Author: Philipp Benner Last-Update: Sat, 31 Oct 2009 21:25:52 +0000 Bug-Debian: http://bugs.debian.org/552821 Description: Fixed conflicting definitions of getline(). --- wise-2.4.1.orig/src/HMMer2/sqio.c +++ wise-2.4.1/src/HMMer2/sqio.c @@ -213,7 +213,7 @@ } } -/* Function: getline() +/* Function: getline_() * 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 @@ * Returns: (void) */ static void -getline(struct ReadSeqVars *V) +getline_(struct ReadSeqVars *V) { char *cp; @@ -299,7 +299,7 @@ V->seqlen = 0; if (addfirst) addseq(V->sbuffer, V); do { - getline(V); + getline_(V); /* feof() alone is a bug; files not necessarily \n terminated */ if (*(V->sbuffer) == '\0' && feof(V->f)) done = TRUE; @@ -327,7 +327,7 @@ char *sptr; /* load first line of entry */ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) - getline(V); + getline_(V); if (feof(V->f)) return; if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) @@ -336,7 +336,7 @@ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); } do { - getline(V); + getline_(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 @@ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); } } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); - getline(V); /* skip next line, coords */ + getline_(V); /* skip next line, coords */ readLoop(0, endPIR, V); @@ -359,7 +359,7 @@ /* get next line */ while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) - getline(V); + getline_(V); } @@ -377,7 +377,7 @@ char *nm; /* position past ';' comments */ do { - getline(V); + getline_(V); } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); if (!feof(V->f)) @@ -389,7 +389,7 @@ } while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) - getline(V); + getline_(V); } static int @@ -411,7 +411,7 @@ if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); } - getline(V); + getline_(V); } if (! feof(V->f)) @@ -420,7 +420,7 @@ /* load next line */ while ((!feof(V->f)) && (*V->sbuffer != ';')) - getline(V); + getline_(V); } @@ -438,7 +438,7 @@ int in_definition; while (strncmp(V->sbuffer, "LOCUS", 5) != 0) - getline(V); + getline_(V); if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) { @@ -449,7 +449,7 @@ in_definition = FALSE; while (! feof(V->f)) { - getline(V); + getline_(V); if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) { if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) @@ -482,11 +482,11 @@ while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) - getline(V); + getline_(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); + getline_(V); } static int @@ -515,7 +515,7 @@ Die("bogus GCGdata format? %s", V->sbuffer); /* second line contains free text description */ - getline(V); + getline_(V); SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); if (binary) { @@ -535,7 +535,7 @@ else readLoop(0, endGCGdata, V); while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) - getline(V); + getline_(V); } static int @@ -555,12 +555,12 @@ 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)) getline_(V); readLoop(0, endPearson, V); while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) - getline(V); + getline_(V); } @@ -587,7 +587,7 @@ /* make sure we have first line */ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) - getline(V); + getline_(V); if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) { @@ -596,7 +596,7 @@ } do { - getline(V); + getline_(V); if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) { if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) @@ -620,7 +620,7 @@ /* load next record's ID line */ while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) - getline(V); + getline_(V); } @@ -636,7 +636,7 @@ { char *sptr; - getline(V); /*s == "seqLen seqid string..."*/ + getline_(V); /*s == "seqLen seqid string..."*/ if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); @@ -647,7 +647,7 @@ readLoop(0, endZuker, V); while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) - getline(V); + getline_(V); } static void @@ -669,7 +669,7 @@ do { done = feof(V->f); - getline(V); + getline_(V); if (! done) addseq(V->sbuffer, V); } while (!done); } @@ -681,7 +681,7 @@ char *sptr; int dostruc = FALSE; - while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); + while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); @@ -689,7 +689,7 @@ /*CONSTCOND*/ while (1) { - getline(V); + getline_(V); if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } if (strncmp(V->sbuffer, "SRC ", 4) == 0) @@ -721,14 +721,14 @@ while (1) { /* sequence line */ - getline(V); + getline_(V); if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) break; addseq(V->sbuffer, V); /* structure line */ if (dostruc) { - getline(V); + getline_(V); if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } addstruc(V->sbuffer, V); } @@ -736,7 +736,7 @@ while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) - getline(V); + getline_(V); } @@ -816,7 +816,7 @@ /* Load the first line. */ - getline(dbfp); + getline_(dbfp); return dbfp; } @@ -833,7 +833,7 @@ Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); fseek(sqfp->f, offset, SEEK_SET); - getline(sqfp); + getline_(sqfp); } @@ -853,7 +853,7 @@ if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; else { rewind(sqfp->f); - getline(sqfp); + getline_(sqfp); } } @@ -949,7 +949,7 @@ do { /* skip leading comments on GCG file */ gotuw = (strstr(V->sbuffer,"..") != NULL); if (gotuw) readUWGCG(V); - getline(V); + getline_(V); } while (! feof(V->f)); break;