pal.treesearch
Class FixedSRDTGlobalClockModel
java.lang.Object
pal.treesearch.FixedSRDTGlobalClockModel
- All Implemented Interfaces:
- MolecularClockLikelihoodModel.HeightConverter, ConstraintModel, ConstraintModel.GroupManager
public class FixedSRDTGlobalClockModel
- extends java.lang.Object
- implements ConstraintModel, ConstraintModel.GroupManager, MolecularClockLikelihoodModel.HeightConverter
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FixedSRDTGlobalClockModel
public FixedSRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double rate)
getRateModelSummary
public java.lang.String getRateModelSummary()
- Specified by:
getRateModelSummary
in interface ConstraintModel
getGlobalClockConstraintGrouping
public ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
- Description copied from interface:
ConstraintModel
- Enquire about the clock constraint grouping of the leaf
- Specified by:
getGlobalClockConstraintGrouping
in interface ConstraintModel
- Returns:
- the grouping of the leaf, or null if outside the leaf is unconstrained (free)
getCladeConstraints
public java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
- Description copied from interface:
ConstraintModel
- Obtain the permanent clade sets. That is, when randomly building the tree, and when tree searching, what labels must always
form a clade.
- Specified by:
getCladeConstraints
in interface ConstraintModel
- Parameters:
allLabelSet
- The set of all leaf labels in the tree
- Returns:
- An array of string arrays dividing up the label set
createNewFreeLeaf
public UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup,
int numberOfPatterns)
- Specified by:
createNewFreeLeaf
in interface ConstraintModel
createNewFreeExternal
public UnconstrainedLikelihoodModel.External createNewFreeExternal()
- Specified by:
createNewFreeExternal
in interface ConstraintModel
createNewFreeInternal
public UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
- Specified by:
createNewFreeInternal
in interface ConstraintModel
createAppropriateConditionalProbabilityStore
public ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
- Specified by:
createAppropriateConditionalProbabilityStore
in interface ConstraintModel
getSubstitutionRate
public double getSubstitutionRate()
getGlobalParameterAccess
public NeoParameterized getGlobalParameterAccess()
- Specified by:
getGlobalParameterAccess
in interface ConstraintModel
getLeafBaseHeight
public double getLeafBaseHeight(java.lang.String leafLabel)
- Specified by:
getLeafBaseHeight
in interface ConstraintModel.GroupManager
getBaseHeight
public double getBaseHeight(double originalExpectSubstitutionHeight)
- Specified by:
getBaseHeight
in interface ConstraintModel.GroupManager
getBaseHeightUnits
public int getBaseHeightUnits()
- Specified by:
getBaseHeightUnits
in interface ConstraintModel.GroupManager
initialiseParameters
public void initialiseParameters(java.lang.String[] leafNames,
double[] leafHeights)
- Specified by:
initialiseParameters
in interface ConstraintModel.GroupManager
getAllGroupRelatedParameterAccess
public NeoParameterized getAllGroupRelatedParameterAccess()
- Specified by:
getAllGroupRelatedParameterAccess
in interface ConstraintModel.GroupManager
getPrimaryGroupRelatedParameterAccess
public NeoParameterized getPrimaryGroupRelatedParameterAccess()
- Specified by:
getPrimaryGroupRelatedParameterAccess
in interface ConstraintModel.GroupManager
getSecondaryGroupRelatedParameterAccess
public NeoParameterized getSecondaryGroupRelatedParameterAccess()
- Specified by:
getSecondaryGroupRelatedParameterAccess
in interface ConstraintModel.GroupManager
createNewClockLeaf
public MolecularClockLikelihoodModel.Leaf createNewClockLeaf(PatternInfo pattern,
int[] patternStateMatchup)
- Specified by:
createNewClockLeaf
in interface ConstraintModel.GroupManager
createNewClockExternal
public MolecularClockLikelihoodModel.External createNewClockExternal()
- Specified by:
createNewClockExternal
in interface ConstraintModel.GroupManager
createNewClockInternal
public MolecularClockLikelihoodModel.Internal createNewClockInternal()
- Specified by:
createNewClockInternal
in interface ConstraintModel.GroupManager
getExpectedSubstitutionHeight
public double getExpectedSubstitutionHeight(double baseHeight)
- Specified by:
getExpectedSubstitutionHeight
in interface MolecularClockLikelihoodModel.HeightConverter
- Specified by:
getExpectedSubstitutionHeight
in interface ConstraintModel.GroupManager
getExpectedSubstitutionDistance
public double getExpectedSubstitutionDistance(double lowerBaseHeight,
double upperBaseHeight)
- Specified by:
getExpectedSubstitutionDistance
in interface MolecularClockLikelihoodModel.HeightConverter