Package pal.substmodel
Class SingleClassSubstitutionModel
- java.lang.Object
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- pal.misc.PalObjectListener.EventGenerator
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- pal.misc.Parameterized.ParameterizedUser
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- pal.substmodel.SingleClassSubstitutionModel
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- All Implemented Interfaces:
java.io.Serializable
,Parameterized
,Report
,SubstitutionModel
public class SingleClassSubstitutionModel extends Parameterized.ParameterizedUser implements SubstitutionModel
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
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Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel
SubstitutionModel.Utils
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Constructor Summary
Constructors Constructor Description SingleClassSubstitutionModel(NeoRateMatrix base, DataType dt, double[] frequencies)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addPalObjectListener(PalObjectListener l)
java.lang.Object
clone()
SubstitutionModel
getCopy()
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[][][] 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(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model)java.lang.String
toString()
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Methods inherited from class pal.misc.Parameterized.ParameterizedUser
getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE
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Methods inherited from class pal.misc.PalObjectListener.EventGenerator
fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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Constructor Detail
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SingleClassSubstitutionModel
public SingleClassSubstitutionModel(NeoRateMatrix base, DataType dt, double[] frequencies)
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Method Detail
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getDataType
public DataType getDataType()
- Specified by:
getDataType
in interfaceSubstitutionModel
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getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()
- Specified by:
getNumberOfTransitionCategories
in interfaceSubstitutionModel
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getTransitionCategoryProbability
public double getTransitionCategoryProbability(int category)
- Specified by:
getTransitionCategoryProbability
in interfaceSubstitutionModel
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getTransitionCategoryProbabilities
public double[] getTransitionCategoryProbabilities()
- Specified by:
getTransitionCategoryProbabilities
in interfaceSubstitutionModel
- Returns:
- all the category probabilites for each category respectively.
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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 interfaceSubstitutionModel
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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 interfaceSubstitutionModel
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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 interfaceSubstitutionModel
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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 interfaceSubstitutionModel
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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 interfaceSubstitutionModel
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addPalObjectListener
public void addPalObjectListener(PalObjectListener l)
- Specified by:
addPalObjectListener
in interfaceSubstitutionModel
- Overrides:
addPalObjectListener
in classPalObjectListener.EventGenerator
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removePalObjectListener
public void removePalObjectListener(PalObjectListener l)
- Specified by:
removePalObjectListener
in interfaceSubstitutionModel
- Overrides:
removePalObjectListener
in classPalObjectListener.EventGenerator
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getOrthogonalHints
public OrthogonalHints getOrthogonalHints()
Description copied from interface:SubstitutionModel
May return null- Specified by:
getOrthogonalHints
in interfaceSubstitutionModel
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report
public void report(java.io.PrintWriter out)
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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clone
public java.lang.Object clone()
- Specified by:
clone
in interfaceSubstitutionModel
- Overrides:
clone
in classjava.lang.Object
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getCopy
public SubstitutionModel getCopy()
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