pal.eval
Class SiteDetails.Utils

java.lang.Object
  extended by pal.eval.SiteDetails.Utils
Enclosing interface:
SiteDetails

public static final class SiteDetails.Utils
extends java.lang.Object


Constructor Summary
SiteDetails.Utils()
           
 
Method Summary
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

SiteDetails.Utils

public SiteDetails.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