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gentoo-overlay/sci-biology/qrna/files/qrna-2.0.3c-glibc-2.10.patch

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diff -ur qrna-2.0.3c.orig/squid/sqio.c qrna-2.0.3c/squid/sqio.c
--- qrna-2.0.3c.orig/squid/sqio.c 2005-05-11 19:30:51.000000000 +0300
+++ qrna-2.0.3c/squid/sqio.c 2009-08-05 22:27:20.000000000 +0300
@@ -215,7 +215,7 @@
}
static void
-getline(struct ReadSeqVars *V)
+get_line(struct ReadSeqVars *V)
{
readline(V->f, V->sbuffer);
}
@@ -277,7 +277,7 @@
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
- getline(V);
+ get_line(V);
/* feof() alone is a bug; files not necessarily \n terminated */
if (*(V->sbuffer) == '\0' && feof(V->f))
done = TRUE;
@@ -305,7 +305,7 @@
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)
@@ -314,7 +314,7 @@
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)
@@ -323,7 +323,7 @@
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);
@@ -337,7 +337,7 @@
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
}
@@ -355,7 +355,7 @@
char *nm;
/* position past ';' comments */
do {
- getline(V);
+ get_line(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
@@ -367,7 +367,7 @@
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
- getline(V);
+ get_line(V);
}
static int
@@ -389,7 +389,7 @@
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
- getline(V);
+ get_line(V);
}
if (! feof(V->f))
@@ -398,7 +398,7 @@
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
- getline(V);
+ get_line(V);
}
@@ -416,7 +416,7 @@
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
- getline(V);
+ get_line(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
@@ -427,7 +427,7 @@
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)
@@ -460,11 +460,11 @@
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
@@ -494,12 +494,12 @@
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);
}
@@ -529,7 +529,7 @@
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) {
@@ -549,7 +549,7 @@
else readLoop(0, endGCGdata, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
static int
@@ -571,7 +571,7 @@
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
@@ -598,7 +598,7 @@
/* 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)
{
@@ -607,7 +607,7 @@
}
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)
@@ -631,7 +631,7 @@
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -647,7 +647,7 @@
{
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);
@@ -658,7 +658,7 @@
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
- getline(V);
+ get_line(V);
}
static void
@@ -680,7 +680,7 @@
do {
done = feof(V->f);
- getline(V);
+ get_line(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
@@ -692,7 +692,7 @@
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);
@@ -700,7 +700,7 @@
/*CONSTCOND*/
while (1)
{
- getline(V);
+ get_line(V);
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
if (strncmp(V->sbuffer, "SRC ", 4) == 0)
@@ -732,14 +732,14 @@
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);
}
@@ -747,7 +747,7 @@
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -786,7 +786,7 @@
/* Load the first line.
*/
- getline(dbfp);
+ get_line(dbfp);
return dbfp;
}
@@ -800,7 +800,7 @@
SeqfilePosition(SQFILE *sqfp, long offset)
{
fseek(sqfp->f, offset, SEEK_SET);
- getline(sqfp);
+ get_line(sqfp);
}
@@ -817,7 +817,7 @@
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
else {
rewind(sqfp->f);
- getline(sqfp);
+ get_line(sqfp);
}
}
@@ -912,7 +912,7 @@
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;
@@ -991,7 +991,7 @@
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;
@@ -1098,7 +1098,7 @@
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;
@@ -1204,7 +1204,7 @@
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;
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