Package pal.substmodel
Interface SubstitutionModel
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- 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
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Nested Class Summary
Nested Classes Modifier and Type Interface Description 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
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description 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 nulldouble[]
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)
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Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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Method Detail
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getDataType
DataType getDataType()
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getNumberOfTransitionCategories
int getNumberOfTransitionCategories()
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getTransitionCategoryProbability
double getTransitionCategoryProbability(int category)
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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]
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getTransitionProbabilitiesTranspose
void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
Table is organized as [transition_group][to][from]
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getTransitionProbabilities
void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
Table is organized as [transition_group][from][to]
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getTransitionProbabilitiesTranspose
void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
Table is organized as [transition_group][to][from]
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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)
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addPalObjectListener
void addPalObjectListener(PalObjectListener l)
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removePalObjectListener
void removePalObjectListener(PalObjectListener l)
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getOrthogonalHints
OrthogonalHints getOrthogonalHints()
May return null
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clone
java.lang.Object clone()
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