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
 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