X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=37cd8b312898798ad709d3537bda47304001d7fe;hb=400b50efffaa43ae2c3b4d3f653bf8215c5d1edc;hp=838b5340420594ee07531a08bae19389992eefd6;hpb=b5699e7d9cc2045f623609948ee10a736256abc4;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 838b534..37cd8b3 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,25 +38,17 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.io.FileFormat;
+import jalview.gui.ColourMenuHelper.ColourChangeListener;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ClustalxColourScheme;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TCoffeeColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
+import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -76,13 +68,11 @@ import java.util.SortedMap;
 import java.util.TreeMap;
 import java.util.Vector;
 
-import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
 
 /**
  * DOCUMENT ME!
@@ -90,48 +80,20 @@ import javax.swing.JRadioButtonMenuItem;
  * @author $author$
  * @version $Revision: 1.118 $
  */
-public class PopupMenu extends JPopupMenu
+public class PopupMenu extends JPopupMenu implements ColourChangeListener
 {
   JMenu groupMenu = new JMenu();
 
   JMenuItem groupName = new JMenuItem();
 
-  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 JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
 
-  protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
-
-  JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
-
-  protected JRadioButtonMenuItem tcoffeeColour = new JRadioButtonMenuItem();
-
-  // protected JRadioButtonMenuItem RNAInteractionColour;
-
-  JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+  protected JMenuItem modifyPID = new JMenuItem();
 
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
 
+  protected JMenuItem modifyConservation = new JMenuItem();
+
   AlignmentPanel ap;
 
   JMenu sequenceMenu = new JMenu();
@@ -242,11 +204,11 @@ public class PopupMenu extends JPopupMenu
     this.ap = ap;
     sequence = seq;
 
-    for (String ff : FileFormat.getWritableFormats(true))
+    for (String ff : FileFormats.getInstance().getWritableFormats(true))
     {
       JMenuItem item = new JMenuItem(ff);
 
-      item.addActionListener(new java.awt.event.ActionListener()
+      item.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent e)
@@ -330,7 +292,7 @@ public class PopupMenu extends JPopupMenu
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_structure_line",
                       new Object[] { aa.label }));
-              menuItem.addActionListener(new java.awt.event.ActionListener()
+              menuItem.addActionListener(new ActionListener()
               {
                 @Override
                 public void actionPerformed(ActionEvent e)
@@ -358,7 +320,7 @@ public class PopupMenu extends JPopupMenu
               menuItem.setText(MessageManager.formatMessage(
                       "label.2d_rna_sequence_name",
                       new Object[] { seq.getName() }));
-              menuItem.addActionListener(new java.awt.event.ActionListener()
+              menuItem.addActionListener(new ActionListener()
               {
                 @Override
                 public void actionPerformed(ActionEvent e)
@@ -379,7 +341,7 @@ public class PopupMenu extends JPopupMenu
 
       menuItem = new JMenuItem(
               MessageManager.getString("action.hide_sequences"));
-      menuItem.addActionListener(new java.awt.event.ActionListener()
+      menuItem.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent e)
@@ -395,7 +357,7 @@ public class PopupMenu extends JPopupMenu
         menuItem = new JMenuItem(MessageManager.formatMessage(
                 "label.represent_group_with",
                 new Object[] { seq.getName() }));
-        menuItem.addActionListener(new java.awt.event.ActionListener()
+        menuItem.addActionListener(new ActionListener()
         {
           @Override
           public void actionPerformed(ActionEvent e)
@@ -464,72 +426,21 @@ public class PopupMenu extends JPopupMenu
       groupName.setText(MessageManager
               .getString("label.edit_name_and_description_current_group"));
 
-      if (sg.cs instanceof ZappoColourScheme)
-      {
-        zappoColour.setSelected(true);
-      }
-      else if (sg.cs instanceof TaylorColourScheme)
-      {
-        taylorColour.setSelected(true);
-      }
-      else if (sg.cs instanceof PIDColourScheme)
-      {
-        PIDColour.setSelected(true);
-      }
-      else if (sg.cs instanceof Blosum62ColourScheme)
-      {
-        BLOSUM62Colour.setSelected(true);
-      }
-      else if (sg.cs instanceof UserColourScheme)
-      {
-        userDefinedColour.setSelected(true);
-      }
-      else if (sg.cs instanceof HydrophobicColourScheme)
-      {
-        hydrophobicityColour.setSelected(true);
-      }
-      else if (sg.cs instanceof HelixColourScheme)
-      {
-        helixColour.setSelected(true);
-      }
-      else if (sg.cs instanceof StrandColourScheme)
-      {
-        strandColour.setSelected(true);
-      }
-      else if (sg.cs instanceof TurnColourScheme)
-      {
-        turnColour.setSelected(true);
-      }
-      else if (sg.cs instanceof BuriedColourScheme)
-      {
-        buriedColour.setSelected(true);
-      }
-      else if (sg.cs instanceof ClustalxColourScheme)
-      {
-        clustalColour.setSelected(true);
-      }
-      else if (sg.cs instanceof PurinePyrimidineColourScheme)
-      {
-        purinePyrimidineColour.setSelected(true);
-      }
-      else if (sg.cs instanceof NucleotideColourScheme)
-      {
-        nucleotideColour.setSelected(true);
-      }
+      ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
 
