JAL-2361 apply any saved changes to current colour scheme

diff --git a/src/jalview/gui/ColourMenuHelper.java b/src/jalview/gui/ColourMenuHelper.java
index 19ad939..801615c 100644 (file)
--- a/src/jalview/gui/ColourMenuHelper.java
+++ b/src/jalview/gui/ColourMenuHelper.java
@@ -104,14 +104,14 @@ public class ColourMenuHelper
         /*
          * user-defined colour scheme loaded on startup or during the
          * Jalview session; right-click on this offers the option to
-         * remove it as a colour choice
+         * remove it as a colour choice (unless currently selected)
          */
         radioItem.addMouseListener(new MouseAdapter()
         {
           @Override
           public void mousePressed(MouseEvent evt)
           {
-            if (evt.isPopupTrigger()) // Mac
+            if (evt.isPopupTrigger() && !radioItem.isSelected()) // Mac
             {
               offerRemoval();
             }
@@ -120,7 +120,7 @@ public class ColourMenuHelper
           @Override
           public void mouseReleased(MouseEvent evt)
           {
-            if (evt.isPopupTrigger()) // Windows
+            if (evt.isPopupTrigger() && !radioItem.isSelected()) // Windows
             {
               offerRemoval();
             }

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 9ab4327..5ec95ed 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.SequenceGroup;
 import jalview.io.JalviewFileChooser;
@@ -40,7 +39,6 @@ import jalview.util.MessageManager;
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.Insets;
-import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.io.File;
@@ -82,14 +80,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   SequenceGroup seqGroup;
 
-  List<JButton> selectedButtons;
-
   ColourSchemeI oldColourScheme;
 
   JInternalFrame frame;
 
-  JalviewStructureDisplayI structureViewer;
-
   List<JButton> upperCaseButtons;
 
   List<JButton> lowerCaseButtons;
@@ -140,29 +134,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     showFrame();
   }
 
-  public UserDefinedColours(JalviewStructureDisplayI viewer,
-          ColourSchemeI oldcs)
-  {
-    this();
-    this.structureViewer = viewer;
-
-    colorChooser.getSelectionModel().addChangeListener(this);
-
-    oldColourScheme = oldcs;
-
-    if (oldColourScheme instanceof UserColourScheme)
-    {
-      schemeName.setText(((UserColourScheme) oldColourScheme)
-              .getSchemeName());
-    }
-
-    resetButtonPanel(false);
-
-    showFrame();
-
-  }
-
-  public UserDefinedColours()
+  UserDefinedColours()
   {
     super();
     selectedButtons = new ArrayList<JButton>();
@@ -509,8 +481,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
   }
 
   /**
-   * Applies the current colour scheme to the alignment, sequence group or
-   * structure view.
+   * Applies the current colour scheme to the alignment or sequence group
    */
   @Override
   protected void applyButton_actionPerformed()
@@ -534,12 +505,14 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       ap.alignFrame.changeColour(ucs);
     }
-    else if (structureViewer != null)
-    {
-      structureViewer.setJalviewColourScheme(ucs);
-    }
   }
 
+  /**
+   * Constructs an instance of UserColourScheme with the residue colours
+   * currently set on the buttons on the panel
+   * 
+   * @return
+   */
   UserColourScheme getSchemeFromButtons()
   {
 
@@ -595,13 +568,15 @@ public class UserDefinedColours extends GUserDefinedColours implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on clicking Load scheme button.
+   * <ul>
+   * <li>Open a file chooser to browse for files with extension .jc</li>
+   * <li>Load in the colour scheme and transfer it to this panel's buttons</li>
+   * <li>Register the loaded colour scheme</li>
+   * </ul>
    */
   @Override
-  protected void loadbutton_actionPerformed(ActionEvent e)
+  protected void loadbutton_actionPerformed()
   {
     upperCaseButtons = new ArrayList<JButton>();
     lowerCaseButtons = new ArrayList<JButton>();
@@ -683,13 +658,20 @@ public class UserDefinedColours extends GUserDefinedColours implements
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
+   * Action on pressing the Save button.
+   * <ul>
+   * <li>Check a name has been entered</li>
+   * <li>Warn if the name already exists, remove any existing scheme of the same
+   * name if overwriting</li>
+   * <li>Do the standard file chooser thing to write with extension .jc</li>
+   * <li>If saving changes (possibly not yet applied) to the currently selected
+   * colour scheme, then apply the changes, as it is too late to back out now</li>
+   * <li>Don't apply the changes if the currently selected scheme is different,
+   * to allow a new scheme to be configured and saved but not applied</li>
+   * </ul>
    */
   @Override
-  protected void savebutton_actionPerformed(ActionEvent e)
+  protected void savebutton_actionPerformed()
   {
     String name = schemeName.getText().trim();
     if (name.length() < 1)
@@ -731,6 +713,16 @@ public class UserDefinedColours extends GUserDefinedColours implements
       File file = chooser.getSelectedFile();
       addNewColourScheme(file.getPath());
       saveToFile(file);
+
+      /*
+       * changes saved - apply to alignment if we are changing 
+       * the currently selected colour scheme
+       */
+      if (oldColourScheme != null
+              && name.equals(oldColourScheme.getSchemeName()))
+      {
+        applyButton_actionPerformed();
+      }
     }
   }
 
