X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=88cc0a8394d719fdce4a689f21c0ddc606401a11;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=dc173973ec69a349604ed7be690fae5a50dadbf3;hpb=8677e6e34e291edc58c1da2fc9c958473754143f;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index dc17397..88cc0a8 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,12 +23,11 @@ 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.FileFormats;
-import jalview.schemes.ColourSchemeProperty;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -66,15 +65,13 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu colourMenu = new JMenu();
-
   protected JMenu webService = new JMenu();
 
   protected JMenuItem webServiceNoServices;
 
-  public JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
 
   protected JMenu sortByAnnotScore = new JMenu();
 
@@ -82,58 +79,19 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu outputTextboxMenu = new JMenu();
 
-  protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
-  // protected JRadioButtonMenuItem covariationColour = new
-  // JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
 
-  protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
-  public JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
-
-  public JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
-
-  public JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem showNonconservedMenuItem = new JCheckBoxMenuItem();
 
   protected JMenuItem undoMenuItem = new JMenuItem();
 
   protected JMenuItem redoMenuItem = new JMenuItem();
 
-  public JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
-
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-
-  public JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
-
-  public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
@@ -143,23 +101,35 @@ public class GAlignFrame extends JInternalFrame
 
   JMenu pasteMenu = new JMenu();
 
-  public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+
+  protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 
-  public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem applyToAllGroups;
 
-  public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenuItem textColour;
+
+  protected JCheckBoxMenuItem conservationMenuItem;
+
+  protected JMenuItem modifyConservation;
 
-  protected JMenuItem modifyConservation = new JMenuItem();
+  protected JCheckBoxMenuItem abovePIDThreshold;
+
+  protected JMenuItem modifyPID;
+
+  protected JMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
 
   protected JMenu sort = new JMenu();
 
-  protected JMenu calculateTree = new JMenu();
+  protected JMenuItem calculateTree = new JMenuItem();
 
   protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
 
@@ -167,8 +137,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem showDbRefsMenuitem = new JCheckBoxMenuItem();
 
-  protected ButtonGroup colours = new ButtonGroup();
-
   protected JMenuItem showTranslation = new JMenuItem();
 
   protected JMenuItem showReverse = new JMenuItem();
@@ -179,8 +147,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
-  protected JMenuItem rnahelicesColour = new JMenuItem();
-
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -265,7 +231,7 @@ public class GAlignFrame extends JInternalFrame
       System.err.println(e.toString());
     }
 
