crossrefs have properly updated pdbId lists

[jalview.git] / src / jalview / io / StockholmFile.java

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index d0d84f5..e7b1c6e 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -31,9 +31,15 @@ import jalview.datamodel.*;
 \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
@@ -158,9 +164,8 @@ public class StockholmFile extends AlignFile
             {\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