JAL-1641 docs for ComplexAlignFile interface

[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 9fa6bf4..3df8957 100644 (file)
--- a/src/jalview/ext/jmol/PDBFileWithJmol.java
+++ b/src/jalview/ext/jmol/PDBFileWithJmol.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -177,18 +177,25 @@ public class PDBFileWithJmol extends AlignFile implements
                   PDBEntry pdbe = new PDBEntry();
                   pdbe.setFile(getDataName());
                   pdbe.setId(getDataName());
-                  sq.addPDBId(pdbe);
                   pdbe.setProperty(new Hashtable());
-                  pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+                  // pdbe.getProperty().put("CHAIN", "" + _lastChainId);
+                  pdbe.setChainCode(String.valueOf(_lastChainId));
+                  sq.addPDBId(pdbe);
                   // JAL-1533
                   // Need to put the number of models for this polymer somewhere for Chimera/others to grab
                   //                  pdbe.getProperty().put("PDBMODELS", biopoly.)
                   seqs.add(sq);
                   if (!isNa)
                   {
+                    String mt = model.getModelTitle() == null ? getDataName()
+                            : model.getModelTitle();
+                    if (_lastChainId >= ' ')
+                    {
+                      mt += _lastChainId;
+                    }
                     AlignmentAnnotation ann = new AlignmentAnnotation(
                             "Secondary Structure",
-                            "Secondary Structure from PDB File", asecstr);
+                            "Secondary Structure for " + mt, asecstr);
                     ann.belowAlignment=true;
                     ann.visible=true;
                     ann.autoCalculated=false;