pal.substmodel.SingleClassSubstitutionModel

All Implemented Interfaces:: 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.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser

Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel
SubstitutionModel.Utils
Constructor Summary

Constructors

Constructor

Description

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

Modifier and Type

Method

Description

void

addPalObjectListener(PalObjectListener l)

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(PrintWriter out)

print human readable report (e.g., on parameters and associated model)

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 Details
- SingleClassSubstitutionModel
  
  public SingleClassSubstitutionModel(NeoRateMatrix base, DataType dt, double[] frequencies)
Method Details
- 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(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 String toString()
  
  Overrides:
  
  toString in class Object
- clone
  
  public Object clone()
  
  Specified by:
  
  clone in interface SubstitutionModel
  
  Overrides:
  
  clone in class Object
- getCopy
  
  public SubstitutionModel getCopy()

Class SingleClassSubstitutionModel

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel

Constructor Summary

Method Summary

Methods inherited from class pal.misc.Parameterized.ParameterizedUser

Methods inherited from class pal.misc.PalObjectListener.EventGenerator

Methods inherited from class java.lang.Object

Methods inherited from interface pal.misc.Parameterized

Constructor Details

SingleClassSubstitutionModel

Method Details

getDataType

getNumberOfTransitionCategories

getTransitionCategoryProbability

getTransitionCategoryProbabilities

getEquilibriumFrequencies

getTransitionProbabilities

getTransitionProbabilities

getTransitionProbabilitiesTranspose

getTransitionProbabilitiesTranspose

addPalObjectListener

removePalObjectListener

getOrthogonalHints

report

toString

clone

getCopy