read_cxml.c

General Hidden Markov Model Library 一个通用的隐马尔科夫模型的C代码库

/*******************************************************************************
*
*       This file is part of the General Hidden Markov Model Library,
*       GHMM version 0.8_beta1, see http://ghmm.org
*
*       Filename: read_cxml.c
*       Authors:   Wasinee Rungsarityotin, 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: [e-mail]
*
*       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: 1451 $
*                       from $Date: 2005-10-18 12:21:55 +0200 (Tue, 18 Oct 2005) $
*             last change by $Author: grunau $.
*
*******************************************************************************/

/* XXX FIXME: breaks out of tree build of ghmmwrapper */
#include "../config.h"

#include <stdio.h>
#include <stdlib.h>
#include <ghmm/rng.h>
#include <ghmm/sequence.h>
#include <ghmm/sdmodel.h>
#include <ghmm++/GHMM_convertXMLtoC.h>
#include "sdclass_change.h"

/*int cp_class_change(int *seq, int len) {
  int sum = 0;
  int i;
  for(i=0;i<=len;i++){
	  sum += seq[i];
  }
  //printf("sum = %d\n",sum);
  if (sum >= 6) {
    //printf("\n++++++++++++++++++++++++++++++++Switching class .... ");    
    return 1;
  }
  else {
    return 0;
  } 
} 		
		

void setSwitchingFunction( ghmm_dsmodel *smd ) {
  smd->get_class = cp_class_change;
} */


/*========================================================================*/


/* the actual pointer to C struct ghmm_dmodel */

void mat_2d_print(double **mat, int rows, int cols) {
  int i,j;

  printf("double ** Rows = %d, Cols = %d\n", rows, cols);
  for(i=0; i < rows; i++) {
    printf("\t");
    for(j=0; j < cols; j++) {
      printf("%g ", mat[i][j]);
    }
    printf("\n");
  }
}

int __seq_d_class(const double *O, int index, double *osum) {
  return 0; 
}

ghmm_dsmodel *graphmlTosdModel(char *filename)
{
  model_t   *mymodel;
  ghmm_dsmodel     *cmodel;
  int nsilents=0;

  mymodel = graphmldoc_cwrapper(filename);

  if (mymodel != NULL)
    {
      if (mymodel->model_id == DISCRETE)
	{
	  cmodel = (ghmm_dsmodel*)(mymodel->model_pt); /* the actual pointer to C struct ghmm_dmodel */
	  nsilents = ghmm_ds_init_silent_states (cmodel);
	  fprintf(stderr, "In Main: # Silent States %d\n", nsilents);

	  if ( cmodel->cos > 1 ) {
	    fprintf(stderr, "Warning: I set the function pointer sdmodel->get_class\n");
	    /* cmodel->get_class = __seq_d_class; */
	    cmodel->get_class = cp_class_change;
	  } else {
	    /* cmodel->get_class = __seq_d_class; */
	    cmodel->get_class = cp_class_change;
	  }

 	  fprintf(stderr, "In read_cxml.c\n");
	  ghmm_ds_topo_order (cmodel);
	  free((void*) mymodel);
	  return cmodel;
	}
      else
	{
	  fprintf(stderr, "graphmlToModel: I need a DISCRETE model\n");
	  free((void*) mymodel);
	  return NULL;
	}
    }
}