JAL-2344 added FileFormatI.isStructureFile()

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 6b94559..cbeb93c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,6 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
+import jalview.io.FileFormat;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
 
@@ -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()
         {
@@ -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