X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJalviewJmolBinding.java;h=61926dc32f7025f890a0842dc5f96f5ed39ee905;hb=f001dc68c5066e79837f0785c587043a2976e446;hp=b1b5ce4ecef8620d4db6f19b18c041e069ab53c9;hpb=ab889432b2f2ebea75aca36e814efc42ab50b9ac;p=jalview.git

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index b1b5ce4..61926dc 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -20,35 +20,18 @@
  */
 package jalview.ext.jmol;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.StructureFile;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-
-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.Hashtable;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
+import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javajs.awt.Dimension;
+import javax.swing.SwingUtilities;
 
 import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.api.JmolAppConsoleInterface;
@@ -56,14 +39,31 @@ import org.jmol.api.JmolSelectionListener;
 import org.jmol.api.JmolStatusListener;
 import org.jmol.api.JmolViewer;
 import org.jmol.c.CBK;
-import org.jmol.script.T;
 import org.jmol.viewer.Viewer;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.SequenceRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.ws.dbsources.Pdb;
+import javajs.util.BS;
+
 public abstract class JalviewJmolBinding extends AAStructureBindingModel
-        implements JmolStatusListener, JmolSelectionListener,
-        ComponentListener
-{
-  boolean allChainsSelected = false;
+    implements JmolStatusListener, JmolSelectionListener, ComponentListener {
+  private String lastMessage;
 
   /*
    * when true, try to search the associated datamodel for sequences that are
@@ -71,59 +71,36 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private boolean associateNewStructs = false;
 
-  Vector<String> atomsPicked = new Vector<String>();
-
-  public Vector<String> chainNames;
-
-  Hashtable<String, String> chainFile;
-
-  public String fileLoadingError;
-
-  /*
-   * the default or current model displayed if the model cannot be identified
-   * from the selection message
-   */
-  int frameNo = 0;
-
-  // protected JmolGenericPopup jmolpopup; // not used - remove?
-
-  String lastCommand;
-
-  String lastMessage;
+  private Vector<String> atomsPicked = new Vector<>();
 
-  boolean loadedInline;
+  private String lastCommand;
 
-  /**
-   * current set of model filenames loaded in the Jmol instance
-   */
-  String[] modelFileNames = null;
+  private boolean loadedInline;
 
-  StringBuffer resetLastRes = new StringBuffer();
+  private StringBuffer resetLastRes = new StringBuffer();
 
-  public Viewer viewer;
+  public Viewer jmolViewer;
 
-  public JalviewJmolBinding(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
-  {
-    super(ssm, pdbentry, sequenceIs, chains, protocol);
+  public JalviewJmolBinding(StructureSelectionManager ssm, PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+      DataSourceType protocol) {
+    super(ssm, pdbentry, sequenceIs, protocol);
+    setStructureCommands(new JmolCommands());
     /*
      * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),
-     * "jalviewJmol", ap.av.applet .getDocumentBase(),
-     * ap.av.applet.getCodeBase(), "", this);
+     * "jalviewJmol", ap.av.applet .getDocumentBase(), ap.av.applet.getCodeBase(),
+     * "", this);
      * 
      * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
      */
   }
 
-  public JalviewJmolBinding(StructureSelectionManager ssm,
-          SequenceI[][] seqs, Viewer theViewer)
-  {
+  public JalviewJmolBinding(StructureSelectionManager ssm, SequenceI[][] seqs, Viewer theViewer) {
     super(ssm, seqs);
 
-    viewer = theViewer;
-    viewer.setJmolStatusListener(this);
-    viewer.addSelectionListener(this);
+    jmolViewer = theViewer;
+    jmolViewer.setJmolStatusListener(this);
+    jmolViewer.addSelectionListener(this);
+    setStructureCommands(new JmolCommands());
   }
 
   /**
@@ -132,434 +109,45 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * 
    * @return
    */
-  public String getViewerTitle()
-  {
+  public String getViewerTitle() {
     return getViewerTitle("Jmol", true);
   }
 
