pal.eval
public static interface LHCalculator.External extends java.io.Serializable
Modifier and Type | Method and Description |
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void |
calculateExtended(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
void |
calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
ConditionalProbabilityStore resultStore) |
double |
calculateLogLikelihood(double distance,
SubstitutionModel model,
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(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
Calculate the likelihood given two sub trees (left, right) and their extended likeihood probabilities
|
double |
calculateLogLikelihoodSingle(SubstitutionModel model,
int[] patternWeights,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilityStore)
Calculate the likelihood given the conditional probabilites at the root
|
void |
calculateSingleExtendedDirect(double distance,
SubstitutionModel model,
int numberOfPatterns,
ConditionalProbabilityStore conditionalProbabilities)
Extend the conditionals back in time by some distance, with some model
|
void |
calculateSingleExtendedIndirect(double distance,
SubstitutionModel model,
int numberOfPatterns,
ConditionalProbabilityStore baseConditionalProbabilities,
ConditionalProbabilityStore resultConditionalProbabilities)
Extend the conditionals back in time by some distance, with some model
|
SiteDetails |
calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore)
Calculate the conditional probabilities of each pattern for each category
|
SiteDetails |
calculateSiteDetailsUnrooted(double distance,
SubstitutionModel model,
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, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities, ConditionalProbabilityStore resultStore)
distance
- model
- centerPattern
- 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, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilities)
distance
- The distance to extend bymodel
- The model to useconditionalProbabilities
- The probabilities to extendvoid calculateSingleExtendedIndirect(double distance, SubstitutionModel model, int numberOfPatterns, ConditionalProbabilityStore baseConditionalProbabilities, ConditionalProbabilityStore resultConditionalProbabilities)
distance
- The distance to extend bymodel
- The model to usebaseConditionalProbabilities
- The probabilities to extendresultConditionalProbabilities
- The probabilities to extenddouble calculateLogLikelihood(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftFlatConditionalProbabilities, ConditionalProbabilityStore rightFlatConditionalProbabilities, ConditionalProbabilityStore tempStore)
distance
- model
- centerPattern
- the pattern informationleftFlatConditionalProbabilities
- rightFlatConditionalProbabilities
- tempStore
- may be used internally to calculate likelihooddouble calculateLogLikelihood(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilities, ConditionalProbabilityStore rightConditionalProbabilities)
model
- centerPattern
- the pattern informationleftConditionalProbabilities
- rightConditionalProbabilities
- double calculateLogLikelihoodSingle(SubstitutionModel model, int[] patternWeights, int numberOfPatterns, ConditionalProbabilityStore conditionalProbabilityStore)
model
- The substitution model usedpatternWeights
- the weights of each patternnumberOfPatterns
- the number of patternsconditionalProbabilities
- The conditionalsSiteDetails calculateSiteDetailsRooted(SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore)
model
- centerPattern
- the pattern informationleftConditionalProbabilities
- rightConditionalProbabilities
- categoryPatternLogLikelihoodStore
- 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 weightsSiteDetails calculateSiteDetailsUnrooted(double distance, SubstitutionModel model, PatternInfo centerPattern, ConditionalProbabilityStore leftConditionalProbabilitiesStore, ConditionalProbabilityStore rightConditionalProbabilitiesStore, ConditionalProbabilityStore tempStore)
distance
- The distance between the two nodesmodel
- centerPattern
- the pattern informationleftConditionalProbabilities
- rightConditionalProbabilities
- categoryPatternLogLikelihoodStore
- 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