X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=65c27d940c5bd4dc753b80370f0bf57eb6fdf98d;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=af83e484f0fa72aa795200da0f9b61f24d6809c9;hpb=b32b824388dea3107cd1598d63f8759f00b75e1f;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index af83e48..65c27d9 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1,58 +1,74 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ext.jmol;
 
-import java.io.File;
-import java.net.URL;
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.SequenceStructureBindingModel;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.event.ComponentEvent;
+import java.awt.event.ComponentListener;
+import java.io.File;
+import java.net.URL;
+import java.security.AccessControlException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
 
-import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
-import jalview.schemes.*;
-
-public abstract class JalviewJmolBinding implements StructureListener,
-        JmolStatusListener, SequenceStructureBinding
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolSelectionListener;
+import org.jmol.api.JmolStatusListener;
+import org.jmol.api.JmolViewer;
+import org.jmol.constant.EnumCallback;
+import org.jmol.popup.JmolPopup;
+
+public abstract class JalviewJmolBinding extends SequenceStructureBindingModel implements StructureListener,
+        JmolStatusListener, SequenceStructureBinding,
+        JmolSelectionListener, ComponentListener,
+        StructureSelectionManagerProvider
 
 {
   /**
-   * set if Jmol state is being restored from some source - instructs binding
-   * not to apply default display style when structure set is updated for first
-   * time.
-   */
-  private boolean loadingFromArchive = false;
-  /**
    * state flag used to check if the Jmol viewer's paint method can be called
    */
-  private boolean finishedInit=false;
-  
+  private boolean finishedInit = false;
+
   public boolean isFinishedInit()
   {
     return finishedInit;
@@ -75,7 +91,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
 
   public Vector chainNames;
 
-  String[] chains;
+  Hashtable chainFile;
+
+  /**
+   * array of target chains for seuqences - tied to pdbentry and sequence[]
+   */
+  protected String[][] chains;
 
   boolean colourBySequence = true;
 
@@ -105,26 +126,34 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public PDBEntry[] pdbentry;
 
   /**
-   * datasource protocol for access to PDBEntry
+   * datasource protocol for access to PDBEntrylatest
    */
   String protocol = null;
 
   StringBuffer resetLastRes = new StringBuffer();
 
-  public SequenceI[] sequence;
+  /**
+   * sequences mapped to each pdbentry
+   */
+  public SequenceI[][] sequence;
 
-  StructureSelectionManager ssm;
+  public StructureSelectionManager ssm;
 
   public JmolViewer viewer;
 
-  public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[] seq,
-          String[] chains, String protocol)
+  public JalviewJmolBinding(StructureSelectionManager ssm,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          String protocol)
   {
-    this.sequence = seq;
+    this.ssm = ssm;
+    this.sequence = sequenceIs;
     this.chains = chains;
     this.pdbentry = pdbentry;
     this.protocol = protocol;
-
+    if (chains == null)
+    {
+      this.chains = new String[pdbentry.length][];
+    }
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
      * "jalviewJmol", ap.av.applet .getDocumentBase(),
@@ -134,16 +163,31 @@ public abstract class JalviewJmolBinding implements StructureListener,
      */
   }
 
+  public JalviewJmolBinding(StructureSelectionManager ssm,
+          JmolViewer viewer2)
+  {
+    this.ssm = ssm;
+    viewer = viewer2;
+    viewer.setJmolStatusListener(this);
+    viewer.addSelectionListener(this);
+  }
+
   /**
-   * construct a title string for the viewer window based on the data jalview knows about
-   * @return 
+   * construct a title string for the viewer window based on the data jalview
+   * knows about
+   * 
+   * @return
    */
-  public String getViewerTitle() {
-    if (sequence==null || pdbentry==null || sequence.length<1 || pdbentry.length<1)
+  public String getViewerTitle()
+  {
+    if (sequence == null || pdbentry == null || sequence.length < 1
+            || pdbentry.length < 1 || sequence[0].length < 1)
     {
-      return("Jalview Jmol Window");
+      return ("Jalview Jmol Window");
     }
-    StringBuffer title = new StringBuffer(sequence[0].getName() + ":"
+    // TODO: give a more informative title when multiple structures are
+    // displayed.
+    StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"
             + pdbentry[0].getId());
 
     if (pdbentry[0].getProperty() != null)
@@ -183,31 +227,40 @@ public abstract class JalviewJmolBinding implements StructureListener,
         p = mlength;
         mlength = lbl.indexOf(":", p);
       } while (p < mlength && mlength < (lbl.length() - 2));
+      // TODO: lookup each pdb id and recover proper model number for it.
       cmd.append(":" + lbl.substring(mlength + 1) + " /"
-              + getModelNum(lbl.substring(0, mlength)) + " or ");
+              + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");
     }
     if (cmd.length() > 0)
       cmd.setLength(cmd.length() - 4);
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center "
-                    + cmd);
+    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
   }
 
   public void closeViewer()
   {
     viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);
     // remove listeners for all structures in viewer
-    StructureSelectionManager.getStructureSelectionManager()
-            .removeStructureViewerListener(this, this.getPdbFile());
+    ssm.removeStructureViewerListener(this, this.getPdbFile());
     // and shut down jmol
     viewer.evalStringQuiet("zap");
     viewer.setJmolStatusListener(null);
-    lastCommand=null;
+    lastCommand = null;
     viewer = null;
+    releaseUIResources();
   }
 
+  /**
+   * called by JalviewJmolbinding after closeViewer is called - release any
+   * resources and references so they can be garbage collected.
+   */
+  protected abstract void releaseUIResources();
+
   public void colourByChain()
   {
     colourBySequence = false;
+    // TODO: colour by chain should colour each chain distinctly across all
+    // visible models
+    // TODO: http://issues.jalview.org/browse/JAL-628
     evalStateCommand("select *;color chain");
   }
 