-    if (!jalview.util.Platform.isAMac())
+    if (!Platform.isAMac())
     {
       closeMenuItem.setMnemonic('C');
       outputTextboxMenu.setMnemonic('T');
@@ -276,201 +242,12 @@ public class GAlignFrame extends JInternalFrame
       pasteMenu.setMnemonic('P');
       reload.setMnemonic('R');
     }
-
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
-    {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
-              .getUserColourSchemes().keys();
-
-      while (userColours.hasMoreElements())
-      {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-                userColours.nextElement().toString());
-        radioItem.setName("USER_DEFINED");
-        radioItem.addMouseListener(new MouseAdapter()
-        {
-          @Override
-          public void mousePressed(MouseEvent evt)
-          {
-            if (evt.isPopupTrigger()) // Mac
-            {
-              offerRemoval(radioItem);
-            }
-          }
-
-          @Override
-          public void mouseReleased(MouseEvent evt)
-          {
-            if (evt.isPopupTrigger()) // Windows
-            {
-              offerRemoval(radioItem);
-            }
-          }
-
-          /**
-           * @param radioItem
-           */
-          void offerRemoval(final JRadioButtonMenuItem radioItem)
-          {
-            radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-            int option = JvOptionPane.showInternalConfirmDialog(
-                    jalview.gui.Desktop.desktop, MessageManager
-                            .getString("label.remove_from_default_list"),
-                    MessageManager
-                            .getString("label.remove_user_defined_colour"),
-                    JvOptionPane.YES_NO_OPTION);
-            if (option == JvOptionPane.YES_OPTION)
-            {
-              jalview.gui.UserDefinedColours
-                      .removeColourFromDefaults(radioItem.getText());
-              colourMenu.remove(radioItem);
-            }
-            else
-            {
-              radioItem.addActionListener(new ActionListener()
-              {
-                @Override
-                public void actionPerformed(ActionEvent evt)
-                {
-                  userDefinedColour_actionPerformed(evt);
-                }
-              });
-            }
-          }
-        });
-        radioItem.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent evt)
-          {
-            userDefinedColour_actionPerformed(evt);
-          }
-        });
-        colourMenu.insert(radioItem, 15);
-        colours.add(radioItem);
-      }
-    }
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(userDefinedColour);
-    colours.add(PIDColour);
-    colours.add(BLOSUM62Colour);
-    colours.add(nucleotideColour);
-    colours.add(purinePyrimidineColour);
-    // colours.add(covariationColour);
-    colours.add(tcoffeeColour);
-    colours.add(RNAInteractionColour);
-    setColourSelected(jalview.bin.Cache.getDefault(
-            Preferences.DEFAULT_COLOUR, "None"));
-  }
-
-  public void setColourSelected(String defaultColour)
-  {
-
-    if (defaultColour != null)
-    {
-      int index = ColourSchemeProperty
-              .getColourIndexFromName(defaultColour);
-
-      switch (index)
-      {
-      case ColourSchemeProperty.CLUSTAL:
-        clustalColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.BLOSUM:
-        BLOSUM62Colour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.PID:
-        PIDColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.ZAPPO:
-        zappoColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.TAYLOR:
-        taylorColour.setSelected(true);
-        break;
-
-      case ColourSchemeProperty.HYDROPHOBIC:
-        hydrophobicityColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.HELIX:
-        helixColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.STRAND:
-        strandColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.TURN:
-        turnColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.BURIED:
-        buriedColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.NUCLEOTIDE:
-        nucleotideColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.TCOFFEE:
-        tcoffeeColour.setSelected(true);
-        break;
-
-      case ColourSchemeProperty.PURINEPYRIMIDINE:
-        purinePyrimidineColour.setSelected(true);
-
-        break;
-
-      case ColourSchemeProperty.RNAINTERACTION:
-        RNAInteractionColour.setSelected(true);
-
-        break;
-      /*
-       * case ColourSchemeProperty.COVARIATION:
-       * covariationColour.setSelected(true);
-       * 
-       * break;
-       */
-      case ColourSchemeProperty.USER_DEFINED:
-        userDefinedColour.setSelected(true);
-
-        break;
-      case ColourSchemeProperty.NONE:
-      default:
-        noColourmenuItem.setSelected(true);
-        break;
-
-      }
-    }
-
   }
 
   private void jbInit() throws Exception
   {
+    initColourMenu();
+
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
     ActionListener al = new ActionListener()
@@ -481,6 +258,8 @@ public class GAlignFrame extends JInternalFrame
         saveAs_actionPerformed(e);
       }
     };
+
+    // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask()
             | KeyEvent.SHIFT_MASK, false);
@@ -669,7 +448,7 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     showNonconservedMenuItem.setText(MessageManager
-            .getString("label.show_non_conversed"));
+            .getString("label.show_non_conserved"));
     showNonconservedMenuItem.setState(false);
     showNonconservedMenuItem.addActionListener(new ActionListener()
     {
@@ -744,36 +523,6 @@ public class GAlignFrame extends JInternalFrame
         pairwiseAlignmentMenuItem_actionPerformed(e);
       }
     });
-    JMenuItem PCAMenuItem = new JMenuItem(
-            MessageManager.getString("label.principal_component_analysis"));
-    PCAMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PCAMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem averageDistanceTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_identity"));
-    averageDistanceTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        averageDistanceTreeMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem neighbourTreeMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_joining_identity"));
-    neighbourTreeMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        neighbourTreeMenuItem_actionPerformed(e);
-      }
-    });
 
