| 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; |
| |