getall.c

GESPI 2.0动态系统模拟工具

#include "copyleft.h"

/*
    GEPASI - a simulator of metabolic pathways and other dynamical systems
    Copyright (C) 1989, 1992, 1993  Pedro Mendes
*/

/*************************************/
/*                                   */
/*             data input            */
/*                                   */
/*        Zortech C/C++ 3.0 r4       */
/*          MICROSOFT C 6.00         */
/*          Visual C/C++ 1.0         */
/*           QuickC/WIN 1.0          */
/*             ULTRIX cc             */
/*              GNU gcc              */
/*                                   */
/*   (include here compilers that    */
/*   compiled GEPASI successfully)   */
/*                                   */
/*************************************/


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#ifdef MSDOS
#include <io.h>
#endif
#include <fcntl.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <math.h>
#include "globals.h"
#include "globvar.h"
#include "datab.h"
#include "newton.h"
#include "strtbl.h"
#include "gauss.h"
#include "kinetics.h"
#include "pmu.h"                                    /* several utilities     */
#include "heapchk.h"

#if ( _MSC_VER >= 610 )
 #define open _open
 #define close _close
 #define stat _stat
 #define fstat _fstat
 #define read _read
 #define write _write
 #define O_RDONLY _O_RDONLY
#endif

#ifdef _ZTC
#define MEM_DEBUG 1
#include "mem.h"
#else
#define mem_malloc malloc
#define mem_free free
#define mem_realloc realloc
#endif

/*
	get the list of files to process
*/

void getlist( char *inpf )
{
 int i;
 FILE *chg;

 if ( inpf )
 {
  if (!(chg=fopen(inpf,"r")))
  {
   printf(errormsg[6],inpf);
   term_gepasi();
  }
 }
 else
 {
  chg = stdin;
  fprintf( stderr, "\n\n%s\n\n", gepasi );
  fprintf( stderr, "input filenames one at a line, a dot followed by ENTER ends.\n\n");
 }
 for(i=0;i<MAX_FIL;i++)                              /* stop at MAX_FIL     */
 {
  fgets( filename[i], PWIDTH, chg );
  if (   ( filename[i][0] == '.' )
      || ( feof( chg ) )
     ) break;                                        /* stop if EOF or .    */
  filename[i][strlen(filename[i])-1] = 0;            /* put /0 at the end   */
  fixext( filename[i], '.', ".sim" );
 }
 nrunfiles = i;
 if ( inpf ) fclose( chg );
 return;
}



/*
	read topology from file
*/

int BufToTop( char *Buff, char **endoftop )
{
 int i,j;
 int daux;
 unsigned char uaux;
 char *paux;
 char saux[NAME_L];

/* reset the version number to zero                                                    */
 ver_no = 0;
 /* copy the first line                                                                                 */
 paux = strchr( Buff, '\n' );
 if( paux == NULL ) return IDS_ERR_BAD_TOPNAM;
 /* take care of CR if one existed before LF                                            */
 if( *(paux-1)=='\r' ) *(paux-1) = '\0';
 *paux = '\0';
 if( strlen( Buff ) > 255 ) Buff[255] = '\0';
 strcpy( topname, Buff );
 Buff = paux+1;
 /* is this line a version number ?                                                                     */
 sscanf( topname, "version %f", &ver_no );
 if( ver_no != 0 )
 {
  /* YES! so let's read another line, with the title                            */
  paux = strchr( Buff, '\n' );
  if( paux == NULL ) return IDS_ERR_BAD_TOPNAM;
  if( *(paux-1)=='\r' ) *(paux-1) = '\0';
  *paux = '\0';
  if( strlen( Buff ) > 255 ) Buff[255] = '\0';
  strcpy( topname, Buff );
  Buff = paux+1;
 }

 /* read nstep from the buffer                                                                          */
 if ( ( sscanf( Buff, " %d", &daux ) < 1) ||
      ( daux < 1 ) || ( daux > MAX_STEP ) )
  return IDS_ERR_BAD_NSTEP;
 nsteps = daux;

 Buff = strchr( Buff, ' ' );
 /* read totmet from the buffer                                                                 */
 if( (Buff == NULL ) || ( sscanf( ++Buff, " %d", &daux ) < 1) ||
     ( daux < 1 )   || ( daux > MAX_MET ) )
  return IDS_ERR_BAD_TOTMET;
 totmet = daux;

