Package pal.substmodel

Class CachedRateMatrix

java.lang.Object
pal.substmodel.CachedRateMatrix
All Implemented Interfaces:
Serializable, Cloneable, NamedParameterized, PalObjectListener, Parameterized, Report, RateMatrix
public abstract class CachedRateMatrix extends Object implements RateMatrix, PalObjectListener
a cached rate matrix. This model caches transition probabilities by distance in order to increase speed of likelihood calculations for repeated calls with same/similar branch lengths.
AS OF 11 November 2003 this class has been made abstract and will be removed at a later point (as it never really helped much)
Version:
$Id: CachedRateMatrix.java,v 1.13 2003/11/13 04:05:39 matt Exp $
Author:
Alexei Drummond
See Also:

  • Constructor Details

    • CachedRateMatrix

      public CachedRateMatrix(RateMatrix rateMatrix, DoubleKeyCache cache)
      Parameters:
      model - the underlying substitution model
      cache - the caching method used

    • CachedRateMatrix

      public CachedRateMatrix(RateMatrix rateMatrix, int maxCacheSize)
      Parameters:
      model - the underlying substitution model

    • CachedRateMatrix

      public CachedRateMatrix(CachedRateMatrix cachedRateMatrix)
      Parameters:
      model - the previous cached model.

  • Method Details

    • report

      public final void report(PrintWriter out)
      Description copied from interface: Report
      print human readable report (e.g., on parameters and associated model)
      Specified by:
      report in interface Report
      Parameters:
      out - output stream

    • getTypeID

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

    • getModelID

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

    • getDimension

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

    • getEquilibriumFrequencies

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

    • getEquilibriumFrequency

      public final double getEquilibriumFrequency(int i)
      Specified by:
      getEquilibriumFrequency in interface RateMatrix
      Returns:
      stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.

    • getRelativeRates

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

    • toString

      public String toString()
      Return string representation of substitution model.
      Overrides:
      toString in class Object

    • getNumParameters

      public final int getNumParameters()
      Description copied from interface: Parameterized
      get number of parameters
      Specified by:
      getNumParameters in interface Parameterized
      Returns:
      number of parameters

    • setParameter

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

    • getParameter

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

    • setParameterSE

      public final void setParameterSE(double paramSE, int n)
      Description copied from interface: Parameterized
      set standard errors for model parameter
      Specified by:
      setParameterSE in interface Parameterized
      Parameters:
      paramSE - standard error of parameter value
      n - parameter number

    • getLowerLimit

      public final double getLowerLimit(int n)
      Description copied from interface: Parameterized
      get lower parameter limit
      Specified by:
      getLowerLimit in interface Parameterized
      Parameters:
      n - parameter number
      Returns:
      lower bound

    • getUpperLimit

      public final double getUpperLimit(int n)
      Description copied from interface: Parameterized
      get upper parameter limit
      Specified by:
      getUpperLimit in interface Parameterized
      Parameters:
      n - parameter number
      Returns:
      upper bound

    • getDefaultValue

      public final double getDefaultValue(int n)
      Description copied from interface: Parameterized
      get default value of parameter
      Specified by:
      getDefaultValue in interface Parameterized
      Parameters:
      n - parameter number
      Returns:
      default value

    • getParameterName

      public final String getParameterName(int i)
      Specified by:
      getParameterName in interface NamedParameterized
      Returns:
      a short identifier for this parameter type. Should be the same for all instances of a given class!

    • setDistance

      public final void setDistance(double k)
      set distance and corresponding computation transition probabilities
      Specified by:
      setDistance in interface RateMatrix
      Parameters:
      k - distance

    • setDistanceTranspose

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

    • getTransitionProbability

      public final double getTransitionProbability(int i, int j)
      get transition probability for the preselected model and the previously specified distance
      Specified by:
      getTransitionProbability in interface RateMatrix
      Parameters:
      i - start state
      j - end state
      Returns:
      transition probability

    • getTransitionProbabilities

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

    • clone

      public final Object clone()
      A non shallow implementation of clone()
      Specified by:
      clone in interface RateMatrix
      Overrides:
      clone in class Object

    • getDataType

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

    • getUniqueName

      public final String getUniqueName()
      Specified by:
      getUniqueName in interface RateMatrix
      Returns:
      a short unique human-readable identifier for this rate matrix.

    • structureChanged

      public void structureChanged(PalObjectEvent pe)
      Description copied from interface: PalObjectListener
      Signifies that the structure of the object has changed (for example in trees to topology has changed)
      Specified by:
      structureChanged in interface PalObjectListener

    • parametersChanged

      public void parametersChanged(PalObjectEvent pe)
      Description copied from interface: PalObjectListener
      Signifies that parametric valued governing the state of this Object have changed. Parameters don't have to be visible ones For example, in trees the branch lengths have changed.
      Specified by:
      parametersChanged in interface PalObjectListener

    • 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

    • getOrthogonalHints

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