     this.getContentPane().setLayout(new BorderLayout());
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));
@@ -783,167 +532,7 @@ public class GAlignFrame extends JInternalFrame
     statusBar.setText(MessageManager.getString("label.status_bar"));
     outputTextboxMenu.setText(MessageManager
             .getString("label.out_to_textbox"));
-    clustalColour.setText(MessageManager.getString("label.clustalx"));
-    clustalColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
-    zappoColour.setText(MessageManager.getString("label.zappo"));
-    zappoColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
-    taylorColour.setText(MessageManager.getString("label.taylor"));
-    taylorColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
-    hydrophobicityColour.setText(MessageManager
-            .getString("label.hydrophobicity"));
-    hydrophobicityColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
-    helixColour.setText(MessageManager.getString("label.helix_propensity"));
-    helixColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
-    strandColour.setText(MessageManager
-            .getString("label.strand_propensity"));
-    strandColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
-    turnColour.setText(MessageManager.getString("label.turn_propensity"));
-    turnColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
-    buriedColour.setText(MessageManager.getString("label.buried_index"));
-    buriedColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
-    userDefinedColour.setText(MessageManager
-            .getString("action.user_defined"));
-    userDefinedColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
-    PIDColour
-            .setText(MessageManager.getString("label.percentage_identity"));
-    PIDColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
-    BLOSUM62Colour
-            .setText(MessageManager.getString("label.blosum62_score"));
-    BLOSUM62Colour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
-    nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
-    nucleotideColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideColour_actionPerformed(e);
-      }
-    });
-
-    purinePyrimidineColour.setText(MessageManager
-            .getString("label.purine_pyrimidine"));
-    purinePyrimidineColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        purinePyrimidineColour_actionPerformed(e);
-      }
-    });
-
-    RNAInteractionColour.setText("RNA Interaction type");
-    RNAInteractionColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        RNAInteractionColour_actionPerformed(e);
-      }
-    });
-    /*
-     * covariationColour.setText("Covariation");
-     * covariationColour.addActionListener(new ActionListener() { public void
-     * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(e); }
-     * });
-     */
 
-    JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_bloslum62"));
-    avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        avTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
-    JMenuItem njTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.neighbour_blosum62"));
-    njTreeBlosumMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        njTreeBlosumMenuItem_actionPerformed(e);
-      }
-    });
     annotationPanelMenuItem.setActionCommand("");
     annotationPanelMenuItem.setText(MessageManager
             .getString("label.show_annotations"));
@@ -1039,7 +628,8 @@ public class GAlignFrame extends JInternalFrame
         sortAnnotations_actionPerformed();
       }
     });
-    colourTextMenuItem.setText(MessageManager
+    colourTextMenuItem = new JCheckBoxMenuItem(
+            MessageManager
             .getString("label.colour_text"));
     colourTextMenuItem.addActionListener(new ActionListener()
     {
@@ -1111,25 +701,6 @@ 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(e);
-      }
-    });
-    noColourmenuItem.setText(MessageManager.getString("label.none"));
-    noColourmenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -1182,16 +753,6 @@ 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(e);
-      }
-    });
     showSeqFeatures.setText(MessageManager
             .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
@@ -1337,28 +898,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    nucleotideColour.setText(MessageManager.getString("label.nucleotide"));
-    nucleotideColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideColour_actionPerformed(e);
-      }
-    });
-
-    tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
-    tcoffeeColour.setEnabled(false);
-    tcoffeeColour.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        tcoffeeColorScheme_actionPerformed(e);
-      }
-    });
-
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U, Toolkit
@@ -1373,8 +912,19 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, deleteGroups, al);
 
+    JMenuItem annotationColumn = new JMenuItem(
+            MessageManager.getString("action.select_by_annotation"));
+    annotationColumn.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColumn_actionPerformed(e);
+      }
+    });
+
     JMenuItem createGroup = new JMenuItem(
-            MessageManager.getString("action.create_groups"));
+            MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1470,16 +1020,6 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, pasteThis, al);
 
