JAL-3387 no-annotation too early

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d87f0f0..01aa9b0 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -107,6 +107,7 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
+import java.awt.Dimension;
 import java.awt.Rectangle;
 import java.awt.Toolkit;
 import java.awt.datatransfer.Clipboard;
@@ -299,9 +300,6 @@ public class AlignFrame extends GAlignFrame
 
     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 
-    alignPanel = new AlignmentPanel(this, viewport);
-
-    addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -321,8 +319,6 @@ public class AlignFrame extends GAlignFrame
     {
       viewport.hideSequence(hiddenSeqs);
     }
-    alignPanel = new AlignmentPanel(this, viewport);
-    addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -338,7 +334,6 @@ public class AlignFrame extends GAlignFrame
   {
     viewport = ap.av;
     alignPanel = ap;
-    addAlignmentPanel(ap, false);
     init();
   }
 
@@ -348,7 +343,28 @@ public class AlignFrame extends GAlignFrame
    */
   void init()
   {
-//       setBackground(Color.white); // BH 2019
+    boolean newPanel = (alignPanel == null);
+    viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    if (newPanel)
+    {
+      if (Platform.isJS())
+      {
+        // need to set this up front if NOANNOTATION is
+        // used in conjunction with SHOWOVERVIEW.
+
+        // I have not determined if this is appropriate for
+        // Jalview/Java, as it means we are setting this flag
+        // for all subsequent AlignFrames. For now, at least,
+        // I am setting it to be JalviewJS-only.
+
+        boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+        viewport.setShowAnnotation(showAnnotation);
+      }
+      alignPanel = new AlignmentPanel(this, viewport);
+    }
+    addAlignmentPanel(alignPanel, newPanel);
+
+    // setBackground(Color.white); // BH 2019
                  
     if (!Jalview.isHeadlessMode())
     {
@@ -381,9 +397,6 @@ public class AlignFrame extends GAlignFrame
       sortPairwiseMenuItem_actionPerformed(null);
     }
 
-    this.alignPanel.av
-            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
-
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
     calculateTree.addActionListener(new ActionListener()
@@ -556,7 +569,7 @@ public class AlignFrame extends GAlignFrame
         switch (evt.getKeyCode())
         {
 
-        case 27: // escape key
+        case KeyEvent.VK_ESCAPE: // escape key
           deselectAllSequenceMenuItem_actionPerformed(null);
 
           break;
@@ -829,8 +842,6 @@ public class AlignFrame extends GAlignFrame
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
-                // // System.out.println("Discoverer property change.");
-                // if (evt.getPropertyName().equals("services"))
                 {
                   SwingUtilities.invokeLater(new Runnable()
                   {