All Known Implementing Classes:

SimpleUnconstrainedLikelihoodModel.InternalImpl

Enclosing interface:

UnconstrainedLikelihoodModel
```
public static interface UnconstrainedLikelihoodModel.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`	`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).

Method Detail

calculateFlat

ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern,
                                          ConditionalProbabilityStore leftConditionalProbabilities,
                                          ConditionalProbabilityStore rightConditionalProbabilities)

calculate flat probability information (not extended over a branch).

Parameters:: centerPattern - the pattern information; leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases; rightConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
Returns:: true if results built from cached information

calculateExtended

ConditionalProbabilityStore calculateExtended(double distance,
                                              PatternInfo centerPattern,
                                              ConditionalProbabilityStore leftConditionalProbabilities,
                                              ConditionalProbabilityStore rightConditionalProbabilities)

Parameters:: distance - The evolutionary distance; centerPattern - the pattern information; leftConditionalProbabilities - Implementations should be allowed to overwrite in certain cases; rightConditionalProbabilities - Implementations should be allowed to overwrite in certain cases
Returns:: resulting conditional probabilities

Interface UnconstrainedLikelihoodModel.Internal

Method Summary

Method Detail

calculateFlat

calculateExtended