-    applyToAllGroups.setText(MessageManager
-            .getString("label.apply_colour_to_all_groups"));
-    applyToAllGroups.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        applyToAllGroups_actionPerformed(e);
-      }
-    });
     JMenuItem createPNG = new JMenuItem("PNG");
     createPNG.addActionListener(new ActionListener()
     {
@@ -1604,26 +1144,6 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    JMenuItem modifyPID = new JMenuItem(
-            MessageManager.getString("label.modify_identity_threshold"));
-    modifyPID.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyPID_actionPerformed(e);
-      }
-    });
-    modifyConservation.setText(MessageManager
-            .getString("label.modify_conservation_threshold"));
-    modifyConservation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed(e);
-      }
-    });
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1632,7 +1152,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void menuSelected(MenuEvent e)
       {
-        buildTreeMenu();
+        buildTreeSortMenu();
       }
 
       @Override
@@ -1669,8 +1189,8 @@ public class GAlignFrame extends JInternalFrame
     });
     sortByAnnotScore.setVisible(false);
 
-    calculateTree
-            .setText(MessageManager.getString("action.calculate_tree"));
+    calculateTree.setText(MessageManager
+            .getString("action.calculate_tree_pca"));
 
     padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
     padGapsMenuitem.setState(jalview.bin.Cache
@@ -1773,39 +1293,6 @@ public class GAlignFrame extends JInternalFrame
       }
     });
 
-    JMenuItem annotationColour = new JMenuItem(
-            MessageManager.getString("action.by_annotation"));
-    annotationColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        annotationColour_actionPerformed(e);
-      }
-    });
-
-    JMenuItem annotationColumn = new JMenuItem(
-            MessageManager.getString("action.select_by_annotation"));
-    annotationColumn.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        annotationColumn_actionPerformed(e);
-      }
-    });
-
-    rnahelicesColour.setText(MessageManager
-            .getString("action.by_rna_helixes"));
-    rnahelicesColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        rnahelicesColour_actionPerformed(e);
-      }
-    });
-
     JMenuItem associatedData = new JMenuItem(
             MessageManager.getString("label.load_features_annotations"));
     associatedData.addActionListener(new ActionListener()
@@ -2112,18 +1599,10 @@ public class GAlignFrame extends JInternalFrame
     tabbedPane.setToolTipText("<html><i>"
             + MessageManager.getString("label.rename_tab_eXpand_reGroup")
             + "</i></html>");
-    JMenuItem textColour = new JMenuItem(
-            MessageManager.getString("action.set_text_colour"));
-    textColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        textColour_actionPerformed(e);
-      }
-    });
+
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -2303,33 +1782,6 @@ public class GAlignFrame extends JInternalFrame
     autoAnnMenu.add(showGroupConsensus);
     annotationsMenu.add(autoAnnMenu);
 
-    colourMenu.add(applyToAllGroups);
-    colourMenu.add(textColour);
-    colourMenu.addSeparator();
-    colourMenu.add(noColourmenuItem);
-    colourMenu.add(clustalColour);
-    colourMenu.add(BLOSUM62Colour);
-    colourMenu.add(PIDColour);
-    colourMenu.add(zappoColour);
-    colourMenu.add(taylorColour);
-    colourMenu.add(hydrophobicityColour);
-    colourMenu.add(helixColour);
-    colourMenu.add(strandColour);
-    colourMenu.add(turnColour);
-    colourMenu.add(buriedColour);
-    colourMenu.add(nucleotideColour);
-    colourMenu.add(purinePyrimidineColour);
-    // colourMenu.add(RNAInteractionColour);
-    // colourMenu.add(covariationColour);
-    colourMenu.add(tcoffeeColour);
-    colourMenu.add(userDefinedColour);
-    colourMenu.addSeparator();
-    colourMenu.add(conservationMenuItem);
-    colourMenu.add(modifyConservation);
-    colourMenu.add(abovePIDThreshold);
-    colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
-    colourMenu.add(rnahelicesColour);
 
