Package pal.eval

Class SiteDetails.Utils

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

  • Constructor Summary

    Constructors
    Constructor
    Description
    Utils()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    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
    static final 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 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 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