Enclosing interface:

LHCalculator
```
public static interface LHCalculator.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, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)`
`ConditionalProbabilityStore`	`calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)`	calculate flat probability information (not extended over a branch).
`ConditionalProbabilityStore`	`calculatePostExtendedFlat(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, boolean modelChangedSinceLastCall)`

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,
                                              SubstitutionModel model,
                                              PatternInfo centerPattern,
                                              ConditionalProbabilityStore leftConditionalProbabilities,
                                              ConditionalProbabilityStore rightConditionalProbabilities,
                                              boolean modelChangedSinceLastCall)

Parameters:: distance -; model -; centerPattern - the pattern information; leftConditionalProbabilities -; rightConditionalProbabilities -; modelChangedSinceLastCall - this should be true if the substituion model has altered since the last call to this method on this particular object, false otherwise
Returns:: resulting conditional probabilities

calculatePostExtendedFlat

ConditionalProbabilityStore calculatePostExtendedFlat(double distance,
                                                      SubstitutionModel model,
                                                      PatternInfo centerPattern,
                                                      ConditionalProbabilityStore leftConditionalProbabilities,
                                                      ConditionalProbabilityStore rightConditionalProbabilities,
                                                      boolean modelChangedSinceLastCall)

Interface LHCalculator.Internal

Method Summary

Method Detail

calculateFlat

calculateExtended

calculatePostExtendedFlat