pal.substmodel
Class MatrixExponential

java.lang.Object
  |
  +--pal.substmodel.MatrixExponential
All Implemented Interfaces:
java.lang.Cloneable, java.io.Serializable

public class MatrixExponential
extends java.lang.Object
implements java.lang.Cloneable, java.io.Serializable

compute matrix exponential and, subsequently, transition probabilities for a given rate matrix

See Also:
Serialized Form

Field Summary
 int dimension
          dimension of rate matrix
 double[][] transProb
          transition probability matrix
 
Constructor Summary
MatrixExponential(RateMatrix r)
          create module
 
Method Summary
 int getDimension()
           
 void getTransitionProbabilities(double[][] probabilityStore)
          A utility method for speed, transfers trans prob information quickly into store
 double getTransitionProbability(int from, int to)
           
 void setDistance(double arc)
          compute transition probabilities for a expected distance using the prespecified rate matrix
 void setMatrix(RateMatrix r)
          update rate matrix used in present module
 void setSpan(double start, double end)
          compute transition probabilities for a expected distance using the prespecified rate matrix
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dimension

public int dimension
dimension of rate matrix

transProb

public double[][] transProb
transition probability matrix
Constructor Detail

MatrixExponential

public MatrixExponential(RateMatrix r)
create module
Parameters:
r - rate matrix
Method Detail

getTransitionProbability

public final double getTransitionProbability(int from,
                                             int to)

getDimension

public int getDimension()

setMatrix

public void setMatrix(RateMatrix r)
update rate matrix used in present module
Parameters:
r - rate matrix

setSpan

public void setSpan(double start,
                    double end)
compute transition probabilities for a expected distance using the prespecified rate matrix
Parameters:
arc - expected distance

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