Package pal.eval
Class SimpleUnconstrainedLikelihoodModel.InternalImpl
- java.lang.Object
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- pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
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- All Implemented Interfaces:
UnconstrainedLikelihoodModel.Internal
- Enclosing class:
- SimpleUnconstrainedLikelihoodModel
public static final class SimpleUnconstrainedLikelihoodModel.InternalImpl extends java.lang.Object implements UnconstrainedLikelihoodModel.Internal
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Constructor Summary
Constructors Constructor Description InternalImpl(LHCalculator.Internal base, SubstitutionModel model)
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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).
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Constructor Detail
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InternalImpl
public InternalImpl(LHCalculator.Internal base, SubstitutionModel model)
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Method Detail
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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 interfaceUnconstrainedLikelihoodModel.Internal
- Parameters:
centerPattern
- the pattern informationleftConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities
- Implementations should be allowed to overwrite in certain cases- Returns:
- true if results built from cached information
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calculateExtended
public ConditionalProbabilityStore calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
- Specified by:
calculateExtended
in interfaceUnconstrainedLikelihoodModel.Internal
- Parameters:
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- Returns:
- resulting conditional probabilities
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