pal.eval
Class LHCalculator.AbstractExternal
java.lang.Object
pal.eval.LHCalculator.AbstractExternal
- Enclosing interface:
- LHCalculator
public abstract static class LHCalculator.AbstractExternal
- extends java.lang.Object
Method Summary |
protected abstract void |
calculateCategoryPatternProbabilities(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore,
double[][] categoryPatternLogLikelihoodStore)
|
protected abstract void |
calculateCategoryPatternProbabilities(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
double[][] categoryPatternLikelihoodStore)
|
SiteDetails |
calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore)
|
SiteDetails |
calculateSiteDetailsUnrooted(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
LHCalculator.AbstractExternal
public LHCalculator.AbstractExternal()
calculateSiteDetailsUnrooted
public final SiteDetails calculateSiteDetailsUnrooted(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore)
calculateSiteDetailsRooted
public final SiteDetails calculateSiteDetailsRooted(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilitiesStore,
ConditionalProbabilityStore rightConditionalProbabilitiesStore)
calculateCategoryPatternProbabilities
protected abstract void calculateCategoryPatternProbabilities(double distance,
SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftFlatConditionalProbabilities,
ConditionalProbabilityStore rightFlatConditionalProbabilities,
ConditionalProbabilityStore tempStore,
double[][] categoryPatternLogLikelihoodStore)
calculateCategoryPatternProbabilities
protected abstract void calculateCategoryPatternProbabilities(SubstitutionModel model,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities,
double[][] categoryPatternLikelihoodStore)