JAL-2360 ColourSchemes holds configured schemes, AlignFrame colour menu
[jalview.git] / src / jalview / jbgui / GAlignFrame.java
index fba0efa..faa0d5d 100755 (executable)
@@ -23,15 +23,9 @@ package jalview.jbgui;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
-import jalview.gui.UserDefinedColours;
 import jalview.io.FileFormat;
-import jalview.schemes.JalviewColourScheme;
-import jalview.schemes.ResidueColourScheme;
-import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -90,38 +84,8 @@ public class GAlignFrame extends JInternalFrame
 
   protected JRadioButtonMenuItem textColour;
 
-  protected JRadioButtonMenuItem clustalColour;
-
-  protected JRadioButtonMenuItem zappoColour;
-
-  protected JRadioButtonMenuItem taylorColour;
-
-  protected JRadioButtonMenuItem hydrophobicityColour;
-
-  protected JRadioButtonMenuItem helixColour;
-
-  protected JRadioButtonMenuItem strandColour;
-
-  protected JRadioButtonMenuItem turnColour;
-
-  protected JRadioButtonMenuItem buriedColour;
-
   protected JRadioButtonMenuItem userDefinedColour;
 
-  protected JRadioButtonMenuItem PIDColour;
-
-  protected JRadioButtonMenuItem BLOSUM62Colour;
-
-  protected JRadioButtonMenuItem nucleotideColour;
-
-  protected JRadioButtonMenuItem purinePyrimidineColour;
-
-  protected JRadioButtonMenuItem RNAInteractionColour;
-
-  // protected JRadioButtonMenuItem covariationColour;
-
-  protected JRadioButtonMenuItem tcoffeeColour;
-
   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
@@ -134,7 +98,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem conservationMenuItem;
 
-  JRadioButtonMenuItem noColourmenuItem;
+  protected JRadioButtonMenuItem noColourmenuItem;
 
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
@@ -178,8 +142,6 @@ 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();
@@ -190,8 +152,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem runGroovy = new JMenuItem();
 
-  protected JMenuItem rnahelicesColour;
-
   protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem();
@@ -323,7 +283,6 @@ public class GAlignFrame extends JInternalFrame
   private void jbInit() throws Exception
   {
     initColourMenu();
-    buildColourMenu();
 
     JMenuItem saveAs = new JMenuItem(
             MessageManager.getString("action.save_as"));
@@ -642,7 +601,7 @@ public class GAlignFrame extends JInternalFrame
 
