X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=b14d9c63412d2c2ffda7a3903943d37ec95d0b3f;hb=85de15725d1b74ba9e0c35a104132206615d8c13;hp=62d8d9248e98ff9ccfc7c9adf94bbcd215157bbe;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 62d8d92..b14d9c6 100755
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -87,7 +87,7 @@ public class ResidueProperties
     aaIndex['b'] = 20;
     aaIndex['z'] = 21;
     aaIndex['x'] = 22;
-    aaIndex['u'] = 22;
+    aaIndex['u'] = 22; // TODO: selenocystine triplet and codons needed. also extend subt. matrices
   }
 
   static
@@ -1167,12 +1167,7 @@ public class ResidueProperties
 
   public static int getPAM250(String A1, String A2)
   {
-    int a = aaIndex[A1.charAt(0)];
-    int b = aaIndex[A2.charAt(0)];
-
-    int pog = ResidueProperties.PAM250[a][b];
-
-    return pog;
+    return getPAM250(A1.charAt(0), A2.charAt(0));
   }
 
   public static int getBLOSUM62(char c1, char c2)
@@ -1246,4 +1241,14 @@ public class ResidueProperties
     }
     return null;
   }
+
+  public static int getPAM250(char c, char d)
+  {
+    int a = aaIndex[c];
+    int b = aaIndex[d];
+
+    int pog = ResidueProperties.PAM250[a][b];
+
+    return pog;
+  }
 }