Package pal.eval

Class SiteDetails.Utils

  • Enclosing interface:
    SiteDetails
    public static final class SiteDetails.Utils
extends java.lang.Object

    • Constructor Summary

      Constructors 
      Constructor Description
      Utils()  

    • 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 model
      static SiteDetails create​(double[][] categoryPatternConditionalProbabilities, boolean isLoggedConditionals, SubstitutionModel model, int numberOfPatterns, int[] sitePatternMatchup, int numberOfSites, double[] siteLikelihoods)
      Create a Postriors object

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • Utils

        public Utils()

    • Method Detail

      • 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 site
        isLoggedConditionals - should be true if the conditional probabilities are stored as logged values, false if not
        model - the related substitution models
        numberOfPatterns - the number of patterns
        sitePatternMatchup - an array that identifies what pattern is to used at which site
        numberOfSites - the number of sites
        siteLikelihoods - 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 site
        isLoggedConditionals - should be true if the conditional probabilities are stored as logged values, false if not
        numberOfPatterns - the number of patterns
        sitePatternMatchup - an array that identifies what pattern is to used at which site
        numberOfSites - the number of sites
        siteLikelihoods - the site likelihood (unlogged) at each site
        Returns:
        an appropriate Posteriors object