] endingSequenceStore)
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getSimulated
public int[] getSimulated(int[] startingSequence, double distance)
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generateRoot
public int[] generateRoot()
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