X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=4cc888dd3ccc3faa9f58d292c12bbab581f39d01;hb=6c73ca9c7f82edea4e8c4889969e72e917f3296d;hp=70ef47cab0e895072ccc83f925d4c7b5a9e2ef7e;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 70ef47c..4cc888d 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * 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(" "))
@@ -430,7 +437,11 @@ public class DBRefUtils
ref = new DBRefEntry(locsrc, version, pdbid + chaincode);
PDBEntry pdbr = new PDBEntry();
pdbr.setId(pdbid);
+ pdbr.setProperty(new Hashtable());
+ pdbr.getProperty().put("CHAIN", chaincode);
seq.addPDBId(pdbr);
+ } else {
+ System.err.println("Malformed PDB DR line:"+acn);
}
}
else