added 3 letter IUB codes for ambiguous residues/bases

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

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index fbaab81..4906eb7 100755 (executable)
--- 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));\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