svn commit: r415128 - head/biology/tRNAscan-SE/files
Baptiste Daroussin
bapt at FreeBSD.org
Fri May 13 18:38:36 UTC 2016
Author: bapt
Date: Fri May 13 18:38:34 2016
New Revision: 415128
URL: https://svnweb.freebsd.org/changeset/ports/415128
Log:
Prevent collision with getline(3)
Added:
head/biology/tRNAscan-SE/files/patch-sqio.c (contents, props changed)
Added: head/biology/tRNAscan-SE/files/patch-sqio.c
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/tRNAscan-SE/files/patch-sqio.c Fri May 13 18:38:34 2016 (r415128)
@@ -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;
+
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