JAL-845 map 'STOP' codons correctly

[jalview.git] / src / jalview / util / DBRefUtils.java

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 14ace19..9a4ffc8 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.util;
 
@@ -415,11 +418,15 @@ public class DBRefUtils
         // check for chaincode and mapping
         // PFAM style stockhom PDB citation
         com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
-                "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;([0-9]+)-([0-9]+)");
+                "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
         if (r.search(acn.trim()))
         {
           String pdbid = r.stringMatched(1);
           String chaincode = r.stringMatched(2);
+          if (chaincode==null)
+          {
+            chaincode = " ";
+          }
           String mapstart = r.stringMatched(3);
           String mapend = r.stringMatched(4);
           if (chaincode.equals(" "))
@@ -430,8 +437,11 @@ public class DBRefUtils
           ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
           PDBEntry pdbr = new PDBEntry();
           pdbr.setId(pdbid);
-          pdbr.getProperty().put("CHAIN",chaincode);
+          pdbr.setProperty(new Hashtable());
+          pdbr.getProperty().put("CHAIN", chaincode);
           seq.addPDBId(pdbr);
+        } else {
+          System.err.println("Malformed PDB DR line:"+acn);
         }
       }
       else