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 1c6c015..8503167 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -1,5 +1,5 @@
 /*
- * 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.
@@ -21,6 +21,7 @@
 package jalview.ws.dbsources;
 
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -37,6 +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;
 
@@ -192,13 +194,19 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
         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