Package pal.eval
Interface MolecularClockLikelihoodModel.Internal
- 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
-
Method Summary
Modifier and TypeMethodDescriptioncalculateAscendentExtendedConditionals
(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) calculateAscendentFlatConditionals
(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) calculateExtendedConditionals
(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) calculateFlatConditionals
(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) calculatePostExtendedFlatConditionals
(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) Extends left and right conditionals by type and then calculates flat conditionals
-
Method Details
-
calculateExtendedConditionals
ConditionalProbabilityStore calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilityProbabilties, ConditionalProbabilityStore rightConditionalProbabilityProbabilties) - Parameters:
leftConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casespatternLookup
-numberOfPatterns
-- Returns:
- true if result build on cached information
-
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:
leftConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilityProbabilties
- Implementations should be allowed to overwrite in certain casespatternLookup
-numberOfPatterns
-- Returns:
- true if result build on cached information
-
calculateAscendentExtendedConditionals
ConditionalProbabilityStore calculateAscendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) -
calculateAscendentFlatConditionals
ConditionalProbabilityStore calculateAscendentFlatConditionals(PatternInfo centerPattern, ConditionalProbabilityStore ascenedentConditionalProbabilityProbabilties, ConditionalProbabilityStore otherConditionalProbabilityProbabilties) -
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
-