fix for JAL-1495 - initialise menu entry from current state of apply to all groups...

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 564f28c..fbb61de 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,11 +14,13 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
@@ -92,7 +94,7 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
-        ItemListener, KeyListener
+        ItemListener, KeyListener, AlignViewControllerGuiI
 {
   public AlignViewControllerI avc;
   public AlignmentPanel alignPanel;
@@ -120,10 +122,31 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       ex.printStackTrace();
     }
-
+    // need to get window geometry before we calculate alignment layout
+    if (applet != null)
+    {
+      String param;
+      try
+      {
+        param = applet.getParameter("windowWidth");
+        if (param != null)
+        {
+          int width = Integer.parseInt(param);
+          DEFAULT_WIDTH = width;
+        }
+        param = applet.getParameter("windowHeight");
+        if (param != null)
+        {
+          int height = Integer.parseInt(param);
+          DEFAULT_HEIGHT = height;
+        }
+      } catch (Exception ex)
+      {
+      }
+    }
     viewport = new AlignViewport(al, applet);
     alignPanel = new AlignmentPanel(this, viewport);
-    avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+    avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
 
@@ -135,7 +158,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
     showSequenceLogo.setState(viewport.isShowSequenceLogo());
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
-
+    applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+    
     seqLimits.setState(viewport.showJVSuffix);
 
     if (applet != null)
@@ -172,23 +196,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         centreColumnLabelFlag.setState(true);
         centreColumnLabelFlag_stateChanged();
       }
-      try
-      {
-        param = applet.getParameter("windowWidth");
-        if (param != null)
-        {
-          int width = Integer.parseInt(param);
-          DEFAULT_WIDTH = width;
-        }
-        param = applet.getParameter("windowHeight");
-        if (param != null)
-        {
-          int height = Integer.parseInt(param);
-          DEFAULT_HEIGHT = height;
-        }
-      } catch (Exception ex)
-      {
-      }
 
     }
     if (viewport.getAlignment().isNucleotide())
@@ -3149,7 +3156,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     menu1.setLabel(MessageManager.getString("action.show"));
     showColumns.setLabel(MessageManager.getString("label.all_columns"));
     showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
-    menu2.setLabel(MessageManager.getString("aciton.hide"));
+    menu2.setLabel(MessageManager.getString("action.hide"));
     hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
     hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
     hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
@@ -3320,6 +3327,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   }
 
+  
+  public void setStatus(String string) {
+    statusBar.setText(string);
+  };
+
   MenuItem featureSettings = new MenuItem();
 
   CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();