--- ureadseq.c~ 2003-01-25 23:48:36.000000000 +0100 +++ ureadseq.c 2009-08-19 09:48:03.000000000 +0200 @@ -136,7 +136,7 @@ } } -Local void getline(struct ReadSeqVars *V) +Local void parseline(struct ReadSeqVars *V) { readline(V->f, V->s, &V->linestart); } @@ -215,7 +215,7 @@ if (addfirst) addseq(V->s, V); do { - getline(V); + parseline(V); V->done = feof(V->f); V->done |= (*endTest)( &addend, &ungetend, V); if (V->addit && (addend || !V->done) && (strlen(V->s) > margin)) { @@ -246,7 +246,7 @@ while (!V->allDone) { do { - getline(V); + parseline(V); for (si= V->s; *si != 0 && *si < ' '; si++) *si= ' '; /* drop controls */ if (*si == 0) *V->s= 0; /* chop line to empty */ } while (! (feof(V->f) || ((*V->s != 0) && (*V->s != ';') ) )); @@ -272,13 +272,13 @@ { /* ? only 1 seq/file ? */ while (!V->allDone) { - getline(V); + parseline(V); if (strstr(V->s,"; DNA sequence ") == V->s) strcpy(V->seqid, (V->s)+16); else strcpy(V->seqid, (V->s)+1); while ((!feof(V->f)) && (*V->s == ';')) { - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; else readLoop(0, true, endStrider, V); @@ -298,16 +298,16 @@ while (!V->allDone) { while (! (feof(V->f) || strstr(V->s,"ENTRY") || strstr(V->s,"SEQUENCE")) ) - getline(V); + parseline(V); strcpy(V->seqid, (V->s)+16); while (! (feof(V->f) || strstr(V->s,"SEQUENCE") == V->s)) - getline(V); + parseline(V); readLoop(0, false, endPIR, V); if (!V->allDone) { while (! (feof(V->f) || ((*V->s != 0) && (strstr( V->s,"ENTRY") == V->s)))) - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; } @@ -327,13 +327,13 @@ while (!V->allDone) { strcpy(V->seqid, (V->s)+12); while (! (feof(V->f) || strstr(V->s,"ORIGIN") == V->s)) - getline(V); + parseline(V); readLoop(0, false, endGB, V); if (!V->allDone) { while (! (feof(V->f) || ((*V->s != 0) && (strstr( V->s,"LOCUS") == V->s)))) - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; } @@ -364,11 +364,11 @@ { while (!V->allDone) { strcpy(V->seqid, (V->s)+4); - getline(V); /*skip title-junk line*/ + parseline(V); /*skip title-junk line*/ readLoop(0, false, endNBRF, V); if (!V->allDone) { while (!(feof(V->f) || (*V->s != 0 && *V->s == '>'))) - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; } @@ -390,7 +390,7 @@ readLoop(0, false, endPearson, V); if (!V->allDone) { while (!(feof(V->f) || ((*V->s != 0) && (*V->s == '>')))) - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; } @@ -410,14 +410,14 @@ while (!V->allDone) { strcpy(V->seqid, (V->s)+5); do { - getline(V); + parseline(V); } while (!(feof(V->f) | (strstr(V->s,"SQ ") == V->s))); readLoop(0, false, endEMBL, V); if (!V->allDone) { while (!(feof(V->f) | ((*V->s != '\0') & (strstr(V->s,"ID ") == V->s)))) - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; } @@ -437,13 +437,13 @@ /*! 1st string is Zuker's Fortran format */ while (!V->allDone) { - getline(V); /*s == "seqLen seqid string..."*/ + parseline(V); /*s == "seqLen seqid string..."*/ strcpy(V->seqid, (V->s)+6); readLoop(0, false, endZuker, V); if (!V->allDone) { while (!(feof(V->f) | ((*V->s != '\0') & (*V->s == '(')))) - getline(V); + parseline(V); } if (feof(V->f)) V->allDone = true; } @@ -486,7 +486,7 @@ do { addseq(V->s, V); V->done = feof(V->f); - getline(V); + parseline(V); } while (!V->done); if (V->choice == kListSequences) addinfo(V->seqid, V); V->allDone = true; @@ -498,7 +498,7 @@ /* 10nov91: Reading GCG files casued duplication of last line when EOF followed that line !!! - fix: getline now sets *V->s = 0 + fix: parseline now sets *V->s = 0 */ char *si; @@ -512,7 +512,7 @@ else if (si = strstr(V->seqid,"..")) *si = 0; do { V->done = feof(V->f); - getline(V); + parseline(V); if (!V->done) addseq((V->s), V); } while (!V->done); if (V->choice == kListSequences) addinfo(V->seqid, V); @@ -531,7 +531,7 @@ if (V->addit) V->seqlen = 0; rewind(V->f); V->nseq= 0; do { - getline(V); + parseline(V); V->done = feof(V->f); if (V->done && !(*V->s)) break; @@ -614,7 +614,7 @@ if (V->addit) V->seqlen = 0; rewind(V->f); V->nseq= 0; do { - getline(V); + parseline(V); V->done = feof(V->f); if (V->done && !(*V->s)) break; @@ -685,7 +685,7 @@ domatch= (V->matchchar > 0); do { - getline(V); + parseline(V); V->done = feof(V->f); if (V->done && !(*V->s)) break; @@ -766,7 +766,7 @@ /* rewind(V->f); V->nseq= 0; << do in caller !*/ indata= true; /* call here after we find "matrix" */ do { - getline(V); + parseline(V); V->done = feof(V->f); if (V->done && !(*V->s)) break; @@ -851,7 +851,7 @@ /* fprintf(stderr,"Phylip-ileaf: topnseq=%d topseqlen=%d\n",V->topnseq, V->topseqlen); */ do { - getline(V); + parseline(V); V->done = feof(V->f); if (V->done && !(*V->s)) break; @@ -904,7 +904,7 @@ while (isdigit(*si)) si++; skipwhitespace(si); V->topseqlen= atol(si); - getline(V); + parseline(V); while (!V->allDone) { V->seqlencount= 0; strncpy(V->seqid, (V->s), 10); @@ -935,10 +935,10 @@ V->err = eFileNotFound; else { - for (l = skiplines_; l > 0; l--) getline( V); + for (l = skiplines_; l > 0; l--) parseline( V); do { - getline( V); + parseline( V); for (l= strlen(V->s); (l > 0) && (V->s[l] == ' '); l--) ; } while ((l == 0) && !feof(V->f)); @@ -963,7 +963,7 @@ char *cp; /* rewind(V->f); V->nseq= 0; ?? assume it is at top ?? skiplines ... */ while (!done) { - getline( V); + parseline( V); tolowerstr( V->s); if (strstr( V->s, "matrix")) done= true; if (strstr( V->s, "interleav")) interleaved= true; @@ -995,7 +995,7 @@ break; case kFitch : - strcpy(V->seqid, V->s); getline(V); + strcpy(V->seqid, V->s); parseline(V); readFitch(V); break; @@ -1003,7 +1003,7 @@ do { gotuw = (strstr(V->s,"..") != NULL); if (gotuw) readUWGCG(V); - getline(V); + parseline(V); } while (!(feof(V->f) || V->allDone)); break; }