Package pal.substmodel

Class AbstractRateMatrix

java.lang.Object
pal.substmodel.AbstractRateMatrix
All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix
Direct Known Subclasses:
AminoAcidModel, CodonModel, NucleotideModel, TwoStateModel
public abstract class AbstractRateMatrix extends Object implements RateMatrix, ExternalParameterListener
abstract base class for all rate matrices
Version:
$Id: AbstractRateMatrix.java,v 1.30 2004/04/05 05:14:39 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Field Details

  • Constructor Details

    • AbstractRateMatrix

      protected AbstractRateMatrix(int dim)

  • Method Details

    • getTypeID

      public int getTypeID()
      get numerical code describing the data type
      Specified by:
      getTypeID in interface RateMatrix
      Returns:
      integer code identifying a data type

    • getModelID

      public abstract int getModelID()
      get numerical code describing the model type
      Specified by:
      getModelID in interface RateMatrix
      Returns:
      integer code identifying a substitution model

    • getDimension

      public int getDimension()
      Specified by:
      getDimension in interface RateMatrix
      Returns:
      the dimension of this rate matrix.

    • getEquilibriumFrequencies

      public double[] getEquilibriumFrequencies()
      Specified by:
      getEquilibriumFrequencies in interface RateMatrix
      Returns:
      stationary frequencies (sum = 1.0)

    • getEquilibriumFrequency

      public double getEquilibriumFrequency(int i)
      Specified by:
      getEquilibriumFrequency in interface RateMatrix
      Returns:
      stationary frequencie (sum = 1.0) for ith state

    • getDataType

      public DataType getDataType()
      Description copied from interface: RateMatrix
      Get the data type of this rate matrix
      Specified by:
      getDataType in interface RateMatrix

    • setDataType

      protected final void setDataType(DataType dt)

    • getRelativeRates

      public double[][] getRelativeRates()
      Specified by:
      getRelativeRates in interface RateMatrix
      Returns:
      rate matrix (transition: from 1st index to 2nd index)

    • getTransitionProbability

      public double getTransitionProbability(int fromState, int toState)
      Returns the probability of going from one state to another given the current distance
      Specified by:
      getTransitionProbability in interface RateMatrix
      Parameters:
      fromState - The state from which we are starting
      toState - The resulting state
      Returns:
      the probability of going from one state to another given the current distance

    • rebuild

      public final void rebuild()

    • setDistance

      public final void setDistance(double distance)
      Sets the distance (such as time/branch length) used when calculating the probabilities.
      Specified by:
      setDistance in interface RateMatrix

    • setDistanceTranspose

      public final void setDistanceTranspose(double distance)
      Sets the distance (such as time/branch length) used when calculating the probabilities.
      Specified by:
      setDistanceTranspose in interface RateMatrix

    • getTransitionProbabilities

      public final void getTransitionProbabilities(double[][] probabilityStore)
      A utility method for speed, transfers trans prob information quickly into store
      Specified by:
      getTransitionProbabilities in interface RateMatrix

    • scale

      public void scale(double scale)
      Specified by:
      scale in interface RateMatrix

    • printFrequencies

      protected void printFrequencies(PrintWriter out)

    • setFrequencies

      protected void setFrequencies(double[] f)

    • setParametersNoScale

      public double setParametersNoScale(double[] parameters)
      Specified by:
      setParametersNoScale in interface RateMatrix

    • setParameters

      public void setParameters(double[] parameters)

    • setParameter

      public final void setParameter(double value, int parameter)
      Description copied from interface: Parameterized
      set model parameter
      Specified by:
      setParameter in interface Parameterized
      Parameters:
      value - parameter value
      parameter - parameter number

    • getParameter

      public final double getParameter(int parameter)
      Description copied from interface: Parameterized
      get model parameter
      Specified by:
      getParameter in interface Parameterized
      Parameters:
      parameter - parameter number
      Returns:
      parameter value

    • rebuildRateMatrix

      protected abstract void rebuildRateMatrix(double[][] rate, double[] parameters)

    • addPalObjectListener

      public void addPalObjectListener(PalObjectListener pol)
      Description copied from interface: RateMatrix
      Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called
      Specified by:
      addPalObjectListener in interface RateMatrix

    • removePalObjectListener

      public void removePalObjectListener(PalObjectListener pol)
      Specified by:
      removePalObjectListener in interface RateMatrix

    • fireParametersChangedEvent

      protected void fireParametersChangedEvent()

    • fireParametersChangedEvent

      protected void fireParametersChangedEvent(PalObjectEvent pe)

    • updateMatrixExp

      protected void updateMatrixExp()

    • parameterChanged

      public void parameterChanged(ParameterEvent pe)
      For the external parameter interface. This can be ignored unless you want to use this Rate Matrix as an external parameter listener This method does two things.First it sets a flag indicating that rebuild method should be called the next time a setDistance method is called, and then it notifies any PalObject listeners that a parameter has changed
      Specified by:
      parameterChanged in interface ExternalParameterListener

    • clone

      public Object clone()
      Specified by:
      clone in interface RateMatrix
      Overrides:
      clone in class Object

    • getOrthogonalHints

      public OrthogonalHints getOrthogonalHints()
      Specified by:
      getOrthogonalHints in interface RateMatrix
      Returns:
      null

    • getFrequencies

      protected final double[] getFrequencies()