X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FUserDefinedColours.java;h=463d8cdddc49b1e45d1d55c2c53da8e615e579d8;hb=e529f0aa0690ac7a6f58677fd043135d21e5e148;hp=5314c5c1472335289497db1a2fc759fee4a13042;hpb=89911f9bb8cd7c981cbeefb0445af265fc2b0d0b;p=jalview.git

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 5314c5c..463d8cd 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -29,6 +29,7 @@ import jalview.jbgui.GUserDefinedColours;
 import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
 import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
@@ -101,7 +102,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
    */
   public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
   {
-    super();
+    this();
 
     lcaseColour.setEnabled(false);
 
@@ -110,7 +111,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -142,7 +143,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
   public UserDefinedColours(JalviewStructureDisplayI viewer,
           ColourSchemeI oldcs)
   {
-    super();
+    this();
     this.structureViewer = viewer;
 
     colorChooser.getSelectionModel().addChangeListener(this);
@@ -161,6 +162,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
   }
 
+  public UserDefinedColours()
+  {
+    super();
+    selectedButtons = new ArrayList<JButton>();
+  }
+
   void showFrame()
   {
     colorChooser.getSelectionModel().addChangeListener(this);
@@ -256,33 +263,33 @@ 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++)
     {
-      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 (lcaseColour.isSelected())
+    {
+      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()));
       }
     }
   }
@@ -307,11 +314,6 @@ 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())
@@ -437,7 +439,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
       col = Color.white;
       if (oldColourScheme != null && oldColourScheme.isSimple())
       {
-        col = oldColourScheme.findColour(residue.charAt(0));
+        col = oldColourScheme.findColour(residue.charAt(0), 0, null, null,
+                0f);
       }
     }
 
@@ -523,7 +526,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (seqGroup != null)
     {
-      seqGroup.cs = ucs;
+      seqGroup.setColourScheme(ucs);
       ap.paintAlignment(true);
     }
     else if (ap != null)
@@ -587,10 +590,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
       ucs.setLowerCaseColours(newColours);
     }
 
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     return ucs;
   }
@@ -623,7 +626,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     File choice = chooser.getSelectedFile();
     Cache.setProperty(LAST_DIRECTORY, choice.getParent());
 
-    UserColourScheme ucs = ColourSchemes.loadColourScheme(choice
+    UserColourScheme ucs = ColourSchemeLoader.loadColourScheme(choice
             .getAbsolutePath());
     Color[] colors = ucs.getColours();
     schemeName.setText(ucs.getSchemeName());
@@ -672,7 +675,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
       {
         colours = colours.substring(0, colours.indexOf("|"));
       }
-      ret = ColourSchemes.loadColourScheme(colours);
+      ret = ColourSchemeLoader.loadColourScheme(colours);
     }
 
     if (ret == null)
@@ -822,7 +825,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = oldColourScheme;
+        seqGroup.setColourScheme(oldColourScheme);
       }
       else
       {
@@ -847,21 +850,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
   @Override
   public void caseSensitive_actionPerformed(ActionEvent e)
   {
-    resetButtonPanel(caseSensitive.isSelected());
-    lcaseColour.setEnabled(caseSensitive.isSelected());
-  }
-
-  @Override
-  public void lcaseColour_actionPerformed(ActionEvent e)
-  {
-    if (selectedButtons == null)
-    {
-      selectedButtons = new ArrayList<JButton>();
-    }
-    else
-    {
-      selectedButtons.clear();
-    }
-    selectedButtons.add(lcaseColour);
+    boolean selected = caseSensitive.isSelected();
+    resetButtonPanel(selected);
+    lcaseColour.setEnabled(selected);
   }
 }