Package pal.substmodel
Interface SubstitutionModel
- All Superinterfaces:
Parameterized
,Report
,Serializable
- All Known Implementing Classes:
GeneralRateDistributionSubstitutionModel
,SingleClassSubstitutionModel
,YangCodonModel.SimpleNeutralSelection
,YangCodonModel.SimplePositiveSelection
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
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
A small Utility class for things relating to Substitution Models in generalNested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
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Method Summary
Modifier and TypeMethodDescriptionvoid
clone()
double[]
Should return a double[] array of the related equilibrium frequencies.int
May return nulldouble[]
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
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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Method Details
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getDataType
DataType getDataType() -
getNumberOfTransitionCategories
int getNumberOfTransitionCategories() -
getTransitionCategoryProbability
double getTransitionCategoryProbability(int category) -
getTransitionCategoryProbabilities
double[] getTransitionCategoryProbabilities()- Returns:
- all the category probabilites for each category respectively.
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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
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removePalObjectListener
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getOrthogonalHints
OrthogonalHints getOrthogonalHints()May return null -
clone
Object clone()
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