Package pal.eval
Class SiteDetails.Utils
java.lang.Object
pal.eval.SiteDetails.Utils
- Enclosing interface:
- SiteDetails
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final SiteDetails
create
(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods) Create a Postriors object with no related substitution modelstatic final SiteDetails
create
(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods) Create a Postriors object
-
Constructor Details
-
Utils
public Utils()
-
-
Method Details
-
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
-
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
-