From e77ec70cef4efba54974739e86673925396f0e92 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 7 Feb 2017 15:59:37 +0000
Subject: [PATCH] JAL-2401 Lower Case Colour toggleable, help text added

---
 help/html/colourSchemes/user.html          |    3 ++
 src/jalview/gui/UserDefinedColours.java    |   67 +++++++++++++++-------------
 src/jalview/jbgui/GUserDefinedColours.java |    6 +++
 3 files changed, 45 insertions(+), 31 deletions(-)

diff --git a/help/html/colourSchemes/user.html b/help/html/colourSchemes/user.html
index 7239e4d..fb6c356 100755
--- a/help/html/colourSchemes/user.html
+++ b/help/html/colourSchemes/user.html
@@ -41,6 +41,9 @@
     The <strong>Case Sensitive</strong> option allows you to choose
     distinct colours for upper and lower case residue codes.
   <p>
+    The <strong>Lower Case Colour</strong> option allows you to apply a selected colour
+    to all lower case residues.
+  <p>
     Click <strong>Apply</strong> or <strong>OK</strong> to set your new
     colours on the active alignment window.<br /> Click <strong>Cancel</strong>
     to undo your changes if you pressed the <strong>Apply</strong>
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 6b4bd10..e6ff3c8 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -70,8 +70,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   SequenceGroup seqGroup;
 
-  ArrayList<JButton> selectedButtons;
-
   ColourSchemeI oldColourScheme;
 
   JInternalFrame frame;
@@ -248,33 +246,34 @@ public class UserDefinedColours extends GUserDefinedColours implements
   }
 
   /**
-   * DOCUMENT ME!
+   * ChangeListener handler for when a colour is picked in the colour chooser.
+   * The action is to apply the colour to all selected buttons as their
+   * background colour. Foreground colour (text) is set to a lighter shade in
+   * order to highlight which buttons are selected. If 'Lower Case Colour' is
+   * active, then the colour is applied to all lower case buttons (as well as
+   * the Lower Case Colour button itself).
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void stateChanged(ChangeEvent evt)
   {
-    if (selectedButtons != null)
+    JButton button = null;
+    final Color newColour = colorChooser.getColor();
+    for (int i = 0; i < selectedButtons.size(); i++)
+    {
+      button = selectedButtons.get(i);
+      button.setBackground(newColour);
+      button.setForeground(ColorUtils.brighterThan(newColour));
+    }
+    if (button == lcaseColour)
     {
-      JButton button = null;
-      final Color newColour = colorChooser.getColor();
-      for (int i = 0; i < selectedButtons.size(); i++)
+      button.setForeground(Color.black);
+      for (int i = 0; i < lowerCaseButtons.size(); i++)
       {
-        button = selectedButtons.get(i);
+        button = lowerCaseButtons.get(i);
         button.setBackground(newColour);
-        button.setForeground(ColorUtils.brighterThan(newColour));
-      }
-      if (button == lcaseColour)
-      {
-        for (int i = 0; i < lowerCaseButtons.size(); i++)
-        {
-          button = lowerCaseButtons.get(i);
-          button.setBackground(newColour);
-          button.setForeground(ColorUtils.brighterThan(button
-                  .getBackground()));
-        }
+        button.setForeground(ColorUtils.brighterThan(button.getBackground()));
       }
     }
   }
@@ -299,11 +298,6 @@ public class UserDefinedColours extends GUserDefinedColours implements
    */
   public void colourButtonPressed(MouseEvent e)
   {
-    if (selectedButtons == null)
-    {
-      selectedButtons = new ArrayList<JButton>();
-    }
-
     JButton pressed = (JButton) e.getSource();
 
     if (e.isShiftDown())
@@ -1026,21 +1020,32 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   public void caseSensitive_actionPerformed(ActionEvent e)
   {
-    resetButtonPanel(caseSensitive.isSelected());
-    lcaseColour.setEnabled(caseSensitive.isSelected());
+    boolean selected = caseSensitive.isSelected();
+    resetButtonPanel(selected);
+    lcaseColour.setEnabled(selected);
+    lcaseColour.setForeground(Color.GRAY);
   }
 
+  /**
+   * Action on clicking 'Lower case colour', which results in changing colour of
+   * all lower-case buttons when a colour is picked. A second click of the
+   * button turns off this behaviour.
+   */
   @Override
   public void lcaseColour_actionPerformed(ActionEvent e)
   {
-    if (selectedButtons == null)
+    boolean enable = !selectedButtons.contains(lcaseColour);
+    selectedButtons.clear();
+    if (enable)
     {
-      selectedButtons = new ArrayList<JButton>();
+      selectedButtons.add(lcaseColour);
+      lcaseColour.setForeground(lowerCaseButtons.get(0).getForeground());
+      lcaseColour.setForeground(Color.black);
     }
     else
     {
-      selectedButtons.clear();
+      lcaseColour.setBackground(Color.white);
+      lcaseColour.setForeground(Color.gray);
     }
-    selectedButtons.add(lcaseColour);
   }
 }
diff --git a/src/jalview/jbgui/GUserDefinedColours.java b/src/jalview/jbgui/GUserDefinedColours.java
index b5695b2..65d02df 100755
--- a/src/jalview/jbgui/GUserDefinedColours.java
+++ b/src/jalview/jbgui/GUserDefinedColours.java
@@ -32,6 +32,8 @@ import java.awt.GridBagLayout;
 import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
 
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
@@ -104,6 +106,8 @@ public class GUserDefinedColours extends JPanel
 
   protected JButton lcaseColour = new JButton();
 
+  protected List<JButton> selectedButtons;
+
   /**
    * Creates a new GUserDefinedColours object.
    */
@@ -253,6 +257,8 @@ public class GUserDefinedColours extends JPanel
       colorChooser
               .setChooserPanels(new AbstractColorChooserPanel[] { choosers[0] });
     }
+
+    selectedButtons = new ArrayList<JButton>();
   }
 
   /**
-- 
1.7.10.2