pal.eval
Class SimpleUnconstrainedLikelihoodModel.InternalImpl

java.lang.Object
  extended by pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
All Implemented Interfaces:
UnconstrainedLikelihoodModel.Internal
Enclosing class:
SimpleUnconstrainedLikelihoodModel

public static final class SimpleUnconstrainedLikelihoodModel.InternalImpl
extends java.lang.Object
implements UnconstrainedLikelihoodModel.Internal


Constructor Summary
SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal base, SubstitutionModel model)
           
 
Method Summary
 ConditionalProbabilityStore calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
           
 ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
          calculate flat probability information (not extended over a branch).
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleUnconstrainedLikelihoodModel.InternalImpl

public SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal base,
                                                       SubstitutionModel model)
Method Detail

calculateFlat

public ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern,
                                                 ConditionalProbabilityStore leftConditionalProbabilities,
                                                 ConditionalProbabilityStore rightConditionalProbabilities)
Description copied from interface: UnconstrainedLikelihoodModel.Internal
calculate flat probability information (not extended over a branch).

Specified by:
calculateFlat in interface UnconstrainedLikelihoodModel.Internal
Parameters:
centerPattern - the pattern information
leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
rightConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
Returns:
true if results built from cached information

calculateExtended

public ConditionalProbabilityStore calculateExtended(double distance,
                                                     PatternInfo centerPattern,
                                                     ConditionalProbabilityStore leftConditionalProbabilities,
                                                     ConditionalProbabilityStore rightConditionalProbabilities)
Specified by:
calculateExtended in interface UnconstrainedLikelihoodModel.Internal
Parameters:
distance - The evolutionary distance
centerPattern - the pattern information
leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
rightConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
Returns:
resulting conditional probabilities