Package 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 Object
implements UnconstrainedLikelihoodModel.Internal
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncalculateExtended
(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculateFlat
(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities) calculate flat probability information (not extended over a branch).
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Constructor Details
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InternalImpl
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Method Details
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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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