[med-svn] r280 - in trunk/packages/seaview/trunk: . debian

[Charles Plessy]

Author: charles-guest
Date: 2007-04-29 13:48:45 +0000 (Sun, 29 Apr 2007)
New Revision: 280

Modified:
   trunk/packages/seaview/trunk/debian/changelog
   trunk/packages/seaview/trunk/use_mase_files.cxx
Log:
New usptream release

Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog	2007-04-29 13:42:49 UTC (rev 279)
+++ trunk/packages/seaview/trunk/debian/changelog	2007-04-29 13:48:45 UTC (rev 280)
@@ -1,3 +1,9 @@
+seaview (20070417-1) UNRELEASED; urgency=low
+
+  * New upstream release adding processing of comments in FASTA format.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org>  Sun, 29 Apr 2007 22:46:26 +0900
+
 seaview (20070215-1) unstable; urgency=low
 
   * New upstream release, adding a new "Edit sequence" option in the Edit menu.

Modified: trunk/packages/seaview/trunk/use_mase_files.cxx
===================================================================
--- trunk/packages/seaview/trunk/use_mase_files.cxx	2007-04-29 13:42:49 UTC (rev 279)
+++ trunk/packages/seaview/trunk/use_mase_files.cxx	2007-04-29 13:48:45 UTC (rev 280)
@@ -15,7 +15,7 @@
 int read_msf_align(const char *fname, char ***pseq, char ***pseqname, 
 		char ***pcomments, char **pheader, char **err_message);
 int is_a_protein_seq(char *seq);
-int save_fasta_file(const char *fname, char **seq,
+int save_fasta_file(const char *fname, char **seq, char **comments,
 	char **seqname, int totseqs, int *eachlength, region *region_used,
 	int *sel_seqs, int tot_sel_seqs);
 int save_phylip_file(const char *fname, char **seq,
@@ -249,7 +249,7 @@
 {
 FILE *in;
 int totseqs, lseq, l2, l, lenseqs;
-char line[200], *p, *i, *provseq = NULL;
+char line[300], *p, *i, *provseq = NULL, c, *q;
 static char ret_message[200];
 char **seq, **seqname, **comments;
 
@@ -282,17 +282,33 @@
 	totseqs = -1; goto fini;
 	}
 while( i != NULL ){
+	/* finish reading very long title line */
+	c = line[strlen(line) - 1];
+	while(c != '\n' && c != '\r' && c != EOF) c = getc(in);
+	q = line + strlen(line) - 1;
+	while(q > line + 1 && (*q == '\n' || *q == '\r')) *(q--) = 0;
 	totseqs++;
-	comments[totseqs] = NULL;
 	p = line + 1; while(*p != ' ' && *p != '\n') p++;
 	l = p - line - 1;
 	if( (seqname[totseqs] = (char *)malloc(l+1)) == NULL)goto nomem;
 	memcpy(seqname[totseqs], line + 1, l); seqname[totseqs][l] = 0;
+	/* use rest of title line, if any, as comment */
+	while(*p == ' ') p++;
+	l = q - p + 1;
+	if( l > 0) {
+		comments[totseqs] = (char *)malloc(l + 3);
+		if(comments[totseqs] != NULL) {
+			strcpy(comments[totseqs], ";");
+			strcpy(comments[totseqs] + 1, p);
+			strcpy(comments[totseqs] + l + 1, "\n");
+			}
+		}
+	else comments[totseqs] = NULL;
 	seq[totseqs] = (char *)malloc(lenseqs+1);
 	if(seq[totseqs] == NULL) goto nomem;
 	lseq = 0;
 	while( (i=fgets(line, sizeof(line), in))!= NULL && *i != '>' ) {
-	    	l2 = strlen(line);
+		l2 = strlen(line);
 		if( line[l2 - 1] == '\n' ) l2--;
 	   	while(l2>0 && line[l2-1]==' ')l2--;
 		if(lseq + l2 > lenseqs) {
@@ -872,7 +888,7 @@
 }
 
 
-int save_fasta_file(const char *fname, char **seq,
+int save_fasta_file(const char *fname, char **seq, char **comments,
 	char **seqname, int totseqs, int *eachlength, region *region_used,
 	int *sel_seqs, int tot_sel_seqs)
 /* sauver des sequences ou des regions au format fasta
@@ -886,6 +902,7 @@
 int num, retval = 1, current, ecrit;
 list_segments *psegment, all_sequence;
 region maregion;
+char *p;
 
 if(totseqs == 0) return 0;
 if( (out = fopen(fname,"w")) == NULL) return 1;
@@ -904,7 +921,13 @@
 	if( tot_sel_seqs != 0 && ! sel_seqs[num] ) continue;
 	current = 0; psegment = region_used->list;
 	all_sequence.fin = eachlength[num];
-	fprintf(out,">%s\n",seqname[num]);
+	fprintf(out,">%s", seqname[num]);
+	if(comments[num] != NULL) {
+		putc(' ', out); 
+		p = comments[num] + 1;
+		while(*p != '\n' && *p != 0) putc(*(p++), out);
+		}
+	putc('\n', out);
 	if(ferror(out)) goto fin;
 	do	{
 		ecrit = output_next_res_from_region(seq[num], eachlength[num], 
@@ -1163,7 +1186,7 @@
 		seqname, totseqs, eachlength, region_used, protein,
 		sel_seqs, tot_sel_seqs);
 else if(format == FASTA_FORMAT) 
-	err = save_fasta_file(fname, seq,
+	err = save_fasta_file(fname, seq, comments,
 		seqname, totseqs, eachlength, region_used,
 		sel_seqs, tot_sel_seqs);
 if(err == 0)