Merge branch 'hotfix/JAL-1530' into Release_2_8_2_Branch

[jalview.git] / src / jalview / ext / jmol / PDBFileWithJmol.java

diff --git a/src/jalview/ext/jmol/PDBFileWithJmol.java b/src/jalview/ext/jmol/PDBFileWithJmol.java
index 77755f8..6553e26 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,23 +1,27 @@
 /*
- * 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 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 <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.ext.jmol;
 
 import java.io.IOException;
+import java.util.Hashtable;
 import java.util.Map;
 
 import org.jmol.api.JmolStatusListener;
@@ -53,12 +57,10 @@ public class PDBFileWithJmol extends AlignFile implements
 
   Viewer viewer = null;
 
-  public PDBFileWithJmol(String inFile, String type)
-          throws IOException
+  public PDBFileWithJmol(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
-  
 
   public PDBFileWithJmol(FileParse fp) throws IOException
   {
@@ -171,12 +173,15 @@ public class PDBFileWithJmol extends AlignFile implements
                   pdbe.setFile(getDataName());
                   pdbe.setId(getDataName());
                   sq.addPDBId(pdbe);
+                  pdbe.setProperty(new Hashtable());
+                  pdbe.getProperty().put("CHAIN", "" + _lastChainId);
                   seqs.add(sq);
                   if (!(biopoly.isDna() || biopoly.isRna()))
                   {
                     AlignmentAnnotation ann = new AlignmentAnnotation(
                             "Secondary Structure",
                             "Secondary Structure from PDB File", asecstr);
+                    ann.setCalcId(getClass().getName());
                     sq.addAlignmentAnnotation(ann);
                     annotations.add(ann);
                   }