pal.eval
Class LikelihoodSummary

java.lang.Object
  extended by pal.eval.LikelihoodSummary
All Implemented Interfaces:
java.io.Serializable

public class LikelihoodSummary
extends java.lang.Object
implements java.io.Serializable

See Also:
Serialized Form

Constructor Summary
LikelihoodSummary(DataType dt, double overallLogLikelihood, double[] categoryProbabilities, double[][] individualLikelihoods, int[] sitePatternMatchup)
           
 
Method Summary
 int[] generateCategoryRanking(int site)
           
 int[][] generateCategoryRankings()
           
 double[] generateSiteLikelihoods(int site)
           
 double[] generateSitePosteriors(int site)
           
 double getOverallLogLikelihood()
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

LikelihoodSummary

public LikelihoodSummary(DataType dt,
                         double overallLogLikelihood,
                         double[] categoryProbabilities,
                         double[][] individualLikelihoods,
                         int[] sitePatternMatchup)
Parameters:
dt - The data type used (for reference)
overallLogLikelihood - (the overall log likelihood found)
categoryProbabilities - (the probabilities of each category ([1] if not separate categories)
individualLikelihoods - The individual likelihoods of each pattern/category (organised [site][category])
sitePatternMatchup - for each site indicates which is the related pattern (it is assumed categoryProbabilities given with regard to patterns, if not sitePatternMatchup should contain {0,1,2, ... numberOfSites-1)
Method Detail

getOverallLogLikelihood

public final double getOverallLogLikelihood()

generateCategoryRankings

public final int[][] generateCategoryRankings()

generateSiteLikelihoods

public final double[] generateSiteLikelihoods(int site)

generateSitePosteriors

public final double[] generateSitePosteriors(int site)

generateCategoryRanking

public final int[] generateCategoryRanking(int site)

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object