-  /**
-   * prepare the view for a given set of models/chains. chainList contains
-   * strings of the form 'pdbfilename:Chaincode'
-   * 
-   * @param chainList
-   *          list of chains to make visible
-   */
-  public void centerViewer(Vector<String> chainList)
-  {
-    StringBuilder cmd = new StringBuilder(128);
-    int mlength, p;
-    for (String lbl : chainList)
-    {
-      mlength = 0;
-      do
-      {
-        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) + " /"
-              + (1 + getModelNum(chainFile.get(lbl))) + " or ");
-    }
-    if (cmd.length() > 0)
-    {
-      cmd.setLength(cmd.length() - 4);
-    }
-    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);
-  }
-
-  public void closeViewer()
-  {
-    // remove listeners for all structures in viewer
-    getSsm().removeStructureViewerListener(this, this.getPdbFile());
-     viewer.dispose();
-    lastCommand = null;
-    viewer = null;
-    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");
-  }
+  private String jmolScript(String script) {
+    Cache.log.debug(">>Jmol>> " + script);
+    String s = jmolViewer.evalStringQuiet(script); // scriptWait(script); BH
+    Cache.log.debug("<<Jmol<< " + s);
 
-  public void colourByCharge()
-  {
-    colourBySequence = false;
-    evalStateCommand("select *;color white;select ASP,GLU;color red;"
-            + "select LYS,ARG;color blue;select CYS;color yellow");
-  }
-
-  /**
-   * superpose the structures associated with sequences in the alignment
-   * according to their corresponding positions.
-   */
-  public void superposeStructures(AlignmentI alignment)
-  {
-    superposeStructures(alignment, -1, 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)
-   */
-  public void superposeStructures(AlignmentI alignment, int refStructure)
-  {
-    superposeStructures(alignment, refStructure, null);
+    return s;
   }
 
-  /**
-   * 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 });
-  }
-
-  /**
-   * Construct and send a command to align structures against a reference
-   * structure, based on one or more sequence alignments
-   * 
-   * @param _alignment
-   *          an array of alignments to process
-   * @param _refStructure
-   *          an array of corresponding reference structures (index into pdb
-   *          file array); if a negative value is passed, the first PDB file
-   *          mapped to an alignment sequence is used as the reference for
-   *          superposition
-   * @param _hiddenCols
-   *          an array of corresponding hidden columns for each alignment
-   */
-  public void superposeStructures(AlignmentI[] _alignment,
-          int[] _refStructure, ColumnSelection[] _hiddenCols)
-  {
-    while (viewer.isScriptExecuting())
-    {
-      try
-      {
-        Thread.sleep(10);
-      } catch (InterruptedException i)
-      {
-      }
-      ;
-    }
-    String[] files = getPdbFile();
-    if (!waitForFileLoad(files))
-    {
-      return;
-    }
-
-    StringBuilder selectioncom = new StringBuilder(256);
-    // 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 = " 0.005 ";
-    }
-    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++)
-    {
-      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;
-      }
-
-      /*
-       * 'matched' array will hold 'true' for visible alignment columns where
-       * all sequences have a residue with a mapping to the PDB structure
-       */
-      boolean matched[] = new boolean[alignment.getWidth()];
-      for (int m = 0; m < matched.length; m++)
-      {
-        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
-      }
-
-      SuperposeData[] structures = new SuperposeData[files.length];
-      for (int f = 0; f < files.length; f++)
-      {
-        structures[f] = new SuperposeData(alignment.getWidth());
-      }
-
-      /*
-       * Calculate the superposable alignment columns ('matched'), and the
-       * corresponding structure residue positions (structures.pdbResNo)
-       */
-      int candidateRefStructure = findSuperposableResidues(alignment,
-              matched, structures);
-      if (refStructure < 0)
-      {
-        /*
-         * If no reference structure was specified, pick the first one that has
-         * a mapping in the alignment
-         */
-        refStructure = candidateRefStructure;
-      }
-
-      String[] selcom = new String[files.length];
-      int nmatched = 0;
-      for (boolean b : matched)
-      {
-        if (b)
-        {
-          nmatched++;
-        }
-      }
-      if (nmatched < 4)
-      {
-        // TODO: bail out here because superposition illdefined?
-      }
-
-      /*
-       * generate select statements to select regions to superimpose structures
-       */
-      {
-        for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-        {
-          String chainCd = ":" + structures[pdbfnum].chain;
-          int lpos = -1;
-          boolean run = false;
-          StringBuilder molsel = new StringBuilder();
-          molsel.append("{");
-          for (int r = 0; r < matched.length; r++)
-          {
-            if (matched[r])
-            {
-              int pdbResNo = structures[pdbfnum].pdbResNo[r];
-              if (lpos != pdbResNo - 1)
-              {
-                // discontinuity
-                if (lpos != -1)
-                {
-                  molsel.append(lpos);
-                  molsel.append(chainCd);
-                  molsel.append("|");
-                }
-                run = false;
-              }
-              else
-              {
-                // continuous run - and lpos >-1
-                if (!run)
-                {
-                  // at the beginning, so add dash
-                  molsel.append(lpos);
-                  molsel.append("-");
-                }
-                run = true;
-              }
-              lpos = pdbResNo;
-            }
-          }
-          /*
-           * add final selection phrase
-           */
-          if (lpos != -1)
-          {
-            molsel.append(lpos);
-            molsel.append(chainCd);
-            molsel.append("}");
-          }
-          if (molsel.length() > 1)
-          {
-            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("|");
-            }
-          }
-          else
-          {
-            selcom[pdbfnum] = null;
-          }
-        }
-      }
-      StringBuilder command = new StringBuilder(256);
-      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(structures[pdbfnum].pdbId);
-        command.append(") against reference (");
-        command.append(structures[refStructure].pdbId);
-        command.append(")\";\ncompare " + nSeconds);
-        command.append("{");
-        command.append(Integer.toString(1 + pdbfnum));
-        command.append(".1} {");
-        command.append(Integer.toString(1 + refStructure));
-        // conformation=1 excludes alternate locations for CA (JAL-1757)
-        command.append(".1} SUBSET {(*.CA | *.P) and conformation=1} ATOMS ");
-
-        // for (int s = 0; s < 2; s++)
-        // {
-        // command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);
-        // }
-        command.append(selcom[pdbfnum]);
-        command.append(selcom[refStructure]);
-        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; ");
-        String cmdString = command.toString();
-        // System.out.println("Superimpose command(s):\n" + cmdString);
-
-        evalStateCommand(cmdString);
-      }
-    }
-    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());
+  @Override
+  public List<String> executeCommand(StructureCommandI command, boolean getReply) {
+    if (command == null) {
+      return null;
     }
-  }
-
-  public void evalStateCommand(String command)
-  {
+    String cmd = command.getCommand();
     jmolHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command))
-    {
-      viewer.evalStringQuiet(command + "\n");
+    if (lastCommand == null || !lastCommand.equals(cmd)) {
+      jmolScript(cmd + "\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(AlignmentViewPanel alignmentv)
-  {
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
-    if (!colourBySequence || !isLoadingFinished())
-    {
-      return;
-    }
-    if (getSsm() == null)
-    {
-      return;
-    }
-    String[] files = getPdbFile();
-
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-    AlignmentI alignment = alignmentv.getAlignment();
-
-    for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
-            files, sr, fr, alignment))
-    {
-      for (String cbyseq : cpdbbyseq.commands)
-      {
-        executeWhenReady(cbyseq);
-      }
-    }
-  }
-
-  /**
-   * @param files
-   * @param sr
-   * @param fr
-   * @param alignment
-   * @return
-   */
-  protected StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
-  {
-    return JmolCommands.getColourBySequenceCommand(getSsm(), files,
-            getSequence(), sr, fr, alignment);
-  }
-
-  /**
-   * @param command
-   */
-  protected void executeWhenReady(String command)
-  {
-    evalStateCommand(command);
+    lastCommand = cmd;
+    return null;
   }
 
