pal.eval
public static final class SimpleUnconstrainedLikelihoodModel.InternalImpl extends java.lang.Object implements UnconstrainedLikelihoodModel.Internal
Constructor and Description |
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SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal base,
SubstitutionModel model) |
Modifier and Type | Method and Description |
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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).
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public SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal base, SubstitutionModel model)
public ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
UnconstrainedLikelihoodModel.Internal
calculateFlat
in interface UnconstrainedLikelihoodModel.Internal
centerPattern
- the pattern informationleftConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities
- Implementations should be allowed to overwrite in certain casespublic ConditionalProbabilityStore calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
calculateExtended
in interface UnconstrainedLikelihoodModel.Internal
distance
- The evolutionary distancecenterPattern
- the pattern informationleftConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities
- Implementations should be allowed to overwrite in certain cases