/*******************************************************************************
*
* This file is part of the General Hidden Markov Model Library,
* GHMM version __VERSION__, see http://ghmm.org
*
* Filename: ghmm/ghmm/pmodel.c
* Authors: Matthias Heinig
*
* 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: 1713 $
* from $Date: 2006-10-16 10:06:28 -0400 (Mon, 16 Oct 2006) $
* last change by $Author: grunau $.
*
*******************************************************************************/
#ifdef HAVE_CONFIG_H
# include "../config.h"
#endif
#include "pmodel.h"
#include "mes.h"
#include "ghmm_internals.h"
int ghmm_dpmodel_state_alloc(ghmm_dpstate * s, int M, int in_states, int out_states) {
# define CUR_PROC "ghmm_dpmodel_state_alloc"
int res = -1;
ARRAY_CALLOC (s->b, M);
if (out_states > 0) {
ARRAY_CALLOC (s->out_id, out_states);
ARRAY_CALLOC (s->out_a, out_states);
}
if (in_states > 0) {
ARRAY_CALLOC (s->in_id, in_states);
ARRAY_CALLOC (s->in_a, in_states);
}
res = 0;
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
return(res);
# undef CUR_PROC
} /* ghmm_dpmodel_state_alloc */
void ghmm_dpmodel_state_clean(ghmm_dpstate *my_state) {
#define CUR_PROC "ghmm_dpmodel_state_clean"
if (!my_state) return;
if (my_state->b)
m_free(my_state->b);
if (my_state->out_id)
m_free(my_state->out_id);
if (my_state->in_id)
m_free(my_state->in_id);
if (my_state->out_a)
m_free(my_state->out_a);
if (my_state->in_a)
m_free(my_state->in_a);
if (my_state->class_change)
m_free(my_state->class_change);
my_state->pi = 0;
my_state->b = NULL;
my_state->out_id = NULL;
my_state->in_id = NULL;
my_state->out_a = NULL;
my_state->in_a = NULL;
my_state->out_states = 0;
my_state->in_states = 0;
my_state->fix = 0;
#undef CUR_PROC
} /* ghmm_dpmodel_state_clean */
/* use this to allocate the memory for a ghmm_dpmodel and set the pointers to NULL */
ghmm_dpmodel * ghmm_dpmodel_init() {
#define CUR_PROC "ghmm_dpmodel_init"
ghmm_dpmodel * mo;
ARRAY_CALLOC (mo, 1);
return mo;
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
return NULL;
#undef CUR_PROC
}
ghmm_dpmodel_class_change_context * ghmm_dpmodel_init_class_change() {
#define CUR_PROC "ghmm_dpmodel_init_class_change"
ghmm_dpmodel_class_change_context * pccc;
ARRAY_CALLOC (pccc, 1);
pccc->get_class = &ghmm_dpmodel_default_transition_class;
pccc->user_data = NULL;
return pccc;
STOP: /* Label STOP from ARRAY_[CM]ALLOC */
return NULL;
#undef CUR_PROC
}
int ghmm_dpmodel_free(ghmm_dpmodel *mo) {
#define CUR_PROC "ghmm_dpmodel_free"
int i;
mes_check_ptr(mo, return(-1));
if( !mo ) return(0);
if (mo->s) {
for (i = 0; i < mo->N; i++)
ghmm_dpmodel_state_clean(&(mo->s[i]));
m_free(mo->s);
}
if (mo-> silent)
m_free(mo->silent);
if (mo -> tied_to)
m_free(mo->tied_to);
/*if ((*mo) -> emission_order) Moved to state
m_free((*mo)->emission_order);*/
if (mo-> topo_order)
m_free(mo->topo_order);
if (mo->number_of_alphabets > 0)
m_free(mo->size_of_alphabet);
m_free(mo);
return(0);
#undef CUR_PROC
} /* ghmm_dpmodel_free */
/* get the emission index for a pair of symbols
if the pair cannot be emmited this returns the size of the emission table
plus 1 => emission table[size of table] should be 1 and the actual size
should be one more... */
int ghmm_dpmodel_pair(int symbol_x, int symbol_y, int alphabet_size, int off_x, int off_y) {
if (off_x == 0 && symbol_y >= 0)
return symbol_y;
if (off_y == 0 && symbol_x >= 0)
return symbol_x;
if (symbol_x < 0 || symbol_y < 0) {
if (off_x == 0 || off_y == 0)
return alphabet_size;
else
return (alphabet_size - 1) * (alphabet_size - 1) + 1;
}
return(symbol_x * alphabet_size + symbol_y);
}
int ghmm_dpmodel_emission_table_size(ghmm_dpmodel* mo, int state_index) {
/* the alphabet is over single sequences so get the maximal index for the
lookup of emission probabilities and use it to determine the size of
the lookup table */
int size = mo->size_of_alphabet[mo->s[state_index].alphabet];
return ghmm_dpmodel_pair(size - 1, size - 1, size, mo->s[state_index].offset_x, mo->s[state_index].offset_y) + 1;
}
void ghmm_dpmodel_state_print(ghmm_dpstate * s) {
int i;
printf("offset x: %i\n", s->offset_x);
printf("offset y: %i\n", s->offset_y);
printf("alphabet: %i\n", s->alphabet);
printf("kclasses: %i\n", s->kclasses);
printf("in_state: %i\n", s->in_states);
for (i=0; i<s->in_states; i++)
printf("%i ", s->in_id[i]);
printf("\n");
printf("probabilities...\n");
}
void ghmm_dpmodel_print(ghmm_dpmodel* mo) {
int i;
printf("Pair HMM model\n");
printf("max offset x: %i\n", mo->max_offset_x);
printf("max offset y: %i\n", mo->max_offset_y);
printf("Number of states: %i\n", mo->N);
for (i=0; i<mo->N; i++) {
printf("State %i:\n", i);
ghmm_dpmodel_state_print(&(mo->s[i]));
}
}
int ghmm_dpmodel_default_transition_class(ghmm_dpmodel * mo, ghmm_dpseq * X, ghmm_dpseq * Y, int index_x, int index_y, void * user_data) {
return 0;
}
void ghmm_dpmodel_set_to_default_transition_class(ghmm_dpmodel_class_change_context * pccc) {
if (pccc){
pccc->get_class = &ghmm_dpmodel_default_transition_class;
pccc->user_data = NULL;
}
else
fprintf(stderr, "set_to_default_transition_class: No class change context\n");
}