-  public void createImage(String file, String type, int quality)
-  {
+  public void createImage(String file, String type, int quality) {
     System.out.println("JMOL CREATE IMAGE");
   }
 
   @Override
-  public String createImage(String fileName, String type,
-          Object textOrBytes, int quality)
-  {
+  public String createImage(String fileName, String type, Object textOrBytes, int quality) {
     System.out.println("JMOL CREATE IMAGE");
     return null;
   }
 
   @Override
-  public String eval(String strEval)
-  {
+  public String eval(String strEval) {
     // System.out.println(strEval);
     // "# 'eval' is implemented only for the applet.";
     return null;
@@ -569,66 +157,16 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   // //////////////////////////
 
   @Override
-  public float[][] functionXY(String functionName, int x, int y)
-  {
+  public float[][] functionXY(String functionName, int x, int y) {
     return null;
   }
 
   @Override
-  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)
-  {
+  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) {
     // TODO Auto-generated method stub
     return null;
   }
 
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (getModelNum(pdbfile) < 0)
-    {
-      return null;
-    }
-    // TODO: verify atomIndex is selecting correct model.
-    // return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
-    int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
-    return new Color(colour);
-  }
-
-  /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  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)
-  {
-    String[] mfn = getPdbFile();
-    if (mfn == null)
-    {
-      return -1;
-    }
-    for (int i = 0; i < mfn.length; i++)
-    {
-      if (mfn[i].equalsIgnoreCase(modelFileName))
-      {
-        return i;
-      }
-    }
-    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 -
@@ -636,67 +174,31 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   private int _modelFileNameMap[];
 
