pal.eval
Interface MolecularClockLikelihoodModel.External

Enclosing interface:
MolecularClockLikelihoodModel

public static interface MolecularClockLikelihoodModel.External

The External calculator does not maintain any state and is approapriate for calculation where a store is provided


Method Summary
 void calculateExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
           
 void calculateFlatConditionals(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore resultConditionalProbabilitiesStore)
           
 double calculateLogLikelihood(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
          Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
 double calculateLogLikelihoodNonRoot(double nodeHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilitiesStore, ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
          Calculate the likelihood given a non root node
 double calculateLogLikelihoodSingle(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore conditionalProbabilitiesStore)
           
 void calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties)
           
 void calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties, ConditionalProbabilityStore resultConditionalProbabilityProbabilties)
           
 void calculateSingleDescendentExtendedConditionals(double topBaseHeight, double bottomBaseHeight, PatternInfo centerPattern, ConditionalProbabilityStore descendentConditionalProbabilities)
           
 SiteDetails calculateSiteDetails(double rootHeight, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
           
 

Method Detail

calculateSingleDescendentExtendedConditionals

void calculateSingleDescendentExtendedConditionals(double topBaseHeight,
                                                   double bottomBaseHeight,
                                                   PatternInfo centerPattern,
                                                   ConditionalProbabilityStore descendentConditionalProbabilities)

calculateSingleAscendentExtendedConditionalsDirect

void calculateSingleAscendentExtendedConditionalsDirect(double topBaseHeight,
                                                        double bottomBaseHeight,
                                                        PatternInfo centerPattern,
                                                        ConditionalProbabilityStore ascendentConditionalProbabilityProbabilties)

calculateSingleAscendentExtendedConditionalsIndirect

void calculateSingleAscendentExtendedConditionalsIndirect(double topBaseHeight,
                                                          double bottomBaseHeight,
                                                          PatternInfo centerPattern,
                                                          ConditionalProbabilityStore baseAscendentConditionalProbabilityProbabilties,
                                                          ConditionalProbabilityStore resultConditionalProbabilityProbabilties)

calculateExtendedConditionals

void calculateExtendedConditionals(double topBaseHeight,
                                   double bottomBaseHeight,
                                   PatternInfo centerPattern,
                                   ConditionalProbabilityStore leftConditionalProbabilities,
                                   ConditionalProbabilityStore rightConditionalProbabilities,
                                   ConditionalProbabilityStore resultStore)
Parameters:
distance -
model -
patternLookup -
numberOfPatterns -
leftConditionalProbabilityProbabilties - Implementations must not overwrite or change
rightConditionalProbabilityProbabilties - Implementations must not overwrite or change
resultStore - Where to stick the created categoryPatternState information

calculateLogLikelihood

double calculateLogLikelihood(double rootHeight,
                              PatternInfo centerPattern,
                              ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                              ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities

Parameters:
rootHeight - the height of the likelihood calculation
leftConditionalProbabilities - Assumed to be extended to the rootHeight
rightConditionalProbabilities - Assumed to be extended to the rootHeight
Returns:
the Log likelihood

calculateLogLikelihoodNonRoot

double calculateLogLikelihoodNonRoot(double nodeHeight,
                                     PatternInfo centerPattern,
                                     ConditionalProbabilityStore ascendentConditionalProbabilitiesStore,
                                     ConditionalProbabilityStore descendentConditionalProbabilitiesStore)
Calculate the likelihood given a non root node

Parameters:
nodeHeight - the height of node doing the likelihood calculation
centerPatter - assumed left is ascendent component, right is descendent
ascendentConditionalProbabilities - Assumed to be extended (downwards) to the nodeHeight
descendentConditionalProbabilities - Assumed to be extended (upwards) to the nodeHeight
Returns:
the Log likelihood

calculateLogLikelihoodSingle

double calculateLogLikelihoodSingle(double rootHeight,
                                    PatternInfo centerPattern,
                                    ConditionalProbabilityStore conditionalProbabilitiesStore)

calculateSiteDetails

SiteDetails calculateSiteDetails(double rootHeight,
                                 PatternInfo centerPattern,
                                 ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                                 ConditionalProbabilityStore rightConditionalProbabilitiesStore)

calculateFlatConditionals

void calculateFlatConditionals(double rootHeight,
                               PatternInfo centerPattern,
                               ConditionalProbabilityStore leftConditionalProbabilitiesStore,
                               ConditionalProbabilityStore rightConditionalProbabilitiesStore,
                               ConditionalProbabilityStore resultConditionalProbabilitiesStore)