JAL-3387 no-annotation too early

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 6f902af..060d6ad 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -145,6 +145,8 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
 
   private boolean noCalculation, noMenuBar, noStatus;
 
+  private boolean noAnnotation;
+
   public boolean getStartCalculations()
   {
     return !noCalculation;
@@ -160,6 +162,10 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
     return !noStatus;
   }
 
+  public boolean getShowAnnotation()
+  {
+    return !noAnnotation;
+  }
 
   public static AlignFrame getCurrentAlignFrame()
   {
@@ -654,6 +660,12 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
         System.out.println("CMD [nostatus] executed successfully!");
       }
 
+      if (aparser.contains(ArgsParser.NOANNOTATION)
+              || aparser.contains(ArgsParser.NOANNOTATION2))
+      {
+        noAnnotation = true;
+        System.out.println("CMD no-annotation executed successfully!");
+      }
       if (aparser.contains(ArgsParser.NOCALCULATION))
       {
         noCalculation = true;
@@ -754,18 +766,30 @@ public class Jalview implements ApplicationSingletonI, JalviewJSApi
             System.out.println("CMD [-sortbytree] executed successfully!");
           }
         }
-        
+
         boolean doUpdateAnnotation = false;
-        
 
-        if (aparser.contains(ArgsParser.NOANNOTATION)
-                || aparser.contains(ArgsParser.NOANNOTATION2))
+        /**
+         * we do this earlier in JalviewJS because of a complication with
+         * SHOWOVERVIEW
+         * 
+         * For now, just fixing this in JalviewJS.
+         *
+         * 
+         * @j2sIgnore
+         * 
+         */
         {
-          af.getViewport().setShowAnnotation(false);
-          if (!af.getViewport().isShowAnnotation())
+          if (aparser.contains(ArgsParser.NOANNOTATION)
+                  || aparser.contains(ArgsParser.NOANNOTATION2))
           {
-            doUpdateAnnotation = true;
-            System.out.println("CMD no-annotation executed successfully!");
+            af.getViewport().setShowAnnotation(false);
+            if (!af.getViewport().isShowAnnotation())
+            {
+              doUpdateAnnotation = true;
+              System.out
+                      .println("CMD no-annotation executed successfully!");
+            }
           }
         }
         if (aparser.contains(ArgsParser.NOSORTBYTREE))

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()
                   {

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index f723794..5fa8fdf 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -56,6 +56,7 @@ import java.awt.event.AdjustmentEvent;
 import java.awt.event.AdjustmentListener;
 import java.awt.event.ComponentAdapter;
 import java.awt.event.ComponentEvent;
+import java.awt.image.BufferedImage;
 import java.awt.print.PageFormat;
 import java.awt.print.Printable;
 import java.awt.print.PrinterException;
@@ -136,7 +137,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     annotationScroller.setViewportView(getAnnotationPanel());
     annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
-
+    if (!av.isShowAnnotation())
+    {
+      annotationScroller.setVisible(false);
+      annotationSpaceFillerHolder.setVisible(false);
+    }
     scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
     seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);