pal.eval

Class SiteDetails.Utils

java.lang.Object

pal.eval.SiteDetails.Utils

Enclosing interface:

SiteDetails

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

Constructor Summary

Constructors

Constructor and Description
SiteDetails.Utils()

Method Summary

Methods

Modifier and Type	Method and 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

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