/*******************************************************************************
*
* This file is part of the General Hidden Markov Model Library,
* GHMM version __VERSION__, see http://ghmm.org
*
* Filename: ghmm/ghmm/sgenerate.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: 2262 $
* from $Date: 2009-04-22 09:44:25 -0400 (Wed, 22 Apr 2009) $
* last change by $Author: grunau $.
*
*******************************************************************************/
#ifndef GHMM_SGENERATE_H
#define GHMM_SGENERATE_H
#include "smodel.h"
#include "sequence.h"
#ifdef __cplusplus
extern "C" {
#endif
/**
@name generation and extension of sequences from shmm
*/
/*@{
*/
/**
Help "modus" for sgenerate_extensions.
*/
typedef enum {
viterbi_viterbi,
viterbi_all,
all_viterbi,
all_all
} sgeneration_mode_t;
/**
Makes part sequences longer given a model. There are some different possibilities
to do this (only Viterbi or take all paths into account, combined with
sequence begin and end).
Which method to use (@todo ?only all_all implemented):
0 = viterbi_viterbi,
1 = viterbi_all,
2 = all_viterbi,
3 = all_all
@return pointer to a vector of all sequences (given initial sequence and
generated end sequence)
@param smo: given Model
@param sqd_short: vector of initial sequences
@param seed: initial value for random value generator (int)
@param global_len: wanted length of sequences (=0: automatically over final
states)
@param mode: which method to use for the generator
*/
ghmm_cseq *ghmm_sgenerate_extensions (ghmm_cmodel * smo, ghmm_cseq * sqd_short,
int seed, int global_len,
sgeneration_mode_t mode);
/**
Makes one sequences longer given a model. See ghmm_sgenerate_extensions()
for details.
@return pointer to the whole sequence
@param smo: model
@param O: given sequence to make longer
@param len: original length of sequence
@param new_len: wanted length of sequence
@param alpha:
@param mode:
*/
double *ghmm_sgenerate_single_ext (ghmm_cmodel * smo, double *O, const int len,
int *new_len, double **alpha,
sgeneration_mode_t mode);
/** Generate a single next value based on a trained model and on a seq of
length "len". Use the most prob. state given the seq as an initial state
and determin the next state und the symbol with the RNG.
@param smo: given model
@param O: given sequence
@param len: length of sequence
*/
double ghmm_sgenerate_next_value (ghmm_cmodel * smo, double *O, const int len);
/*@} sgenerate section */
#ifdef __cplusplus
}
#endif
#endif /* GHMM_SGENERATE_H */