merge

diff --combined src/jalview/gui/StructureChooser.java
index 976b77b,23b688c..765c214
--- 1/src/jalview/gui/StructureChooser.java
--- 2/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@@ -49,7 -49,6 +49,6 @@@ import javax.swing.JLabel
  import javax.swing.JOptionPane;
  import javax.swing.table.DefaultTableModel;
  
- 
  /**
   * Provides the behaviors for the Structure chooser Panel
   * 
@@@ -189,8 -188,7 +188,7 @@@ public class StructureChooser extends G
      }
      else
      {
-       mainFrame
- .setTitle("Structure Chooser - Manual association");
+       mainFrame.setTitle("Structure Chooser - Manual association");
        if (errors.size() > 0)
        {
          StringBuilder errorMsg = new StringBuilder();
@@@ -232,16 -230,13 +230,13 @@@
            String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
                    .getChainCode();
            Object[] pdbEntryRowData = new Object[]
-           { seq, pdbEntry.getId(),
-  chain,
-               pdbEntry.getType(),
+           { seq, pdbEntry.getId(), chain, pdbEntry.getType(),
                pdbEntry.getFile() };
            if (pdbEntry.getFile() != null)
            {
              tableModel.addRow(pdbEntryRowData);
            }
-           cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
-                   pdbEntry);
+           cachedEntryMap.put(pdbEntry.getId().toLowerCase(), pdbEntry);
          }
        }
      }
@@@ -461,7 -456,6 +456,6 @@@
      filterThread.start();
    }
  
- 
    /**
     * Handles action event for btn_pdbFromFile
     */
@@@ -628,8 -622,7 +622,7 @@@
              .getCmb_assSeq().getSelectedItem();
      lbl_fromFileStatus.setIcon(errorImage);
      if (selectedSequences.length == 1
-             || (assSeqOpt != null
-             && !assSeqOpt.getName().equalsIgnoreCase(
+             || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
                      "-Select Associated Seq-")))
      {
        btn_pdbFromFile.setEnabled(true);
@@@ -713,7 -706,8 +706,8 @@@
        launchStructureViewer(ap.getStructureSelectionManager(),
                pdbEntriesToView, ap, selectedSeqs);
      }
-     else if(currentView == VIEWS_LOCAL_PDB){
+     else if (currentView == VIEWS_LOCAL_PDB)
+     {
        int[] selectedRows = tbl_local_pdb.getSelectedRows();
        PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
        int count = 0;
@@@ -725,13 -719,11 +719,12 @@@
        for (int row : selectedRows)
        {
          String entryKey = tbl_local_pdb.getValueAt(row, pdbIdColIndex)
-                 .toString()
-                 .toLowerCase();
+                 .toString().toLowerCase();
          pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
 -        SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
 +        SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
                  refSeqColIndex);
          selectedSeqsToView.add(selectedSeq);
 +
        }
        SequenceI[] selectedSeqs = selectedSeqsToView
                .toArray(new SequenceI[selectedSeqsToView.size()]);
@@@ -772,9 -764,9 +765,9 @@@
          selectedSequence = userSelectedSeq;
        }
        PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-               .associatePdbWithSeq(
-               selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
-               selectedSequence, true, Desktop.instance);
+               .associatePdbWithSeq(selectedPdbFileName,
+                       jalview.io.AppletFormatAdapter.FILE,
+                       selectedSequence, true, Desktop.instance);
  
        launchStructureViewer(ap.getStructureSelectionManager(),
                new PDBEntry[]
@@@ -784,31 -776,35 +777,35 @@@
      mainFrame.dispose();
    }
  
-   private void launchStructureViewer(StructureSelectionManager ssm,
-           PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
-           SequenceI[] sequences)
+   private void launchStructureViewer(final StructureSelectionManager ssm,
+           final PDBEntry[] pdbEntriesToView,
+           final AlignmentPanel alignPanel, final SequenceI[] sequences)
    {
-     StructureViewer sViewer = new StructureViewer(ssm);
-     if (pdbEntriesToView.length > 1)
+     final StructureViewer sViewer = new StructureViewer(ssm);
+     new Thread(new Runnable()
      {
-       ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
-       for (SequenceI seq : sequences)
+       public void run()
        {
-         seqsMap.add(new SequenceI[]
-         { seq });
+         if (pdbEntriesToView.length > 1)
+         {
+           ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+           for (SequenceI seq : sequences)
+           {
+             seqsMap.add(new SequenceI[]
+             { seq });
+           }
+           SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+           sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
+           // sViewer.viewStructures(pdbEntriesToView,
+           // alignPanel.av.collateForPDB(pdbEntriesToView),
+           // alignPanel);
+         }
+         else
+         {
+           sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+         }
        }
-       SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
-       sViewer.viewStructures(pdbEntriesToView, collatedSeqs,
-               alignPanel);
-       // sViewer.viewStructures(pdbEntriesToView,
-       // alignPanel.av.collateForPDB(pdbEntriesToView),
-       // alignPanel);
-     }
-     else
-     {
-       sViewer.viewStructures(pdbEntriesToView[0], sequences,
-               alignPanel);
-     }
+     }).start();
    }
  
    /**