-  // ////////////////////////////////
-  // /StructureListener
   @Override
-  public synchronized String[] getPdbFile()
-  {
-    if (viewer == null)
-    {
+  public synchronized String[] getStructureFiles() {
+    if (jmolViewer == null) {
       return new String[0];
     }
-    if (modelFileNames == null)
-    {
-      String mset[] = new String[viewer.ms.mc];
-      _modelFileNameMap = new int[mset.length];
-      String m = viewer.ms.getModelFileName(0);
-      if (m != null)
-      {
-        mset[0] = m;
-        try
-        {
-          mset[0] = new File(m).getAbsolutePath();
-        } catch (AccessControlException x)
-        {
-          // usually not allowed to do this in applet
-          System.err
-                  .println("jmolBinding: Using local file string from Jmol: "
-                          + m);
-        }
-        if (mset[0].indexOf("/file:") != -1)
-        {
-          // applet path with docroot - discard as format won't match pdbfile
-          mset[0] = m;
+
+    if (modelFileNames == null) {
+      int modelCount = jmolViewer.ms.mc;
+      String filePath = null;
+      List<String> mset = new ArrayList<>();
+      for (int i = 0; i < modelCount; ++i) {
+        /*
+         * defensive check for null as getModelFileName can return null even when model
+         * count ms.mc is > 0
+         */
+        filePath = jmolViewer.ms.getModelFileName(i);
+        if (filePath != null && !mset.contains(filePath)) {
+          mset.add(filePath);
         }
-        _modelFileNameMap[0] = 0; // filename index for first model is always 0.
       }
-      int j = 1;
-      for (int i = 1; i < mset.length; i++)
-      {
-        m = viewer.ms.getModelFileName(i);
-        mset[j] = m;
-        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
-            // 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++;
-        }
+      if (!mset.isEmpty()) {
+        modelFileNames = mset.toArray(new String[mset.size()]);
       }
-      modelFileNames = new String[j];
-      System.arraycopy(mset, 0, modelFileNames, 0, j);
     }
+
     return modelFileNames;
   }
 
@@ -704,28 +206,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * map from string to applet
    */
   @Override
-  public Map<String, Object> getRegistryInfo()
-  {
+  public Map<String, Object> getRegistryInfo() {
     // TODO Auto-generated method stub
     return null;
   }
 
-  /**
-   * returns the current sequenceRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment);
-
   // ///////////////////////////////
   // JmolStatusListener
 
-  public void handlePopupMenu(int x, int y)
-  {
+  public void handlePopupMenu(int x, int y) {
     // jmolpopup.show(x, y);
     // jmolpopup.jpiShow(x, y);
   }
@@ -734,84 +223,52 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * Highlight zero, one or more atoms on the structure
    */
   @Override
-  public void highlightAtoms(List<AtomSpec> atoms)
-  {
-    if (atoms != null)
-    {
-      if (resetLastRes.length() > 0)
-      {
-        viewer.evalStringQuiet(resetLastRes.toString());
+  public void highlightAtoms(List<AtomSpec> atoms) {
+    if (atoms != null) {
+      if (resetLastRes.length() > 0) {
+        jmolScript(resetLastRes.toString());
         resetLastRes.setLength(0);
       }
-      for (AtomSpec atom : atoms)
-      {
-        highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(),
-                atom.getChain(), atom.getPdbFile());
+      for (AtomSpec atom : atoms) {
+        highlightAtom(atom.getAtomIndex(), atom.getPdbResNum(), atom.getChain(), atom.getPdbFile());
       }
     }
   }
 
   // jmol/ssm only
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (modelFileNames == null)
-    {
-      return;
-    }
-
-    // look up file model number for this pdbfile
-    int mdlNum = 0;
-    // may need to adjust for URLencoding here - we don't worry about that yet.
-    while (mdlNum < modelFileNames.length
-            && !pdbfile.equals(modelFileNames[mdlNum]))
-    {
-      mdlNum++;
-    }
-    if (mdlNum == modelFileNames.length)
-    {
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile) {
+    String modelId = getModelIdForFile(pdbfile);
+    if (modelId.isEmpty()) {
       return;
     }
 
     jmolHistory(false);
 
