X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=87efddc2d927e5126859386eeae669d5a345bef4;hb=7418f2aca1d88b04abebcce7940006e202c5f19c;hp=4906eb700f2138659142192e03ffb414552c89b4;hpb=952ede10e4daf14f554d5867e5eb74591aafddb3;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 4906eb7..87efddc 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -164,6 +164,7 @@ public class ResidueProperties
     aa3Hash.put("*", new Integer(23));
     aa3Hash.put(".", new Integer(23));
     aa3Hash.put(" ", new Integer(23));
+    aa3Hash.put("Gap", new Integer(23));
   }
 
   static
@@ -824,27 +825,6 @@ public class ResidueProperties
     Phe.addElement("TTT");
   }
 
-  public static Color[][] groupColors =
-      {
-      {
-      Color.red, Color.red.brighter(), Color.red.brighter().brighter()},
-      {
-      Color.orange, Color.orange.brighter(),
-      Color.orange.brighter().brighter()
-  },
-      {
-      Color.green, Color.green.brighter(), Color.green.brighter().brighter()},
-      {
-      Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()},
-      {
-      Color.magenta, Color.magenta.brighter(),
-      Color.magenta.brighter().brighter()
-  },
-      {
-      Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()},
-      {
-      Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()},
-  };
 
   //Stores residue codes/names and colours and other things
   public static Hashtable propHash = new Hashtable();
@@ -1135,20 +1115,6 @@ public class ResidueProperties
     propHash.put("polar", polar);
   }
 
-  public static Hashtable chainColours = new Hashtable();
-
-  static
-  {
-    chainColours.put("A", Color.red);
-    chainColours.put("B", Color.orange);
-    chainColours.put("C", Color.yellow);
-    chainColours.put("D", Color.green);
-    chainColours.put("E", Color.cyan);
-    chainColours.put("F", Color.blue);
-    chainColours.put("G", Color.magenta);
-    chainColours.put("H", Color.pink);
-  }
-
   private ResidueProperties()
   {
   }
@@ -1234,7 +1200,7 @@ public class ResidueProperties
       String key = (String) e.nextElement();
       Vector tmp = (Vector) codonHash.get(key);
 
-      if (tmp.contains(codon))
+      if (tmp.contains(codon.toUpperCase()))
       {
         return key;
       }
@@ -1242,9 +1208,4 @@ public class ResidueProperties
 
     return null;
   }
-
-  public static Hashtable getChainColours()
-  {
-    return chainColours;
-  }
 }