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Prevent collision with getline(3)

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This commit is contained in:
Baptiste Daroussin 2016-05-13 18:38:34 +00:00
parent 7250841fe9
commit b8902fca51
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=415128
1 changed files with 291 additions and 0 deletions
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291
biology/tRNAscan-SE/files/patch-sqio.c Normal file
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@ -0,0 +1,291 @@
--- sqio.c.orig 2002-04-12 20:12:04 UTC
+++ sqio.c
@@ -235,7 +235,7 @@ readline(FILE *f, char *s)
}
static void
-getline(struct ReadSeqVars *V)
+get_line(struct ReadSeqVars *V)
{
readline(V->f, V->sbuffer);
}
@@ -306,7 +306,7 @@ readLoop(int addfirst, int (*endTest)(ch
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
- getline(V);
+ get_line(V);
done = feof(V->f);
done |= (*endTest)(V->sbuffer, &addend);
if (addend || !done)
@@ -332,7 +332,7 @@ readPIR(struct ReadSeqVars *V)
char *sptr;
/* load first line of entry */
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
if (feof(V->f)) return;
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
@@ -341,7 +341,7 @@ readPIR(struct ReadSeqVars *V)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
- getline(V);
+ get_line(V);
if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
@@ -350,7 +350,7 @@ readPIR(struct ReadSeqVars *V)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
- getline(V); /* skip next line, coords */
+ get_line(V); /* skip next line, coords */
readLoop(0, endPIR, V);
@@ -364,7 +364,7 @@ readPIR(struct ReadSeqVars *V)
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
}
@@ -382,7 +382,7 @@ readIG(struct ReadSeqVars *V)
char *nm;
/* position past ';' comments */
do {
- getline(V);
+ get_line(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
@@ -394,7 +394,7 @@ readIG(struct ReadSeqVars *V)
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
- getline(V);
+ get_line(V);
}
static int
@@ -416,7 +416,7 @@ readStrider(struct ReadSeqVars *V)
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
- getline(V);
+ get_line(V);
}
if (! feof(V->f))
@@ -425,7 +425,7 @@ readStrider(struct ReadSeqVars *V)
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
- getline(V);
+ get_line(V);
}
@@ -443,7 +443,7 @@ readGenBank(struct ReadSeqVars *V)
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
@@ -454,7 +454,7 @@ readGenBank(struct ReadSeqVars *V)
in_definition = FALSE;
while (! feof(V->f))
{
- getline(V);
+ get_line(V);
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
@@ -487,11 +487,11 @@ readGenBank(struct ReadSeqVars *V)
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
- getline(V);
+ get_line(V);
/* SRE: V->s now holds "//", so sequential
reads are wedged: fixed Tue Jul 13 1993 */
while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer)
- getline(V);
+ get_line(V);
}
static int
@@ -521,12 +521,12 @@ readNBRF(struct ReadSeqVars *V)
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
- getline(V); /*skip title-junk line*/
+ get_line(V); /*skip title-junk line*/
readLoop(0, endNBRF, V);
while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
- getline(V);
+ get_line(V);
}
@@ -559,7 +559,7 @@ readGCGdata(struct ReadSeqVars *V)
} else Die("bogus GCGdata format? %s", V->sbuffer);
/* second line contains free text description */
- getline(V);
+ get_line(V);
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
if (binary) {
@@ -579,7 +579,7 @@ readGCGdata(struct ReadSeqVars *V)
else readLoop(0, endGCGdata, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
static int
@@ -625,7 +625,7 @@ readPearson(struct ReadSeqVars *V)
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
@@ -652,7 +652,7 @@ readEMBL(struct ReadSeqVars *V)
/* make sure we have first line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
{
@@ -661,7 +661,7 @@ readEMBL(struct ReadSeqVars *V)
}
do {
- getline(V);
+ get_line(V);
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
@@ -685,7 +685,7 @@ readEMBL(struct ReadSeqVars *V)
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -701,7 +701,7 @@ readZuker(struct ReadSeqVars *V)
{
char *sptr;
- getline(V); /*s == "seqLen seqid string..."*/
+ get_line(V); /*s == "seqLen seqid string..."*/
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -712,7 +712,7 @@ readZuker(struct ReadSeqVars *V)
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
- getline(V);
+ get_line(V);
}
static void
@@ -734,7 +734,7 @@ readUWGCG(struct ReadSeqVars *V)
do {
done = feof(V->f);
- getline(V);
+ get_line(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
@@ -746,7 +746,7 @@ readSquid(struct ReadSeqVars *V)
char *sptr;
int dostruc = FALSE;
- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -754,7 +754,7 @@ readSquid(struct ReadSeqVars *V)
/*CONSTCOND*/
while (1)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
if (strncmp(V->sbuffer, "SRC ", 4) == 0)
@@ -786,14 +786,14 @@ readSquid(struct ReadSeqVars *V)
while (1)
{
/* sequence line */
- getline(V);
+ get_line(V);
if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
break;
addseq(V->sbuffer, V);
/* structure line */
if (dostruc)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
addstruc(V->sbuffer, V);
}
@@ -801,7 +801,7 @@ readSquid(struct ReadSeqVars *V)
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -848,7 +848,7 @@ SeqfileOpen(char *filename, int format,
/* Load the first line.
*/
- getline(dbfp);
+ get_line(dbfp);
return dbfp;
}
@@ -862,7 +862,7 @@ void
SeqfilePosition(SQFILE *sqfp, long offset)
{
fseek(sqfp->f, offset, SEEK_SET);
- getline(sqfp);
+ get_line(sqfp);
}
@@ -954,7 +954,7 @@ ReadSeq(SQFILE *V, int format, char **re
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ get_line(V);
} while (! feof(V->f));
break;