X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=25707ea0f0549570b224dd58be8e4b6fca08affd;hb=a0d1b1826f8ab0792c589946746d52ad0316fc99;hp=f92bfd12601c61862a61f5f7086d55444123003a;hpb=c3a5f5735df3a8e85818a6dd1e3f1d614060b721;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index f92bfd1..25707ea 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -29,6 +29,7 @@ public class ResidueProperties
   public static final Hashtable aa3Hash = new Hashtable();
   public static final Hashtable aa2Triplet = new Hashtable();
   public static final Hashtable nucleotideHash = new Hashtable();
+  public static final Hashtable nucleotideName = new Hashtable();
 
   static
   {
@@ -55,6 +56,7 @@ public class ResidueProperties
     aaHash.put("B", new Integer(20));
     aaHash.put("Z", new Integer(21));
     aaHash.put("X", new Integer(22));
+    aaHash.put("U", new Integer(22));
     aaHash.put("a", new Integer(0));
     aaHash.put("r", new Integer(1));
     aaHash.put("n", new Integer(2));
@@ -78,6 +80,7 @@ public class ResidueProperties
     aaHash.put("b", new Integer(20));
     aaHash.put("z", new Integer(21));
     aaHash.put("x", new Integer(22));
+    aaHash.put("u", new Integer(22));
     aaHash.put("-", new Integer(23));
     aaHash.put("*", new Integer(23));
     aaHash.put(".", new Integer(23));
@@ -87,27 +90,49 @@ public class ResidueProperties
   static
   {
     nucleotideHash.put("A", new Integer(0));
-    nucleotideHash.put("C", new Integer(1));
-    nucleotideHash.put("G", new Integer(2));
-    nucleotideHash.put("T", new Integer(3));
-    nucleotideHash.put("U", new Integer(4));
     nucleotideHash.put("a", new Integer(0));
+    nucleotideHash.put("C", new Integer(1));
     nucleotideHash.put("c", new Integer(1));
+    nucleotideHash.put("G", new Integer(2));
     nucleotideHash.put("g", new Integer(2));
+    nucleotideHash.put("T", new Integer(3));
     nucleotideHash.put("t", new Integer(3));
+    nucleotideHash.put("U", new Integer(4));
     nucleotideHash.put("u", new Integer(4));
+    nucleotideHash.put("I", new Integer(5));
+    nucleotideHash.put("i", new Integer(5));
+    nucleotideHash.put("X", new Integer(6));
+    nucleotideHash.put("x", new Integer(6));
+    nucleotideHash.put("R", new Integer(7));
+    nucleotideHash.put("r", new Integer(7));
+    nucleotideHash.put("Y", new Integer(8));
+    nucleotideHash.put("y", new Integer(8));
+    nucleotideHash.put("N", new Integer(9));
+    nucleotideHash.put("n", new Integer(9));
+
+
+    nucleotideName.put("A", "Adenine");
+    nucleotideName.put("a", "Adenine");
+    nucleotideName.put("G", "Guanine");
+    nucleotideName.put("g", "Guanine");
+    nucleotideName.put("C", "Cytosine");
+    nucleotideName.put("c", "Cytosine");
+    nucleotideName.put("T", "Thymine");
+    nucleotideName.put("t", "Thymine");
+    nucleotideName.put("U", "Uracil");
+    nucleotideName.put("u", "Uracil");
+    nucleotideName.put("I", "Inosine");
+    nucleotideName.put("i", "Inosine");
+    nucleotideName.put("X", "Xanthine");
+    nucleotideName.put("x", "Xanthine");
+    nucleotideName.put("R", "Unknown Purine");
+    nucleotideName.put("r", "Unknown Purine");
+    nucleotideName.put("Y", "Unknown Pyrimidine");
+    nucleotideName.put("y", "Unknown Pyrimidine");
+    nucleotideName.put("N", "Unknown");
+    nucleotideName.put("n", "Unknown");
   }
 
-  // These numbers should correspond to the indices in the Color hashes
-  public static final Hashtable aaSpecialsHash = new Hashtable();
-
-  static
-  {
-    aaSpecialsHash.put("-", new Integer(23));
-    aaSpecialsHash.put("*", new Integer(24));
-    aaSpecialsHash.put(".", new Integer(25));
-    aaSpecialsHash.put(" ", new Integer(26));
-  }
 
   static
   {
@@ -1208,7 +1233,7 @@ 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;
       }