Merge branch 'feature/JAL-4159_pasimap' into spike/JAL-4159_pasimap_2113_series

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

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 851bd32..9658a92 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -40,6 +40,7 @@ import javax.swing.JComboBox;
 import javax.swing.JLabel;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
+import javax.swing.JProgressBar;
 import javax.swing.JTable;
 import javax.swing.SwingUtilities;
 import javax.swing.table.AbstractTableModel;
@@ -1347,7 +1348,7 @@ public class StructureChooser extends GStructureChooser
           // TODO - tidy up this ugly hack so we call launchStructureViewer too
           StructureChooser.openStructureFileForSequence(ssm, sc, ap,
                   selectedSequence, true, pdbFilename, tft, paeFilename,false,
-                  true,true,getTargetedStructureViewer(ssm).getViewerType());
+                  true,false,getTargetedStructureViewer(ssm).getViewerType());
         }
         SwingUtilities.invokeLater(new Runnable()
         {
@@ -1856,10 +1857,13 @@ public class StructureChooser extends GStructureChooser
       sv = sc.launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
               new SequenceI[]
               { seq }, viewerType);
+      // foo
+      sv.getJalviewStructureDisplay().raiseViewer();
     }
 
     sc.mainFrame.dispose();
 
+    // TODO should honor preferences - only show reference annotation that is requested - JAL-4415 JAL-3124
     if (showRefAnnotations)
     {
       showReferenceAnnotationsForSequence(ap.alignFrame, seq);
@@ -1889,4 +1893,10 @@ public class StructureChooser extends GStructureChooser
     }
 
   }
+
+  @Override
+  public JProgressBar getProgressBar(long id)
+  {
+    return progressBar.getProgressBar(id);
+  }
 }