pal.eval

Class SimpleUnconstrainedLikelihoodModel.InternalImpl

java.lang.Object

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

Constructors

Constructor and Description
SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal base, SubstitutionModel model)

Method Summary

Methods

Modifier and Type	Method and Description
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