117 lines
2.5 KiB
Text
117 lines
2.5 KiB
Text
--- fmtseq.c.orig Wed Jul 10 12:58:39 1996
|
|
+++ fmtseq.c Tue Aug 21 13:17:23 2001
|
|
@@ -37,7 +37,6 @@
|
|
#include <sys/stat.h>
|
|
#include "seqio.h"
|
|
|
|
-extern char *sys_errlist[];
|
|
|
|
|
|
#ifdef WIN32
|
|
@@ -70,6 +69,7 @@
|
|
#define ASK 2
|
|
#define ITEMLIST 3
|
|
|
|
+#define MAXLINE 128
|
|
|
|
int pretty_flag, pretty_count;
|
|
FILE *fpout;
|
|
@@ -81,7 +81,7 @@
|
|
} pretty;
|
|
|
|
|
|
-char dna_complement[128], rna_complement[128];
|
|
+char dna_complement[MAXLINE], rna_complement[MAXLINE];
|
|
|
|
|
|
/*
|
|
@@ -222,7 +222,7 @@
|
|
void print_options(int flag)
|
|
{
|
|
int i, j;
|
|
- char line[128];
|
|
+ char line[MAXLINE];
|
|
|
|
printf("Program Options (text in [...] is optional):\n");
|
|
printf(" -al[l] select all sequences\n");
|
|
@@ -249,7 +249,7 @@
|
|
|
|
if (flag) {
|
|
printf("More? ");
|
|
- gets(line);
|
|
+ fgets(line,MAXLINE-1,stdin);
|
|
if (line[0] == 'q' || line[0] == 'Q')
|
|
return;
|
|
}
|
|
@@ -264,7 +264,7 @@
|
|
|
|
if (flag) {
|
|
printf("More? ");
|
|
- gets(line);
|
|
+ fgets(line,MAXLINE-1,stdin);
|
|
if (line[0] == 'q' || line[0] == 'Q')
|
|
return;
|
|
}
|
|
@@ -1646,7 +1646,7 @@
|
|
s = line;
|
|
while (*s == '\0') {
|
|
printf("Enter: ");
|
|
- gets(line);
|
|
+ fgets(line,MAXLINE-1,stdin);
|
|
for (s=line; *s && isspace(*s); s++) ;
|
|
}
|
|
printf("----------------------\n\n");
|
|
@@ -1701,7 +1701,7 @@
|
|
{
|
|
static char defch = 'y';
|
|
int init_print, count;
|
|
- char *s, *entry, *eptr, line[128];
|
|
+ char *s, *entry, *eptr, line[MAXLINE];
|
|
|
|
putchar('\n');
|
|
if (seqcount == 1) {
|
|
@@ -1717,7 +1717,7 @@
|
|
eptr = entry = NULL;
|
|
while (1) {
|
|
printf("Select? [%c] ", defch);
|
|
- gets(line);
|
|
+ fgets(line,MAXLINE-1,stdin);
|
|
|
|
if (line[0] == '\0')
|
|
line[0] = defch;
|
|
@@ -1771,7 +1771,7 @@
|
|
SEQINFO *info, int mode)
|
|
{
|
|
int len;
|
|
- char *temp, tempbuffer[128];
|
|
+ char *temp, tempbuffer[MAXLINE];
|
|
|
|
if (buf != NULL)
|
|
temp = buf;
|
|
@@ -1803,7 +1803,7 @@
|
|
|
|
int pretty_store(char *seq, int seqlen, SEQINFO *info)
|
|
{
|
|
- char buffer[128];
|
|
+ char buffer[MAXLINE];
|
|
|
|
if (pretty_count == psize) {
|
|
if (psize == 0) {
|
|
@@ -2582,7 +2582,7 @@
|
|
|
|
void blastout_store(SEQFILE *sfp, char *seq, int seqlen, SEQINFO *info)
|
|
{
|
|
- static otherstrand = 0;
|
|
+ static int otherstrand = 0;
|
|
int pos, al_start, ingap, len;
|
|
char *s, *t1, *entry, *end, *line1, *line2;
|
|
ALIGN newalign;
|
|
@@ -3017,7 +3017,7 @@
|
|
{
|
|
int i;
|
|
|
|
- for (i=0; i < 128; i++)
|
|
+ for (i=0; i < MAXLINE; i++)
|
|
dna_complement[i] = dna_complement[i] = i;
|
|
|
|
dna_complement['a'] = 't'; dna_complement['A'] = 'T';
|