MolecularClockLikelihoodModel.HeightConverter
, NeoParameterized
, ConstraintModel
, ConstraintModel.GroupManager
public class MRDTGlobalClockModel extends java.lang.Object implements ConstraintModel, ConstraintModel.GroupManager, NeoParameterized, MolecularClockLikelihoodModel.HeightConverter
ConstraintModel.GroupManager
Constructor | Description |
---|---|
MRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel) |
|
MRDTGlobalClockModel(SampleInformation sampleInformation,
MolecularClockLikelihoodModel.Instance likelihoodModel,
double[] rateChangeTimes) |
public MRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel)
public MRDTGlobalClockModel(SampleInformation sampleInformation, MolecularClockLikelihoodModel.Instance likelihoodModel, double[] rateChangeTimes)
public java.lang.String getRateModelSummary()
getRateModelSummary
in interface ConstraintModel
public ConstraintModel.GroupManager getGlobalClockConstraintGrouping(java.lang.String[] leafLabelSet)
ConstraintModel
getGlobalClockConstraintGrouping
in interface ConstraintModel
public java.lang.String[][] getCladeConstraints(java.lang.String[] allLabelSet)
ConstraintModel
getCladeConstraints
in interface ConstraintModel
allLabelSet
- The set of all leaf labels in the treepublic UnconstrainedLikelihoodModel.Leaf createNewFreeLeaf(int[] patternStateMatchup, int numberOfPatterns)
createNewFreeLeaf
in interface ConstraintModel
public UnconstrainedLikelihoodModel.External createNewFreeExternal()
createNewFreeExternal
in interface ConstraintModel
public UnconstrainedLikelihoodModel.Internal createNewFreeInternal()
createNewFreeInternal
in interface ConstraintModel
public ConditionalProbabilityStore createAppropriateConditionalProbabilityStore(boolean isForLeaf)
createAppropriateConditionalProbabilityStore
in interface ConstraintModel
public NeoParameterized getGlobalParameterAccess()
getGlobalParameterAccess
in interface ConstraintModel
public double getLeafBaseHeight(java.lang.String leafLabel)
getLeafBaseHeight
in interface ConstraintModel.GroupManager
public double getBaseHeight(double originalExpectSubstitutionHeight)
getBaseHeight
in interface ConstraintModel.GroupManager
public int getBaseHeightUnits()
getBaseHeightUnits
in interface ConstraintModel.GroupManager
public void initialiseParameters(java.lang.String[] leafNames, double[] leafHeights)
initialiseParameters
in interface ConstraintModel.GroupManager
public NeoParameterized getAllGroupRelatedParameterAccess()
getAllGroupRelatedParameterAccess
in interface ConstraintModel.GroupManager
public NeoParameterized getPrimaryGroupRelatedParameterAccess()
getPrimaryGroupRelatedParameterAccess
in interface ConstraintModel.GroupManager
public NeoParameterized getSecondaryGroupRelatedParameterAccess()
getSecondaryGroupRelatedParameterAccess
in interface ConstraintModel.GroupManager
public MolecularClockLikelihoodModel.Leaf createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
createNewClockLeaf
in interface ConstraintModel.GroupManager
public MolecularClockLikelihoodModel.External createNewClockExternal()
createNewClockExternal
in interface ConstraintModel.GroupManager
public MolecularClockLikelihoodModel.Internal createNewClockInternal()
createNewClockInternal
in interface ConstraintModel.GroupManager
public double getExpectedSubstitutionHeight(double baseHeight)
getExpectedSubstitutionHeight
in interface ConstraintModel.GroupManager
getExpectedSubstitutionHeight
in interface MolecularClockLikelihoodModel.HeightConverter
public double getExpectedSubstitutionDistance(double lowerBaseHeight, double upperBaseHeight)
getExpectedSubstitutionDistance
in interface MolecularClockLikelihoodModel.HeightConverter
public int getNumberOfParameters()
NeoParameterized
getNumberOfParameters
in interface NeoParameterized
public void setParameters(double[] parameters, int startIndex)
NeoParameterized
setParameters
in interface NeoParameterized
parameters
- the array holding the parametersstartIndex
- the index into the array that the related parameters start atpublic void getParameters(double[] store, int startIndex)
NeoParameterized
getParameters
in interface NeoParameterized
startIndex
- the index into the array that the related parameters start atpublic double getLowerLimit(int n)
NeoParameterized
getLowerLimit
in interface NeoParameterized
n
- parameter numberpublic double getUpperLimit(int n)
NeoParameterized
getUpperLimit
in interface NeoParameterized
n
- parameter numberpublic void getDefaultValues(double[] store, int startIndex)
NeoParameterized
getDefaultValues
in interface NeoParameterized