static FILE *gunzip(const char *fn,const char *mode)
{
FILE *fp;
char buf[256];
sprintf(buf,"gunzip -c < %s",fn);
fprintf(stderr,"Going to execute '%s'\n",buf);
if ((fp=popen(buf,mode)) == NULL)
gmx_open(fn);
push_ps(fp);
return fp;
}
static FILE *uncompress(const char *fn, const char *mode)
{
FILE *fp;
char buf[256];
sprintf(buf, "uncompress -c < %s", fn);
fprintf(stderr, "Going to execute '%s'\n", buf);
if ((fp = popen(buf, mode)) == NULL)
{
gmx_open(fn);
}
push_ps(fp);
return fp;
}
/*****************************************************************
*
* EXPORTED SECTION
*
*****************************************************************/
t_fileio *gmx_fio_open(const char *fn, const char *mode)
{
t_fileio *fio = NULL;
int i;
char newmode[5];
gmx_bool bRead, bReadWrite;
int xdrid;
if (fn2ftp(fn) == efTPA)
{
strcpy(newmode, mode);
}
else
{
/* sanitize the mode string */
if (strncmp(mode, "r+", 2) == 0)
{
strcpy(newmode, "r+");
}
else if (mode[0] == 'r')
{
strcpy(newmode, "r");
}
else if (strncmp(mode, "w+", 2) == 0)
{
strcpy(newmode, "w+");
}
else if (mode[0] == 'w')
{
strcpy(newmode, "w");
}
else if (strncmp(mode, "a+", 2) == 0)
{
strcpy(newmode, "a+");
}
else if (mode[0] == 'a')
{
strcpy(newmode, "a");
}
else
{
gmx_fatal(FARGS, "DEATH HORROR in gmx_fio_open, mode is '%s'", mode);
}
}
/* Check if it should be opened as a binary file */
if (strncmp(ftp2ftype(fn2ftp(fn)), "ASCII", 5))
{
/* Not ascii, add b to file mode */
if ((strchr(newmode, 'b') == NULL) && (strchr(newmode, 'B') == NULL))
{
strcat(newmode, "b");
}
}
snew(fio, 1);
#ifdef GMX_THREAD_MPI
tMPI_Lock_init(&(fio->mtx));
#endif
bRead = (newmode[0] == 'r' && newmode[1] != '+');
bReadWrite = (newmode[1] == '+');
fio->fp = NULL;
fio->xdr = NULL;
if (fn)
{
fio->iFTP = fn2ftp(fn);
fio->fn = strdup(fn);
fio->bStdio = FALSE;
/* If this file type is in the list of XDR files, open it like that */
if (in_ftpset(fio->iFTP, asize(ftpXDR), ftpXDR))
{
/* First check whether we have to make a backup,
* only for writing, not for read or append.