 /* read stoiu from the buffer                                                                          */
 for(i=0;i<totmet;i++)
  for(j=0;j<nsteps;j++)
  {
   if(j==0)
   {
    Buff = strchr( Buff, '\n' );
    if( Buff != NULL )
    {
     Buff++;
     for( ;*Buff == ' '; Buff++);
    }
   }
   else
   {
    Buff = strchr( Buff, ' ' );
    if( Buff != NULL ) for( ;*Buff == ' '; Buff++);
   }
   if ( (Buff == NULL) || (sscanf( Buff, "%d", &daux ) < 1) )
    return IDS_ERR_BAD_STOI;
   stoiu[i][j] = daux;
  }
 Buff = strchr( Buff, '\n' );
 if( Buff == NULL ) return IDS_ERR_BAD_KINTYPE;
 Buff++;
 /* read kinetu, revers and metname from the buffer                             */
 for( i=0; i<nsteps; i++ )
 {
  for( ;*Buff == ' '; Buff++);
  if ( (Buff == NULL) || (sscanf( Buff, "%d", &daux ) < 1)
       || (daux < -1) )
   return IDS_ERR_BAD_KINTYPE;
  kinetu[i] = daux;
  Buff = strchr( Buff, ' ' );
  if( Buff != NULL ) for( ;*Buff == ' '; Buff++);
  if ( (Buff == NULL) || (sscanf( Buff, "%d", &daux ) < 1) )
   return IDS_ERR_BAD_KINTYPE;
  revers[i] = daux;

  Buff = strchr( Buff, ' ' );
  if( Buff != NULL ) for( ;*Buff == ' '; Buff++);
  paux = strchr( Buff, '\n' );
  if( paux == NULL ) return IDS_ERR_BAD_KINTYPE;
  /* take care of CR if one existed before LF                                           */
  if( *(paux-1)=='\r' ) *(paux-1) = '\0';
  *paux = '\0';
  if( strlen( Buff ) >= NAME_L ) Buff[NAME_L-1] = '\0';
  strcpy( stepname[i], Buff );
  Buff = paux+1;
 }

 *(--Buff) = '\n';
 /* read rstr from the buffer                                                                           */
 for(i=0;i<nsteps;i++)
  for(j=0;j<MAX_MOL;j++)
  {
   if(j==0)
   {
    Buff = strchr( Buff, '\n' );
    if( Buff != NULL )
    {
     Buff++;
     for( ;*Buff == ' '; Buff++);
    }
   }
   else
   {
    Buff = strchr( Buff, ' ' );
    if( Buff != NULL ) for( ;*Buff == ' '; Buff++);
   }
   if ( (Buff == NULL) || (sscanf( Buff,"%d", &daux ) < 1) )
    return IDS_ERR_BAD_LOOP;
   (*rstr)[i][j] = (signed char) daux;
  }

 /* read loop from the buffer                                                                           */
 for(i=0;i<nsteps;i++)
  for(j=0;j<totmet;j++)
  {
   if(j==0)
   {
    Buff = strchr( Buff, '\n' );
    if( Buff != NULL )
    {
     Buff++;
     for( ;*Buff == ' '; Buff++);
    }
   }
   else
   {
    Buff = strchr( Buff, ' ' );
    if( Buff != NULL ) for( ;*Buff == ' '; Buff++);
   }
   if ( (Buff == NULL) || (sscanf( Buff,"%u", &uaux ) < 1)
	 || (uaux < 0) )
    return IDS_ERR_BAD_LOOP;
   (*loop)[i][j] = uaux;
  }

 /* read metabolite status and names from the buffer                            */
 for(i=0;i<totmet;i++)
 {
  Buff = strchr( Buff, '\n' );
  if ( (Buff == NULL) || (sscanf( ++Buff, "%d %21s", &daux, saux ) < 2) )
   return IDS_ERR_BAD_INTMET;
  intmet[i] = daux;
  strcpy( metname[i], saux );
 }

 /* point endofbuf to the end of the topology section                           */
 if( endoftop != NULL )
  *endoftop = Buff;
 /* return and signal that function was successful                                      */
 return 0;
}

int BufToTree( char *Buff, char **endoftree )
{
 int i;
 char  *paux;
 int daux, daux1, daux2;
 char caux[10];
 float faux;

 /* copy the title from the buffer                                                              */
 paux = strchr( Buff, '\n' );
 if( paux == NULL ) return IDS_ERR_LOAD;
 /* take care of CR if one existed before LF                                            */
 if( *(paux-1)=='\r' ) *(paux-1) = '\0';
 *paux = '\0';
 if( strlen( Buff ) > 63 ) Buff[63] = '\0';
 strcpy( tr.descr, Buff );
 Buff = paux+1;

 /* read nnode from the buffer                                                                          */
 if ( sscanf( Buff, "%d", &daux ) < 1 )
  return IDS_ERR_LOAD;
 tr.nnode = daux;

 Buff = strchr( Buff, ' ' );
 /* read nid from the buffer                                                                            */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.nid = daux;

 Buff = strchr( Buff, ' ' );
 /* read nnum from the buffer                                                                           */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.nnum = daux;

 Buff = strchr( Buff, ' ' );
 /* read nconst from the buffer                                                                 */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.nconst = daux;

 Buff = strchr( Buff, ' ' );
 /* read nsub from the buffer                                                                           */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.nsub = daux;