 
     JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem(
-            MessageManager.getString("label.average_distance_bloslum62"));
+            MessageManager.getString("label.average_distance_blosum62"));
     avDistanceTreeBlosumMenuItem.addActionListener(new ActionListener()
     {
       @Override
@@ -1982,144 +1941,6 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
-   * Rebuilds the Colour menu, including any user-defined colours which have
-   * been loaded either on startup or during the session
-   */
-  public void buildColourMenu()
-  {
-    colourMenu.removeAll();
-    colours = new ButtonGroup();
-
-    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);
-
-    /*
-     * add any user-defined colours
-     */
-    Map<String, UserColourScheme> userColourSchemes = UserDefinedColours
-            .getUserColourSchemes();
-    if (userColourSchemes != null)
-    {
-      for (String userColour : userColourSchemes.keySet())
-      {
-        final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
-                userColour);
-        radioItem.setName(userColour);
-        radioItem.addMouseListener(new MouseAdapter()
-        {
-          @Override
-          public void mousePressed(MouseEvent evt)
-          {
-            if (evt.isPopupTrigger()) // Mac
-            {
-              offerRemoval();
-            }
-          }
-
-          @Override
-          public void mouseReleased(MouseEvent evt)
-          {
-            if (evt.isPopupTrigger()) // Windows
-            {
-              offerRemoval();
-            }
-          }
-
-          void offerRemoval()
-          {
-            radioItem.removeActionListener(radioItem.getActionListeners()[0]);
-
-            int option = JvOptionPane.showInternalConfirmDialog(
-                    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)
-            {
-              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.add(radioItem);
-        colours.add(radioItem);
-      }
-    }
-
-    colourMenu.add(userDefinedColour);
-    colourMenu.addSeparator();
-    colourMenu.add(conservationMenuItem);
-    colourMenu.add(modifyConservation);
-    colourMenu.add(abovePIDThreshold);
-    colourMenu.add(modifyPID);
-    colourMenu.add(annotationColour);
-    colourMenu.add(rnahelicesColour);
-
-    /*
-     * add colours to a ButtonGroup to make their 
-     * selection mutually exclusive
-     */
-    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(Cache.getDefault(Preferences.DEFAULT_COLOUR,
-            ResidueColourScheme.NONE));
-
-  }
-
-  /**
    * 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
@@ -2148,101 +1969,10 @@ public class GAlignFrame extends JInternalFrame
         textColour_actionPerformed();
       }
     });
-    clustalColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.clustalx"));
-    clustalColour.setName(JalviewColourScheme.Clustal.toString());
-    clustalColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed();
-      }
-    });
-    zappoColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.zappo"));
-    zappoColour.setName(JalviewColourScheme.Zappo.toString());
-    zappoColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed();
-      }
-    });
-    taylorColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.taylor"));
-    taylorColour.setName(JalviewColourScheme.Taylor.toString());
-    taylorColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed();
-      }
-    });
-    hydrophobicityColour = new JRadioButtonMenuItem(
-            MessageManager
-            .getString("label.hydrophobicity"));
-    hydrophobicityColour
-            .setName(JalviewColourScheme.Hydrophobic.toString());
-    hydrophobicityColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed();
-      }
-    });
-    helixColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.helix_propensity"));
-    helixColour.setName(JalviewColourScheme.Helix.toString());
-    helixColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed();
-      }
-    });
-    strandColour = new JRadioButtonMenuItem(
-            MessageManager
-            .getString("label.strand_propensity"));
-    strandColour.setName(JalviewColourScheme.Strand.toString());
-    strandColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed();
-      }
-    });
-    turnColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.turn_propensity"));
-    turnColour.setName(JalviewColourScheme.Turn.toString());
-    turnColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed();
-      }
-    });
-    buriedColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.buried_index"));
-    buriedColour.setName(JalviewColourScheme.Buried.toString());
-    buriedColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed();
-      }
-    });
+
     userDefinedColour = new JRadioButtonMenuItem(
             MessageManager
             .getString("action.user_defined"));
-    userDefinedColour.setName(JalviewColourScheme.UserDefined.toString());
     userDefinedColour.addActionListener(new ActionListener()
     {
       @Override
@@ -2251,81 +1981,6 @@ public class GAlignFrame extends JInternalFrame
         userDefinedColour_actionPerformed(e);
       }
     });
-    PIDColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.percentage_identity"));
-    PIDColour.setName(JalviewColourScheme.PID.toString());
-    PIDColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed();
-      }
-    });
-    BLOSUM62Colour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.blosum62_score"));
-    BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
-    BLOSUM62Colour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed();
-      }
-    });
-    nucleotideColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.nucleotide"));
-    nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
-    nucleotideColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideColour_actionPerformed();
-      }
-    });
-    purinePyrimidineColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.purine_pyrimidine"));
-    purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine.toString());
-    purinePyrimidineColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        purinePyrimidineColour_actionPerformed();
-      }
-    });
-
-    tcoffeeColour = new JRadioButtonMenuItem(
-            MessageManager.getString("label.tcoffee_scores"));
-    tcoffeeColour.setName(JalviewColourScheme.TCoffee.toString());
-    tcoffeeColour.setEnabled(false);
-    tcoffeeColour.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        tcoffeeColorScheme_actionPerformed();
-      }
-    });
-
-    // RNAInteractionColour = new JRadioButtonMenuItem("RNA Interaction type");
-    // RNAInteractionColour.setName("RNA Interaction");
-    // RNAInteractionColour.addActionListener(new ActionListener()
-    // {
-    // @Override
-    // public void actionPerformed(ActionEvent e)
-    // {
-    // RNAInteractionColour_actionPerformed();
-    // }
-    // });
-    /*
-     * covariationColour = new JRadioButtonMenuItem("Covariation");
-     * covariationColour.addActionListener(new ActionListener() { public void
-     * actionPerformed(ActionEvent e) { covariationColour_actionPerformed(); }
-     * });
-     */
 
     conservationMenuItem = new JCheckBoxMenuItem(
             MessageManager.getString("action.by_conservation"));
@@ -2391,17 +2046,6 @@ public class GAlignFrame extends JInternalFrame
         annotationColour_actionPerformed();
       }
     });
-
-    rnahelicesColour = new JMenuItem(
-            MessageManager.getString("action.by_rna_helixes"));
-    rnahelicesColour.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        rnahelicesColour_actionPerformed();
-      }
-    });
   }
 
   protected void selectHighlightedColumns_actionPerformed(
@@ -2759,57 +2403,11 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void clustalColour_actionPerformed()
-  {
-  }
-
-  protected void zappoColour_actionPerformed()
-  {
-  }
-
-  protected void taylorColour_actionPerformed()
-  {
-  }
-
-  protected void hydrophobicityColour_actionPerformed()
-  {
-  }
-
-  protected void helixColour_actionPerformed()
-  {
-  }
-
-  protected void strandColour_actionPerformed()
-  {
-  }
-
-  protected void turnColour_actionPerformed()
-  {
-  }
-
-  protected void buriedColour_actionPerformed()
-  {
-  }
-
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
   }
 
-  protected void PIDColour_actionPerformed()
-  {
-  }
-
-  protected void BLOSUM62Colour_actionPerformed()
-  {
-  }
-
-  protected void purinePyrimidineColour_actionPerformed()
-  {
-  }
-
-  protected void RNAInteractionColour_actionPerformed()
-  {
-  }
+  
 
   /*
    * protected void covariationColour_actionPerformed() { }
@@ -2843,10 +2441,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void nucleotideColour_actionPerformed()
-  {
-  }
-
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
   }
@@ -2927,16 +2521,6 @@ 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.
-   */
-  protected void tcoffeeColorScheme_actionPerformed()
-  {
-
-  }
-
   protected void jpred_actionPerformed(ActionEvent e)
   {
   }
@@ -3007,11 +2591,6 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  public void rnahelicesColour_actionPerformed()
-  {
-
-  }
-
   public void associatedData_actionPerformed(ActionEvent e)
   {