pal.eval
Class SimpleUnconstrainedLikelihoodModel.InternalImpl
java.lang.Object
pal.eval.SimpleUnconstrainedLikelihoodModel.InternalImpl
- All Implemented Interfaces:
- UnconstrainedLikelihoodModel.Internal
- Enclosing class:
- SimpleUnconstrainedLikelihoodModel
public static final class SimpleUnconstrainedLikelihoodModel.InternalImpl
- extends java.lang.Object
- implements UnconstrainedLikelihoodModel.Internal
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SimpleUnconstrainedLikelihoodModel.InternalImpl
public SimpleUnconstrainedLikelihoodModel.InternalImpl(LHCalculator.Internal base,
SubstitutionModel model)
calculateFlat
public ConditionalProbabilityStore calculateFlat(PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
- Description copied from interface:
UnconstrainedLikelihoodModel.Internal
- calculate flat probability information (not extended over a branch).
- Specified by:
calculateFlat
in interface UnconstrainedLikelihoodModel.Internal
- Parameters:
centerPattern
- the pattern informationleftConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities
- Implementations should be allowed to overwrite in certain cases
- Returns:
- true if results built from cached information
calculateExtended
public ConditionalProbabilityStore calculateExtended(double distance,
PatternInfo centerPattern,
ConditionalProbabilityStore leftConditionalProbabilities,
ConditionalProbabilityStore rightConditionalProbabilities)
- Specified by:
calculateExtended
in interface UnconstrainedLikelihoodModel.Internal
- Parameters:
distance
- The evolutionary distancecenterPattern
- the pattern informationleftConditionalProbabilities
- Implementations should be allowed to overwrite in certain casesrightConditionalProbabilities
- Implementations should be allowed to overwrite in certain cases
- Returns:
- resulting conditional probabilities