JAL-1620 version bump and release notes

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index b28ce8a..8503167 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,24 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * 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.ws.dbsources;
 
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -35,6 +38,7 @@ import com.stevesoft.pat.Regex;
 
 import jalview.datamodel.AlignmentI;
 import jalview.io.FormatAdapter;
+import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -136,7 +140,7 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
               jalview.io.AppletFormatAdapter.FILE, "PDB");
       if (pdbfile != null)
       {
-        List<SequenceI> toremove=new ArrayList<SequenceI>();
+        List<SequenceI> toremove = new ArrayList<SequenceI>();
         for (SequenceI pdbcs : pdbfile.getSequences())
         {
           String chid = null;
@@ -181,21 +185,28 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
           }
           else
           {
-            // mark this sequence to be removed from the alignment 
+            // mark this sequence to be removed from the alignment
             // - since it's not from the right chain
             toremove.add(pdbcs);
           }
         }
-        // now remove marked sequences 
-        for (SequenceI pdbcs:toremove) {
+        // now remove marked sequences
+        for (SequenceI pdbcs : toremove)
+        {
           pdbfile.deleteSequence(pdbcs);
+          if (pdbcs.getAnnotation()!=null)
+          {
+            for (AlignmentAnnotation aa: pdbcs.getAnnotation())
+            {
+              pdbfile.deleteAnnotation(aa);
+            }
+          }
         }
       }
-      
+
       if (pdbfile == null || pdbfile.getHeight() < 1)
       {
-        throw new Exception("No PDB Records for " + id + " chain "
-                + ((chain == null) ? "' '" : chain));
+        throw new Exception(MessageManager.formatMessage("exception.no_pdb_records_for_chain", new String[]{id, ((chain == null) ? "' '" : chain)}));
       }
 
     } catch (Exception ex) // Problem parsing PDB file