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gentoo-overlay/sci-biology/wise/files/wise-2.4.0_alpha-glibc-2.10...

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diff --git a/src/HMMer2/sqio.c b/src/HMMer2/sqio.c
index 5889e7d..bc95629 100644
--- a/src/HMMer2/sqio.c
+++ b/src/HMMer2/sqio.c
@@ -213,7 +213,7 @@ readline(FILE *f, char *s)
}
}
-/* Function: getline()
+/* Function: get_line()
* Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis]
*
* Purpose: read a line from a sequence file into V->sbuffer.
@@ -229,7 +229,7 @@ readline(FILE *f, char *s)
* Returns: (void)
*/
static void
-getline(struct ReadSeqVars *V)
+get_line(struct ReadSeqVars *V)
{
char *cp;
@@ -299,7 +299,7 @@ readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
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;
@@ -327,7 +327,7 @@ 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)
@@ -336,7 +336,7 @@ 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)
@@ -345,7 +345,7 @@ 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);
@@ -359,7 +359,7 @@ readPIR(struct ReadSeqVars *V)
/* get next line
*/
while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
- getline(V);
+ get_line(V);
}
@@ -377,7 +377,7 @@ 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))
@@ -389,7 +389,7 @@ readIG(struct ReadSeqVars *V)
}
while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
- getline(V);
+ get_line(V);
}
static int
@@ -411,7 +411,7 @@ 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))
@@ -420,7 +420,7 @@ readStrider(struct ReadSeqVars *V)
/* load next line
*/
while ((!feof(V->f)) && (*V->sbuffer != ';'))
- getline(V);
+ get_line(V);
}
@@ -438,7 +438,7 @@ 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)
{
@@ -449,7 +449,7 @@ 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)
@@ -482,11 +482,11 @@ 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
@@ -515,7 +515,7 @@ readGCGdata(struct ReadSeqVars *V)
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) {
@@ -535,7 +535,7 @@ 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
@@ -555,12 +555,12 @@ readPearson(struct ReadSeqVars *V)
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)) get_line(V);
readLoop(0, endPearson, V);
while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
- getline(V);
+ get_line(V);
}
@@ -587,7 +587,7 @@ 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)
{
@@ -596,7 +596,7 @@ 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)
@@ -620,7 +620,7 @@ 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);
}
@@ -636,7 +636,7 @@ 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);
@@ -647,7 +647,7 @@ readZuker(struct ReadSeqVars *V)
readLoop(0, endZuker, V);
while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
- getline(V);
+ get_line(V);
}
static void
@@ -669,7 +669,7 @@ readUWGCG(struct ReadSeqVars *V)
do {
done = feof(V->f);
- getline(V);
+ get_line(V);
if (! done) addseq(V->sbuffer, V);
} while (!done);
}
@@ -681,7 +681,7 @@ 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);
@@ -689,7 +689,7 @@ 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)
@@ -721,14 +721,14 @@ 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);
}
@@ -736,7 +736,7 @@ readSquid(struct ReadSeqVars *V)
while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
- getline(V);
+ get_line(V);
}
@@ -816,7 +816,7 @@ SeqfileOpen(char *filename, int format, char *env)
/* Load the first line.
*/
- getline(dbfp);
+ get_line(dbfp);
return dbfp;
}
@@ -833,7 +833,7 @@ SeqfilePosition(SQFILE *sqfp, long offset)
Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
fseek(sqfp->f, offset, SEEK_SET);
- getline(sqfp);
+ get_line(sqfp);
}
@@ -853,7 +853,7 @@ SeqfileRewind(SQFILE *sqfp)
if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0;
else {
rewind(sqfp->f);
- getline(sqfp);
+ get_line(sqfp);
}
}
@@ -949,7 +949,7 @@ ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
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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