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

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

Method Detail

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 cases; rightConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
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:: patternLookup -; numberOfPatterns -; leftConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases; rightConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
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 info; leftConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases; rightConditionalProbabilityProbabilties - Implementations should be allowed to overwrite in certain cases
Returns:: true if result build on cached information

Interface MolecularClockLikelihoodModel.Internal

Method Summary

Method Detail

calculateExtendedConditionals

calculatePostExtendedFlatConditionals

calculateAscendentExtendedConditionals

calculateAscendentFlatConditionals

calculateFlatConditionals