*/
if (newmode[0] == 'w')
{
#ifndef GMX_FAHCORE
/* only make backups for normal gromacs */
make_backup(fn);
#endif
}
else
{
/* Check whether file exists */
if (!gmx_fexist(fn))
{
gmx_open(fn);
}
}
/* Open the file */
fio->fp = ffopen(fn, newmode);
/* determine the XDR direction */
if (newmode[0] == 'w' || newmode[0] == 'a')
{
fio->xdrmode = XDR_ENCODE;
}
else
{
fio->xdrmode = XDR_DECODE;
}
snew(fio->xdr, 1);
xdrstdio_create(fio->xdr, fio->fp, fio->xdrmode);
}
else
{
/* If it is not, open it as a regular file */
fio->fp = ffopen(fn, newmode);
}
/* for appending seek to end of file to make sure ftell gives correct position
* important for checkpointing */
if (newmode[0] == 'a')
{
gmx_fseek(fio->fp, 0, SEEK_END);
}
}
else
{
/* Use stdin/stdout for I/O */
fio->iFTP = efTPA;
fio->fp = bRead ? stdin : stdout;
fio->fn = strdup("STDIO");
fio->bStdio = TRUE;
}
fio->bRead = bRead;
fio->bReadWrite = bReadWrite;
fio->bDouble = (sizeof(real) == sizeof(double));
fio->bDebug = FALSE;
fio->bOpen = TRUE;
fio->bLargerThan_off_t = FALSE;
/* set the reader/writer functions */
gmx_fio_set_iotype(fio);
/* and now insert this file into the list of open files. */
gmx_fio_insert(fio);
return fio;
}
/*****************************************************************
*
* EXPORTED SECTION
*
*****************************************************************/
int gmx_fio_open(const char *fn,const char *mode)
{
t_fileio *fio=NULL;
int i,nfio=0;
char *bf,newmode[5];
bool bRead;
int xdrid;
if (fn2ftp(fn)==efTPA)
{
strcpy(newmode,mode);
}
else
{
if (mode[0]=='r')
{
strcpy(newmode,"r");
}
else if (mode[0]=='w')
{
strcpy(newmode,"w");
}
else if (mode[0]=='a')
{
strcpy(newmode,"a");
}
else
{
gmx_fatal(FARGS,"DEATH HORROR in gmx_fio_open, mode is '%s'",mode);
}
}
/* Check if it should be opened as a binary file */
if (strncmp(ftp2ftype(fn2ftp(fn)),"ASCII",5))
{
/* Not ascii, add b to file mode */
if ((strchr(newmode,'b')==NULL) && (strchr(newmode,'B')==NULL))
{
strcat(newmode,"b");
}
}
/* Determine whether we have to make a new one */
for(i=0; (i<nFIO); i++)
{
if (!FIO[i].bOpen)
{
fio = &(FIO[i]);
nfio = i;
break;
}
}
if (i == nFIO)
{
nFIO++;
srenew(FIO,nFIO);
fio = &(FIO[nFIO-1]);
nfio = nFIO-1;
}
bRead = (newmode[0]=='r');
fio->fp = NULL;
fio->xdr = NULL;
if (fn)
{
fio->iFTP = fn2ftp(fn);
fio->fn = strdup(fn);
fio->bStdio = FALSE;
/* If this file type is in the list of XDR files, open it like that */
if (in_ftpset(fio->iFTP,asize(ftpXDR),ftpXDR))
{
/* First check whether we have to make a backup,
* only for writing, not for read or append.
*/
if (newmode[0]=='w')
{
#ifndef GMX_FAHCORE
/* only make backups for normal gromacs */
if (gmx_fexist(fn))
{
bf=(char *)backup_fn(fn);
if (rename(fn,bf) == 0)
{
fprintf(stderr,"\nBack Off! I just backed up %s to %s\n",fn,bf);
}
else
{
fprintf(stderr,"Sorry, I couldn't backup %s to %s\n",fn,bf);
}
}
#endif
}
else
{
/* Check whether file exists */
if (!gmx_fexist(fn))
{
gmx_open(fn);
}
}
snew(fio->xdr,1);
xdrid = xdropen(fio->xdr,fn,newmode);
if (xdrid == 0)
{
if(newmode[0]=='r')
gmx_fatal(FARGS,"Cannot open file %s for reading\nCheck permissions if it exists.",fn);
else
gmx_fatal(FARGS,"Cannot open file %s for writing.\nCheck your permissions, disk space and/or quota.",fn);
}
fio->fp = xdr_get_fp(xdrid);
}
else
{
/* If it is not, open it as a regular file */
fio->fp = ffopen(fn,newmode);
}
}
else
{
/* Use stdin/stdout for I/O */
fio->iFTP = efTPA;
fio->fp = bRead ? stdin : stdout;
fio->fn = strdup("STDIO");
fio->bStdio = TRUE;
}
fio->bRead = bRead;
fio->bDouble= (sizeof(real) == sizeof(double));
fio->bDebug = FALSE;
fio->bOpen = TRUE;
return nfio;
}