+    StringBuilder selection = new StringBuilder(32);
     StringBuilder cmd = new StringBuilder(64);
-    cmd.append("select " + pdbResNum); // +modelNum
-
-    resetLastRes.append("select " + pdbResNum); // +modelNum
-
-    cmd.append(":");
-    resetLastRes.append(":");
-    if (!chain.equals(" "))
-    {
-      cmd.append(chain);
-      resetLastRes.append(chain);
-    }
-    {
-      cmd.append(" /" + (mdlNum + 1));
-      resetLastRes.append("/" + (mdlNum + 1));
+    selection.append("select ").append(String.valueOf(pdbResNum));
+    selection.append(":");
+    if (!chain.equals(" ")) {
+      selection.append(chain);
     }
-    cmd.append(";wireframe 100;" + cmd.toString() + " and not hetero;");
+    selection.append(" /").append(modelId);
 
-    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + " and not hetero; spacefill 0;");
+    cmd.append(selection).append(";wireframe 100;").append(selection).append(" and not hetero;")
+        .append("spacefill 200;select none");
 
-    cmd.append("spacefill 200;select none");
+    resetLastRes.append(selection).append(";wireframe 0;").append(selection).append(" and not hetero; spacefill 0;");
 
-    viewer.evalStringQuiet(cmd.toString());
+    jmolScript(cmd.toString());
     jmolHistory(true);
-
   }
 
-  boolean debug = true;
+  private boolean debug = true;
 
-  private void jmolHistory(boolean enable)
-  {
-    viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
+  private void jmolHistory(boolean enable) {
+    jmolScript("History " + ((debug || enable) ? "on" : "off"));
   }
 
-  public void loadInline(String string)
-  {
+  public void loadInline(String string) {
     loadedInline = true;
     // TODO: re JAL-623
     // viewer.loadInline(strModel, isAppend);
@@ -821,145 +278,133 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     // 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);
+    jmolViewer.openStringInline(string);
   }
 
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
+  protected void mouseOverStructure(int atomIndex, final String strInfo) {
     int pdbResNum;
     int alocsep = strInfo.indexOf("^");
     int mdlSep = strInfo.indexOf("/");
     int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;
 
-    if (chainSeparator == -1)
-    {
+    if (chainSeparator == -1) {
       chainSeparator = strInfo.indexOf(".");
-      if (mdlSep > -1 && mdlSep < chainSeparator)
-      {
+      if (mdlSep > -1 && mdlSep < chainSeparator) {
         chainSeparator1 = chainSeparator;
         chainSeparator = mdlSep;
       }
     }
     // handle insertion codes
-    if (alocsep != -1)
-    {
-      pdbResNum = Integer.parseInt(strInfo.substring(
-              strInfo.indexOf("]") + 1, alocsep));
+    if (alocsep != -1) {
+      pdbResNum = Integer.parseInt(strInfo.substring(strInfo.indexOf("]") + 1, alocsep));
 
-    }
-    else
-    {
-      pdbResNum = Integer.parseInt(strInfo.substring(
-              strInfo.indexOf("]") + 1, chainSeparator));
+    } else {
+      pdbResNum = Integer.parseInt(strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator));
     }
     String chainId;
 
-    if (strInfo.indexOf(":") > -1)
-    {
-      chainId = strInfo.substring(strInfo.indexOf(":") + 1,
-              strInfo.indexOf("."));
-    }
-    else
-    {
+    if (strInfo.indexOf(":") > -1) {
+      chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo.indexOf("."));
+    } else {
       chainId = " ";
     }
 
-    String pdbfilename = modelFileNames[frameNo]; // default is first or current
-    // model
-    if (mdlSep > -1)
-    {
-      if (chainSeparator1 == -1)
-      {
+    String pdbfilename = modelFileNames[0]; // default is first model
+    if (mdlSep > -1) {
+      if (chainSeparator1 == -1) {
         chainSeparator1 = strInfo.indexOf(".", mdlSep);
       }
-      String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,
-              chainSeparator1) : strInfo.substring(mdlSep + 1);
-      try
-      {
+      String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, chainSeparator1)
+          : strInfo.substring(mdlSep + 1);
+      try {
         // recover PDB filename for the model hovered over.
-        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.ms.getModelFileName(mnumber))
-                  .getAbsolutePath();
-        }
+        int mnumber = Integer.valueOf(mdlId).intValue() - 1;
+        if (_modelFileNameMap != null) {
+          int _mp = _modelFileNameMap.length - 1;
 
-      } catch (Exception e)
-      {
+          while (mnumber < _modelFileNameMap[_mp]) {
+            _mp--;
+          }
+          pdbfilename = modelFileNames[_mp];
+        } else {
+          if (mnumber >= 0 && mnumber < modelFileNames.length) {
+            pdbfilename = modelFileNames[mnumber];
+          }
+
+          if (pdbfilename == null) {
+            pdbfilename = new File(jmolViewer.ms.getModelFileName(mnumber)).getAbsolutePath();
+          }
+        }
+      } catch (Exception e) {
       }
-      ;
-    }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-    {
-      getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
     }
 
