Merge branch 'features/JAL-2360colourSchemeApplicability' into

[jalview.git] / src / jalview / appletgui / UserDefinedColours.java

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 57cf669..aecc0c9 100644 (file)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -20,9 +20,11 @@
  */
 package jalview.appletgui;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceGroup;
+import jalview.schemes.CollectionColourScheme;
 import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
@@ -59,7 +61,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
   Button selectedButton;
 
-  Vector oldColours = new Vector();
+  Vector<Color> oldColours = new Vector<Color>();
 
   ColourSchemeI oldColourScheme;
 
@@ -75,7 +77,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
   String originalLabel;
 
-  Object originalColour;
+  FeatureColourI originalColour;
 
   int R = 0, G = 0, B = 0;
 
@@ -92,7 +94,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
     if (seqGroup != null)
     {
-      oldColourScheme = seqGroup.cs;
+      oldColourScheme = seqGroup.getColourScheme();
     }
     else
     {
@@ -117,7 +119,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
   public UserDefinedColours(FeatureRenderer fr, Frame alignframe)
   {
     caller = fr;
-    originalColour = fr.colourPanel.getBackground();
+    originalColour = new FeatureColour(fr.colourPanel.getBackground());
     originalLabel = "Feature Colour";
     setForDialog("Select Feature Colour", alignframe);
     setTargetColour(fr.colourPanel.getBackground());
@@ -134,21 +136,21 @@ public class UserDefinedColours extends Panel implements ActionListener,
    * 
    * @param caller
    *          - handles events
-   * @param col1
+   * @param col
    *          - original colour
    * @param alignframe
    *          - the parent Frame for the dialog
    * @param title
    *          - window title
    */
-  public UserDefinedColours(Component caller, Color col1, Frame alignframe,
+  public UserDefinedColours(Component caller, Color col, Frame alignframe,
           String title)
   {
     this.caller = caller;
-    originalColour = col1;
+    originalColour = new FeatureColour(col);
     originalLabel = title;
     setForDialog(title, alignframe);
-    setTargetColour(col1);
+    setTargetColour(col);
     dialog.setVisible(true);
   }
 
@@ -161,7 +163,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
    */
   public UserDefinedColours(Object caller, String label, Color colour)
   {
-    this(caller, label, colour, colour);
+    this(caller, label, new FeatureColour(colour), colour);
   }
 
   /**
@@ -172,13 +174,13 @@ public class UserDefinedColours extends Panel implements ActionListener,
    * @param graduatedColor
    */
   public UserDefinedColours(FeatureSettings me, String type,
-          GraduatedColor graduatedColor)
+          FeatureColourI graduatedColor)
   {
-    this(me, type, graduatedColor, graduatedColor.getMaxColor());
+    this(me, type, graduatedColor, graduatedColor.getMaxColour());
   }
 
-  private UserDefinedColours(Object caller, String label, Object ocolour,
-          Color colour)
+  private UserDefinedColours(Object caller, String label,
+          FeatureColourI ocolour, Color colour)
   {
     this.caller = caller;
     originalColour = ocolour;
@@ -228,6 +230,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
 
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     final Object source = evt.getSource();
@@ -257,6 +260,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     }
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (evt.getSource() == rScroller)
@@ -404,14 +408,9 @@ public class UserDefinedColours extends Panel implements ActionListener,
   {
     final Button button = new Button();
     Color col = Color.white;
-    if (oldColourScheme != null)
+    if (oldColourScheme != null && oldColourScheme.isSimple())
     {
-      try
-      {
-        col = oldColourScheme.findColour(aa.charAt(0), -1, null);
-      } catch (Exception ex)
-      {
-      }
+      col = oldColourScheme.findColour(aa.charAt(0), 0, null, null, 0f);
     }
     button.setBackground(col);
     oldColours.addElement(col);
@@ -420,6 +419,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     button.setFont(new java.awt.Font("Verdana", 1, 10));
     button.addMouseListener(new java.awt.event.MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         colourButtonPressed(e);
@@ -451,7 +451,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (caller instanceof FeatureSettings)
       {
-        ((FeatureSettings) caller).setUserColour(originalLabel, getColor());
+        ((FeatureSettings) caller).setUserColour(originalLabel,
+                new FeatureColour(getColor()));
       }
       else if (caller instanceof AnnotationColourChooser)
       {
@@ -468,7 +469,8 @@ public class UserDefinedColours extends Panel implements ActionListener,
       }
       else if (caller instanceof FeatureRenderer)
       {
-        ((FeatureRenderer) caller).colourPanel.updateColor(getColor());
+        ((FeatureRenderer) caller).colourPanel
+                .updateColor(new FeatureColour(getColor()));
       }
       else if (caller instanceof FeatureColourChooser)
       {
@@ -495,20 +497,24 @@ public class UserDefinedColours extends Panel implements ActionListener,
     }
 
     UserColourScheme ucs = new UserColourScheme(newColours);
-    if (ap != null)
-    {
-      ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
-    }
+    // if (ap != null)
+    // {
+    // ucs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+    // }
 
     if (ap != null)
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = ucs;
+        seqGroup.cs = new CollectionColourScheme(ucs);
+        seqGroup.getGroupColourScheme().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       else
       {
         ap.av.setGlobalColourScheme(ucs);
+        ap.av.getViewportColourScheme().setThreshold(0,
+                ap.av.isIgnoreGapsConsensus());
       }
       ap.seqPanel.seqCanvas.img = null;
       ap.paintAlignment(true);
@@ -537,12 +543,12 @@ public class UserDefinedColours extends Panel implements ActionListener,
         if (originalLabel.equals("Min Colour"))
         {
           ((AnnotationColourChooser) caller)
-                  .minColour_actionPerformed((Color) originalColour);
+                  .minColour_actionPerformed(originalColour.getColour());
         }
         else
         {
           ((AnnotationColourChooser) caller)
-                  .maxColour_actionPerformed((Color) originalColour);
+                  .maxColour_actionPerformed(originalColour.getColour());
         }
       }
       else if (caller instanceof FeatureRenderer)
@@ -556,12 +562,12 @@ public class UserDefinedColours extends Panel implements ActionListener,
         if (originalLabel.indexOf("inimum") > -1)
         {
           ((FeatureColourChooser) caller)
-                  .minColour_actionPerformed((Color) originalColour);
+                  .minColour_actionPerformed(originalColour.getColour());
         }
         else
         {
           ((FeatureColourChooser) caller)
-                  .maxColour_actionPerformed((Color) originalColour);
+                  .maxColour_actionPerformed(originalColour.getColour());
         }
       }
       if (dialog != null)
@@ -576,7 +582,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     Color[] newColours = new Color[24];
     for (int i = 0; i < 24; i++)
     {
-      newColours[i] = (Color) oldColours.elementAt(i);
+      newColours[i] = oldColours.elementAt(i);
       buttonPanel.getComponent(i).setBackground(newColours[i]);
     }
 
@@ -586,7 +592,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     {
       if (seqGroup != null)
       {
-        seqGroup.cs = ucs;
+        seqGroup.cs = new CollectionColourScheme(ucs);
       }
       else
       {