pal.eval
public static final class SiteDetails.Utils extends java.lang.Object
Constructor and Description |
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SiteDetails.Utils() |
Modifier and Type | Method and Description |
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static SiteDetails |
create(double[][] categoryPatternConditionalProbabilities,
boolean isLoggedConditionals,
int numberOfPatterns,
int[] sitePatternMatchup,
int numberOfSites,
double[] siteLikelihoods)
Create a Postriors object with no related substitution model
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static SiteDetails |
create(double[][] categoryPatternConditionalProbabilities,
boolean isLoggedConditionals,
SubstitutionModel model,
int numberOfPatterns,
int[] sitePatternMatchup,
int numberOfSites,
double[] siteLikelihoods)
Create a Postriors object
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public static final SiteDetails create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
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 sitepublic static final SiteDetails create(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
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