-    lastMessage = strInfo;
+    /*
+     * highlight position on alignment(s); if some text is returned, show this as a
+     * second line on the structure hover tooltip
+     */
+    String label = getSsm().mouseOverStructure(pdbResNum, chainId, pdbfilename);
+    if (label != null) {
+      // change comma to pipe separator (newline token for Jmol)
+      label = label.replace(',', '|');
+      StringTokenizer toks = new StringTokenizer(strInfo, " ");
+      StringBuilder sb = new StringBuilder();
+      sb.append("select ").append(String.valueOf(pdbResNum)).append(":").append(chainId).append("/1");
+      sb.append(";set hoverLabel \"").append(toks.nextToken()).append(" ").append(toks.nextToken());
+      sb.append("|").append(label).append("\"");
+      executeCommand(new StructureCommand(sb.toString()), false);
+    }
   }
 
-  public void notifyAtomHovered(int atomIndex, String strInfo, String data)
-  {
-    if (data != null)
-    {
-      System.err.println("Ignoring additional hover info: " + data
-              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
+  public void notifyAtomHovered(int atomIndex, String strInfo, String data) {
+    if (strInfo.equals(lastMessage)) {
+      return;
+    }
+    lastMessage = strInfo;
+    if (data != null) {
+      System.err.println(
+          "Ignoring additional hover info: " + data + " (other info: '" + strInfo + "' pos " + atomIndex + ")");
     }
     mouseOverStructure(atomIndex, strInfo);
   }
 
   /*
    * { if (history != null && strStatus != null &&
-   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
-   * } }
+   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus); }
+   * }
    */
 
-  public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
-  {
+  public void notifyAtomPicked(int atomIndex, String strInfo, String strData) {
     /**
-     * this implements the toggle label behaviour copied from the original
-     * structure viewer, MCView
+     * this implements the toggle label behaviour copied from the original structure
+     * viewer, mc_view
      */
-    if (strData != null)
-    {
+    if (strData != null) {
       System.err.println("Ignoring additional pick data string " + strData);
     }
     int chainSeparator = strInfo.indexOf(":");
     int p = 0;
-    if (chainSeparator == -1)
-    {
+    if (chainSeparator == -1) {
       chainSeparator = strInfo.indexOf(".");
     }
 
-    String picked = strInfo.substring(strInfo.indexOf("]") + 1,
-            chainSeparator);
+    String picked = strInfo.substring(strInfo.indexOf("]") + 1, chainSeparator);
     String mdlString = "";
-    if ((p = strInfo.indexOf(":")) > -1)
-    {
+    if ((p = strInfo.indexOf(":")) > -1) {
       picked += strInfo.substring(p, strInfo.indexOf("."));
     }
 
-    if ((p = strInfo.indexOf("/")) > -1)
-    {
+    if ((p = strInfo.indexOf("/")) > -1) {
       mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
     }
-    picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
-            + mdlString + "))";
+    picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" + mdlString + "))";
     jmolHistory(false);
 
-    if (!atomsPicked.contains(picked))
-    {
-      viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
+    if (!atomsPicked.contains(picked)) {
+      jmolScript("select " + picked + ";label %n %r:%c");
       atomsPicked.addElement(picked);
-    }
-    else
-    {
-      viewer.evalString("select " + picked + ";label off");
+    } else {
+      jmolViewer.evalString("select " + picked + ";label off");
       atomsPicked.removeElement(picked);
     }
     jmolHistory(true);
@@ -974,36 +419,48 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   }
 
   @Override
-  public void notifyCallback(CBK type, Object[] data)
-  {
-    try
-    {
-      switch (type)
-      {
+  public void notifyCallback(CBK type, Object[] data) {
+    /*
+     * ensure processed in AWT thread to avoid risk of deadlocks
+     */
+    SwingUtilities.invokeLater(new Runnable() {
+
+      @Override
+      public void run() {
+        processCallback(type, data);
+      }
+    });
+  }
+
+  /**
+   * Processes one callback notification from Jmol
+   * 
+   * @param type
+   * @param data
+   */
+  protected void processCallback(CBK type, Object[] data) {
+    try {
+      switch (type) {
       case LOADSTRUCT:
-        notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4],
-                ((Integer) data[5]).intValue());
+        notifyFileLoaded((String) data[1], (String) data[2], (String) data[3], (String) data[4],
+            ((Integer) data[5]).intValue());
 
