Package pal.eval
Interface UnconstrainedLikelihoodModel.External
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- All Superinterfaces:
java.io.Serializable
- Enclosing interface:
- UnconstrainedLikelihoodModel
public static interface UnconstrainedLikelihoodModel.External extends java.io.Serializable
The External calculator does not maintain any state and is approapriate for calculation where a store is provided
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description 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 probabilitiesdouble
calculateLogLikelihood(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilitiesdouble
calculateLogLikelihoodSingle(int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the rootvoid
calculateSingleExtendedDirect(double distance, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distancevoid
calculateSingleExtendedIndirect(double distance, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distanceSiteDetails
calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the conditional probabilities of each pattern for each categorySiteDetails
calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
Calculate the conditional probabilities of each pattern for each category
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Method Detail
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calculateFlat
void calculateFlat(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
- Parameters:
centerPattern
- the pattern informationleftConditionalProbabilities
- Implementations must not overwrite or changerightConditionalProbabilities
- Implementations must not overwrite or changeresultStore
- Where to stick the created categoryPatternState information
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calculateExtended
void calculateExtended(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
- Parameters:
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 information
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calculateSingleExtendedDirect
void calculateSingleExtendedDirect(double distance, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distance- Parameters:
distance
- The evolutionary distance to extend bynumberOfPatterns
- the number of patternsconditionalProbabilities
- The probabilities to extend
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calculateSingleExtendedIndirect
void calculateSingleExtendedIndirect(double distance, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distance- Parameters:
distance
- The evolutionary distance to extend bynumberOfPatterns
- the number of patternsbaseConditionalProbabilities
- The probabilities to extendresultConditionalProbabilities
- The probabilities to extend
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calculateLogLikelihood
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- Parameters:
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 likelihood- Returns:
- the log likelihood
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calculateLogLikelihood
double calculateLogLikelihood(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities- Parameters:
centerPattern
- the pattern informationleftConditionalProbabilities
- The left conditional probabilitiesrightConditionalProbabilities
- The right conditional probabilities- Returns:
- the Log likelihood
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calculateLogLikelihoodSingle
double calculateLogLikelihoodSingle(int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the root- Parameters:
patternWeights
- the weights of each patternnumberOfPatterns
- the number of patterns- Returns:
- the Log likelihood
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calculateSiteDetailsRooted
SiteDetails calculateSiteDetailsRooted(PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the conditional probabilities of each pattern for each category- Parameters:
centerPattern
- the pattern informationleftConditionalProbabilitiesStore
- The left conditional probabilitiesrightConditionalProbabilitiesStore
- The right conditional probabilities
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calculateSiteDetailsUnrooted
SiteDetails calculateSiteDetailsUnrooted(double distance, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
Calculate the conditional probabilities of each pattern for each category- Parameters:
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
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