\r
/**\r
* This class is supposed to parse a Stockholm format file into Jalview\r
- * \r
+ * There are TODOs in this class: we do not know what the database source and\r
+ * version is for the file when parsing the #GS= AC tag which associates accessions\r
+ * with sequences. \r
+ * Database references are also not parsed correctly: a separate reference string\r
+ * parser must be added to parse the database reference form into Jalview's local\r
+ * representation.\r
* @author bsb at sanger.ac.uk\r
- * @version 0.3\r
+ * @version 0.3 + jalview mods\r
+ * \r
*/\r
public class StockholmFile extends AlignFile\r
{\r
{\r
String src = dbr.substring(0, dbr.indexOf(";"));\r
String acn = dbr.substring(dbr.indexOf(";") + 1);\r
- DBRefEntry dbref = new DBRefEntry(jalview.util.DBRefUtils\r
- .getCanonicalName(src), acn, "");\r
- seqO.addDBRef(dbref);\r
+ jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);\r
+ //seqO.addDBRef(dbref);\r
}\r
}\r
Hashtable features = null;\r