new DBRef management and generalised source and entry retrieval mechanism for referen...

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/io/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
similarity index 94%
rename from src/jalview/io/DBRefFetcher.java
rename to src/jalview/ws/DBRefFetcher.java
index 6d589f9..fb7eac9 100644 (file)
--- a/src/jalview/io/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -16,7 +16,7 @@
  * along with this program; if not, write to the Free Software\r
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  */\r
-package jalview.io;\r
+package jalview.ws;\r
 \r
 import java.io.*;\r
 import java.util.*;\r
@@ -310,7 +310,7 @@ public class DBRefFetcher
       {\r
         sequence = (SequenceI) sequenceMatches.elementAt(m);\r
         sequence.addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
-                                         "0",\r
+                                         "0", // TODO: VERSION FROM UNIPROT\r
                                          entry.getAccession().elementAt(0).\r
                                          toString()));\r
 \r
@@ -366,9 +366,11 @@ public class DBRefFetcher
           PDBEntry pdb = (PDBEntry) e.nextElement();\r
           if (!pdb.getType().equals(DBRefSource.PDB))\r
           {\r
+            DBRefEntry xref = new DBRefEntry(pdb.getType(), DBRefSource.UNIPROT, pdb.getId());\r
+            sequence.addDBRef(xref);\r
             continue;\r
           }\r
-\r
+          \r
           sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,\r
                                            "0",\r
                                            pdb.getId()));\r