-      /*
-       * else if (sg.cs instanceof CovariationColourScheme) {
-       * covariationColour.setSelected(true); }
-       */
-      else
+      if (sg.cs != null)
       {
-        noColourmenuItem.setSelected(true);
-      }
-
-      if (sg.cs != null && sg.cs.conservationApplied())
-      {
-        conservationMenuItem.setSelected(true);
+        if (sg.cs.conservationApplied())
+        {
+          conservationMenuItem.setSelected(true);
+        }
+        if (sg.cs.getThreshold() > 0)
+        {
+          abovePIDColour.setSelected(true);
+        }
       }
+      modifyConservation.setEnabled(conservationMenuItem.isSelected());
+      modifyPID.setEnabled(abovePIDColour.isSelected());
       displayNonconserved.setSelected(sg.getShowNonconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
@@ -653,8 +564,6 @@ public class PopupMenu extends JPopupMenu
 
   }
 
-
-
   /**
    * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
    * "All" is added first, followed by a separator. Then add any annotation
@@ -770,7 +679,7 @@ public class PopupMenu extends JPopupMenu
     label = label.substring(1, label.length() - 1); // a, b, c
     final JMenuItem item = new JMenuItem(label);
     item.setToolTipText(calcId);
-    item.addActionListener(new java.awt.event.ActionListener()
+    item.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -952,7 +861,7 @@ public class PopupMenu extends JPopupMenu
     JMenuItem item = new JMenuItem(label);
     item.setToolTipText(MessageManager.formatMessage(
             "label.open_url_param", new Object[] { url }));
-    item.addActionListener(new java.awt.event.ActionListener()
+    item.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1029,7 +938,7 @@ public class PopupMenu extends JPopupMenu
   {
     groupMenu.setText(MessageManager.getString("label.selection"));
     groupName.setText(MessageManager.getString("label.name"));
-    groupName.addActionListener(new java.awt.event.ActionListener()
+    groupName.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1040,7 +949,7 @@ public class PopupMenu extends JPopupMenu
     sequenceMenu.setText(MessageManager.getString("label.sequence"));
     sequenceName.setText(MessageManager
             .getString("label.edit_name_description"));
-    sequenceName.addActionListener(new java.awt.event.ActionListener()
+    sequenceName.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1050,7 +959,7 @@ public class PopupMenu extends JPopupMenu
     });
     chooseAnnotations.setText(MessageManager
             .getString("action.choose_annotations"));
-    chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+    chooseAnnotations.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1060,7 +969,7 @@ public class PopupMenu extends JPopupMenu
     });
     sequenceDetails.setText(MessageManager
             .getString("label.sequence_details"));
-    sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+    sequenceDetails.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1070,19 +979,18 @@ public class PopupMenu extends JPopupMenu
     });
     sequenceSelDetails.setText(MessageManager
             .getString("label.sequence_details"));
-    sequenceSelDetails
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                sequenceSelectionDetails_actionPerformed();
-              }
-            });
-    PIDColour.setFocusPainted(false);
+    sequenceSelDetails.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceSelectionDetails_actionPerformed();
+      }
+    });
+
     unGroupMenuItem
             .setText(MessageManager.getString("action.remove_group"));
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    unGroupMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -1092,36 +1000,24 @@ public class PopupMenu extends JPopupMenu
     });
     createGroupMenuItem.setText(MessageManager
             .getString("action.create_group"));
-    createGroupMenuItem
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                createGroupMenuItem_actionPerformed();
-              }
-            });
-
-    outline.setText(MessageManager.getString("action.border_colour"));
-    outline.addActionListener(new java.awt.event.ActionListener()
+    createGroupMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        outline_actionPerformed();
+        createGroupMenuItem_actionPerformed();
       }
     });
-    nucleotideColour
-            .setText(MessageManager.getString("label.nucleotide"));
-    nucleotideColour.addActionListener(new ActionListener()
+
+    outline.setText(MessageManager.getString("action.border_colour"));
+    outline.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        nucleotideMenuItem_actionPerformed();
+        outline_actionPerformed();
       }
     });
-    colourMenu.setText(MessageManager.getString("label.group_colour"));
     showBoxes.setText(MessageManager.getString("action.boxes"));
     showBoxes.setState(true);
     showBoxes.addActionListener(new ActionListener()
@@ -1228,15 +1124,6 @@ public class PopupMenu extends JPopupMenu
         sequenceFeature_actionPerformed();
       }
     });
-    textColour.setText(MessageManager.getString("label.text_colour"));
-    textColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        textColour_actionPerformed();
-      }
-    });
     jMenu1.setText(MessageManager.getString("label.group"));
     pdbStructureDialog.setText(MessageManager
             .getString("label.show_pdbstruct_dialog"));
@@ -1329,6 +1216,7 @@ public class PopupMenu extends JPopupMenu
     sequenceMenu.add(sequenceDetails);
     sequenceMenu.add(makeReferenceSeq);
 
