JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 0d2ec68..0e17779 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -38,6 +38,8 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Point;
@@ -2505,21 +2507,29 @@ public class Jalview2XML
         parentseq = jds;
       }
     }
+
+    /*
+     * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+     */
     if (dbrefs != null)
     {
       for (int d = 0; d < dbrefs.length; d++)
       {
         DBRef dbref = new DBRef();
-        dbref.setSource(dbrefs[d].getSource());
-        dbref.setVersion(dbrefs[d].getVersion());
-        dbref.setAccessionId(dbrefs[d].getAccessionId());
-        if (dbrefs[d].hasMap())
+        DBRefEntry dbRefEntry = dbrefs[d];
+        dbref.setSource(dbRefEntry.getSource());
+        dbref.setVersion(dbRefEntry.getVersion());
+        dbref.setAccessionId(dbRefEntry.getAccessionId());
+        if (dbRefEntry instanceof GeneLocus)
         {
-          Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+          dbref.setLocus(true);
+        }
+        if (dbRefEntry.hasMap())
+        {
+          Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq,
                   jds, recurse);
           dbref.setMapping(mp);
         }
-        // vamsasSeq.addDBRef(dbref);
         vamsasSeq.getDBRef().add(dbref);
       }
     }
@@ -5798,13 +5808,29 @@ public class Jalview2XML
     return datasetId;
   }
 
+  /**
+   * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
+   * constructed as a special subclass GeneLocus.
+   * 
+   * @param datasetSequence
+   * @param sequence
+   */
   private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
   {
     for (int d = 0; d < sequence.getDBRef().size(); d++)
     {
       DBRef dr = sequence.getDBRef().get(d);
-      jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
-              dr.getSource(), dr.getVersion(), dr.getAccessionId());
+      DBRefEntry entry;
+      if (dr.isLocus())
+      {
+        entry = new GeneLocus(dr.getSource(), dr.getVersion(),
+                dr.getAccessionId());
+      }
+      else
+      {
+        entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
+                dr.getAccessionId());
+      }
       if (dr.getMapping() != null)
       {
         entry.setMap(addMapping(dr.getMapping()));