From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Thu, 10 Nov 2016 16:11:36 +0000 (+0000)
Subject: Merge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop
X-Git-Tag: Release_2_10_1~11^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b9c160cf930b03268b2a0caa9e45ebfca305da04;hp=3da04c960983caa8614a123b96084933a46a4f46;p=jalview.git

Merge branch 'bug/JAL-2317_jmol_chimera-chain-factorisation' into develop
---

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index b925284..133cc94 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -180,7 +180,7 @@ public class AppletJmol extends EmbmenuFrame implements
     this.ap = ap;
     jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
             new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
-            new String[][] { chains }, protocol);
+            protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -369,7 +369,7 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector<String> chains)
+  void setChainMenuItems(List<String> chains)
   {
     chainMenu.removeAll();
 
@@ -588,7 +588,7 @@ public class AppletJmol extends EmbmenuFrame implements
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
     jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());
diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 6ec5b4d..3a36ed5 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -45,9 +45,9 @@ class AppletJmolBinding extends JalviewJmolBinding
 
   public AppletJmolBinding(AppletJmol appletJmol,
           StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] seq, String[][] chains, String protocol)
+          SequenceI[][] seq, String protocol)
   {
-    super(sSm, pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, protocol);
     appletJmolBinding = appletJmol;
   }
 
@@ -113,12 +113,14 @@ class AppletJmolBinding extends JalviewJmolBinding
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
     colourBySequence(ap);
   }
 
+  @Override
   public void showUrl(String url)
   {
     try
@@ -143,6 +145,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     // do nothing.
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 929a871..5ffbaa4 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -49,11 +49,11 @@ public class ExtJmol extends JalviewJmolBinding
   private AlignmentPanel ap;
 
   protected ExtJmol(jalview.appletgui.AlignFrame alframe,
-          PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+          PDBEntry[] pdbentry, SequenceI[][] seq,
           String protocol)
   {
     super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
-            chains, protocol);
+            protocol);
   }
 
   public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
@@ -64,6 +64,7 @@ public class ExtJmol extends JalviewJmolBinding
     notifyFileLoaded(null, null, null, null, 0);
   }
 
+  @Override
   public void updateColours(Object source)
   {
 
@@ -71,6 +72,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
   public void showUrl(String arg0)
   {
     showUrl(arg0, "jmol");
@@ -126,6 +128,7 @@ public class ExtJmol extends JalviewJmolBinding
     // ignore
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     System.out.println(arg0);
diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 6a6ccd0..9c3a8e7 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -121,16 +121,6 @@ public class PDBEntry
   {
   }
 
-  /**
-   * Constructor given file path and PDB id.
-   * 
-   * @param filePath
-   */
-  // public PDBEntry(String filePath, String pdbId)
-  // {
-  // this.file = filePath;
-  // this.id = pdbId;
-  // }
 
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index fbac400..56287a9 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -74,7 +74,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
   Vector<String> atomsPicked = new Vector<String>();
 
-  public Vector<String> chainNames;
+  private List<String> chainNames;
 
   Hashtable<String, String> chainFile;
 
@@ -99,10 +99,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public Viewer viewer;
 
   public JalviewJmolBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           String protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -1083,7 +1083,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new Vector<String>();
+    chainNames = new ArrayList<String>();
     chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
@@ -1143,6 +1143,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       for (int pe = 0; pe < getPdbCount(); pe++)
       {
         boolean matches = false;
+        addSequence(pe, getSequence()[pe]);
         if (fileName == null)
         {
           if (false)
@@ -1194,7 +1195,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
             String chid = new String(pdb.getId() + ":"
                     + pdb.getChains().elementAt(i).id);
             chainFile.put(chid, fileName);
-            chainNames.addElement(chid);
+            chainNames.add(chid);
           }
           notifyLoaded = true;
         }
@@ -1242,6 +1243,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setLoadingFromArchive(false);
   }
 