+    initColourMenu();
     buildColourMenu();
 
     editMenu.add(copy);
@@ -1348,240 +1236,119 @@ public class PopupMenu extends JPopupMenu
     jMenu1.add(showColourText);
     jMenu1.add(outline);
     jMenu1.add(displayNonconserved);
-    noColourmenuItem.setText(MessageManager.getString("label.none"));
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+  }
+  
+  /**
+   * Constructs the entries for the colour menu
+   */
+  protected void initColourMenu()
+  {
+    colourMenu.setText(MessageManager.getString("label.group_colour"));
+    textColour.setText(MessageManager.getString("label.text_colour"));
+    textColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        noColourmenuItem_actionPerformed();
+        textColour_actionPerformed();
       }
     });
 
-    clustalColour.setText(MessageManager.getString("label.clustalx"));
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed();
-      }
-    });
-    zappoColour.setText(MessageManager.getString("label.zappo"));
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed();
-      }
-    });
-    taylorColour.setText(MessageManager.getString("label.taylor"));
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed();
-      }
-    });
-    hydrophobicityColour.setText(MessageManager
-            .getString("label.hydrophobicity"));
-    hydrophobicityColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                hydrophobicityColour_actionPerformed();
-              }
-            });
-    helixColour.setText(MessageManager.getString("label.helix_propensity"));
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed();
-      }
-    });
-    strandColour.setText(MessageManager
-            .getString("label.strand_propensity"));
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed();
-      }
-    });
-    turnColour.setText(MessageManager.getString("label.turn_propensity"));
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed();
-      }
-    });
-    buriedColour.setText(MessageManager.getString("label.buried_index"));
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed();
-      }
-    });
     abovePIDColour.setText(MessageManager
             .getString("label.above_identity_threshold"));
-    abovePIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDColour_actionPerformed();
-      }
-    });
-    userDefinedColour.setText(MessageManager
-            .getString("action.user_defined"));
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+    abovePIDColour.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        userDefinedColour_actionPerformed(e);
+        abovePIDColour_actionPerformed(abovePIDColour.isSelected());
       }
     });
-    PIDColour
-            .setText(MessageManager.getString("label.percentage_identity"));
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
+
+    modifyPID.setText(MessageManager
+            .getString("label.modify_identity_threshold"));
+    modifyPID.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        PIDColour_actionPerformed();
+        modifyPID_actionPerformed();
       }
     });
-    BLOSUM62Colour
-            .setText(MessageManager.getString("label.blosum62_score"));
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+
+    conservationMenuItem.setText(MessageManager
+            .getString("action.by_conservation"));
+    conservationMenuItem.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        BLOSUM62Colour_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
-    purinePyrimidineColour.setText(MessageManager
-            .getString("label.purine_pyrimidine"));
-    purinePyrimidineColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              @Override
-              public void actionPerformed(ActionEvent e)
-              {
-                purinePyrimidineColour_actionPerformed();
-              }
-            });
 
-    tcoffeeColour.setText(MessageManager.getString("label.tcoffee_scores"));
-    tcoffeeColour.addActionListener(new ActionListener()
+    modifyConservation.setText(MessageManager
+            .getString("label.modify_conservation_threshold"));
+    modifyConservation.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        tcoffeeColorScheme_actionPerformed();
+        modifyConservation_actionPerformed();
       }
     });
-
-    /*
-     * covariationColour.addActionListener(new java.awt.event.ActionListener() {
-     * public void actionPerformed(ActionEvent e) {
-     * covariationColour_actionPerformed(); } });
-     */
-
-    conservationMenuItem.setText(MessageManager
-            .getString("action.by_conservation"));
-    conservationMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed();
-              }
-            });
   }
 
