Package pal.substmodel
Class MatrixExponential
java.lang.Object
pal.substmodel.MatrixExponential
- All Implemented Interfaces:
Serializable
,Cloneable
compute matrix exponential and, subsequently, transition probabilities
for a given rate matrix
- Version:
- $Id: MatrixExponential.java,v 1.20 2004/08/05 03:00:22 matt Exp $
- Author:
- Korbinian Strimmer
- See Also:
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
final void
getTransitionProbabilities
(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into storefinal double
getTransitionProbability
(int from, int to) final void
setDistance
(double arc) compute transition probabilities for a expected distance using the prespecified rate matrixfinal void
setDistanceTranspose
(double arc) compute transition probabilities for a expected distance using the prespecified rate matrixvoid
update rate matrix used in present modulevoid
updateByRelativeRates
(double[][] relativeRates)
-
Constructor Details
-
MatrixExponential
public MatrixExponential(int dimension) create module- Parameters:
r
- rate matrix
-
MatrixExponential
create module- Parameters:
r
- rate matrix
-
-
Method Details
-
getTransitionProbability
public final double getTransitionProbability(int from, int to) -
getDimension
public int getDimension() -
updateByRelativeRates
public void updateByRelativeRates(double[][] relativeRates) -
setMatrix
update rate matrix used in present module- Parameters:
r
- rate matrix
-
getTransitionProbabilities
public final void getTransitionProbabilities(double[][] probabilityStore) A utility method for speed, transfers trans prob information quickly into store -
setDistance
public final void setDistance(double arc) compute transition probabilities for a expected distance using the prespecified rate matrix- Parameters:
arc
- expected distance
-
setDistanceTranspose
public final void setDistanceTranspose(double arc) compute transition probabilities for a expected distance using the prespecified rate matrix- Parameters:
arc
- expected distance
-