header updated

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index fbaab81..8cffae5 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -156,9 +156,10 @@ public class ResidueProperties
     aa3Hash.put("TRP", new Integer(17));\r
     aa3Hash.put("TYR", new Integer(18));\r
     aa3Hash.put("VAL", new Integer(19));\r
-    aa3Hash.put("B", new Integer(20));\r
-    aa3Hash.put("Z", new Integer(21));\r
-    aa3Hash.put("X", new Integer(22));\r
+    // IUB Nomenclature for ambiguous peptides\r
+    aa3Hash.put("ASX", new Integer(20)); // "B";\r
+    aa3Hash.put("GLX", new Integer(21)); // X\r
+    aa3Hash.put("XAA", new Integer(22));// X unknown\r
     aa3Hash.put("-", new Integer(23));\r
     aa3Hash.put("*", new Integer(23));\r
     aa3Hash.put(".", new Integer(23));\r
@@ -823,27 +824,6 @@ public class ResidueProperties
     Phe.addElement("TTT");\r
   }\r
 \r
-  public static Color[][] groupColors =\r
-      {\r
-      {\r
-      Color.red, Color.red.brighter(), Color.red.brighter().brighter()},\r
-      {\r
-      Color.orange, Color.orange.brighter(),\r
-      Color.orange.brighter().brighter()\r
-  },\r
-      {\r
-      Color.green, Color.green.brighter(), Color.green.brighter().brighter()},\r
-      {\r
-      Color.blue, Color.blue.brighter(), Color.blue.brighter().brighter()},\r
-      {\r
-      Color.magenta, Color.magenta.brighter(),\r
-      Color.magenta.brighter().brighter()\r
-  },\r
-      {\r
-      Color.cyan, Color.cyan.brighter(), Color.cyan.brighter().brighter()},\r
-      {\r
-      Color.pink, Color.pink.brighter(), Color.pink.brighter().brighter()},\r
-  };\r
 \r
   //Stores residue codes/names and colours and other things\r
   public static Hashtable propHash = new Hashtable();\r
@@ -1134,20 +1114,6 @@ public class ResidueProperties
     propHash.put("polar", polar);\r
   }\r
 \r
-  public static Hashtable chainColours = new Hashtable();\r
-\r
-  static\r
-  {\r
-    chainColours.put("A", Color.red);\r
-    chainColours.put("B", Color.orange);\r
-    chainColours.put("C", Color.yellow);\r
-    chainColours.put("D", Color.green);\r
-    chainColours.put("E", Color.cyan);\r
-    chainColours.put("F", Color.blue);\r
-    chainColours.put("G", Color.magenta);\r
-    chainColours.put("H", Color.pink);\r
-  }\r
-\r
   private ResidueProperties()\r
   {\r
   }\r
@@ -1233,7 +1199,7 @@ public class ResidueProperties
       String key = (String) e.nextElement();\r
       Vector tmp = (Vector) codonHash.get(key);\r
 \r
-      if (tmp.contains(codon))\r
+      if (tmp.contains(codon.toUpperCase()))\r
       {\r
         return key;\r
       }\r
@@ -1241,9 +1207,4 @@ public class ResidueProperties
 \r
     return null;\r
   }\r
-\r
-  public static Hashtable getChainColours()\r
-  {\r
-    return chainColours;\r
-  }\r
 }\r