JAL-1641 cherry-picked changes into develop compatible branch

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

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 5f45dc1..9e5bbff 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,6 +20,23 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.io.JSONFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GSplitFrame;
+import jalview.jbgui.GStructureViewer;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.ParamManager;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -84,22 +101,6 @@ import javax.swing.event.HyperlinkEvent.EventType;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
-import jalview.io.IdentifyFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GSplitFrame;
-import jalview.jbgui.GStructureViewer;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.ws.params.ParamManager;
-
 /**
  * Jalview Desktop
  * 
@@ -169,6 +170,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private static final int THREE = 3;
 
+  private static AlignFrame currentAlignFrame;
+
   public static jalview.ws.jws1.Discoverer discoverer;
 
   public static Object[] jalviewClipboard;
@@ -1022,6 +1025,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
                 format);
+        viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled());
+        AlignFrame af = viewport.getAlignPanel().alignFrame;
+        if (af != null)
+        {
+          af.changeColour(JSONFile.getColourScheme());
+          af.setMenusForViewport();
+        }
       }
       else
       {
@@ -3073,4 +3083,16 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     myTopFrame.setDisplayedView(myTopFrame.alignPanel);
 
   }
+
+  public static AlignFrame getCurrentAlignFrame()
+  {
+    return currentAlignFrame;
+  }
+
+  public static void setCurrentAlignFrame(AlignFrame currentAlignFrame)
+  {
+    Desktop.currentAlignFrame = currentAlignFrame;
+  }
+
+
 }