Package pal.substmodel
Interface NeoRateMatrix
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- All Superinterfaces:
java.io.Serializable
- All Known Implementing Classes:
GeneralPoissonRateMatrix
,GeneralREVRateMatrix
public interface NeoRateMatrix extends java.io.Serializable
The new RateMatrix class. Replaces the old RateMatrix, and will in turn be renamed to RateMatrix at a later point. A NeoRateMatix object should be stateless (with regard to parameters used in likelihood searching). State is given by the parameter values which are administered externally.- Version:
- $Id: NeoRateMatrix.java,v 1.3 2004/08/15 03:00:37 matt Exp $
- Author:
- Matthew Goode
- 3 May 2004 - Created file
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)
Create the relative rates arrayvoid
getDefaultRateParameters(double[] parameterStore, int startIndex)
int
getDimension()
int
getNumberOfRateParameters()
double
getRateParameterLowerBound(int parameter)
double
getRateParameterUpperBound(int parameter)
java.lang.String
getUniqueName()
boolean
isDataTypeCompatible(DataType dt)
Check the compatibility of a data type to be used with the rate matrixboolean
isReversible()
Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );
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Method Detail
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getUniqueName
java.lang.String getUniqueName()
- Returns:
- a short unique human-readable identifier for this rate matrix.
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isReversible
boolean isReversible()
Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );- Returns:
- true if reversible
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getDimension
int getDimension()
- Returns:
- the dimension of this rate matrix.
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isDataTypeCompatible
boolean isDataTypeCompatible(DataType dt)
Check the compatibility of a data type to be used with the rate matrix- Parameters:
dt
- the data type to test- Returns:
- true if data type compatible (false otherwise)
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createRelativeRates
void createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)
Create the relative rates array- Parameters:
rateStore
- The place where the relative rates are stored (should be assumed to be large enough - based on dimension)rateParameters
- The parameters to be used to construct the rate storestartIndex
- The index into the rateParameters to start reading parameters
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getNumberOfRateParameters
int getNumberOfRateParameters()
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getRateParameterLowerBound
double getRateParameterLowerBound(int parameter)
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getRateParameterUpperBound
double getRateParameterUpperBound(int parameter)
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getDefaultRateParameters
void getDefaultRateParameters(double[] parameterStore, int startIndex)
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