add more IUB codes

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@15560 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/variant/MultipleAlleleVariant.java

-
+/* MultipleAlleleVariant
+ *
+ * created: 2011
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2011  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ *
+ */
 package uk.ac.sanger.artemis.components.variant;
 
 public class MultipleAlleleVariant
 {
-
-  private static String IUB[][] = 
+  private static String IUB_2[][] = 
   { 
       {"m", "a", "c"},
       {"r", "a", "g"},
@@ -17,11 +38,22 @@ public class MultipleAlleleVariant
       {"k", "g", "u"}
   };
 
+  private static String IUB_3[][] = 
+  { 
+      {"b", "c", "g", "t"},
+      {"b", "c", "g", "u"},
+      {"d", "a", "g", "t"},
+      {"d", "a", "g", "u"},
+      {"h", "a", "c", "t"},
+      {"h", "a", "c", "u"},
+      {"v", "a", "c", "g"}
+  };
+  
   /**
-   * M (A or C)
-   * R (A or G)
-   * W (A or T/U)
-   * S (C or G)
+   * M (A or C)             B (C, G or T/U)
+   * R (A or G)             D (A, G or T/U)
+   * W (A or T/U)           H (A, C or T/U)
+   * S (C or G)             V (A, C or G)
    * Y (C or T/U)
    * K (G or T/U)
    * @param base
@@ -30,7 +62,7 @@ public class MultipleAlleleVariant
   protected static String getIUBCode(VCFRecord record)
   {
     String alt = record.getAlt().toString();
-    String alleles[] = alt.split(",");
+    String alleles[] = alt.toLowerCase().split(",");
     String pl;
     if ((pl = record.getFormatValue("PL")) != null && pl.split(",").length == 3 &&
          pl.split(",")[1].equals("0")) 
@@ -39,26 +71,45 @@ public class MultipleAlleleVariant
       String[] temp = new String[alleles.length+1];
       System.arraycopy(alleles, 0, temp, 0, alleles.length);
       alleles = temp;
-      alleles[alleles.length-1] = record.getRef();
+      alleles[alleles.length-1] = record.getRef().toLowerCase();
     }
 
     boolean isSNP = true;
     for(int i=0; i<alleles.length; i++)
     {
-      alleles[i] = alleles[i].toLowerCase();
+      alleles[i] = alleles[i];
       if(alleles[i].length() > 1)
         isSNP = false;
     }
 
     if(isSNP && alleles.length == 2)
     {
-      for(int i=0; i<IUB.length; i++)
+      for(int i=0; i<IUB_2.length; i++)
       {
-        if(IUB[i][1].equals(alleles[0]) && IUB[i][2].equals(alleles[1]) ||
-           IUB[i][1].equals(alleles[1]) && IUB[i][2].equals(alleles[0]))
-          return IUB[i][0];
+        if( (IUB_2[i][1].equals(alleles[0]) && IUB_2[i][2].equals(alleles[1])) ||
+            (IUB_2[i][1].equals(alleles[1]) && IUB_2[i][2].equals(alleles[0])) )
+          return IUB_2[i][0];
       }
     }
+
+    if(isSNP && alleles.length == 3)
+    {
+      System.out.println(record.toString());
+      for(int i=0; i<IUB_3.length; i++)
+      {
+        if( (IUB_3[i][1].equals(alleles[0]) && IUB_3[i][2].equals(alleles[1]) && IUB_3[i][3].equals(alleles[2])) ||
+            (IUB_3[i][1].equals(alleles[1]) && IUB_3[i][2].equals(alleles[0]) && IUB_3[i][3].equals(alleles[2])) ||
+            (IUB_3[i][1].equals(alleles[2]) && IUB_3[i][2].equals(alleles[0]) && IUB_3[i][3].equals(alleles[1])) ||
+            (IUB_3[i][1].equals(alleles[2]) && IUB_3[i][2].equals(alleles[1]) && IUB_3[i][3].equals(alleles[0])) ||
+            (IUB_3[i][1].equals(alleles[0]) && IUB_3[i][2].equals(alleles[2]) && IUB_3[i][3].equals(alleles[1])) ||
+            (IUB_3[i][1].equals(alleles[1]) && IUB_3[i][2].equals(alleles[2]) && IUB_3[i][3].equals(alleles[0])))
+          return IUB_3[i][0];
+      }
+    }
+    
+    if(isSNP)
+      return "n";
+
     return null;
   }