@@ -787,7 +779,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
      * marshal to file
      */
     JalviewUserColours ucs = new JalviewUserColours();
-    ucs.setSchemeName(schemeName.getText());
+    String name = schemeName.getText();
+    ucs.setSchemeName(name);
     try
     {
       PrintWriter out = new PrintWriter(new OutputStreamWriter(
@@ -810,12 +803,11 @@ public class UserDefinedColours extends GUserDefinedColours implements
   }
 
   /**
-   * On cancel, restores the colour scheme before the dialogue was opened
-   * 
-   * @param e
+   * On cancel, restores the colour scheme that was selected before the dialogue
+   * was opened
    */
   @Override
-  protected void cancelButton_actionPerformed(ActionEvent e)
+  protected void cancelButton_actionPerformed()
   {
     if (ap != null)
     {
@@ -830,11 +822,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ap.paintAlignment(true);
     }
 
-    if (structureViewer != null)
-    {
-      structureViewer.setJalviewColourScheme(oldColourScheme);
-    }
-
     try
     {
       frame.setClosed(true);
@@ -843,8 +830,14 @@ public class UserDefinedColours extends GUserDefinedColours implements
     }
   }
 
+  /**
+   * Action on selecting or deselecting the Case Sensitive option. When
+   * selected, separate buttons are shown for lower case residues, and the panel
+   * is resized to accommodate them. Also, the checkbox for 'apply colour to all
+   * lower case' is enabled.
+   */
   @Override
-  public void caseSensitive_actionPerformed(ActionEvent e)
+  public void caseSensitive_actionPerformed()
   {
     boolean selected = caseSensitive.isSelected();
     resetButtonPanel(selected);

diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index aa5319c..c3645a8 100755 (executable)
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -137,7 +137,7 @@ public class GUserDefinedColours extends JPanel
     gridLayout.setRows(5);
     okButton.setFont(new java.awt.Font("Verdana", 0, 11));
     okButton.setText(MessageManager.getString("action.ok"));
-    okButton.addActionListener(new java.awt.event.ActionListener()
+    okButton.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
@@ -157,32 +157,32 @@ public class GUserDefinedColours extends JPanel
     });
     loadbutton.setFont(new java.awt.Font("Verdana", 0, 11));
     loadbutton.setText(MessageManager.getString("action.load_scheme"));
-    loadbutton.addActionListener(new java.awt.event.ActionListener()
+    loadbutton.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        loadbutton_actionPerformed(e);
+        loadbutton_actionPerformed();
       }
     });
     savebutton.setFont(new java.awt.Font("Verdana", 0, 11));
     savebutton.setText(MessageManager.getString("action.save_scheme"));
-    savebutton.addActionListener(new java.awt.event.ActionListener()
+    savebutton.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        savebutton_actionPerformed(e);
+        savebutton_actionPerformed();
       }
     });
     cancelButton.setFont(JvSwingUtils.getLabelFont());
     cancelButton.setText(MessageManager.getString("action.cancel"));
-    cancelButton.addActionListener(new java.awt.event.ActionListener()
+    cancelButton.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        cancelButton_actionPerformed(e);
+        cancelButton_actionPerformed();
       }
     });
     this.setBackground(new Color(212, 208, 223));
@@ -218,7 +218,7 @@ public class GUserDefinedColours extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        caseSensitive_actionPerformed(e);
+        caseSensitive_actionPerformed();
       }
     });
     lcaseColour
@@ -282,17 +282,11 @@ public class GUserDefinedColours extends JPanel
    * @param e
    *          DOCUMENT ME!
    */
-  protected void loadbutton_actionPerformed(ActionEvent e)
+  protected void loadbutton_actionPerformed()
   {
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param e
-   *          DOCUMENT ME!
-   */
-  protected void savebutton_actionPerformed(ActionEvent e)
+  protected void savebutton_actionPerformed()
   {
   }
 
@@ -302,16 +296,16 @@ public class GUserDefinedColours extends JPanel
    * @param e
    *          DOCUMENT ME!
    */
-  protected void cancelButton_actionPerformed(ActionEvent e)
+  protected void cancelButton_actionPerformed()
   {
   }
 
-  public void caseSensitive_actionPerformed(ActionEvent e)
+  public void caseSensitive_actionPerformed()
   {
 
   }
 
-  public void lcaseColour_actionPerformed(ActionEvent e)
+  public void lcaseColour_actionPerformed()
   {
 
   }

diff --git a/src/jalview/schemes/ColourSchemes.java b/src/jalview/schemes/ColourSchemes.java
index dc7e403..269811b 100644 (file)
--- a/src/jalview/schemes/ColourSchemes.java
+++ b/src/jalview/schemes/ColourSchemes.java
@@ -15,7 +15,7 @@ public class ColourSchemes
   private static ColourSchemes instance = new ColourSchemes();
 
   /*
-   * a map from scheme name to an instance of it
+   * a map from scheme name (lower-cased) to an instance of it
    */
   private Map<String, ColourSchemeI> schemes;
 
@@ -94,7 +94,10 @@ public class ColourSchemes
    */
   public void removeColourScheme(String name)
   {
-    schemes.remove(name);
+    if (name != null)
+    {
+      schemes.remove(name.toLowerCase());
+    }
   }
   
   /**
@@ -162,14 +165,6 @@ public class ColourSchemes
     {
       return false;
     }
-    name = name.toLowerCase();
-    for (ColourSchemeI scheme : getColourSchemes())
-    {
-      if (name.equals(scheme.getSchemeName().toLowerCase()))
-      {
-        return true;
-      }
-    }
-    return false;
+    return schemes.containsKey(name.toLowerCase());
   }
 }