@@ -224,171 +277,382 @@ public abstract class JalviewJmolBinding implements StructureListener,
    */
   public void superposeStructures(AlignmentI alignment)
   {
-    String[] files = getPdbFile();
+    superposeStructures(alignment, -1, null);
+  }
 
-    StringBuffer command = new StringBuffer();
-    boolean matched[] = new boolean[alignment.getWidth()];
-    String commonpositions[][] = new String[files.length][alignment
-            .getWidth()];
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+  /**
+   * superpose the structures associated with sequences in the alignment
+   * according to their corresponding positions. ded)
+   * 
+   * @param refStructure
+   *          - select which pdb file to use as reference (default is -1 - the
+   *          first structure in the alignment)
+   */
+  public void superposeStructures(AlignmentI alignment, int refStructure)
+  {
+    superposeStructures(alignment, refStructure, null);
+  }
+
+  /**
+   * superpose the structures associated with sequences in the alignment
+   * according to their corresponding positions. ded)
+   * 
+   * @param refStructure
+   *          - select which pdb file to use as reference (default is -1 - the
+   *          first structure in the alignment)
+   * @param hiddenCols
+   *          TODO
+   */
+  public void superposeStructures(AlignmentI alignment, int refStructure,
+          ColumnSelection hiddenCols)
+  {
+    superposeStructures(new AlignmentI[]
+    { alignment }, new int[]
+    { refStructure }, new ColumnSelection[]
+    { hiddenCols });
+  }
+
+  public void superposeStructures(AlignmentI[] _alignment,
+          int[] _refStructure, ColumnSelection[] _hiddenCols)
+  {
+    assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
+
+    String[] files = getPdbFile();
+    // check to see if we are still waiting for Jmol files
+    long starttime = System.currentTimeMillis();
+    boolean waiting = true;
+    do
+    {
+      waiting = false;
+      for (String file : files)
+      {
+        try
+        {
+          // HACK - in Jalview 2.8 this call may not be threadsafe so we catch
+          // every possible exception
+          StructureMapping[] sm = ssm.getMapping(file);
+          if (sm == null || sm.length == 0)
+          {
+            waiting = true;
+          }
+        } catch (Exception x)
+        {
+          waiting = true;
+        } catch (Error q)
+        {
+          waiting = true;
+        }
+      }
+      // we wait around for a reasonable time before we give up
+    } while (waiting
+            && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime));
+    if (waiting)
+    {
+      System.err
+              .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures.");
+      return;
+    }
+    StringBuffer selectioncom = new StringBuffer();
+    // In principle - nSeconds specifies the speed of animation for each
+    // superposition - but is seems to behave weirdly, so we don't specify it.
+    String nSeconds = " ";
+    if (files.length > 10)
+    {
+      nSeconds = " 0.00001 ";
+    }
+    else
+    {
+      nSeconds = " " + (2.0 / files.length) + " ";
+      // if (nSeconds).substring(0,5)+" ";
+    }
+    // see JAL-1345 - should really automatically turn off the animation for
+    // large numbers of structures, but Jmol doesn't seem to allow that.
+    nSeconds = " ";
+    // union of all aligned positions are collected together.
+    for (int a = 0; a < _alignment.length; a++)
     {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+      int refStructure = _refStructure[a];
+      AlignmentI alignment = _alignment[a];
+      ColumnSelection hiddenCols = _hiddenCols[a];
+      if (a > 0
+              && selectioncom.length() > 0
+              && !selectioncom.substring(selectioncom.length() - 1).equals(
+                      "|"))
+      {
+        selectioncom.append("|");
+      }
+      // process this alignment
+      if (refStructure >= files.length)
+      {
+        System.err.println("Invalid reference structure value "
+                + refStructure);
+        refStructure = -1;
+      }
+      if (refStructure < -1)
+      {
+        refStructure = -1;
+      }
+      StringBuffer command = new StringBuffer();
 
-      if (mapping == null || mapping.length < 1)
-        continue;
+      boolean matched[] = new boolean[alignment.getWidth()];
+      for (int m = 0; m < matched.length; m++)
+      {
+
+        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
+      }
 
-      int lastPos = -1;
-      for (int s = 0; s < sequence.length; s++)
+      int commonrpositions[][] = new int[files.length][alignment.getWidth()];
+      String isel[] = new String[files.length];
+      // reference structure - all others are superposed in it
+      String[] targetC = new String[files.length];
+      String[] chainNames = new String[files.length];
+      for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
       {
-        for (int sp, m = 0; m < mapping.length; m++)
+        StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+        // RACE CONDITION - getMapping only returns Jmol loaded filenames once
+        // Jmol callback has completed.
+        if (mapping == null || mapping.length < 1)
         {
-          if (mapping[m].getSequence() == sequence[s]
-                  && (sp = alignment.findIndex(sequence[s])) > -1)
+          throw new Error(MessageManager.getString("error.implementation_error_jmol_getting_data"));
+        }
+        int lastPos = -1;
+        for (int s = 0; s < sequence[pdbfnum].length; s++)
+        {
+          for (int sp, m = 0; m < mapping.length; m++)
           {
-            SequenceI asp = alignment.getSequenceAt(sp);
-            for (int r = 0; r < asp.getLength(); r++)
+            if (mapping[m].getSequence() == sequence[pdbfnum][s]
+                    && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
             {
-              // no mapping to gaps in sequence
-              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+              if (refStructure == -1)
               {
-                matched[r] = false; // exclude from common set
-                continue;
+                refStructure = pdbfnum;
               }
-              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
-              if (pos < 1 || pos == lastPos)
-                continue;
+              SequenceI asp = alignment.getSequenceAt(sp);
+              for (int r = 0; r < matched.length; r++)
+              {
+                if (!matched[r])
+                {
+                  continue;
+                }
+                matched[r] = false; // assume this is not a good site
+                if (r >= asp.getLength())
+                {
+                  continue;
+                }
 
