X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=cab1ac7569f8ecc551f146db55a7a2cf32e44a0b;hb=43b415c68805f3dec44a6ddc666d52220483c120;hp=65d81799c8e8b779a515e3ff16b5dc9e704b7de2;hpb=3ef44bef1f825d26977dedd1608469712a87fe15;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 65d8179..cab1ac7 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -121,7 +121,7 @@ public class Sequence implements SequenceI
               .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
-    // Does sequence have the /start-end signiature?
+    // Does sequence have the /start-end signature?
     if (limitrx.search(name))
     {
       name = limitrx.left();
@@ -355,19 +355,32 @@ public class Sequence implements SequenceI
     {
       pdbIds = new Vector<PDBEntry>();
     }
-    if (!pdbIds.contains(entry))
+    if (pdbIds.contains(entry))
+    {
+      updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+    }
+    else
     {
       pdbIds.addElement(entry);
     }
   }
 
+  private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+  {
+    if (newEntry.getFile() != null)
+    {
+      oldEntry.setFile(newEntry.getFile());
+    }
+  }
+
   /**
    * DOCUMENT ME!
    * 
    * @param id
    *          DOCUMENT ME!
    */
-  public void setPDBId(Vector id)
+  @Override
+  public void setPDBId(Vector<PDBEntry> id)
   {
     pdbIds = id;
   }
@@ -377,7 +390,8 @@ public class Sequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
-  public Vector getPDBId()
+  @Override
+  public Vector<PDBEntry> getPDBId()
   {
     return pdbIds;
   }
@@ -935,7 +949,7 @@ public class Sequence implements SequenceI
   {
     if (this.annotation == null)
     {
-      this.annotation = new Vector();
+      this.annotation = new Vector<AlignmentAnnotation>();
     }
     if (!this.annotation.contains(annotation))
     {