Package jebl.evolution.substmodel
Interface RateMatrix
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- All Superinterfaces:
java.lang.Cloneable
,java.io.Serializable
- All Known Implementing Classes:
AbstractRateMatrix
,AminoAcidModel
,WAG
public interface RateMatrix extends java.lang.Cloneable, java.io.Serializable
abstract base class for all rate matrices- Version:
- $Id: RateMatrix.java 185 2006-01-23 23:03:18Z rambaut $
- Author:
- Korbinian Strimmer, Alexei Drummond, Matthew Goode
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int
getDimension()
double[]
getEquilibriumFrequencies()
double
getEquilibriumFrequency(int i)
double[][]
getRelativeRates()
SequenceType
getSequenceType()
Get the data type of this rate matrixvoid
getTransitionProbabilities(double[][] probabilityStore)
A utility method for speed, transfers trans prob information quickly into store.double
getTransitionProbability(int fromState, int toState)
java.lang.String
getUniqueName()
void
setDistance(double distance)
Sets the distance (such as time/branch length) used when calculating the probabilities.
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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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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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getSequenceType
SequenceType getSequenceType()
Get the data type of this rate matrix
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getRelativeRates
double[][] getRelativeRates()
- 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.
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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!
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