JAL-2361 simplify constructors, select unsaved but applied user defined

colour scheme in menu

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 507bfab..d4c87d8 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3335,7 +3335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     if (ResidueColourScheme.USER_DEFINED.equals(name))
     {
-      new UserDefinedColours(alignPanel, null);
+      new UserDefinedColours(alignPanel);
       return;
     }
 
@@ -3356,10 +3356,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void changeColour(ColourSchemeI cs)
   {
     // TODO: pull up to controller method
-    if (cs != null)
-    {
-      ColourMenuHelper.setColourSelected(colourMenu, cs.getSchemeName());
-    }
+    ColourMenuHelper.setColourSelected(colourMenu, cs);
 
     viewport.setGlobalColourScheme(cs);
 
@@ -5708,10 +5705,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     colourMenu.add(annotationColour);
 
     ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
-    String schemeName = colourScheme == null ? null : colourScheme
-            .getSchemeName();
-
-    ColourMenuHelper.setColourSelected(colourMenu, schemeName);
+    ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
   }
 }
 

diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index 801615c..b2b9574 100644 (file)
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -23,6 +23,12 @@ public class ColourMenuHelper
 {
   public interface ColourChangeListener
   {
+    /**
+     * Change colour scheme to the selected scheme
+     * 
+     * @param name
+     *          the registered (unique) name of a colour scheme
+     */
     void changeColour_actionPerformed(String name);
   }
 
@@ -37,7 +43,7 @@ public class ColourMenuHelper
    * <li>Clustal</li>
    * <li>...other 'built-in' colours</li>
    * <li>...any user-defined colours</li>
-   * <li>User Defined..</li>
+   * <li>User Defined..(only for AlignFrame menu)</li>
    * </ul>
    * 
    * @param colourMenu
@@ -77,7 +83,7 @@ public class ColourMenuHelper
     }
 
     /*
-     * scan registered colour schemes (built-in or user-defined
+     * scan registered colour schemes (built-in or user-defined)
      * and add them to the menu (in the order they were registered)
      */
     Iterable<ColourSchemeI> colourSchemes = ColourSchemes.getInstance()
@@ -171,6 +177,7 @@ public class ColourMenuHelper
       final String label = MessageManager.getString("action.user_defined");
       JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(
               label);
+      userDefinedColour.setName(ResidueColourScheme.USER_DEFINED);
       userDefinedColour.addActionListener(new ActionListener()
       {
         @Override
@@ -187,20 +194,22 @@ public class ColourMenuHelper
   }
 
   /**
-   * Marks as selected the colour menu item matching the given name, or the
-   * first item ('None') if no match is found
+   * Marks as selected the colour menu item matching the given colour scheme, or
+   * the first item ('None') if no match is found. If the colour scheme is a
+   * user defined scheme, but not in the menu (this arises if a new scheme is
+   * defined and applied but not saved to file), then menu option
+   * "User Defined.." is selected.
    * 
    * @param colourMenu
-   * @param colourName
+   * @param cs
    */
-  public static void setColourSelected(JMenu colourMenu, String colourName)
+  public static void setColourSelected(JMenu colourMenu, ColourSchemeI cs)
   {
-    if (colourName == null)
-    {
-      return;
-    }
+    String colourName = cs == null ? ResidueColourScheme.NONE : cs
+            .getSchemeName();
 
     JRadioButtonMenuItem none = null;
+    JRadioButtonMenuItem userDefined = null;
 
     /*
      * select the radio button whose name matches the colour name
@@ -210,38 +219,39 @@ public class ColourMenuHelper
     {
       if (menuItem instanceof JRadioButtonMenuItem)
       {
-        String buttonName = ((JRadioButtonMenuItem) menuItem).getName();
-        if (colourName.equals(buttonName))
+        JRadioButtonMenuItem radioButton = (JRadioButtonMenuItem) menuItem;
+        String buttonName = radioButton.getName();
+        if (buttonName.equals(colourName))
         {
-          ((JRadioButtonMenuItem) menuItem).setSelected(true);
+          radioButton.setSelected(true);
           return;
         }
         if (ResidueColourScheme.NONE.equals(buttonName))
         {
-          none = (JRadioButtonMenuItem) menuItem;
+          none = radioButton;
+        }
+        if (ResidueColourScheme.USER_DEFINED.equals(buttonName))
+        {
+          userDefined = radioButton;
         }
       }
     }
-    if (none != null)
+
+    /*
+     * no match by name; select User Defined.. if current scheme is a 
+     * user defined one, else select None
+     */
+    if (cs instanceof UserColourScheme && userDefined != null)
+    {
+      userDefined.setSelected(true);
+    }
+    else if (none != null)
     {
       none.setSelected(true);
     }
   }
 