-              lastPos = pos;
+                if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+                {
+                  // no mapping to gaps in sequence
+                  continue;
+                }
+                int t = asp.findPosition(r); // sequence position
+                int apos = mapping[m].getAtomNum(t);
+                int pos = mapping[m].getPDBResNum(t);
 
-              commonpositions[m][r] = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/" + (pdbfnum + 1) + ".1";
+                if (pos < 1 || pos == lastPos)
+                {
+                  // can't align unmapped sequence
+                  continue;
+                }
+                matched[r] = true; // this is a good ite
+                lastPos = pos;
+                // just record this residue position
+                commonrpositions[pdbfnum][r] = pos;
+              }
+              // create model selection suffix
+              isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";
+              if (mapping[m].getChain() == null
+                      || mapping[m].getChain().trim().length() == 0)
+              {
+                targetC[pdbfnum] = "";
+              }
+              else
+              {
+                targetC[pdbfnum] = ":" + mapping[m].getChain();
+              }
+              chainNames[pdbfnum] = mapping[m].getPdbId()
+                      + targetC[pdbfnum];
+              // move on to next pdb file
+              s = sequence[pdbfnum].length;
+              break;
             }
-            break;
           }
         }
       }
-    }
-    command.append("select ");
-    // form the matched pair selection strings
-    String sep = "";
-    for (int r = 0; r < matched.length; r++)
-    {
-      if (matched[r])
+
+      // TODO: consider bailing if nmatched less than 4 because superposition
+      // not
+      // well defined.
+      // TODO: refactor superposable position search (above) from jmol selection
+      // construction (below)
+
+      String[] selcom = new String[files.length];
+      int nmatched = 0;
+      // generate select statements to select regions to superimpose structures
       {
-        command.append(sep);
-        command.append("(");
-        for (int s = 0; s < commonpositions.length; s++)
+        for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
         {
-          if (s > 0)
+          String chainCd = targetC[pdbfnum];
+          int lpos = -1;
+          boolean run = false;
+          StringBuffer molsel = new StringBuffer();
+          molsel.append("{");
+          for (int r = 0; r < matched.length; r++)
+          {
+            if (matched[r])
+            {
+              if (pdbfnum == 0)
+              {
+                nmatched++;
+              }
+              if (lpos != commonrpositions[pdbfnum][r] - 1)
+              {
+                // discontinuity
+                if (lpos != -1)
+                {
+                  molsel.append(lpos);
+                  molsel.append(chainCd);
+                  // molsel.append("} {");
+                  molsel.append("|");
+                }
+              }
+              else
+              {
+                // continuous run - and lpos >-1
+                if (!run)
+                {
+                  // at the beginning, so add dash
+                  molsel.append(lpos);
+                  molsel.append("-");
+                }
+                run = true;
+              }
+              lpos = commonrpositions[pdbfnum][r];
+              // molsel.append(lpos);
+            }
+          }
+          // add final selection phrase
+          if (lpos != -1)
+          {
+            molsel.append(lpos);
+            molsel.append(chainCd);
+            molsel.append("}");
+          }
+          if (molsel.length() > 1)
           {
-            command.append(" | ");
+            selcom[pdbfnum] = molsel.toString();
+            selectioncom.append("((");
+            selectioncom.append(selcom[pdbfnum].substring(1,
+                    selcom[pdbfnum].length() - 1));
+            selectioncom.append(" )& ");
+            selectioncom.append(pdbfnum + 1);
+            selectioncom.append(".1)");
+            if (pdbfnum < files.length - 1)
+            {
+              selectioncom.append("|");
+            }
           }
-          command.append(commonpositions[s][r]);
+          else
+          {
+            selcom[pdbfnum] = null;
+          }
+        }
+      }
+      for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+      {
+        if (pdbfnum == refStructure || selcom[pdbfnum] == null
+                || selcom[refStructure] == null)
+        {
+          continue;
+        }
+        command.append("echo ");
+        command.append("\"Superposing (");
+        command.append(chainNames[pdbfnum]);
+        command.append(") against reference (");
+        command.append(chainNames[refStructure]);
+        command.append(")\";\ncompare " + nSeconds);
+        command.append("{");
+        command.append(1 + pdbfnum);
+        command.append(".1} {");
+        command.append(1 + refStructure);
+        command.append(".1} SUBSET {*.CA | *.P} ATOMS ");
+
+        // form the matched pair strings
+        String sep = "";
+        for (int s = 0; s < 2; s++)
+        {
+          command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
         }
-        command.append(")");
-        sep = " | ";
+        command.append(" ROTATE TRANSLATE;\n");
+      }
+      if (selectioncom.length() > 0)
+      {
+        System.out.println("Select regions:\n" + selectioncom.toString());
+        evalStateCommand("select *; cartoons off; backbone; select ("
+                + selectioncom.toString() + "); cartoons; ");
+        // selcom.append("; ribbons; ");
+        System.out
+                .println("Superimpose command(s):\n" + command.toString());
+
+        evalStateCommand(command.toString());
       }
     }
-    evalStateCommand(command.toString());
+    if (selectioncom.length() > 0)
+    {// finally, mark all regions that were superposed.
+      if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
+      {
+        selectioncom.setLength(selectioncom.length() - 1);
+      }
+      System.out.println("Select regions:\n" + selectioncom.toString());
+      evalStateCommand("select *; cartoons off; backbone; select ("
+              + selectioncom.toString() + "); cartoons; ");
+      // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
+    }
   }
 
