X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b1a4fee90d33aae9fbd2b05c0816979559225419;hb=4316d20b437d529be1d9ddafc0118fadd1b6a4ce;hp=692cd18b2156671387b096322853087c9768a51f;hpb=f4c55ce8e067fc6ae84a6ae614cebed6c88a81f0;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 692cd18..b1a4fee 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -683,27 +683,42 @@ public class AlignViewport extends AlignmentViewport implements
     List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
     for (PDBEntry pdb : pdbEntries)
     {
-      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
-        if (pdbs == null)
+        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+        if (pdbRefEntries == null)
         {
           continue;
         }
-        for (PDBEntry p1 : pdbs)
+        for (PDBEntry pdbRefEntry : pdbRefEntries)
         {
-          if (p1.getId().equals(pdb.getId()))
+          if (pdbRefEntry.getId().equals(pdb.getId()))
           {
-            if (!seqs.contains(sq))
+            if (pdbRefEntry.getChainCode() != null
+                    && pdb.getChainCode() != null)
             {
-              seqs.add(sq);
-              continue;
+              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+                      pdb.getChainCode())
+                      && !choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
             }
+            else
+            {
+              if (!choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
+            }
+
           }
         }
       }
-      seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+      seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
@@ -1103,6 +1118,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @param featureSettings
    */
+  @Override
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
     if (featureSettings == null)