Package pal.eval
Class SiteDetails.Utils
- java.lang.Object
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- pal.eval.SiteDetails.Utils
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- Enclosing interface:
- SiteDetails
public static final class SiteDetails.Utils extends java.lang.Object
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Constructor Summary
Constructors Constructor Description Utils()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static SiteDetails
create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
Create a Postriors object with no related substitution modelstatic SiteDetails
create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
Create a Postriors object
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Method Detail
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create
public static final SiteDetails create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
Create a Postriors object- Parameters:
categoryPatternConditionalProbabilities
- An array arranged [category][pattern] that holds the conditional probabilities for each category at each siteisLoggedConditionals
- should be true if the conditional probabilities are stored as logged values, false if notmodel
- the related substitution modelsnumberOfPatterns
- the number of patternssitePatternMatchup
- an array that identifies what pattern is to used at which sitenumberOfSites
- the number of sitessiteLikelihoods
- the site likelihood (unlogged) at each site- Returns:
- an appropriate Posteriors object
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create
public static final SiteDetails create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
Create a Postriors object with no related substitution model- Parameters:
categoryPatternConditionalProbabilities
- An array arranged [category][pattern] that holds the conditional probabilities for each category at each siteisLoggedConditionals
- should be true if the conditional probabilities are stored as logged values, false if notnumberOfPatterns
- the number of patternssitePatternMatchup
- an array that identifies what pattern is to used at which sitenumberOfSites
- the number of sitessiteLikelihoods
- the site likelihood (unlogged) at each site- Returns:
- an appropriate Posteriors object
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