-  public void evalStateCommand(String command) {
+  public void evalStateCommand(String command)
+  {
     jmolHistory(false);
     if (lastCommand == null || !lastCommand.equals(command))
     {
-      viewer.evalStringQuiet(command+"\n");
+      viewer.evalStringQuiet(command + "\n");
     }
     jmolHistory(true);
     lastCommand = command;
   }
+
   /**
    * colour any structures associated with sequences in the given alignment
    * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
    * if colourBySequence is enabled.
    */
-  public void colourBySequence(boolean showFeatures, AlignmentI alignment)
+  public void colourBySequence(boolean showFeatures,
+          jalview.api.AlignmentViewPanel alignmentv)
   {
-    if (!colourBySequence)
+    if (!colourBySequence || !isLoadingFinished())
       return;
-    if (ssm==null)
+    if (ssm == null)
     {
       return;
     }
     String[] files = getPdbFile();
-    SequenceRenderer sr = getSequenceRenderer();
+
+    SequenceRenderer sr = getSequenceRenderer(alignmentv);
 
     FeatureRenderer fr = null;
     if (showFeatures)
     {
-      fr = getFeatureRenderer();
+      fr = getFeatureRenderer(alignmentv);
     }
+    AlignmentI alignment = alignmentv.getAlignment();
 
-    StringBuffer command = new StringBuffer();
-
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-    {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
-      if (mapping == null || mapping.length < 1)
-        continue;
-
-      int lastPos = -1;
-      for (int s = 0; s < sequence.length; s++)
+    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : JmolCommands
+            .getColourBySequenceCommand(ssm, files, sequence, sr, fr,
+                    alignment))
+      for (String cbyseq : cpdbbyseq.commands)
       {
-        for (int sp, m = 0; m < mapping.length; m++)
-        {
-          if (mapping[m].getSequence() == sequence[s]
-                  && (sp = alignment.findIndex(sequence[s])) > -1)
-          {
-            SequenceI asp = alignment.getSequenceAt(sp);
-            for (int r = 0; r < asp.getLength(); r++)
-            {
-              // no mapping to gaps in sequence
-              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
-              {
-                continue;
-              }
-              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
-              if (pos < 1 || pos == lastPos)
-                continue;
-
-              lastPos = pos;
-
-              Color col = sr.getResidueBoxColour(sequence[s], r);
-
-              if (showFeatures)
-                col = fr.findFeatureColour(col, sequence[s], r);
-              String newSelcom = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
-                      + col.getBlue() + "]";
-              if (command.toString().endsWith(newSelcom))
-              {
-                command = condenseCommand(command.toString(), pos);
-                continue;
-              }
-              // TODO: deal with case when buffer is too large for Jmol to parse
-              // - execute command and flush
-
-              command.append(";select " + pos);
-              command.append(newSelcom);
-            }
-            break;
-          }
-        }
+        evalStateCommand(cbyseq);
       }
-    }
-    evalStateCommand(command.toString());
   }
 
   public boolean isColourBySequence()
@@ -401,30 +665,6 @@ public abstract class JalviewJmolBinding implements StructureListener,
     this.colourBySequence = colourBySequence;
   }
 
-  StringBuffer condenseCommand(String command, int pos)
-  {
-
-    StringBuffer sb = new StringBuffer(command.substring(0, command
-            .lastIndexOf("select") + 7));
-
-    command = command.substring(sb.length());
-
-    String start;
-
-    if (command.indexOf("-") > -1)
-    {
-      start = command.substring(0, command.indexOf("-"));
-    }
-    else
-    {
-      start = command.substring(0, command.indexOf(":"));
-    }
-
-    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-
-    return sb;
-  }
-
   public void createImage(String file, String type, int quality)
   {
     System.out.println("JMOL CREATE IMAGE");
@@ -471,9 +711,19 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * returns the current featureRenderer that should be used to colour the
    * structures
    * 
+   * @param alignment
+   * 
    * @return
    */
-  public abstract FeatureRenderer getFeatureRenderer();
+  public abstract FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment);
+
+  /**
+   * instruct the Jalview binding to update the pdbentries vector if necessary
+   * prior to matching the jmol view's contents to the list of structure files
+   * Jalview knows about.
+   */
+  public abstract void refreshPdbEntries();
 
   private int getModelNum(String modelFileName)
   {
@@ -490,23 +740,73 @@ public abstract class JalviewJmolBinding implements StructureListener,
     return -1;
   }
 
+  /**
+   * map between index of model filename returned from getPdbFile and the first
+   * index of models from this file in the viewer. Note - this is not trimmed -
+   * use getPdbFile to get number of unique models.
+   */
+  private int _modelFileNameMap[];
+
   // ////////////////////////////////
   // /StructureListener
-  public String[] getPdbFile()
+  public synchronized String[] getPdbFile()
   {
+    if (viewer == null)
+    {
+      return new String[0];
+    }
     if (modelFileNames == null)
     {
+
       String mset[] = new String[viewer.getModelCount()];
-      for (int i = 0; i < mset.length; i++)
+      _modelFileNameMap = new int[mset.length];
+      int j = 1;
+      String m = viewer.getModelFileName(0);
+      if (m != null)
       {
-        mset[i] = viewer.getModelFileName(i);
+        try
+        {
+          mset[0] = new File(m).getAbsolutePath();
+        } catch (AccessControlException x)
+        {
+          // usually not allowed to do this in applet, so keep raw handle
+          mset[0] = m;
+          // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+        }
       }
-      modelFileNames = mset;
+      for (int i = 1; i < mset.length; i++)
+      {
+        m = viewer.getModelFileName(i);
+        if (m != null)
+        {
+          try
+          {
+            mset[j] = new File(m).getAbsolutePath();
+          } catch (AccessControlException x)
+          {
+            // usually not allowed to do this in applet, so keep raw handle
+            mset[j] = m;
+            // System.err.println("jmolBinding: Using local file string from Jmol: "+m);
+          }
+        }
+        _modelFileNameMap[j] = i; // record the model index for the filename
+        // skip any additional models in the same file (NMR structures)
+        if ((mset[j] == null ? mset[j] != mset[j - 1]
+                : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))
+        {
+          j++;
+        }
+      }
+      modelFileNames = new String[j];
+      System.arraycopy(mset, 0, modelFileNames, 0, j);
     }
     return modelFileNames;
   }
 
