X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FResidueProperties.java;h=9ac87ab231940b27ce6f3c89f95ef7bb48a01878;hb=4dd6a7731413d5fc38e2eda95548085bb07e7baf;hp=62d8d9248e98ff9ccfc7c9adf94bbcd215157bbe;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 62d8d92..9ac87ab 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 +1241,52 @@ 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;
+  }
+
+  public static Hashtable toDssp3State;
+  static {
+    toDssp3State = new Hashtable();
+    toDssp3State.put("H", "H");
+    toDssp3State.put("E", "E");
+    toDssp3State.put("C", " ");
+    toDssp3State.put(" ", " ");
+    toDssp3State.put("T", " ");
+    toDssp3State.put("B", "E");
+    toDssp3State.put("G", "H");
+    toDssp3State.put("I", "H");
+    toDssp3State.put("X", " ");
+  }
+  /**
+   * translate from other dssp secondary structure alphabets to 3-state
+   * @param ssstring
+   * @return ssstring as a three-state secondary structure assignment.
+   */
+  public static String getDssp3state(String ssstring)
+  {
+    if (ssstring==null)
+    {
+      return null;
+    }
+    StringBuffer ss = new StringBuffer();
+    for (int i=0; i<ssstring.length(); i++)
+    {
+      String ssc = ssstring.substring(i, i+1);
+      if (toDssp3State.containsKey(ssc))
+      {
+        ss.append((String) toDssp3State.get(ssc));
+      } else {
+        ss.append(" ");
+      }
+    }
+    return ss.toString();
+  }
 }