+  @Override
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
+
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
   {
     notifyAtomPicked(iatom, strMeasure, null);
diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 7ba9186..4a9bf5f 100644
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -40,6 +40,7 @@ import jalview.util.MessageManager;
 import java.awt.Color;
 import java.net.BindException;
 import java.util.ArrayList;
+import java.util.Hashtable;
 import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
@@ -63,6 +64,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private static final String ALPHACARBON = "CA";
 
+  private List<String> chainNames = new ArrayList<String>();
+
+  private Hashtable<String, String> chainFile = new Hashtable<String, String>();
   /*
    * Object through which we talk to Chimera
    */
@@ -191,10 +195,9 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * @param protocol
    */
   public JalviewChimeraBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     viewer = new ChimeraManager(
             new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
   }
@@ -244,11 +247,14 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     boolean first = true;
     for (String chain : toshow)
     {
+      int modelNumber = getModelNoForChain(chain);
+      String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
+              + chain.split(":")[1];
       if (!first)
       {
         cmd.append(",");
       }
-      cmd.append(":.").append(chain);
+      cmd.append(showChainCmd);
       first = false;
     }
 
@@ -257,7 +263,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
      * window, but it looks more helpful not to (easier to relate chains to the
      * whole)
      */
-    final String command = "~display #*; ~ribbon #*; ribbon "
+    final String command = "~display #*; ~ribbon #*; ribbon :"
             + cmd.toString();
     sendChimeraCommand(command, false);
   }
@@ -758,18 +764,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     {
       return new String[0];
     }
-    // if (modelFileNames == null)
-    // {
-    // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
-    // _modelFileNameMap = new int[chimodels.size()];
-    // int j = 0;
-    // for (ChimeraModel chimodel : chimodels)
-    // {
-    // String mdlName = chimodel.getModelName();
-    // }
-    // modelFileNames = new String[j];
-    // // System.arraycopy(mset, 0, modelFileNames, 0, j);
-    // }
 
     return chimeraMaps.keySet().toArray(
             modelFileNames = new String[chimeraMaps.size()]);
@@ -1067,28 +1061,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    * 
    * @return
    */
-  public List<String> getChainNames()
-  {
-    List<String> names = new ArrayList<String>();
-    String[][] allNames = getChains();
-    if (allNames != null)
-    {
-      for (String[] chainsForPdb : allNames)
-      {
-        if (chainsForPdb != null)
-        {
-          for (String chain : chainsForPdb)
-          {
-            if (chain != null && !names.contains(chain))
-            {
-              names.add(chain);
-            }
-          }
-        }
-      }
-    }
-    return names;
-  }
 
   /**
    * Send a 'focus' command to Chimera to recentre the visible display
@@ -1125,4 +1097,31 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       sm.highlightStructure(this, seq, positions);
     }
   }
+
+
+  @Override
+  public List<String> getChainNames()
+  {
+    return chainNames;
+  }
+
+  public Hashtable<String, String> getChainFile()
+  {
+    return chainFile;
+  }
+
+  public List<ChimeraModel> getChimeraModelByChain(String chain)
+  {
+    return chimeraMaps.get(chainFile.get(chain));
+  }
+
+  public int getModelNoForChain(String chain)
+  {
+    List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
+    if (foundModels != null && !foundModels.isEmpty())
+    {
+      return foundModels.get(0).getModelNumber();
+    }
+    return -1;
+  }
 }
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 1c0dfe6..d7e8305 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -50,7 +50,6 @@ import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Rectangle;
 import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.io.BufferedReader;
@@ -67,7 +66,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
@@ -131,7 +129,7 @@ public class AppJmol extends StructureViewerBase
     // / TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
-            pdbentrys, seqs, null, null);
+            pdbentrys, seqs, null);
 
