pal.substmodel
Interface SubstitutionModel

All Superinterfaces:
Parameterized, Report, java.io.Serializable
All Known Implementing Classes:
GeneralRateDistributionSubstitutionModel, SingleClassSubstitutionModel, YangCodonModel.SimpleNeutralSelection, YangCodonModel.SimplePositiveSelection

public interface SubstitutionModel
extends Parameterized, Report, java.io.Serializable

model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities

Version:
$Id: SubstitutionModel.java,v 1.33 2004/05/19 04:05:21 matt Exp $
Author:
Alexei Drummond, Matthew Goode

Nested Class Summary
static class SubstitutionModel.Utils
          A small Utility class for things relating to Substitution Models in general
 
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
 
Method Summary
 void addPalObjectListener(PalObjectListener l)
           
 java.lang.Object clone()
           
 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[][][] tableStore)
          Table is organized as [transition_group][from][to]
 void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
          Table is organized as [transition_group][from][to]
 void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
          Table is organized as [transition_group][to][from]
 void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
          Table is organized as [transition_group][to][from]
 void removePalObjectListener(PalObjectListener l)
           
 
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
 
Methods inherited from interface pal.misc.Report
report
 

Method Detail

getDataType

DataType getDataType()

getNumberOfTransitionCategories

int getNumberOfTransitionCategories()

getTransitionCategoryProbability

double getTransitionCategoryProbability(int category)

getTransitionCategoryProbabilities

double[] getTransitionCategoryProbabilities()
Returns:
all the category probabilites for each category respectively.

getTransitionProbabilities

void getTransitionProbabilities(double branchLength,
                                double[][][] tableStore)
Table is organized as [transition_group][from][to]


getTransitionProbabilitiesTranspose

void getTransitionProbabilitiesTranspose(double branchLength,
                                         double[][][] tableStore)
Table is organized as [transition_group][to][from]


getTransitionProbabilities

void getTransitionProbabilities(double branchLength,
                                int category,
                                double[][] tableStore)
Table is organized as [transition_group][from][to]


getTransitionProbabilitiesTranspose

void getTransitionProbabilitiesTranspose(double branchLength,
                                         int category,
                                         double[][] tableStore)
Table is organized as [transition_group][to][from]


getEquilibriumFrequencies

double[] getEquilibriumFrequencies()
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)


addPalObjectListener

void addPalObjectListener(PalObjectListener l)

removePalObjectListener

void removePalObjectListener(PalObjectListener l)

getOrthogonalHints

OrthogonalHints getOrthogonalHints()
May return null


clone

java.lang.Object clone()