-  public Hashtable getRegistryInfo()
+  /**
+   * map from string to applet
+   */
+  public Map getRegistryInfo()
   {
     // TODO Auto-generated method stub
     return null;
@@ -516,9 +816,12 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * returns the current sequenceRenderer that should be used to colour the
    * structures
    * 
+   * @param alignment
+   * 
    * @return
    */
-  public abstract SequenceRenderer getSequenceRenderer();
+  public abstract SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment);
 
   // ///////////////////////////////
   // JmolStatusListener
@@ -599,12 +902,21 @@ public abstract class JalviewJmolBinding implements StructureListener,
   public void loadInline(String string)
   {
     loadedInline = true;
+    // TODO: re JAL-623
+    // viewer.loadInline(strModel, isAppend);
+    // could do this:
+    // construct fake fullPathName and fileName so we can identify the file
+    // later.
+    // Then, construct pass a reader for the string to Jmol.
+    // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,
+    // fileName, null, reader, false, null, null, 0);
     viewer.openStringInline(string);
   }
 
   public void mouseOverStructure(int atomIndex, String strInfo)
   {
     int pdbResNum;
+    int alocsep = strInfo.indexOf("^");
     int mdlSep = strInfo.indexOf("/");
     int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
 
@@ -617,14 +929,23 @@ public abstract class JalviewJmolBinding implements StructureListener,
         chainSeparator = mdlSep;
       }
     }
-    pdbResNum = Integer.parseInt(strInfo.substring(
-            strInfo.indexOf("]") + 1, chainSeparator));
+    // handle insertion codes
+    if (alocsep != -1)
+    {
+      pdbResNum = Integer.parseInt(strInfo.substring(
+              strInfo.indexOf("]") + 1, alocsep));
 
+    }
+    else
+    {
+      pdbResNum = Integer.parseInt(strInfo.substring(
+              strInfo.indexOf("]") + 1, chainSeparator));
+    }
     String chainId;
 
     if (strInfo.indexOf(":") > -1)
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo
-              .indexOf("."));
+      chainId = strInfo.substring(strInfo.indexOf(":") + 1,
+              strInfo.indexOf("."));
     else
     {
       chainId = " ";
@@ -643,8 +964,19 @@ public abstract class JalviewJmolBinding implements StructureListener,
       try
       {
         // recover PDB filename for the model hovered over.
-        pdbfilename = viewer
-                .getModelFileName(new Integer(mdlId).intValue() - 1);
+        int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId)
+                .intValue() - 1;
+        while (mnumber < _modelFileNameMap[_mp])
+        {
+          _mp--;
+        }
+        pdbfilename = modelFileNames[_mp];
+        if (pdbfilename == null)
+        {
+          pdbfilename = new File(viewer.getModelFileName(mnumber))
+                  .getAbsolutePath();
+        }
+
       } catch (Exception e)
       {
       }
@@ -660,7 +992,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
   {
     if (data != null)
     {
-      System.err.println("Ignoring additional hover info: " + data+ " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+      System.err.println("Ignoring additional hover info: " + data
+              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
   }
@@ -713,59 +1046,59 @@ public abstract class JalviewJmolBinding implements StructureListener,
     jmolHistory(true);
     // TODO: in application this happens
     //
-//if (scriptWindow != null)
-//    {
-//      scriptWindow.sendConsoleMessage(strInfo);
-//      scriptWindow.sendConsoleMessage("\n");
-//    }
-
+    // if (scriptWindow != null)
+    // {
+    // scriptWindow.sendConsoleMessage(strInfo);
+    // scriptWindow.sendConsoleMessage("\n");
+    // }
 
   }
 
-  public void notifyCallback(int type, Object[] data)
+  @Override
+  public void notifyCallback(EnumCallback type, Object[] data)
   {
     try
     {
       switch (type)
       {
-      case JmolConstants.CALLBACK_LOADSTRUCT:
+      case LOADSTRUCT:
         notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4], ((Integer) data[5])
-                        .intValue());
+                (String) data[3], (String) data[4],
+                ((Integer) data[5]).intValue());
 
         break;
-      case JmolConstants.CALLBACK_PICK:
+      case PICK:
         notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
                 (String) data[0]);
         // also highlight in alignment
-      case JmolConstants.CALLBACK_HOVER:
+      case HOVER:
         notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
                 (String) data[0]);
         break;
-      case JmolConstants.CALLBACK_SCRIPT:
-        notifyScriptTermination((String) data[2], ((Integer) data[3])
-                .intValue());
+      case SCRIPT:
+        notifyScriptTermination((String) data[2],
+                ((Integer) data[3]).intValue());
         break;
-      case JmolConstants.CALLBACK_ECHO:
+      case ECHO:
         sendConsoleEcho((String) data[1]);
         break;
-      case JmolConstants.CALLBACK_MESSAGE:
+      case MESSAGE:
         sendConsoleMessage((data == null) ? ((String) null)
                 : (String) data[1]);
         break;
-      case JmolConstants.CALLBACK_ERROR:
+      case ERROR:
         // System.err.println("Ignoring error callback.");
         break;
-      case JmolConstants.CALLBACK_SYNC:
-      case JmolConstants.CALLBACK_RESIZE:
-        updateUI();
+      case SYNC:
+      case RESIZE:
+        refreshGUI();
         break;
-      case JmolConstants.CALLBACK_MEASURE:
-        
-      case JmolConstants.CALLBACK_CLICK:
-        
+      case MEASURE:
+
+      case CLICK:
       default:
-        System.err.println("Unhandled callback " + type + " " + data[1].toString());
+        System.err.println("Unhandled callback " + type + " "
+                + data[1].toString());
         break;
       }
     } catch (Exception e)
@@ -775,177 +1108,217 @@ public abstract class JalviewJmolBinding implements StructureListener,
     }
   }
 
