X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=08b7abf765df2fc0265e0f206781bfdd3969f7b1;hb=8dac3344cd26815d4f6060500117c0f6559d8090;hp=25c849ee15e5b8f3181de7cea21434b81eb69cac;hpb=9ae641586ebe22e2b01c7ff7a305897f5f666858;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 25c849e..08b7abf 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,24 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
 import java.awt.Color;
+import java.util.Map;
 import java.util.StringTokenizer;
+
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 public class UserColourScheme extends ResidueColourScheme
@@ -37,7 +42,18 @@ public class UserColourScheme extends ResidueColourScheme
     super(ResidueProperties.aaIndex);
     colors = newColors;
   }
-
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    UserColourScheme usc = new UserColourScheme(colors);
+    if (lowerCaseColours!=null) {
+      usc.schemeName = new String(schemeName);
+      usc.lowerCaseColours = new Color[lowerCaseColours.length];
+      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, lowerCaseColours.length);
+    }
+    return usc;
+  }
   public UserColourScheme(String colour)
   {
     super(ResidueProperties.aaIndex);
@@ -142,6 +158,7 @@ public class UserColourScheme extends ResidueColourScheme
 
   public void parseAppletParameter(String paramValue)
   {
+    // TODO: need a function to generate appletParameter colour string from a UCS
     StringTokenizer st = new StringTokenizer(paramValue, ";");
     StringTokenizer st2;
     String token = null, colour, residues;