Package pal.substmodel
Interface RateMatrix
- All Superinterfaces:
Cloneable
,NamedParameterized
,Parameterized
,Report
,Serializable
- All Known Implementing Classes:
AbstractRateMatrix
,AminoAcidModel
,BLOSUM62
,CachedRateMatrix
,CodonModel
,CPREV
,Dayhoff
,F81
,F84
,GTR
,HKY
,JTT
,MTREV24
,NucleotideModel
,TN
,TwoStateModel
,VT
,WAG
,YangCodonModel
abstract base class for all rate matrices
- Version:
- $Id: RateMatrix.java,v 1.34 2003/11/13 04:05:39 matt Exp $
- Author:
- Korbinian Strimmer, Alexei Drummond, Matthew Goode
-
Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Method Summary
Modifier and TypeMethodDescriptionvoid
Add a PalObjectListener to be notified of changes to the model.clone()
Get the data type of this rate matrixint
double[]
double
getEquilibriumFrequency
(int i) int
get numerical code describing the model typedouble[][]
Deprecated.try not to use.void
getTransitionProbabilities
(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into storedouble
getTransitionProbability
(int fromState, int toState) int
get numerical code describing the data typevoid
void
scale
(double scaleValue) void
setDistance
(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities.void
setDistanceTranspose
(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities.double
setParametersNoScale
(double[] parameters) Methods inherited from interface pal.misc.NamedParameterized
getParameterName
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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Method Details
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getTypeID
int getTypeID()get numerical code describing the data type- Returns:
- integer code identifying a data type
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getModelID
int getModelID()get numerical code describing the model type- Returns:
- integer code identifying a substitution model
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getUniqueName
String getUniqueName()- Returns:
- a short unique human-readable identifier for this rate matrix.
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getDimension
int getDimension()- Returns:
- the dimension of this rate matrix.
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getEquilibriumFrequencies
double[] getEquilibriumFrequencies()- Returns:
- stationary frequencies (sum = 1.0)
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getEquilibriumFrequency
double getEquilibriumFrequency(int i) - Returns:
- stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.
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getDataType
DataType getDataType()Get the data type of this rate matrix -
getRelativeRates
double[][] getRelativeRates()Deprecated.try not to use.- Returns:
- rate matrix (transition: from 1st index to 2nd index)
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getTransitionProbability
double getTransitionProbability(int fromState, int toState) - Parameters:
fromState
- The state from which we are startingtoState
- The resulting state- Returns:
- the probability of going from one state to another given the current distance
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getTransitionProbabilities
void getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store -
setDistance
void setDistance(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities. This method may well take the most time! -
setDistanceTranspose
void setDistanceTranspose(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities. -
addPalObjectListener
Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called -
removePalObjectListener
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getOrthogonalHints
OrthogonalHints getOrthogonalHints()- Returns:
- an orthogonal hints object for orthogonal optimisation (may return null for no hints)
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clone
Object clone() -
setParametersNoScale
double setParametersNoScale(double[] parameters) -
scale
void scale(double scaleValue)
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