Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index faa0d5d..c8aa94f 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,13 +25,12 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
-import jalview.io.FileFormat;
+import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
-import java.awt.Component;
 import java.awt.GridLayout;
 import java.awt.Toolkit;
 import java.awt.event.ActionEvent;
@@ -66,8 +65,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu colourMenu = new JMenu();
-
   protected JMenu webService = new JMenu();
 
   protected JMenuItem webServiceNoServices;
@@ -82,10 +79,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu outputTextboxMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
-
-  protected JRadioButtonMenuItem userDefinedColour;
-
   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
@@ -96,16 +89,10 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem redoMenuItem = new JMenuItem();
 
-  protected JCheckBoxMenuItem conservationMenuItem;
-
-  protected JRadioButtonMenuItem noColourmenuItem;
-
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem abovePIDThreshold;
-
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
   JMenuItem copy = new JMenuItem();
@@ -114,8 +101,6 @@ public class GAlignFrame extends JInternalFrame
 
   JMenu pasteMenu = new JMenu();
 
-  protected JCheckBoxMenuItem applyToAllGroups;
-
   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@ -124,10 +109,20 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 
-  protected JMenuItem modifyPID;
+  protected JCheckBoxMenuItem applyToAllGroups;
+
+  protected JMenu colourMenu = new JMenu();
+
+  protected JRadioButtonMenuItem textColour;
+
+  protected JCheckBoxMenuItem conservationMenuItem;
 
   protected JMenuItem modifyConservation;
 
+  protected JCheckBoxMenuItem abovePIDThreshold;
+
+  protected JMenuItem modifyPID;
+
   protected JMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
@@ -216,7 +211,7 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (String ff : FileFormat.getWritableFormats(true))
+      for (String ff : FileFormats.getInstance().getWritableFormats(true))
       {
         JMenuItem item = new JMenuItem(ff);
 
@@ -249,37 +244,6 @@ public class GAlignFrame extends JInternalFrame
     }
   }
 
-  /**
-   * Marks as selected the colour menu item matching the given name, or the
-   * first item ('None') if no match is found
-   * 
-   * @param colourName
-   */
-  protected void setColourSelected(String colourName)
-  {
-    noColourmenuItem.setSelected(true);
-    if (colourName == null)
-    {
-      return;
-    }
-
-    /*
-     * look for a radio button with a name that matches the colour name
-     * (note the button text may not as it may be internationalised)
-     */
-    for (Component menuItem : colourMenu.getMenuComponents())
-    {
-      if (menuItem instanceof JRadioButtonMenuItem)
-      {
-        if (colourName.equals(((JRadioButtonMenuItem) menuItem).getName()))
-        {
-          ((JRadioButtonMenuItem) menuItem).setSelected(true);
-          return;
-        }
-      }
-    }
-  }
-
   private void jbInit() throws Exception
   {
     initColourMenu();
@@ -788,6 +752,17 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 
+    conservationMenuItem.setText(MessageManager
+            .getString("action.by_conservation"));
+    conservationMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed();
+      }
+    });
+
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -840,6 +815,17 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 
+    abovePIDThreshold.setText(MessageManager
+            .getString("label.above_identity_threshold"));
+    abovePIDThreshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed();
+      }
+    });
+
     showSeqFeatures.setText(MessageManager
             .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
@@ -1231,6 +1217,27 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
+    modifyPID = new JMenuItem(
+            MessageManager.getString("label.modify_identity_threshold"));
+    modifyPID.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed();
+      }
+    });
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_threshold"));
+    modifyConservation.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed();
+      }
+    });
+
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1942,9 +1949,7 @@ public class GAlignFrame extends JInternalFrame
 
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
-   * menu). The 'name' property of each item is set to the canonical name of the
-   * corresponding colour scheme (may not match the display name), to allow
-   * selection of items by colour scheme name.
+   * menu).
    */
   protected void initColourMenu()
   {
@@ -1970,18 +1975,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    userDefinedColour = new JRadioButtonMenuItem(
-            MessageManager
-            .getString("action.user_defined"));
-    userDefinedColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-
     conservationMenuItem = new JCheckBoxMenuItem(
             MessageManager.getString("action.by_conservation"));
     conservationMenuItem.addActionListener(new ActionListener()
@@ -1992,17 +1985,6 @@ public class GAlignFrame extends JInternalFrame
         conservationMenuItem_actionPerformed();
       }
     });
-    noColourmenuItem = new JRadioButtonMenuItem(
-            MessageManager.getString("label.none"));
-    noColourmenuItem.setName("None");
-    noColourmenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed();
-      }
-    });
 
     abovePIDThreshold = new JCheckBoxMenuItem(
             MessageManager.getString("label.above_identity_threshold"));
@@ -2403,20 +2385,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  
-
-  /*
-   * protected void covariationColour_actionPerformed() { }
-   */
-
-  protected void noColourmenuItem_actionPerformed()
-  {
-  }
-
   protected void conservationMenuItem_actionPerformed()
   {
   }