X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=d87f0f0eb627215c5b21a4e82a74094ed9fa7f92;hb=1cec732f963ab102c9d8381203df8c8cba2a9ee4;hp=3b53f1817ad0dedce72d61335d04448cdbb69d70;hpb=26ee59562604fa9164e895e3ca07e11398a6c8a0;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3b53f18..d87f0f0 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -353,6 +353,8 @@ public class AlignFrame extends GAlignFrame
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+      statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+      alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
     }
 
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -793,9 +795,12 @@ public class AlignFrame extends GAlignFrame
       {
         ap.av.getAlignment().padGaps();
       }
-      ap.av.updateConservation(ap);
-      ap.av.updateConsensus(ap);
-      ap.av.updateStrucConsensus(ap);
+      if (Jalview.getInstance().getStartCalculations())
+      {
+        ap.av.updateConservation(ap);
+        ap.av.updateConsensus(ap);
+        ap.av.updateStrucConsensus(ap);
+      }
     }
   }
 
@@ -945,7 +950,7 @@ public class AlignFrame extends GAlignFrame
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
-    autoCalculate.setSelected(av.autoCalculateConsensus);
+    autoCalculate.setSelected(av.getAutoCalculateConsensusAndConservation());
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
 
@@ -3374,7 +3379,7 @@ public class AlignFrame extends GAlignFrame
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
-            true, true);
+            true, true, "overview");
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
@@ -3654,8 +3659,8 @@ public class AlignFrame extends GAlignFrame
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
-    viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if (viewport.autoCalculateConsensus)
+    viewport.setAutoCalculateConsensusAndConservation(autoCalculate.isSelected());
+    if (viewport.getAutoCalculateConsensusAndConservation())
     {
       viewport.firePropertyChange("alignment", null,
               viewport.getAlignment().getSequences());