-  public boolean notifyEnabled(int callbackPick)
+  @Override
+  public boolean notifyEnabled(EnumCallback callbackPick)
   {
     switch (callbackPick)
     {
-    case JmolConstants.CALLBACK_ECHO:
-    case JmolConstants.CALLBACK_LOADSTRUCT:
-    case JmolConstants.CALLBACK_MEASURE:
-    case JmolConstants.CALLBACK_MESSAGE:
-    case JmolConstants.CALLBACK_PICK:
-    case JmolConstants.CALLBACK_SCRIPT:
-    case JmolConstants.CALLBACK_HOVER:
-    case JmolConstants.CALLBACK_ERROR:
+    case ECHO:
+    case LOADSTRUCT:
+    case MEASURE:
+    case MESSAGE:
+    case PICK:
+    case SCRIPT:
+    case HOVER:
+    case ERROR:
       return true;
-    case JmolConstants.CALLBACK_RESIZE:
-    case JmolConstants.CALLBACK_SYNC:
-    case JmolConstants.CALLBACK_CLICK:
-    case JmolConstants.CALLBACK_ANIMFRAME:
-    case JmolConstants.CALLBACK_MINIMIZATION:
+    case RESIZE:
+    case SYNC:
+    case CLICK:
+    case ANIMFRAME:
+    case MINIMIZATION:
     }
     return false;
   }
 
+  // incremented every time a load notification is successfully handled -
+  // lightweight mechanism for other threads to detect when they can start
+  // referrring to new structures.
+  private long loadNotifiesHandled = 0;
+
+  public long getLoadNotifiesHandled()
+  {
+    return loadNotifiesHandled;
+  }
+
   public void notifyFileLoaded(String fullPathName, String fileName2,
           String modelName, String errorMsg, int modelParts)
   {
     if (errorMsg != null)
     {
       fileLoadingError = errorMsg;
-      updateUI();
+      refreshGUI();
       return;
     }
+    // TODO: deal sensibly with models loaded inLine:
+    // modelName will be null, as will fullPathName.
+
+    // the rest of this routine ignores the arguments, and simply interrogates
+    // the Jmol view to find out what structures it contains, and adds them to
+    // the structure selection manager.
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
     chainNames = new Vector();
+    chainFile = new Hashtable();
     boolean notifyLoaded = false;
     String[] modelfilenames = getPdbFile();
-    ssm = StructureSelectionManager.getStructureSelectionManager();
     // first check if we've lost any structures
-    if (oldmodels!=null && oldmodels.length>0)
+    if (oldmodels != null && oldmodels.length > 0)
     {
-      int oldm=0;
-      for (int i=0;i<oldmodels.length;i++)
+      int oldm = 0;
+      for (int i = 0; i < oldmodels.length; i++)
       {
-        for (int n=0;n<modelfilenames.length; n++)
+        for (int n = 0; n < modelfilenames.length; n++)
         {
-          if (modelfilenames[n]==oldmodels[i])
+          if (modelfilenames[n] == oldmodels[i])
           {
-            oldmodels[i]=null;
+            oldmodels[i] = null;
             break;
           }
         }
-        if (oldmodels[i]!=null)
+        if (oldmodels[i] != null)
         {
           oldm++;
         }
       }
-      if (oldm>0)
+      if (oldm > 0)
       {
         String[] oldmfn = new String[oldm];
-        oldm=0;
-        for (int i=0;i<oldmodels.length; i++)
+        oldm = 0;
+        for (int i = 0; i < oldmodels.length; i++)
         {
-          if (oldmodels[i]!=null) {
+          if (oldmodels[i] != null)
+          {
             oldmfn[oldm++] = oldmodels[i];
           }
         }
-        // deregister the Jmol instance for these structures - we'll add 
-        // ourselves again at the end for the current structure set. 
+        // deregister the Jmol instance for these structures - we'll add
+        // ourselves again at the end for the current structure set.
         ssm.removeStructureViewerListener(this, oldmfn);
       }
     }
+    refreshPdbEntries();
     for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
     {
       String fileName = modelfilenames[modelnum];
-      if (fileName != null)
+      boolean foundEntry = false;
+      MCview.PDBfile pdb = null;
+      String pdbfile = null, pdbfhash = null;
+      // model was probably loaded inline - so check the pdb file hashcode
+      if (loadedInline)
+      {
+        // calculate essential attributes for the pdb data imported inline.
+        // prolly need to resolve modelnumber properly - for now just use our
+        // 'best guess'
+        pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+                + ".0", "PDB");
+        pdbfhash = "" + pdbfile.hashCode();
+      }
+      if (pdbentry != null)
       {
-        // search pdbentries and sequences to find correct pdbentry and
-        // sequence[] pair for this filename
-        if (pdbentry != null)
+        // search pdbentries and sequences to find correct pdbentry for this
+        // model
+        for (int pe = 0; pe < pdbentry.length; pe++)
         {
-          boolean foundEntry = false;
-          for (int pe = 0; pe < pdbentry.length; pe++)
+          boolean matches = false;
+          if (fileName == null)
           {
-            if (pdbentry[pe].getFile().equals(fileName))
+            if (false)
+            // see JAL-623 - need method of matching pasted data up
             {
+              pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,
+                      AppletFormatAdapter.PASTE);
+              pdbentry[modelnum].setFile("INLINE" + pdb.id);
+              matches = true;
               foundEntry = true;
-              MCview.PDBfile pdb;
-              if (loadedInline)
-              {
-                // TODO: replace with getData ?
-                pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
-                        .getFile(), AppletFormatAdapter.PASTE);
-                pdbentry[pe].setFile("INLINE" + pdb.id);
-              }
-              else
+            }
+          }
+          else
+          {
+            File fl;
+            if (matches = (fl = new File(pdbentry[pe].getFile()))
+                    .equals(new File(fileName)))
+            {
+              foundEntry = true;
+              // TODO: Jmol can in principle retrieve from CLASSLOADER but
+              // this
+              // needs
+              // to be tested. See mantis bug
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
+              String protocol = AppletFormatAdapter.URL;
+              try
               {
-                // TODO: Jmol can in principle retrieve from CLASSLOADER but
-                // this
-                // needs
-                // to be tested. See mantis bug
-                // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-                String protocol = AppletFormatAdapter.URL;
-                try
-                {
-                  File fl = new java.io.File(pdbentry[pe].getFile());
-                  if (fl.exists())
-                  {
-                    protocol = AppletFormatAdapter.FILE;
-                  }
-                } catch (Exception e)
-                {
-                } catch (Error e)
+                if (fl.exists())
                 {
+                  protocol = AppletFormatAdapter.FILE;
                 }
-                ;
-                pdb = ssm.setMapping(sequence, chains, pdbentry[pe]
-                        .getFile(), protocol);
-
-              }
-
-              pdbentry[pe].setId(pdb.id);
-
-              for (int i = 0; i < pdb.chains.size(); i++)
+              } catch (Exception e)
+              {
+              } catch (Error e)
               {
-                chainNames.addElement(new String(pdb.id + ":"
-                        + ((MCview.PDBChain) pdb.chains.elementAt(i)).id));
               }
-              notifyLoaded = true;
+              // Explicitly map to the filename used by Jmol ;
+              pdb = ssm.setMapping(sequence[pe], chains[pe], fileName,
+                      protocol);
+              // pdbentry[pe].getFile(), protocol);
+
             }
           }
-          if (!foundEntry && associateNewStructs)
+          if (matches)
           {
-            // this is a foreign pdb file that jalview doesn't know about - add
-            // it
-            // to the dataset
-            // and try to find a home - either on a matching sequence or as a
-            // new
-            // sequence.
-            String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
-                    "PDB");
-            // parse pdb file into a chain, etc.
-            // locate best match for pdb in associated views and add mapping to
-            // ssm
-            // if properly registered then
+            // add an entry for every chain in the model
+            for (int i = 0; i < pdb.chains.size(); i++)
+            {
+              String chid = new String(pdb.id + ":"
+                      + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);
+              chainFile.put(chid, fileName);
+              chainNames.addElement(chid);
+            }
             notifyLoaded = true;
           }
         }
       }
+      if (!foundEntry && associateNewStructs)
+      {
+        // this is a foreign pdb file that jalview doesn't know about - add
+        // it to the dataset and try to find a home - either on a matching
+        // sequence or as a new sequence.
+        String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",
+                "PDB");
+        // parse pdb file into a chain, etc.
+        // locate best match for pdb in associated views and add mapping to
+        // ssm
+        // if properly registered then
+        notifyLoaded = true;
+
+      }
     }
     // FILE LOADED OK
     // so finally, update the jmol bits and pieces
-    jmolpopup.updateComputedMenus();
+    if (jmolpopup != null)
+    {
+      // potential for deadlock here:
+      // jmolpopup.updateComputedMenus();
+    }
     if (!isLoadingFromArchive())
     {
-      viewer
-              .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
+      viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
     }
-    setLoadingFromArchive(false);
     // register ourselves as a listener and notify the gui that it needs to
     // update itself.
     ssm.addStructureViewerListener(this);
     if (notifyLoaded)
     {
-      FeatureRenderer fr = getFeatureRenderer();
-      if (fr!=null)
+      FeatureRenderer fr = getFeatureRenderer(null);
+      if (fr != null)
       {
         fr.featuresAdded();
       }
-      updateUI();
+      refreshGUI();
+      loadNotifiesHandled++;
     }
+    setLoadingFromArchive(false);
   }
 
