Class SRDTGlobalClockModel

Method Details

• getRateModelSummary

  public String getRateModelSummary()

  Specified by:

  getRateModelSummary in interface ConstraintModel

• getGlobalClockConstraintGrouping

  public ConstraintModel.GroupManager getGlobalClockConstraintGrouping(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 String[][] getCladeConstraints(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()

• setSubstitutionRate

  public void setSubstitutionRate(double rate)

• getGlobalParameterAccess

  public NeoParameterized getGlobalParameterAccess()

  Specified by:

  getGlobalParameterAccess in interface ConstraintModel

• getLeafBaseHeight

  public double getLeafBaseHeight(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(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 ConstraintModel.GroupManager

  Specified by:

  getExpectedSubstitutionHeight in interface MolecularClockLikelihoodModel.HeightConverter

• getExpectedSubstitutionDistance

  public double getExpectedSubstitutionDistance(double lowerBaseHeight, double upperBaseHeight)

  Specified by:

  getExpectedSubstitutionDistance in interface MolecularClockLikelihoodModel.HeightConverter

• getNumberOfParameters

  public int getNumberOfParameters()

  Description copied from interface: NeoParameterized

  get number of parameters

  Specified by:

  getNumberOfParameters in interface NeoParameterized

  Returns:

  number of parameters

• setParameters

  public void setParameters(double[] parameters, int startIndex)

  Description copied from interface: NeoParameterized

  set model parameter

  Specified by:

  setParameters in interface NeoParameterized

  Parameters:

  parameters - the array holding the parameters

  startIndex - the index into the array that the related parameters start at

• getParameters

  public void getParameters(double[] store, int startIndex)

  Description copied from interface: NeoParameterized

  get model parameter

  Specified by:

  getParameters in interface NeoParameterized

  startIndex - the index into the array that the related parameters start at

• getLowerLimit

  public double getLowerLimit(int n)

  Description copied from interface: NeoParameterized

  get lower parameter limit

  Specified by:

  getLowerLimit in interface NeoParameterized

  Parameters:

  n - parameter number

  Returns:

  lower bound

• getUpperLimit

  public double getUpperLimit(int n)

  Description copied from interface: NeoParameterized

  get upper parameter limit

  Specified by:

  getUpperLimit in interface NeoParameterized

  Parameters:

  n - parameter number

  Returns:

  upper bound

• getDefaultValues

  public void getDefaultValues(double[] store, int startIndex)

  Description copied from interface: NeoParameterized

  get default value parameter values

  Specified by:

  getDefaultValues in interface NeoParameterized