     jmb.setLoadingFromArchive(true);
     addAlignmentPanel(ap);
@@ -301,7 +299,7 @@ public class AppJmol extends StructureViewerBase
   {
     progressBar = ap.alignFrame;
     jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
-            pdbentrys, seqs, null, null);
+            pdbentrys, seqs, null);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
     if (pdbentrys.length > 1)
@@ -394,57 +392,12 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  void setChainMenuItems(Vector<String> chains)
-  {
-    chainMenu.removeAll();
-    if (chains == null)
-    {
-      return;
-    }
-    JMenuItem menuItem = new JMenuItem(
-            MessageManager.getString("label.all"));
-    menuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent evt)
-      {
-        allChainsSelected = true;
-        for (int i = 0; i < chainMenu.getItemCount(); i++)
-        {
-          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-          {
-            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
-          }
-        }
-        centerViewer();
-        allChainsSelected = false;
-      }
-    });
-
-    chainMenu.add(menuItem);
-
-    for (String chain : chains)
-    {
-      menuItem = new JCheckBoxMenuItem(chain, true);
-      menuItem.addItemListener(new ItemListener()
-      {
-        @Override
-        public void itemStateChanged(ItemEvent evt)
-        {
-          if (!allChainsSelected)
-          {
-            centerViewer();
-          }
-        }
-      });
 
-      chainMenu.add(menuItem);
-    }
-  }
 
   boolean allChainsSelected = false;
 
-  void centerViewer()
+  @Override
+  void showSelectedChains()
   {
     Vector<String> toshow = new Vector<String>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
@@ -1075,7 +1028,7 @@ public class AppJmol extends StructureViewerBase
       repaint();
       return;
     }
-    setChainMenuItems(jmb.chainNames);
+    setChainMenuItems(jmb.getChainNames());
 
     this.setTitle(jmb.getViewerTitle());
     if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 1c54a5e..546890e 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -41,10 +41,9 @@ public class AppJmolBinding extends JalviewJmolBinding
   private FeatureRenderer fr = null;
 
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
@@ -113,6 +112,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         appJmolWindow.updateTitleAndMenus();
@@ -121,6 +121,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -144,6 +145,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index ce719d0..fe12f40 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -31,6 +31,7 @@ import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.io.StructureFile;
 import jalview.schemes.BuriedColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.HelixColourScheme;
@@ -46,7 +47,6 @@ import jalview.util.Platform;
 import jalview.ws.dbsources.Pdb;
 
 import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.io.BufferedReader;
@@ -66,7 +66,6 @@ import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JColorChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JMenu;
-import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
@@ -248,10 +247,8 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     createProgressBar();
     // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs
-    String[][] chains = extractChains(seqs);
     jmb = new JalviewChimeraBindingModel(this,
-            ap.getStructureSelectionManager(), pdbentrys, seqs, chains,
-            null);
+            ap.getStructureSelectionManager(), pdbentrys, seqs, null);
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
     if (pdbentrys.length > 1)
@@ -278,41 +275,7 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   }
 
-  /**
-   * Retrieve chains for sequences by inspecting their PDB refs. The hope is
-   * that the first will be to the sequence's own chain. Really need a more
-   * managed way of doing this.
-   * 
-   * @param seqs
-   * @return
-   */
-  protected String[][] extractChains(SequenceI[][] seqs)
-  {
-    String[][] chains = new String[seqs.length][];
-    for (int i = 0; i < seqs.length; i++)
-    {
-      chains[i] = new String[seqs[i].length];
-      int seqno = 0;
-      for (SequenceI seq : seqs[i])
-      {
-        String chain = null;
-        if (seq.getDatasetSequence() != null)
-        {
-          Vector<PDBEntry> pdbrefs = seq.getDatasetSequence()
-                  .getAllPDBEntries();
-          if (pdbrefs != null && pdbrefs.size() > 0)
-          {
-            // FIXME: SequenceI.PDBEntry[0] chain mapping used for
-            // ChimeraViewFrame. Is this even used ???
 