 Buff = strchr( Buff, ' ' );
 /* read npro from the buffer                                                                           */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.npro = daux;

 Buff = strchr( Buff, ' ' );
 /* read nmodf from the buffer                                                                  */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.nmodf = daux;

 Buff = strchr( Buff, ' ' );
 /* read revers from the buffer                                                                 */
 if( (Buff == NULL ) || ( sscanf( ++Buff, "%d", &daux ) < 1 ) )
  return IDS_ERR_LOAD;
 tr.revers = daux;

 Buff = strchr( Buff, '\n' );
 if( Buff==NULL ) return IDS_ERR_LOAD;
 Buff++;

 for( i=0; i<tr.nnode; i++ )
 {
  if( ( sscanf( Buff, "%c %d %d %d", &caux[0],
				     &daux,
				     &daux1,
				     &daux2 ) < 4 ) )
   return IDS_ERR_LOAD;
  tr.node[i].item  = caux[0];
  tr.node[i].val   = (unsigned char) daux;
  tr.node[i].left  = (unsigned char) daux1;
  tr.node[i].right = (unsigned char) daux2;
  Buff = strchr( Buff, ',' );
  if( Buff==NULL ) return IDS_ERR_LOAD;
  Buff++;
 }
 for( i=0; i<tr.nid; i++ )
 {
  Buff = strchr( Buff, '\n' );
  if( Buff==NULL ) return IDS_ERR_LOAD;
  Buff++;
  if( sscanf( Buff, "%d %8s", &daux, caux ) < 2 )
   return IDS_ERR_LOAD;
  strcpy( tr.id[i], caux );
  tr.id[i][8] = '\0';
  tr.id[i][9] = (char) daux;
 }
 for( i=0; i<tr.nnum; i++ )
 {
  Buff = strchr( Buff, '\n' );
  if( Buff==NULL ) return IDS_ERR_LOAD;
  Buff++;
  if( sscanf( Buff, "%g", &faux ) < 1 )
   return IDS_ERR_LOAD;
  tr.constant[i] = faux;
 }
 /* point endofbuf to the end of the topology section                           */
 if( endoftree != NULL )
  *endoftree = Buff;
  /**endoftree = strchr( Buff, '\n' );*/
 return 0;
}


int BufToSim( char *Buff )
{
 int i,j, dens, log, lkt, op, adj;
 double faux, low, high, fac;
 char  *ptr;
 char  *paux;

  /* read the kinetic constants from the buffer, one line per step      */
  for(i=0;i<nsteps;i++)
  {
   Buff = strchr( Buff, '\n' );
   if( Buff != NULL ) Buff++;
   for( j=0; j<(int)ktype[kinetype[i]].nconst; j++ )
   {
    Buff = strchr( Buff, ' ' );
    if( Buff != NULL ) for( ;*Buff == ' '; Buff++);
    if ( (Buff == NULL) || (sscanf( Buff,"%le", &faux ) < 1) )
     return IDS_ERR_BAD_KPARAM;
    *(params[i]+j) = faux;
   }
  }
  /* read the concentrations, one per line                                                      */
  for(i=0;i<totmet;i++)
  {
   Buff = strchr( Buff, '\n' );
   if( Buff != NULL )
    Buff++;
   if ( (Buff == NULL) || (sscanf( Buff,"%le", &faux ) < 1) )
    return IDS_ERR_BAD_CONCENT;
   x0[i] = x[i] = faux;
  }

  /* read the units in one line                                                                                 */
  Buff = strchr( Buff, '\n' );
  if( Buff != NULL ) Buff++;
  if ( (Buff == NULL) || (sscanf( Buff,"%s %s", &options.concu[0], &options.timeu[0] ) < 2) )
   return IDS_ERR_BAD_UNITS;

  /* read log, dyn and ss options in one line                                                   */
  Buff = strchr( Buff, '\n' );
  if( Buff != NULL )
   Buff++;
  if ( (Buff == NULL) || (sscanf( Buff,"%d %d %ld %le %le %le %le %d %d %d",
	  &options.debug, &options.dyn, &options.pfo, &options.endtime,
	  &options.reltol, &options.abstol, &options.hrcz, &options.adams,
	  &options.bdf, &options.ss ) < 10 ) )
   return IDS_ERR_BAD_OPTIONS;
  endtime = options.endtime;

  /* read txt options in one line                                                                               */
  Buff = strchr( Buff, '\n' );
  if( Buff != NULL )
   Buff++;
  if ( (Buff == NULL) || (sscanf( Buff,"%d %d %d %d %d %d %d",
	  &options.txt, &options.structan, &options.staban,
	  &options.stdela, &options.nonela, &options.stdcc,
	  &options.noncc ) < 7 ) )
   return IDS_ERR_BAD_OPTIONS;
  /* read the dat options in one line                                                                   */
  Buff = strchr( Buff, '\n' );