X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FUserColourScheme.java;h=80efaca4e85a862fa9dd15b3c4c05104246de912;hb=e0c1dde5b241a8ac5b8c960f1f55f0940da55788;hp=61aed431ef0321daa52454e441f180775e602ac6;hpb=50eb1f492f5c64b56594ee49be8183fab8a2f73b;p=jalview.git

diff --git a/src/jalview/schemes/UserColourScheme.java b/src/jalview/schemes/UserColourScheme.java
index 61aed43..80efaca 100755
--- a/src/jalview/schemes/UserColourScheme.java
+++ b/src/jalview/schemes/UserColourScheme.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
@@ -42,18 +44,22 @@ 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) {
+    if (lowerCaseColours != null)
+    {
       usc.schemeName = new String(schemeName);
       usc.lowerCaseColours = new Color[lowerCaseColours.length];
-      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0, lowerCaseColours.length);
+      System.arraycopy(lowerCaseColours, 0, usc.lowerCaseColours, 0,
+              lowerCaseColours.length);
     }
     return usc;
   }
+
   public UserColourScheme(String colour)
   {
     super(ResidueProperties.aaIndex);
@@ -158,6 +164,8 @@ 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;