/*******************************************************************************
*
*       This file is part of the General Hidden Markov Model Library,
*       GHMM version __VERSION__, see http://ghmm.org
*
*       Filename: ghmm/ghmm/viterbi.h
*       Authors:  Bernhard Knab, Benjamin Georgi
*
*       Copyright (C) 1998-2004 Alexander Schliep 
*       Copyright (C) 1998-2001 ZAIK/ZPR, Universitaet zu Koeln
*	Copyright (C) 2002-2004 Max-Planck-Institut fuer Molekulare Genetik, 
*                               Berlin
*                                   
*       Contact: schliep@ghmm.org             
*
*       This library is free software; you can redistribute it and/or
*       modify it under the terms of the GNU Library General Public
*       License as published by the Free Software Foundation; either
*       version 2 of the License, or (at your option) any later version.
*
*       This library is distributed in the hope that it will be useful,
*       but WITHOUT ANY WARRANTY; without even the implied warranty of
*       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
*       Library General Public License for more details.
*
*       You should have received a copy of the GNU Library General Public
*       License along with this library; if not, write to the Free
*       Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*
*       This file is version $Revision: 2264 $ 
*                       from $Date: 2009-04-22 11:13:40 -0400 (Wed, 22 Apr 2009) $
*             last change by $Author: grunau $.
*
*******************************************************************************/

#ifndef GHMM_PVITERBI_H
#define GHMM_PVITERBI_H

#ifdef __cplusplus
extern "C" {
#endif

#include "pmodel.h"
#include "psequence.h"


/**@name Viterbi-Algorithmus */
/*@{ (Doc++-Group: viterbi) */

/**
  Viterbi algorithm. Calculates the Viterbi path (the optimal path trough
  the model) and the Viterbi probability to a given model and given 
  sequences.
  */
int *ghmm_dpmodel_viterbi(ghmm_dpmodel *mo, ghmm_dpseq * X, ghmm_dpseq * Y,
                          double *log_p, int *path_length);

int *ghmm_dpmodel_viterbi_variable_tb(ghmm_dpmodel *mo, ghmm_dpseq * X,
                                      ghmm_dpseq * Y, double *log_p,
                                      int *path_length,
                                      int start_traceback_with);

int *ghmm_dpmodel_viterbi_test(ghmm_dpmodel *mo, ghmm_dpseq * X, ghmm_dpseq * Y,
			  double *log_p, int *path_length);

/**
  Calculates the logarithmic probability to a given path through the 
  states (does not have to be the Viterbi path), given sequences and
  a model.
  */

double ghmm_dpmodel_viterbi_logp(ghmm_dpmodel *mo, ghmm_dpseq * X,
                                 ghmm_dpseq * Y,
                                 int *state_seq, int state_seq_len);


#ifdef __cplusplus
}
#endif


#endif

/*@} (Doc++-Group: viterbi) */