     sort.add(sortIDMenuItem);
     sort.add(sortLengthMenuItem);
@@ -2340,7 +1792,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
     calculateMenu.add(pairwiseAlignmentMenuItem);
-    calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(showReverse);
@@ -2402,6 +1853,90 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  /**
+   * Constructs the entries on the Colour menu (but does not add them to the
+   * menu).
+   */
+  protected void initColourMenu()
+  {
+    applyToAllGroups = new JCheckBoxMenuItem(
+            MessageManager.getString("label.apply_colour_to_all_groups"));
+    applyToAllGroups.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
+      }
+    });
+
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
+    textColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed();
+      }
+    });
+
+    conservationMenuItem = new JCheckBoxMenuItem(
+            MessageManager.getString("action.by_conservation"));
+    conservationMenuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
+      }
+    });
+
+    abovePIDThreshold = new JCheckBoxMenuItem(
+            MessageManager.getString("label.above_identity_threshold"));
+    abovePIDThreshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
+      }
+    });
+    modifyPID = new JMenuItem(
+            MessageManager.getString("label.modify_identity_threshold"));
+    modifyPID.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyPID_actionPerformed();
+      }
+    });
+    modifyConservation = new JMenuItem(
+            MessageManager
+            .getString("label.modify_conservation_threshold"));
+    modifyConservation.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        modifyConservation_actionPerformed();
+      }
+    });
+
+    annotationColour = new JMenuItem(
+            MessageManager.getString("action.by_annotation"));
+    annotationColour.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed();
+      }
+    });
+  }
+
   protected void selectHighlightedColumns_actionPerformed(
           ActionEvent actionEvent)
   {
@@ -2737,87 +2272,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void PCAMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void clustalColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void zappoColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void taylorColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void helixColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void strandColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void turnColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void buriedColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void PIDColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void RNAInteractionColour_actionPerformed(ActionEvent e)
-  {
-  }
-
-  /*
-   * protected void covariationColour_actionPerformed(ActionEvent e) { }
-   */
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
-  {
-  }
-
-  protected void conservationMenuItem_actionPerformed(ActionEvent e)
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
 
@@ -2833,7 +2292,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed(ActionEvent e)
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2841,10 +2300,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void nucleotideColour_actionPerformed(ActionEvent e)
-  {
-  }
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
   }
@@ -2877,7 +2332,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  protected void applyToAllGroups_actionPerformed(boolean selected)
   {
   }
 
@@ -2925,19 +2380,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  /**
-   * Template method to handle the 'Color T-Coffee scores' menu event.
-   * <p>
-   * Subclasses override this method to provide a custom action.
-   * 
-   * @param event
-   *          The raised event
-   */
-  protected void tcoffeeColorScheme_actionPerformed(ActionEvent event)
-  {
-
-  }
-
   protected void jpred_actionPerformed(ActionEvent e)
   {
   }
@@ -2954,11 +2396,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void modifyPID_actionPerformed(ActionEvent e)
+  protected void modifyPID_actionPerformed()
   {
   }
 
-  protected void modifyConservation_actionPerformed(ActionEvent e)
+  protected void modifyConservation_actionPerformed()
   {
   }
 
@@ -3000,19 +2442,12 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void annotationColour_actionPerformed(ActionEvent e)
+  public void annotationColour_actionPerformed()
   {
-
   }
 
   public void annotationColumn_actionPerformed(ActionEvent e)
   {
-
-  }
-
-  public void rnahelicesColour_actionPerformed(ActionEvent e)
-  {
-
   }
 
   public void associatedData_actionPerformed(ActionEvent e)
@@ -3105,7 +2540,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void textColour_actionPerformed(ActionEvent e)
+  public void textColour_actionPerformed()
   {
 
   }
@@ -3125,7 +2560,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void buildTreeMenu()
+  public void buildTreeSortMenu()
   {
 
   }