   /**
-   * Adds items to the group colour sub-menu
+   * Builds the group colour sub-menu, including any user-defined colours which
+   * were loaded at startup or during the Jalview session
    */
   protected void buildColourMenu()
   {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg == null)
+    {
+      /*
+       * popup menu with no sequence group scope
+       */
+      return;
+    }
     colourMenu.removeAll();
     colourMenu.add(textColour);
-    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(tcoffeeColour);
-
-    SortedMap<String, UserColourScheme> userColourSchemes = UserDefinedColours
-            .getUserColourSchemes();
-    if (userColourSchemes != null)
-    {
-      for (String userColour : userColourSchemes.keySet())
-    {
-        JMenuItem item = new JMenuItem(userColour);
-        item.addActionListener(new ActionListener()
-        {
-          @Override
-          public void actionPerformed(ActionEvent evt)
-          {
-            userDefinedColour_actionPerformed(evt);
-          }
-        });
-        colourMenu.add(item);
-      }
-    }
-    colourMenu.add(userDefinedColour);
+    colourMenu.addSeparator();
+
+    ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
 
     colourMenu.addSeparator();
-    colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
+    colourMenu.add(modifyConservation);
+    colourMenu.add(abovePIDColour);
+    colourMenu.add(modifyPID);
+  }
 
-    /*
-     * add some of these items to a ButtonGroup so their
-     * selection is mutually exclusive
-     */
-    ButtonGroup colours = new ButtonGroup();
-    colours.add(noColourmenuItem);
-    colours.add(clustalColour);
-    colours.add(BLOSUM62Colour);
-    colours.add(PIDColour);
-    colours.add(zappoColour);
-    colours.add(taylorColour);
-    colours.add(hydrophobicityColour);
-    colours.add(helixColour);
-    colours.add(strandColour);
-    colours.add(turnColour);
-    colours.add(buriedColour);
-    colours.add(purinePyrimidineColour);
-    colours.add(tcoffeeColour);
-    colours.add(nucleotideColour);
-    colours.add(userDefinedColour);
-    colours.add(abovePIDColour);
-    // colours.add(RNAInteractionColour);
+  protected void modifyConservation_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs != null)
+    {
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.showConservationSlider();
+    }
+  }
 
+  protected void modifyPID_actionPerformed()
+  {
+    SequenceGroup sg = getGroup();
+    if (sg.cs != null)
+    {
+      // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+      // .getName());
+      // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+      SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+              .getName());
+      SliderPanel.showPIDSlider();
+    }
   }
 
   /**
@@ -1755,127 +1522,6 @@ public class PopupMenu extends JPopupMenu
     PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void clustalColour_actionPerformed()
-  {
-    SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void zappoColour_actionPerformed()
-  {
-    getGroup().cs = new ZappoColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void taylorColour_actionPerformed()
-  {
-    getGroup().cs = new TaylorColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void hydrophobicityColour_actionPerformed()
-  {
-    getGroup().cs = new HydrophobicColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void helixColour_actionPerformed()
-  {
-    getGroup().cs = new HelixColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void strandColour_actionPerformed()
-  {
-    getGroup().cs = new StrandColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void turnColour_actionPerformed()
-  {
-    getGroup().cs = new TurnColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void buriedColour_actionPerformed()
-  {
-    getGroup().cs = new BuriedColourScheme();
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  public void nucleotideMenuItem_actionPerformed()
-  {
-    getGroup().cs = new NucleotideColourScheme();
-    refresh();
-  }
-
-  protected void purinePyrimidineColour_actionPerformed()
-  {
-    getGroup().cs = new PurinePyrimidineColourScheme();
-    refresh();
-  }
-
-  protected void tcoffeeColorScheme_actionPerformed()
-  {
-    getGroup().cs = new TCoffeeColourScheme(getGroup());
-    refresh();
-  }
-
   /*
    * protected void covariationColour_actionPerformed() { getGroup().cs = new
    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
@@ -1883,10 +1529,12 @@ public class PopupMenu extends JPopupMenu
   /**
    * DOCUMENT ME!
    * 
+   * @param selected
+   * 
    * @param e
    *          DOCUMENT ME!
    */
-  protected void abovePIDColour_actionPerformed()
+  protected void abovePIDColour_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -1894,13 +1542,14 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    if (abovePIDColour.isSelected())
+    if (selected)
     {
       sg.cs.setConsensus(AAFrequency.calculate(
               sg.getSequences(ap.av.getHiddenRepSequences()),
               sg.getStartRes(), sg.getEndRes() + 1));
 
