pal.eval
public static interface UnconstrainedLikelihoodModel.External extends java.io.Serializable
Modifier and Type | Method and Description |
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void |
calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
void |
calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
double |
calculateLogLikelihood(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore)
Calculate the likelihood given two sub trees (left, right) and their flat (unextend) likeihood probabilities
|
double |
calculateLogLikelihood(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
|
double |
calculateLogLikelihoodSingle(int[] patternWeights,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the root
|
void |
calculateSingleExtendedDirect(double distance,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distance
|
void |
calculateSingleExtendedIndirect(double distance,
int numberOfPatterns,
ConditionalProbabilityStore baseConditionalProbabilities,
ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distance
|
SiteDetails |
calculateSiteDetailsRooted(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the conditional probabilities of each pattern for each category
|
SiteDetails |
calculateSiteDetailsUnrooted(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore,
ConditionalProbabilityStore tempStore)
Calculate the conditional probabilities of each pattern for each category
|
void calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
centerPattern
- the pattern informationleftConditionalProbabilities
- Implementations must not overwrite or changerightConditionalProbabilities
- Implementations must not overwrite or changeresultStore
- Where to stick the created categoryPatternState informationvoid calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
distance
- the evolutionary distancecenterPattern
- the pattern informationleftConditionalProbabilities
- Implementations must not overwrite or changerightConditionalProbabilities
- Implementations must not overwrite or changeresultStore
- Where to stick the created categoryPatternState informationvoid calculateSingleExtendedDirect(double distance, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
distance
- The evolutionary distance to extend bynumberOfPatterns
- the number of patternsconditionalProbabilities
- The probabilities to extendvoid calculateSingleExtendedIndirect(double distance, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
distance
- The evolutionary distance to extend bynumberOfPatterns
- the number of patternsbaseConditionalProbabilities
- The probabilities to extendresultConditionalProbabilities
- The probabilities to extenddouble calculateLogLikelihood(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
distance
- The evolutionary distancecenterPattern
- the pattern informationleftFlatConditionalProbabilities
- The left conditional probabilities (unextended)rightFlatConditionalProbabilities
- The right conditional probabilities (unextended)tempStore
- may be used internally to calculate likelihooddouble calculateLogLikelihood(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
centerPattern
- the pattern informationleftConditionalProbabilities
- The left conditional probabilitiesrightConditionalProbabilities
- The right conditional probabilitiesdouble calculateLogLikelihoodSingle(int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore)
patternWeights
- the weights of each patternnumberOfPatterns
- the number of patternsSiteDetails calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
centerPattern
- the pattern informationleftConditionalProbabilitiesStore
- The left conditional probabilitiesrightConditionalProbabilitiesStore
- The right conditional probabilitiesSiteDetails calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
distance
- The distance between the two nodescenterPattern
- the pattern informationleftConditionalProbabilitiesStore
- The left conditional probabilitiesrightConditionalProbabilitiesStore
- The right conditional probabilitiestempStore
- after call will hold a matrix of values in the form [cat][pattern], where [cat][pattern] represents the site probability under a particular category/class, *not* multiplied by the category probability or pattern weights