pal.eval
Class LHCalculator.AbstractExternal

java.lang.Object
  extended by pal.eval.LHCalculator.AbstractExternal
Enclosing interface:
LHCalculator

public abstract static class LHCalculator.AbstractExternal
extends java.lang.Object


Constructor Summary
LHCalculator.AbstractExternal()
           
 
Method Summary
protected abstract  void calculateCategoryPatternProbabilities(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore, double[][] categoryPatternLogLikelihoodStore)
           
protected abstract  void calculateCategoryPatternProbabilities(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, double[][] categoryPatternLikelihoodStore)
           
 SiteDetails calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
           
 SiteDetails calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

LHCalculator.AbstractExternal

public LHCalculator.AbstractExternal()
Method Detail

calculateSiteDetailsUnrooted

public final SiteDetails calculateSiteDetailsUnrooted(double distance,
                                                      SubstitutionModel model,
                                                      PatternInfo centerPattern,
                                                      ConditionalProbabilityStore leftFlatConditionalProbabilities,
                                                      ConditionalProbabilityStore rightFlatConditionalProbabilities,
                                                      ConditionalProbabilityStore tempStore)

calculateSiteDetailsRooted

public final SiteDetails calculateSiteDetailsRooted(SubstitutionModel model,
                                                    PatternInfo centerPattern,
                                                    ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                                    ConditionalProbabilityStore rightConditionalProbabilitiesStore)

calculateCategoryPatternProbabilities

protected abstract void calculateCategoryPatternProbabilities(double distance,
                                                              SubstitutionModel model,
                                                              PatternInfo centerPattern,
                                                              ConditionalProbabilityStore leftFlatConditionalProbabilities,
                                                              ConditionalProbabilityStore rightFlatConditionalProbabilities,
                                                              ConditionalProbabilityStore tempStore,
                                                              double[][] categoryPatternLogLikelihoodStore)

calculateCategoryPatternProbabilities

protected abstract void calculateCategoryPatternProbabilities(SubstitutionModel model,
                                                              PatternInfo centerPattern,
                                                              ConditionalProbabilityStore leftConditionalProbabilities,
                                                              ConditionalProbabilityStore rightConditionalProbabilities,
                                                              double[][] categoryPatternLikelihoodStore)