   /**
-   * Marks as selected the colour menu item matching the given colour scheme, or
-   * the first item ('None') if no match is found
-   * 
-   * @param colourMenu
-   * @param cs
-   */
-  public static void setColourSelected(JMenu colourMenu, ColourSchemeI cs)
-  {
-    setColourSelected(colourMenu, cs == null ? ResidueColourScheme.NONE
-            : cs.getSchemeName());
-  }
-
-  /**
    * Updates the USER_DEFINE_COLOURS preference to remove any de-registered
    * colour scheme
    */

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index d91fa70..660c651 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -47,7 +47,6 @@ import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
@@ -1984,28 +1983,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   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)
     {
-      /*
-       * 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));
-      }
+      sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.getHiddenRepSequences()),
+              sg.getStartRes(), sg.getEndRes() + 1));
     }
 
     refresh();

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 5ec95ed..369dde6 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -21,7 +21,6 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
-import jalview.datamodel.SequenceGroup;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GUserDefinedColours;
@@ -78,8 +77,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   AlignmentPanel ap;
 
-  SequenceGroup seqGroup;
-
   ColourSchemeI oldColourScheme;
 
   JInternalFrame frame;
@@ -89,28 +86,19 @@ public class UserDefinedColours extends GUserDefinedColours implements
   List<JButton> lowerCaseButtons;
 
   /**
-   * Creates a new UserDefinedColours object.
+   * Creates and displays a new UserDefinedColours panel
    * 
-   * @param ap
-   * @param sg
+   * @param alignPanel
    */
-  public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
+  public UserDefinedColours(AlignmentPanel alignPanel)
   {
     this();
 
     lcaseColour.setEnabled(false);
 
-    this.ap = ap;
-    seqGroup = sg;
+    this.ap = alignPanel;
 
-    if (seqGroup != null)
-    {
-      oldColourScheme = seqGroup.getColourScheme();
-    }
-    else
-    {
-      oldColourScheme = ap.av.getGlobalColourScheme();
-    }
+    oldColourScheme = alignPanel.av.getGlobalColourScheme();
 
     if (oldColourScheme instanceof UserColourScheme)
     {
@@ -148,11 +136,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
     Desktop.addInternalFrame(frame,
             MessageManager.getString("label.user_defined_colours"),
             MY_FRAME_WIDTH, MY_FRAME_HEIGHT, true);
-
-    if (seqGroup != null)
-    {
-      frame.setTitle(frame.getTitle() + " (" + seqGroup.getName() + ")");
-    }
   }
 
   /**
@@ -496,15 +479,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     }
     UserColourScheme ucs = getSchemeFromButtons();
 
-    if (seqGroup != null)
-    {
-      seqGroup.setColourScheme(ucs);
-      ap.paintAlignment(true);
-    }
-    else if (ap != null)
-    {
-      ap.alignFrame.changeColour(ucs);
-    }
+    ap.alignFrame.changeColour(ucs);
   }
 
   /**
@@ -695,7 +670,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         return;
       }
-      ColourSchemes.getInstance().removeColourScheme(name);
     }
     JalviewFileChooser chooser = new JalviewFileChooser("jc",
             "Jalview User Colours");
@@ -809,18 +783,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   protected void cancelButton_actionPerformed()
   {
-    if (ap != null)
-    {
-      if (seqGroup != null)
-      {
-        seqGroup.setColourScheme(oldColourScheme);
-      }
-      else
-      {
-        ap.alignFrame.changeColour(oldColourScheme);
-      }
-      ap.paintAlignment(true);
-    }
+    ap.alignFrame.changeColour(oldColourScheme);
+    ap.paintAlignment(true);
 
     try
     {