pal.treesearch
Interface ConstraintModel.GroupManager

All Known Implementing Classes:
FixedBSRDTGlobalClockModel, FixedSRDTGlobalClockModel, GlobalClockModel, MRDTGlobalClockModel, SRDTGlobalClockModel
Enclosing interface:
ConstraintModel

public static interface ConstraintModel.GroupManager


Method Summary
 MolecularClockLikelihoodModel.External createNewClockExternal()
           
 MolecularClockLikelihoodModel.Internal createNewClockInternal()
           
 MolecularClockLikelihoodModel.Leaf createNewClockLeaf(PatternInfo pattern, int[] patternStateMatchup)
           
 NeoParameterized getAllGroupRelatedParameterAccess()
           
 double getBaseHeight(double originalExpectSubstitutionHeight)
           
 int getBaseHeightUnits()
           
 double getExpectedSubstitutionHeight(double baseHeight)
           
 double getLeafBaseHeight(java.lang.String leafLabel)
           
 NeoParameterized getPrimaryGroupRelatedParameterAccess()
           
 NeoParameterized getSecondaryGroupRelatedParameterAccess()
           
 void initialiseParameters(java.lang.String[] leafNames, double[] leafHeights)
           
 

Method Detail

getLeafBaseHeight

double getLeafBaseHeight(java.lang.String leafLabel)

getBaseHeight

double getBaseHeight(double originalExpectSubstitutionHeight)

getExpectedSubstitutionHeight

double getExpectedSubstitutionHeight(double baseHeight)

getBaseHeightUnits

int getBaseHeightUnits()

initialiseParameters

void initialiseParameters(java.lang.String[] leafNames,
                          double[] leafHeights)

getAllGroupRelatedParameterAccess

NeoParameterized getAllGroupRelatedParameterAccess()

getPrimaryGroupRelatedParameterAccess

NeoParameterized getPrimaryGroupRelatedParameterAccess()

getSecondaryGroupRelatedParameterAccess

NeoParameterized getSecondaryGroupRelatedParameterAccess()

createNewClockLeaf

MolecularClockLikelihoodModel.Leaf createNewClockLeaf(PatternInfo pattern,
                                                      int[] patternStateMatchup)

createNewClockExternal

MolecularClockLikelihoodModel.External createNewClockExternal()

createNewClockInternal

MolecularClockLikelihoodModel.Internal createNewClockInternal()