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pkgsrc-wip/emboss-hmmer/patches/patch-ac

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$NetBSD: patch-ac,v 1.2 2011/10/26 14:52:36 noud4 Exp $
--- src/sqio.c.orig 2011-10-26 13:18:53.000000000 +0000
+++ src/sqio.c 2011-10-26 13:18:55.000000000 +0000
@@ -219,7 +219,7 @@
}
}
-/* Function: getline()
+/* Function: mygetline()
* Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
*
* Purpose: read a line from a sequence file into V->sbuffer.
@@ -235,7 +235,7 @@
* Returns: (void)
*/
static void
-getline(struct ReadSeqVars *V)
+mygetline(struct ReadSeqVars *V)
{
char *cp;
@@ -305,7 +305,7 @@
V->seqlen = 0;
if (addfirst) addseq(V->sbuffer, V);
do {
- getline(V);
+ mygetline(V);
/* feof() alone is a bug; files not necessarily \n terminated */
if (*(V->sbuffer) == '\0' && feof(V->f))
done = TRUE;
@@ -333,7 +333,7 @@
char *sptr;
/* load first line of entry */
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ mygetline(V);
if (feof(V->f)) return;
if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
@@ -342,7 +342,7 @@
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
}
do {
- getline(V);
+ mygetline(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)
@@ -351,7 +351,7 @@
SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
}
} while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
- getline(V); /* skip next line, coords */
+ mygetline(V); /* skip next line, coords */
readLoop(0, endPIR, V);
@@ -365,7 +365,7 @@
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ mygetline(V);
}
@@ -383,7 +383,7 @@
char *nm;
/* position past ';' comments */
do {
- getline(V);
+ mygetline(V);
} while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
if (!feof(V->f))
@@ -395,7 +395,7 @@
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
- getline(V);
+ mygetline(V);
}
static int
@@ -417,7 +417,7 @@
if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
}
- getline(V);
+ mygetline(V);
}
if (! feof(V->f))
@@ -426,7 +426,7 @@
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
- getline(V);
+ mygetline(V);
}
@@ -444,7 +444,7 @@
int in_definition;
while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
- getline(V);
+ mygetline(V);
if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
{
@@ -455,7 +455,7 @@
in_definition = FALSE;
while (! feof(V->f))
{
- getline(V);
+ mygetline(V);
if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
@@ -488,11 +488,11 @@
while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
- getline(V);
+ mygetline(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);
+ mygetline(V);
}
static int
@@ -521,7 +521,7 @@
Die("bogus GCGdata format? %s", V->sbuffer);
/* second line contains free text description */
- getline(V);
+ mygetline(V);
SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
if (binary) {
@@ -541,7 +541,7 @@
else readLoop(0, endGCGdata, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ mygetline(V);
}
static int
@@ -561,12 +561,12 @@
if ((sptr = strtok(NULL, "\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
/* workaround for long NCBI NR lines */
- while (V->longline && ! feof(V->f)) getline(V);
+ while (V->longline && ! feof(V->f)) mygetline(V);
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ mygetline(V);
}
@@ -593,7 +593,7 @@
/* make sure we have first line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ mygetline(V);
if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
{
@@ -602,7 +602,7 @@
}
do {
- getline(V);
+ mygetline(V);
if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer)
{
if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL)
@@ -626,7 +626,7 @@
/* load next record's ID line */
while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0)
- getline(V);
+ mygetline(V);
}
@@ -642,7 +642,7 @@
{
char *sptr;
- getline(V); /*s == "seqLen seqid string..."*/
+ mygetline(V); /*s == "seqLen seqid string..."*/
if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -653,7 +653,7 @@
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
- getline(V);
+ mygetline(V);
}
static void
@@ -675,7 +675,7 @@
do {
done = feof(V->f);
- getline(V);
+ mygetline(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
@@ -687,7 +687,7 @@
char *sptr;
int dostruc = FALSE;
- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) mygetline(V);
if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
@@ -695,7 +695,7 @@
/*CONSTCOND*/
while (1)
{
- getline(V);
+ mygetline(V);
if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
if (strncmp(V->sbuffer, "SRC ", 4) == 0)
@@ -727,14 +727,14 @@
while (1)
{
/* sequence line */
- getline(V);
+ mygetline(V);
if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0)
break;
addseq(V->sbuffer, V);
/* structure line */
if (dostruc)
{
- getline(V);
+ mygetline(V);
if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
addstruc(V->sbuffer, V);
}
@@ -742,7 +742,7 @@
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
- getline(V);
+ mygetline(V);
}
@@ -822,7 +822,7 @@
/* Load the first line.
*/
- getline(dbfp);
+ mygetline(dbfp);
return dbfp;
}
@@ -839,7 +839,7 @@
Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
fseek(sqfp->f, offset, SEEK_SET);
- getline(sqfp);
+ mygetline(sqfp);
}
@@ -859,7 +859,7 @@
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
else {
rewind(sqfp->f);
- getline(sqfp);
+ mygetline(sqfp);
}
}
@@ -954,7 +954,7 @@
do { /* skip leading comments on GCG file */
gotuw = (strstr(V->sbuffer,"..") != NULL);
if (gotuw) readUWGCG(V);
- getline(V);
+ mygetline(V);
} while (! feof(V->f));
break;
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