X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=e7b1c6e21af5e029d5ab8be3d920c9349f037b1d;hb=ce886100c1eae01eac7d59c961e694f4493d4bcb;hp=dedbd440d9ac5c31d17f25f3ff06f5665a0acc2a;hpb=0812da43d6b8d673aa25d2d7a7c5f65aab1b1642;p=jalview.git

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index dedbd44..e7b1c6e 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -31,9 +31,15 @@ import jalview.datamodel.*;
 
 /**
  * This class is supposed to parse a Stockholm format file into Jalview
- * 
+ * There are TODOs in this class: we do not know what the database source and
+ * version is for the file when parsing the #GS= AC tag which associates accessions
+ * with sequences. 
+ * Database references are also not parsed correctly: a separate reference string
+ * parser must be added to parse the database reference form into Jalview's local
+ * representation.
  * @author bsb at sanger.ac.uk
- * @version 0.3
+ * @version 0.3 + jalview mods
+ * 
  */
 public class StockholmFile extends AlignFile
 {
@@ -158,9 +164,8 @@ public class StockholmFile extends AlignFile
             {
               String src = dbr.substring(0, dbr.indexOf(";"));
               String acn = dbr.substring(dbr.indexOf(";") + 1);
-              DBRefEntry dbref = new DBRefEntry(jalview.util.DBRefUtils
-                      .getCanonicalName(src), acn, "");
-              seqO.addDBRef(dbref);
+              jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn);
+              //seqO.addDBRef(dbref);
             }
           }
           Hashtable features = null;
@@ -493,7 +498,7 @@ public class StockholmFile extends AlignFile
     if (annot == null)
     {
       annot = new AlignmentAnnotation(type, type, els);
-      annotation.add(annot);
+      annotation.addElement(annot);
     }
     else
     {