   public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
@@ -953,7 +1326,8 @@ public abstract class JalviewJmolBinding implements StructureListener,
     notifyAtomPicked(iatom, strMeasure, null);
   }
 
-  public abstract void notifyScriptTermination(String strStatus, int msWalltime);
+  public abstract void notifyScriptTermination(String strStatus,
+          int msWalltime);
 
   /**
    * display a message echoed from the jmol viewer
@@ -1033,25 +1407,96 @@ public abstract class JalviewJmolBinding implements StructureListener,
    * state change. this could be because structures were loaded, or because an
    * error has occured.
    */
-  public abstract void updateUI();
+  public abstract void refreshGUI();
 
-  public void allocateViewer(Component renderPanel, String htmlName,
-          URL documentBase, URL codeBase, String commandOptions)
+  /**
+   * called to show or hide the associated console window container.
+   * 
+   * @param show
+   */
+  public abstract void showConsole(boolean show);
+
+  /**
+   * @param renderPanel
+   * @param jmolfileio
+   *          - when true will initialise jmol's file IO system (should be false
+   *          in applet context)
+   * @param htmlName
+   * @param documentBase
+   * @param codeBase
+   * @param commandOptions
+   */
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,
+          String htmlName, URL documentBase, URL codeBase,
+          String commandOptions)
   {
+    allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,
+            codeBase, commandOptions, null, null);
+  }
+
+  /**
+   * 
+   * @param renderPanel
+   * @param jmolfileio
+   *          - when true will initialise jmol's file IO system (should be false
+   *          in applet context)
+   * @param htmlName
+   * @param documentBase
+   * @param codeBase
+   * @param commandOptions
+   * @param consolePanel
+   *          - panel to contain Jmol console
+   * @param buttonsToShow
+   *          - buttons to show on the console, in ordr
+   */
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,
+          String htmlName, URL documentBase, URL codeBase,
+          String commandOptions, final Container consolePanel,
+          String buttonsToShow)
+  {
+    if (commandOptions == null)
+    {
+      commandOptions = "";
+    }
     viewer = JmolViewer.allocateViewer(renderPanel,
-            new SmarterJmolAdapter(), htmlName+((Object) this).toString(), documentBase, codeBase,
+            (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
+                    + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);
+
+    console = createJmolConsole(viewer, consolePanel, buttonsToShow);
+    if (consolePanel != null)
+    {
+      consolePanel.addComponentListener(this);
+
+    }
+
   }
 
