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public interface SubstitutionModel
model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
Nested Class Summary | |
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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 |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser |
Method Summary | |
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void |
addPalObjectListener(PalObjectListener l)
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java.lang.Object |
clone()
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DataType |
getDataType()
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double[] |
getEquilibriumFrequencies()
Should return a double[] array of the related equilibrium frequencies. |
int |
getNumberOfTransitionCategories()
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OrthogonalHints |
getOrthogonalHints()
May return null |
double[] |
getTransitionCategoryProbabilities()
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double |
getTransitionCategoryProbability(int category)
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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 |
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getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE |
Methods inherited from interface pal.misc.Report |
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report |
Method Detail |
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DataType getDataType()
int getNumberOfTransitionCategories()
double getTransitionCategoryProbability(int category)
double[] getTransitionCategoryProbabilities()
void getTransitionProbabilities(double branchLength, double[][][] tableStore)
void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
double[] getEquilibriumFrequencies()
void addPalObjectListener(PalObjectListener l)
void removePalObjectListener(PalObjectListener l)
OrthogonalHints getOrthogonalHints()
java.lang.Object clone()
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