Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bb22d64..4de3d3a 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -23,8 +23,10 @@ package jalview.jbgui;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 
@@ -50,7 +52,6 @@ import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JTabbedPane;
@@ -244,10 +245,9 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+      for (String ff : FileFormat.getWritableFormats(true))
       {
-        JMenuItem item = new JMenuItem(
-                jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+        JMenuItem item = new JMenuItem(ff);
 
         item.addActionListener(new ActionListener()
         {
@@ -314,13 +314,13 @@ public class GAlignFrame extends JInternalFrame
           {
             radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
-            int option = JOptionPane.showInternalConfirmDialog(
+            int option = JvOptionPane.showInternalConfirmDialog(
                     jalview.gui.Desktop.desktop, MessageManager
                             .getString("label.remove_from_default_list"),
                     MessageManager
                             .getString("label.remove_user_defined_colour"),
-                    JOptionPane.YES_NO_OPTION);
-            if (option == JOptionPane.YES_OPTION)
+                    JvOptionPane.YES_NO_OPTION);
+            if (option == JvOptionPane.YES_OPTION)
             {
               jalview.gui.UserDefinedColours
                       .removeColourFromDefaults(radioItem.getText());
@@ -2181,6 +2181,19 @@ public class GAlignFrame extends JInternalFrame
         alignmentProperties();
       }
     });
+    JMenuItem selectHighlighted = new JMenuItem(
+            MessageManager.getString("action.select_highlighted_columns"));
+    selectHighlighted.setToolTipText(MessageManager
+            .getString("tooltip.select_highlighted_columns"));
+    al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        selectHighlightedColumns_actionPerformed(actionEvent);
+      }
+    };
+    selectHighlighted.addActionListener(al);
     JMenu tooltipSettingsMenu = new JMenu(
             MessageManager.getString("label.sequence_id_tooltip"));
     JMenu autoAnnMenu = new JMenu(
@@ -2382,12 +2395,20 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(grpsFromSelection);
     selectMenu.add(deleteGroups);
     selectMenu.add(annotationColumn);
+    selectMenu.add(selectHighlighted);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
     // selectMenu.addSeparator();
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void selectHighlightedColumns_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   /**
    * Generate the reverse sequence (or reverse complement if the flag is true)
    * and add it to the alignment