-  public void setLoadingFromArchive(boolean loadingFromArchive)
+  protected abstract JmolAppConsoleInterface createJmolConsole(
+          JmolViewer viewer2, Container consolePanel, String buttonsToShow);
+
+  protected org.jmol.api.JmolAppConsoleInterface console = null;
+
+  public void componentResized(ComponentEvent e)
   {
-    this.loadingFromArchive = loadingFromArchive;
+
   }
 
-  public boolean isLoadingFromArchive()
+  public void componentMoved(ComponentEvent e)
   {
-    return loadingFromArchive;
+
   }
+
+  public void componentShown(ComponentEvent e)
+  {
+    showConsole(true);
+  }
+
+  public void componentHidden(ComponentEvent e)
+  {
+    showConsole(false);
+  }
+
   public void setBackgroundColour(java.awt.Color col)
   {
     jmolHistory(false);
@@ -1059,4 +1504,158 @@ public abstract class JalviewJmolBinding implements StructureListener,
             + col.getGreen() + "," + col.getBlue() + "];");
     jmolHistory(true);
   }
+
+  /**
+   * add structures and any known sequence associations
+   * 
+   * @returns the pdb entries added to the current set.
+   */
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
+          SequenceI[][] seq, String[][] chns)
+  {
+    int pe = -1;
+    Vector v = new Vector();
+    Vector rtn = new Vector();
+    for (int i = 0; i < pdbentry.length; i++)
+    {
+      v.addElement(pdbentry[i]);
+    }
+    for (int i = 0; i < pdbe.length; i++)
+    {
+      int r = v.indexOf(pdbe[i]);
+      if (r == -1 || r >= pdbentry.length)
+      {
+        rtn.addElement(new int[]
+        { v.size(), i });
+        v.addElement(pdbe[i]);
+      }
+      else
+      {
+        // just make sure the sequence/chain entries are all up to date
+        addSequenceAndChain(r, seq[i], chns[i]);
+      }
+    }
+    pdbe = new PDBEntry[v.size()];
+    v.copyInto(pdbe);
+    pdbentry = pdbe;
+    if (rtn.size() > 0)
+    {
+      // expand the tied seuqence[] and string[] arrays
+      SequenceI[][] sqs = new SequenceI[pdbentry.length][];
+      String[][] sch = new String[pdbentry.length][];
+      System.arraycopy(sequence, 0, sqs, 0, sequence.length);
+      System.arraycopy(chains, 0, sch, 0, this.chains.length);
+      sequence = sqs;
+      chains = sch;
+      pdbe = new PDBEntry[rtn.size()];
+      for (int r = 0; r < pdbe.length; r++)
+      {
+        int[] stri = ((int[]) rtn.elementAt(r));
+        // record the pdb file as a new addition
+        pdbe[r] = pdbentry[stri[0]];
+        // and add the new sequence/chain entries
+        addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
+      }
+    }
+    else
+    {
+      pdbe = null;
+    }
+    return pdbe;
+  }
+
+  public void addSequence(int pe, SequenceI[] seq)
+  {
+    // add sequences to the pe'th pdbentry's seuqence set.
+    addSequenceAndChain(pe, seq, null);
+  }
+
+  private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+  {
+    if (pe < 0 || pe >= pdbentry.length)
+    {
+      throw new Error(MessageManager.formatMessage("error.implementation_error_no_pdbentry_from_index", new String[]{Integer.valueOf(pe).toString()}));
+    }
+    final String nullChain = "TheNullChain";
+    Vector s = new Vector();
+    Vector c = new Vector();
+    if (chains == null)
+    {
+      chains = new String[pdbentry.length][];
+    }
+    if (sequence[pe] != null)
+    {
+      for (int i = 0; i < sequence[pe].length; i++)
+      {
+        s.addElement(sequence[pe][i]);
+        if (chains[pe] != null)
+        {
+          if (i < chains[pe].length)
+          {
+            c.addElement(chains[pe][i]);
+          }
+          else
+          {
+            c.addElement(nullChain);
+          }
+        }
+        else
+        {
+          if (tchain != null && tchain.length > 0)
+          {
+            c.addElement(nullChain);
+          }
+        }
+      }
+    }
+    for (int i = 0; i < seq.length; i++)
+    {
+      if (!s.contains(seq[i]))
+      {
+        s.addElement(seq[i]);
+        if (tchain != null && i < tchain.length)
+        {
+          c.addElement(tchain[i] == null ? nullChain : tchain[i]);
+        }
+      }
+    }
+    SequenceI[] tmp = new SequenceI[s.size()];
+    s.copyInto(tmp);
+    sequence[pe] = tmp;
+    if (c.size() > 0)
+    {
+      String[] tch = new String[c.size()];
+      c.copyInto(tch);
+      for (int i = 0; i < tch.length; i++)
+      {
+        if (tch[i] == nullChain)
+        {
+          tch[i] = null;
+        }
+      }
+      chains[pe] = tch;
+    }
+    else
+    {
+      chains[pe] = null;
+    }
+  }
+
+  /**
+   * 
+   * @param pdbfile
+   * @return text report of alignment between pdbfile and any associated
+   *         alignment sequences
+   */
+  public String printMapping(String pdbfile)
+  {
+    return ssm.printMapping(pdbfile);
+  }
+
+  @Override
+  public void resizeInnerPanel(String data)
+  {
+    // Jalview doesn't honour resize panel requests
+
+  }
 }