         break;
       case PICK:
-        notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
+        notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
         // also highlight in alignment
+        // deliberate fall through
       case HOVER:
-        notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
+        notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], (String) data[0]);
         break;
       case SCRIPT:
-        notifyScriptTermination((String) data[2],
-                ((Integer) data[3]).intValue());
+        notifyScriptTermination((String) data[2], ((Integer) data[3]).intValue());
         break;
       case ECHO:
         sendConsoleEcho((String) data[1]);
         break;
       case MESSAGE:
-        sendConsoleMessage((data == null) ? ((String) null)
-                : (String) data[1]);
+        sendConsoleMessage((data == null) ? ((String) null) : (String) data[1]);
         break;
       case ERROR:
         // System.err.println("Ignoring error callback.");
@@ -1016,22 +473,18 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
 
       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)
-    {
+    } catch (Exception e) {
       System.err.println("Squashed Jmol callback handler error:");
       e.printStackTrace();
     }
   }
 
   @Override
-  public boolean notifyEnabled(CBK callbackPick)
-  {
-    switch (callbackPick)
-    {
+  public boolean notifyEnabled(CBK callbackPick) {
+    switch (callbackPick) {
     case ECHO:
     case LOADSTRUCT:
     case MEASURE:
@@ -1051,16 +504,13 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   // referrring to new structures.
   private long loadNotifiesHandled = 0;
 
-  public long getLoadNotifiesHandled()
-  {
+  public long getLoadNotifiesHandled() {
     return loadNotifiesHandled;
   }
 
-  public void notifyFileLoaded(String fullPathName, String fileName2,
-          String modelName, String errorMsg, int modelParts)
-  {
-    if (errorMsg != null)
-    {
+  public void notifyFileLoaded(String fullPathName, String fileName2, String modelName, String errorMsg,
+      int modelParts) {
+    if (errorMsg != null) {
       fileLoadingError = errorMsg;
       refreshGUI();
       return;
@@ -1074,37 +524,31 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     fileLoadingError = null;
     String[] oldmodels = modelFileNames;
     modelFileNames = null;
-    chainNames = new Vector<String>();
-    chainFile = new Hashtable<String, String>();
     boolean notifyLoaded = false;
-    String[] modelfilenames = getPdbFile();
+    String[] modelfilenames = getStructureFiles();
+    if (modelfilenames == null) {
+      // Jmol is still loading files!
+      return;
+    }
     // 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++)
-      {
-        for (int n = 0; n < modelfilenames.length; n++)
-        {
-          if (modelfilenames[n] == oldmodels[i])
-          {
+      for (int i = 0; i < oldmodels.length; i++) {
+        for (int n = 0; n < modelfilenames.length; n++) {
+          if (modelfilenames[n] == oldmodels[i]) {
             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++)
-        {
-          if (oldmodels[i] != null)
-          {
+        for (int i = 0; i < oldmodels.length; i++) {
+          if (oldmodels[i] != null) {
             oldmfn[oldm++] = oldmodels[i];
           }
         }
@@ -1114,90 +558,68 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       }
     }
     refreshPdbEntries();
-    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
-    {
+    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) {
       String fileName = modelfilenames[modelnum];
       boolean foundEntry = false;
       StructureFile pdb = null;
       String pdbfile = null;
       // model was probably loaded inline - so check the pdb file hashcode
-      if (loadedInline)
-      {
+      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");
+        pdbfile = jmolViewer.getData("" + (1 + _modelFileNameMap[modelnum]) + ".0", "PDB");
       }
       // search pdbentries and sequences to find correct pdbentry for this
       // model
-      for (int pe = 0; pe < getPdbCount(); pe++)
-      {
+      for (int pe = 0; pe < getPdbCount(); pe++) {
         boolean matches = false;
-        if (fileName == null)
-        {
+        addSequence(pe, getSequence()[pe]);
+        if (fileName == null) {
           if (false)
           // see JAL-623 - need method of matching pasted data up
           {
-            pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    pdbfile, AppletFormatAdapter.PASTE);
+            pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], pdbfile, DataSourceType.PASTE,
+                getIProgressIndicator());
             getPdbEntry(modelnum).setFile("INLINE" + pdb.getId());
             matches = true;
             foundEntry = true;
           }
-        }
-        else
-        {
+        } else {
           File fl = new File(getPdbEntry(pe).getFile());
           matches = fl.equals(new File(fileName));
-          if (matches)
-          {
+          if (matches) {
             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
-            {
-              if (fl.exists())
-              {
-                protocol = AppletFormatAdapter.FILE;
+            DataSourceType protocol = DataSourceType.URL;
+            try {
+              if (fl.exists()) {
+                protocol = DataSourceType.FILE;
               }
-            } catch (Exception e)
-            {
-            } catch (Error e)
-            {
+            } catch (Exception e) {
+            } catch (Error e) {
             }
             // Explicitly map to the filename used by Jmol ;
-            pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe],
-                    fileName, protocol);
+            pdb = getSsm().setMapping(getSequence()[pe], getChains()[pe], fileName, protocol, getIProgressIndicator());
             // pdbentry[pe].getFile(), protocol);
 
