statalign.base.hmm
Class HmmSilent

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

Direct Known Subclasses:

HmmNonParam

public abstract class HmmSilent
extends Hmm

This is the abstract class of pair-HMMs that emit characters into one unobservable sequence, namely that aligns two observable sequences via an unobservable ancestral sequence.

Author:

novak

Field Summary

Fields inherited from class statalign.base.hmm.Hmm

params

Constructor Summary

HmmSilent()

Method Summary

abstract int	getSilent() Returns the index of the silent state.
abstract double[][]	preCalcRedTransMatrix(double[][] redTransMatrix, double[][] transMatrix) Silent state elimination.
abstract double[][]	preCalcTransMatrix(double[][] transMatrix, double t1, double t2) Calculates the transition matrix given edge lengths t1 and t2 of a cherry-motif.
void	updateParam(double[] _P)

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

HmmSilent

public HmmSilent()

Method Detail

preCalcTransMatrix

public abstract double[][] preCalcTransMatrix(double[][] transMatrix,
                                              double t1,
                                              double t2)

Calculates the transition matrix given edge lengths t1 and t2 of a cherry-motif.

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.

t1 - The length of the left edge

t2 - The length of the right edge.

Returns:

The calculated transition matrix.

preCalcRedTransMatrix

public abstract double[][] preCalcRedTransMatrix(double[][] redTransMatrix,
                                                 double[][] transMatrix)

Silent state elimination. Transforms transMatrix into the transition matrix obtained by eliminating the silent state of transMatrix.

Parameters:

redTransMatrix - Array to store the results, may be left null

transMatrix - Input transition matrix with a silent state

Returns:

The calculated ('reduced') transition matrix (redTransMatrix or a newly allocated array if it is null)

getSilent

public abstract int getSilent()

Returns the index of the silent state.

Returns:

Index of the silent state

updateParam

public void updateParam(double[] _P)