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+      int threshold = SliderPanel.setPIDSliderSource(ap,
+              sg.getGroupColourScheme(), getGroup()
               .getName());
 
       sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
@@ -1911,36 +1560,14 @@ public class PopupMenu extends JPopupMenu
     // remove PIDColouring
     {
       sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+      SliderPanel.hidePIDSlider();
     }
+    modifyPID.setEnabled(selected);
 
     refresh();
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
-  {
-    SequenceGroup sg = getGroup();
-
-    if (e.getSource().equals(userDefinedColour))
-    {
-      new UserDefinedColours(ap, sg);
-    }
-    else
-    {
-      UserColourScheme udc = UserDefinedColours
-              .getUserColourSchemes().get(e.getActionCommand());
-
-      sg.cs = udc;
-    }
-    refresh();
-  }
-
-  /**
    * Open a panel where the user can choose which types of sequence annotation
    * to show or hide.
    * 
@@ -1958,54 +1585,7 @@ public class PopupMenu extends JPopupMenu
    * @param e
    *          DOCUMENT ME!
    */
-  protected void PIDColour_actionPerformed()
-  {
-    SequenceGroup sg = getGroup();
-    sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.getHiddenRepSequences()),
-            sg.getStartRes(), sg.getEndRes() + 1));
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void BLOSUM62Colour_actionPerformed()
-  {
-    SequenceGroup sg = getGroup();
-
-    sg.cs = new Blosum62ColourScheme();
-
-    sg.cs.setConsensus(AAFrequency.calculate(
-            sg.getSequences(ap.av.getHiddenRepSequences()),
-            sg.getStartRes(), sg.getEndRes() + 1));
-
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void noColourmenuItem_actionPerformed()
-  {
-    getGroup().cs = null;
-    refresh();
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void conservationMenuItem_actionPerformed()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
     SequenceGroup sg = getGroup();
     if (sg.cs == null)
@@ -2013,7 +1593,7 @@ public class PopupMenu extends JPopupMenu
       return;
     }
 
-    if (conservationMenuItem.isSelected())
+    if (selected)
     {
       // JBPNote: Conservation name shouldn't be i18n translated
       Conservation c = new Conservation("Group", sg.getSequences(ap.av
@@ -2022,17 +1602,19 @@ public class PopupMenu extends JPopupMenu
 
       c.calculate();
       c.verdict(false, ap.av.getConsPercGaps());
-
       sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+              sg.getName());
       SliderPanel.showConservationSlider();
     }
     else
     // remove ConservationColouring
     {
       sg.cs.setConservation(null);
+      SliderPanel.hideConservationSlider();
     }
+    modifyConservation.setEnabled(selected);
 
     refresh();
   }
@@ -2050,7 +1632,7 @@ public class PopupMenu extends JPopupMenu
             AnnotationColourGradient.NO_THRESHOLD);
 
     acg.setPredefinedColours(true);
-    sg.cs = acg;
+    sg.setColourScheme(acg);
 
     refresh();
   }
@@ -2310,7 +1892,7 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
     cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }
 
@@ -2415,4 +1997,41 @@ public class PopupMenu extends JPopupMenu
     }
   }
 
+  /**
+   * Action on user selecting an item from the colour menu (that does not have
+   * its bespoke action handler)
+   * 
+   * @return
+   */
+  @Override
+  public void changeColour_actionPerformed(String colourSchemeName)
+  {
+    SequenceGroup sg = getGroup();
+    if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
+    {
+      /*
+       * open a panel to load or configure a user-defined colour scheme
+       */
+      new UserDefinedColours(ap, sg);
+    }
+    else
+    {
+      /*
+       * switch to the chosen colour scheme (or null for None)
+       */
+      ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
+              colourSchemeName, sg, ap.av.getHiddenRepSequences());
+      sg.setColourScheme(colourScheme);
+      if (colourScheme instanceof Blosum62ColourScheme
+              || colourScheme instanceof PIDColourScheme)
+      {
+        sg.cs.setConsensus(AAFrequency.calculate(
+                sg.getSequences(ap.av.getHiddenRepSequences()),
+                sg.getStartRes(), sg.getEndRes() + 1));
+      }
+    }
+
+    refresh();
+  }
+
 }