static void add (char c, char* *buf, int *buflen, int n)
{
if (!buf)
return ;
if (n >= *buflen)
{ if (*buflen < 0)
{ *buflen = -*buflen ;
*buf = (char*) messalloc (*buflen) ;
}
else
{ char *newbuf ;
*buflen *= 2 ;
newbuf = (char*) messalloc (*buflen) ;
memcpy (newbuf, *buf, n) ;
messfree (*buf) ;
*buf = newbuf ;
}
}
(*buf)[n] = c ;
}
static void add (char c, char* *buf, int *buflen, int n)
{
if (n >= *buflen)
{
int blen = *buflen;
if (blen < 0)
{ blen = -blen ;
*buf = (char*) messalloc (blen) ;
}
else
{ blen *= 2 ;
if ((*buf = realloc(*buf,blen)) == NULL)
{ fprintf (stderr, "REALLOC failure reqesting %d bytes - aborting\n", blen) ;
exit (-1) ;
}
}
*buflen = blen;
}
(*buf)[n] = c;
}
int readMatrix (char *name, int *conv, int** *mat)
{
char matdirname[256] ;
char fullname[512] ;
FILE *fil ;
char line[1024] = "#", *p;
int i, j, nsymb, smax = 0 ;
int symb[128] ;
extern char* strtok (char*, const char*) ;
if (getenv ("BLASTMAT"))
strcpy (matdirname, getenv ("BLASTMAT")) ;
else
strcpy (matdirname, "/nfs/disk100/pubseq/blastdb/") ;
strcpy (fullname, matdirname) ;
strcat (fullname, name) ;
if (!(fil = fopen (name, "r")) && !(fil = fopen (fullname, "r")))
{ fprintf (stderr, "ERROR in readMatrix: could not open %s or %s\n",
name, matdirname) ;
return 0 ;
}
while (!feof(fil) && *line == '#') /* comments */
fgets (line, 1023, fil) ;
/* character set */
p = line ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
for (i = 0 ; *p && i < 128 ; ++i)
{ symb[i] = conv[*p] ;
if (symb[i] < -2)
{ fprintf (stderr, "ERROR in readMatrix: illegal symbol %c\n", *p) ;
fclose (fil) ;
return 0 ;
}
if (symb[i] > smax)
smax = symb[i] ;
++p ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
}
nsymb = i ;
++smax ;
*mat = (int**) messalloc (smax * sizeof (int*)) ;
for (i = 0 ; i < smax ; ++i)
(*mat)[i] = (int*) messalloc (smax * sizeof (int)) ;
for (i = 0 ; fgets(line, 1023, fil) && i < nsymb ; ++i)
{ p = line ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
if (p && conv[*p] == symb[i])
{ ++p ; while (*p == ' ' || *p == '\t' || *p == '\n') ++p ; }
for (j = 0 ; *p && j < 128 ; ++j)
{ if (symb[i] >= 0 && symb[j] >= 0)
(*mat)[symb[i]][symb[j]] = atoi(p) ;
if (*p == '-') ++p ;
while (p && *p >= '0' && *p <= '9') ++p ;
while (*p == ' ' || *p == '\t' || *p == '\n') ++p ;
}
if (j != nsymb)
{ fprintf (stderr, "ERROR in readMatrix: bad line: %s\n", line) ;
fclose (fil) ;
return 0 ;
}
}
fclose (fil) ;
return 1 ;
}
