Package pal.eval
Interface MolecularClockLikelihoodModel.Internal
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- Enclosing interface:
- MolecularClockLikelihoodModel
public static interface MolecularClockLikelihoodModel.Internal
The Internal calculator may maintain state and is approapriate permanent attachment to internal nodes of the tree structure
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description ConditionalProbabilityStore
calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
ConditionalProbabilityStore
calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
ConditionalProbabilityStore
calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
ConditionalProbabilityStore
calculateFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
ConditionalProbabilityStore
calculatePostExtendedFlatConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
Extends left and right conditionals by type and then calculates flat conditionals
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Method Detail
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calculateExtendedConditionals
ConditionalProbabilityStore calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
- Parameters:
patternLookup
-numberOfPatterns
-leftConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain cases- Returns:
- true if result build on cached information
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calculatePostExtendedFlatConditionals
ConditionalProbabilityStore calculatePostExtendedFlatConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
Extends left and right conditionals by type and then calculates flat conditionals- Parameters:
patternLookup
-numberOfPatterns
-leftConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain cases- Returns:
- true if result build on cached information
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calculateAscendentExtendedConditionals
ConditionalProbabilityStore calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
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calculateAscendentFlatConditionals
ConditionalProbabilityStore calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties)
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calculateFlatConditionals
ConditionalProbabilityStore calculateFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties)
- Parameters:
centerPattern
- the center pattern infoleftConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain cases- Returns:
- true if result build on cached information
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