-            chain = pdbrefs.get(0).getChainCode();
-          }
-        }
-        chains[i][seqno++] = chain;
-      }
-    }
-    return chains;
-  }
 
   /**
    * Create a new viewer from saved session state data including Chimera session
@@ -437,63 +400,11 @@ public class ChimeraViewFrame extends StructureViewerBase
     jmb.startChimeraListener();
   }
 
-  /**
-   * If the list is not empty, add menu items for 'All' and each individual
-   * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed.
-   * 
-   * @param chainNames
-   */
-  void setChainMenuItems(List<String> chainNames)
-  {
-    chainMenu.removeAll();
-    if (chainNames == null || chainNames.isEmpty())
-    {
-      return;
-    }
-    JMenuItem menuItem = new JMenuItem(
-            MessageManager.getString("label.all"));
-    menuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent evt)
-      {
-        allChainsSelected = true;
-        for (int i = 0; i < chainMenu.getItemCount(); i++)
-        {
-          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
-          {
-            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
-          }
-        }
-        showSelectedChains();
-        allChainsSelected = false;
-      }
-    });
-
-    chainMenu.add(menuItem);
-
-    for (String chainName : chainNames)
-    {
-      menuItem = new JCheckBoxMenuItem(chainName, true);
-      menuItem.addItemListener(new ItemListener()
-      {
-        @Override
-        public void itemStateChanged(ItemEvent evt)
-        {
-          if (!allChainsSelected)
-          {
-            showSelectedChains();
-          }
-        }
-      });
-
-      chainMenu.add(menuItem);
-    }
-  }
 
   /**
    * Show only the selected chain(s) in the viewer
    */
+  @Override
   void showSelectedChains()
   {
     List<String> toshow = new ArrayList<String>();
@@ -569,6 +480,7 @@ public class ChimeraViewFrame extends StructureViewerBase
     List<PDBEntry> filePDB = new ArrayList<PDBEntry>();
     List<Integer> filePDBpos = new ArrayList<Integer>();
     PDBEntry thePdbEntry = null;
+    StructureFile pdb = null;
     try
     {
       String[] curfiles = jmb.getPdbFile(); // files currently in viewer
@@ -677,8 +589,9 @@ public class ChimeraViewFrame extends StructureViewerBase
               stopProgressBar("", startTime);
             }
             // Explicitly map to the filename used by Chimera ;
-            jmb.getSsm().setMapping(jmb.getSequence()[pos],
+            pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
                     jmb.getChains()[pos], pe.getFile(), protocol);
+            stashFoundChains(pdb, pe.getFile());
           } catch (OutOfMemoryError oomerror)
           {
             new OOMWarning(
@@ -694,6 +607,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           }
         }
       }
+      jmb.refreshGUI();
       jmb.setFinishedInit(true);
       jmb.setLoadingFromArchive(false);
 
@@ -729,6 +643,17 @@ public class ChimeraViewFrame extends StructureViewerBase
    * @return
    * @throws Exception
    */
+
+  private void stashFoundChains(StructureFile pdb, String file)
+  {
+    for (int i = 0; i < pdb.getChains().size(); i++)
+    {
+      String chid = new String(pdb.getId() + ":"
+              + pdb.getChains().elementAt(i).id);
+      jmb.getChainNames().add(chid);
+      jmb.getChainFile().put(chid, file);
+    }
+  }
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
     // FIXME: this is duplicated code with Jmol frame ?
diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index 7a54732..78ab68d 100644
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -32,11 +32,12 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 
   private FeatureRenderer fr = null;
 
+
   public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
           StructureSelectionManager ssm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+          SequenceI[][] sequenceIs, String protocol)
   {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+    super(ssm, pdbentry, sequenceIs, protocol);
     cvf = chimeraViewFrame;
   }
 
@@ -72,6 +73,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
   {
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
         cvf.updateTitleAndMenus();
@@ -80,6 +82,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     });
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
@@ -113,6 +116,7 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
    * Send an asynchronous command to Chimera, in a new thread, optionally with
    * an 'in progress' message in a progress bar somewhere
    */
+  @Override
   protected void sendAsynchronousCommand(final String command,
           final String progressMsg)
   {
@@ -135,4 +139,6 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     thread.start();
 
