JAL-250 prototype ‘hide redundant sequences’ - redundant seqs are represented by...

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 094fa7a..68245b6 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2349,6 +2349,7 @@ public class Jalview2XML
       initSeqRefs();
     }
     AlignFrame af = null, _af = null;
+    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
     Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
     final String file = jprovider.getFilename();
     try
@@ -2376,13 +2377,24 @@ public class Jalview2XML
           if (true) // !skipViewport(object))
           {
             _af = loadFromObject(object, file, true, jprovider);
-            if (object.getJalviewModelSequence().getViewportCount() > 0)
+            if (_af != null
+                    && object.getJalviewModelSequence().getViewportCount() > 0)
             {
-              af = _af;
-              if (af.viewport.isGatherViewsHere())
+              if (af == null)
               {
-                gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+                // store a reference to the first view
+                af = _af;
               }
+              if (_af.viewport.isGatherViewsHere())
+              {
+                // if this is a gathered view, keep its reference since
+                // after gathering views, only this frame will remain
+                af = _af;
+                gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af);
+              }
+              // Save dataset to register mappings once all resolved
+              importedDatasets.put(af.viewport.getAlignment().getDataset(),
+                      af.viewport.getAlignment().getDataset());
             }
           }
           entryCount++;
@@ -2438,11 +2450,6 @@ public class Jalview2XML
       e.printStackTrace();
     }
 
-    if (Desktop.instance != null)
-    {
-      Desktop.instance.stopLoading();
-    }
-
     /*
      * Regather multiple views (with the same sequence set id) to the frame (if
      * any) that is flagged as the one to gather to, i.e. convert them to tabbed
@@ -2456,11 +2463,24 @@ public class Jalview2XML
     }
 
     restoreSplitFrames();
-
+    for (AlignmentI ds : importedDatasets.keySet())
+    {
+      if (ds.getCodonFrames() != null)
+      {
+        StructureSelectionManager.getStructureSelectionManager(
+                Desktop.instance).registerMappings(ds.getCodonFrames());
+      }
+    }
     if (errorMessage != null)
     {
       reportErrors();
     }
+
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+
     return af;
   }