Package jebl.evolution.substmodel
Interface RateMatrix
- All Superinterfaces:
Cloneable
,Serializable
- All Known Implementing Classes:
AbstractRateMatrix
,AminoAcidModel
,WAG
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
-
Method Summary
Modifier and TypeMethodDescriptionint
double[]
double
getEquilibriumFrequency
(int i) double[][]
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) void
setDistance
(double distance) Sets the distance (such as time/branch length) used when calculating the probabilities.
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Method Details
-
getUniqueName
String getUniqueName()- Returns:
- a short unique human-readable identifier for this rate matrix.
-
getDimension
int getDimension()- Returns:
- the dimension of this rate matrix.
-
getEquilibriumFrequencies
double[] getEquilibriumFrequencies()- Returns:
- stationary frequencies (sum = 1.0)
-
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 -
getRelativeRates
double[][] getRelativeRates()- Returns:
- rate matrix (transition: from 1st index to 2nd index)
-
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!
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