   }
+
+
 }
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 7df42fd..4715e48 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -30,10 +30,15 @@ import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
 
 import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
+import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 
@@ -76,6 +81,8 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   protected Thread worker = null;
 
+  protected boolean allChainsSelected = false;
+
   /**
    * 
    * @param ap2
@@ -152,6 +159,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     this.ap = alp;
   }
 
+  @Override
   public AlignmentPanel[] getAllAlignmentPanels()
   {
     AlignmentPanel[] t, list = new AlignmentPanel[0];
@@ -291,6 +299,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         // queue.
         new Thread(new Runnable()
         {
+          @Override
           public void run()
           {
             while (worker != null && worker.isAlive() && _started)
@@ -492,4 +501,55 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
     return finished;
   }
+
+  void setChainMenuItems(List<String> chainNames)
+  {
+    chainMenu.removeAll();
+    if (chainNames == null || chainNames.isEmpty())
+    {
+      return;
+    }
+    JMenuItem menuItem = new JMenuItem(
+            MessageManager.getString("label.all"));
+    menuItem.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent evt)
+      {
+        allChainsSelected = true;
+        for (int i = 0; i < chainMenu.getItemCount(); i++)
+        {
+          if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+          {
+            ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
+          }
+        }
+        showSelectedChains();
+        allChainsSelected = false;
+      }
+    });
+
+    chainMenu.add(menuItem);
+
+    for (String chain : chainNames)
+    {
+      menuItem = new JCheckBoxMenuItem(chain, true);
+      menuItem.addItemListener(new ItemListener()
+      {
+        @Override
+        public void itemStateChanged(ItemEvent evt)
+        {
+          if (!allChainsSelected)
+          {
+            showSelectedChains();
+          }
+        }
+      });
+
+      chainMenu.add(menuItem);
+    }
+  }
+
+  abstract void showSelectedChains();
+
 }
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index b00f1bc..5dc3465 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -135,19 +135,14 @@ public abstract class AAStructureBindingModel extends
    * @param protocol
    */
   public AAStructureBindingModel(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           String protocol)
   {
     this.ssm = ssm;
     this.sequence = sequenceIs;
     this.nucleotide = Comparison.isNucleotide(sequenceIs);
-    this.chains = chains;
     this.pdbEntry = pdbentry;
     this.protocol = protocol;
-    if (chains == null)
-    {
-      this.chains = new String[pdbentry.length][];
-    }
   }
 
   public StructureSelectionManager getSsm()
@@ -674,4 +669,12 @@ public abstract class AAStructureBindingModel extends
   {
     this.finishedInit = fi;
   }
+
+  /**
+   * Returns a list of chains mapped in this viewer.
+   * 
+   * @return
+   */
+  public abstract List<String> getChainNames();
+
 }
diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 0d00169..66e0152 100644
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -104,7 +104,6 @@ public class AAStructureBindingModelTest
     pdbFiles[0] = new PDBEntry("1YCS", "A", Type.PDB, "INLINE1YCS");
     pdbFiles[1] = new PDBEntry("3A6S", "B", Type.PDB, "INLINE3A6S");
     pdbFiles[2] = new PDBEntry("1OOT", "A", Type.PDB, "INLINE1OOT");
-    String[][] chains = new String[3][];
     SequenceI[][] seqs = new SequenceI[3][];
     seqs[0] = new SequenceI[] { seq1a, seq1b };
     seqs[1] = new SequenceI[] { seq2 };
@@ -118,7 +117,7 @@ public class AAStructureBindingModelTest
     ssm.setMapping(new SequenceI[] { seq3 }, null, PDB_3,
             AppletFormatAdapter.PASTE);
 
-    testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, chains, null)
+    testee = new AAStructureBindingModel(ssm, pdbFiles, seqs, null)
     {
       @Override
       public String[] getPdbFile()
@@ -140,6 +139,12 @@ public class AAStructureBindingModelTest
       public void highlightAtoms(List<AtomSpec> atoms)
       {
       }
+
+      @Override
+      public List<String> getChainNames()
+      {
+        return null;
+      }
     };
   }