statalign.base.hmm
Class Hmm2

java.lang.Object
  statalign.base.hmm.Hmm
      statalign.base.hmm.Hmm2

Direct Known Subclasses:

HmmTkf92

public abstract class Hmm2
extends Hmm

This is an abstract class for HMMs that are pair-HMMs and do not emit characters into unobservable sequences.

Author:

novak

Field Summary

Fields inherited from class statalign.base.hmm.Hmm

params

Constructor Summary

Hmm2()

Method Summary

abstract double[][]	preCalcTransMatrix(double[][] transMatrix, double t) Calculates the transition matrix given an edge length t.
abstract double[][]	preCalcTransMatrix(double[][] transMatrix, double t, double[] newParams)

Methods inherited from class statalign.base.hmm.Hmm

getEmitPatt2State, getEnd, getLogStationaryProb, getStart, getStateEmit

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Hmm2

public Hmm2()

Method Detail

preCalcTransMatrix

public abstract double[][] preCalcTransMatrix(double[][] transMatrix,
                                              double t)

Calculates the transition matrix given an edge length t.

Parameters:

transMatrix - If null, the function allocates memory for the return matrix If not, this is used for storing the matrix. For speeding-up purposes, note that allocating memory is time-consuming. In this way we need to allocate memory when asked.

t - The edge length parameter.

Returns:

The calculated transition matrix.

preCalcTransMatrix

public abstract double[][] preCalcTransMatrix(double[][] transMatrix,
                                              double t,
                                              double[] newParams)

Parameters:

transMatrix - If null, the function allocates memory for the return matrix If not, this is used for storing the matrix. For speeding-up purposes, note that allocating memory is time-consuming. In this way we need to allocate memory when asked.

t - The edge length parameter.

newParams - A set of temporary parameters to be used for this particular instance

Returns:

The calculated transition matrix.