X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=d25707f0f7f75a6a1ab404f07e6002a0361ea303;hb=6ddf2d553aee329db44dd36b564211c3880563ec;hp=fbaab81e63deda1bd5f1bcc952aea8bc7a8bfff0;hpb=8ae2f185311811757976eeb142b4767c42a9618f;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index fbaab81..d25707f 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -156,9 +156,10 @@ public class ResidueProperties
     aa3Hash.put("TRP", new Integer(17));
     aa3Hash.put("TYR", new Integer(18));
     aa3Hash.put("VAL", new Integer(19));
-    aa3Hash.put("B", new Integer(20));
-    aa3Hash.put("Z", new Integer(21));
-    aa3Hash.put("X", new Integer(22));
+    // IUB Nomenclature for ambiguous peptides
+    aa3Hash.put("ASX", new Integer(20)); // "B";
+    aa3Hash.put("GLX", new Integer(21)); // X
+    aa3Hash.put("XAA", new Integer(22));// X unknown
     aa3Hash.put("-", new Integer(23));
     aa3Hash.put("*", new Integer(23));
     aa3Hash.put(".", new Integer(23));
@@ -1134,20 +1135,6 @@ 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()
   {
   }
@@ -1233,7 +1220,7 @@ 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;
       }
@@ -1241,9 +1228,4 @@ public class ResidueProperties
 
     return null;
   }
-
-  public static Hashtable getChainColours()
-  {
-    return chainColours;
-  }
 }