merge commit

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 0f94efa..82b94c3 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -21,15 +21,19 @@
 package jalview.io;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
 
+import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import jalview.util.MessageManager;
 import javax.swing.JOptionPane;
 import javax.swing.SwingUtilities;
 
@@ -310,6 +314,21 @@ public class FileLoader implements Runnable
 
         if ((al != null) && (al.getHeight() > 0))
         {
+          for (SequenceI sq : al.getSequences())
+          {
+            while (sq.getDatasetSequence() != null)
+            {
+              sq = sq.getDatasetSequence();
+            }
+            if (sq.getPDBId() != null)
+            {
+              for (PDBEntry pdbe : (List<PDBEntry>) sq.getPDBId())
+              {
+                StructureSelectionManager.getStructureSelectionManager(
+                        Desktop.instance).registerPDBEntry(pdbe);
+              }
+            }
+          }
           if (viewport != null)
           {
             // TODO: create undo object for this JAL-1101
@@ -319,7 +338,6 @@ public class FileLoader implements Runnable
             }
             viewport.firePropertyChange("alignment", null, viewport
                     .getAlignment().getSequences());
-
           }
           else
           {
@@ -331,7 +349,9 @@ public class FileLoader implements Runnable
                     { title }));
 
             if (!protocol.equals(AppletFormatAdapter.PASTE))
+            {
               alignFrame.setFileName(file, format);
+            }
             if (raiseGUI)
             {
               // add the window to the GUI