pal.substmodel
Class SingleClassSubstitutionModel

java.lang.Object
  extended by pal.misc.PalObjectListener.EventGenerator
      extended by pal.misc.Parameterized.ParameterizedUser
          extended by pal.substmodel.SingleClassSubstitutionModel
All Implemented Interfaces:
java.io.Serializable, Parameterized, Report, SubstitutionModel

public class SingleClassSubstitutionModel
extends Parameterized.ParameterizedUser
implements SubstitutionModel

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel
SubstitutionModel.Utils
 
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
 
Constructor Summary
SingleClassSubstitutionModel(NeoRateMatrix base, DataType dt, double[] frequencies)
           
 
Method Summary
 void addPalObjectListener(PalObjectListener l)
           
 java.lang.Object clone()
           
 SubstitutionModel getCopy()
           
 DataType getDataType()
           
 double[] getEquilibriumFrequencies()
          Should return a double[] array of the related equilibrium frequencies.
 int getNumberOfTransitionCategories()
           
 OrthogonalHints getOrthogonalHints()
          May return null
 double[] getTransitionCategoryProbabilities()
           
 double getTransitionCategoryProbability(int category)
           
 void getTransitionProbabilities(double branchLength, double[][][] store)
          Table is organized as [transition_group][from][to]
 void getTransitionProbabilities(double branchLength, int category, double[][] store)
          Table is organized as [transition_group][from][to]
 void getTransitionProbabilitiesTranspose(double branchLength, double[][][] store)
          Table is organized as [transition_group][to][from]
 void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] store)
          Table is organized as [transition_group][to][from]
 void removePalObjectListener(PalObjectListener l)
           
 void report(java.io.PrintWriter out)
          print human readable report (e.g., on parameters and associated model)
 java.lang.String toString()
           
 
Methods inherited from class pal.misc.Parameterized.ParameterizedUser
getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE
 
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
 

Constructor Detail

SingleClassSubstitutionModel

public SingleClassSubstitutionModel(NeoRateMatrix base,
                                    DataType dt,
                                    double[] frequencies)
Method Detail

getDataType

public DataType getDataType()
Specified by:
getDataType in interface SubstitutionModel

getNumberOfTransitionCategories

public int getNumberOfTransitionCategories()
Specified by:
getNumberOfTransitionCategories in interface SubstitutionModel

getTransitionCategoryProbability

public double getTransitionCategoryProbability(int category)
Specified by:
getTransitionCategoryProbability in interface SubstitutionModel

getTransitionCategoryProbabilities

public double[] getTransitionCategoryProbabilities()
Specified by:
getTransitionCategoryProbabilities in interface SubstitutionModel
Returns:
all the category probabilites for each category respectively.

getEquilibriumFrequencies

public double[] getEquilibriumFrequencies()
Description copied from interface: SubstitutionModel
Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)

Specified by:
getEquilibriumFrequencies in interface SubstitutionModel

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       double[][][] store)
Description copied from interface: SubstitutionModel
Table is organized as [transition_group][from][to]

Specified by:
getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilities

public void getTransitionProbabilities(double branchLength,
                                       int category,
                                       double[][] store)
Description copied from interface: SubstitutionModel
Table is organized as [transition_group][from][to]

Specified by:
getTransitionProbabilities in interface SubstitutionModel

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                double[][][] store)
Description copied from interface: SubstitutionModel
Table is organized as [transition_group][to][from]

Specified by:
getTransitionProbabilitiesTranspose in interface SubstitutionModel

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double branchLength,
                                                int category,
                                                double[][] store)
Description copied from interface: SubstitutionModel
Table is organized as [transition_group][to][from]

Specified by:
getTransitionProbabilitiesTranspose in interface SubstitutionModel

addPalObjectListener

public void addPalObjectListener(PalObjectListener l)
Specified by:
addPalObjectListener in interface SubstitutionModel
Overrides:
addPalObjectListener in class PalObjectListener.EventGenerator

removePalObjectListener

public void removePalObjectListener(PalObjectListener l)
Specified by:
removePalObjectListener in interface SubstitutionModel
Overrides:
removePalObjectListener in class PalObjectListener.EventGenerator

getOrthogonalHints

public OrthogonalHints getOrthogonalHints()
Description copied from interface: SubstitutionModel
May return null

Specified by:
getOrthogonalHints in interface SubstitutionModel

report

public void report(java.io.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

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

clone

public java.lang.Object clone()
Specified by:
clone in interface SubstitutionModel
Overrides:
clone in class java.lang.Object

getCopy

public SubstitutionModel getCopy()