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 Description

InternalImpl(LHCalculator.Internal base, SubstitutionModel model)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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

InternalImpl

public 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

Class SimpleUnconstrainedLikelihoodModel.InternalImpl

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

InternalImpl

Method Detail

calculateFlat

calculateExtended