           }
         }
-        if (matches)
-        {
-          // add an entry for every chain in the model
-          for (int i = 0; i < pdb.getChains().size(); i++)
-          {
-            String chid = new String(pdb.getId() + ":"
-                    + pdb.getChains().elementAt(i).id);
-            chainFile.put(chid, fileName);
-            chainNames.addElement(chid);
-          }
+        if (matches) {
+          stashFoundChains(pdb, fileName);
           notifyLoaded = true;
         }
       }
 
-      if (!foundEntry && associateNewStructs)
-      {
+      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");
+        String pdbcontent = jmolViewer.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
@@ -1213,19 +635,17 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     // // potential for deadlock here:
     // // jmolpopup.updateComputedMenus();
     // }
-    if (!isLoadingFromArchive())
-    {
-      viewer.evalStringQuiet("model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
+    if (!isLoadingFromArchive()) {
+      jmolScript("model *; select backbone;restrict;cartoon;wireframe off;spacefill off");
     }
     // register ourselves as a listener and notify the gui that it needs to
     // update itself.
     getSsm().addStructureViewerListener(this);
-    if (notifyLoaded)
-    {
+    if (notifyLoaded) {
       FeatureRenderer fr = getFeatureRenderer(null);
-      if (fr != null)
-      {
-        fr.featuresAdded();
+      if (fr != null) {
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av.applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;
@@ -1233,13 +653,15 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     setLoadingFromArchive(false);
   }
 
-  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
-  {
+  protected IProgressIndicator getIProgressIndicator() {
+    return null;
+  }
+
+  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) {
     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
@@ -1249,57 +671,29 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public abstract void sendConsoleEcho(String strEcho); /*
                                                          * { showConsole(true);
                                                          * 
-                                                         * history.append("\n" +
-                                                         * strEcho); }
+                                                         * history.append("\n" + strEcho); }
                                                          */
 
   // /End JmolStatusListener
   // /////////////////////////////
 
   /**
-   * @param strStatus
-   *          status message - usually the response received after a script
-   *          executed
+   * @param strStatus status message - usually the response received after a
+   *                  script executed
    */
   public abstract void sendConsoleMessage(String strStatus);
 
   @Override
-  public void setCallbackFunction(String callbackType,
-          String callbackFunction)
-  {
-    System.err.println("Ignoring set-callback request to associate "
-            + callbackType + " with function " + callbackFunction);
+  public void setCallbackFunction(String callbackType, String callbackFunction) {
+    System.err
+        .println("Ignoring set-callback request to associate " + callbackType + " with function " + callbackFunction);
 
   }
 
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    colourBySequence = false;
-
-    if (cs == null)
-    {
-      return;
-    }
-
-    jmolHistory(false);
-    StringBuilder command = new StringBuilder(128);
-    command.append("select *;color white;");
-    List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
-            false);
-    for (String res : residueSet)
-    {
-      Color col = cs.findColour(res.charAt(0));
-      command.append("select " + res + ";color[" + col.getRed() + ","
-              + col.getGreen() + "," + col.getBlue() + "];");
-    }
-
-    evalStateCommand(command.toString());
-    jmolHistory(true);
-  }
-
-  public void showHelp()
-  {
-    showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");
+  public void showHelp() {
+    showUrl("http://wiki.jmol.org"
+    // BH 2018 "http://jmol.sourceforge.net/docs/JmolUserGuide/"
+        , "jmolHelp");
   }
 
   /**
@@ -1310,93 +704,80 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   public abstract void showUrl(String url, String target);
 
   /**
-   * called when the binding thinks the UI needs to be refreshed after a Jmol
-   * state change. this could be because structures were loaded, or because an
-   * error has occured.
-   */
-  public abstract void refreshGUI();
-
-  /**
    * called to show or hide the associated console window container.
    * 
    * @param show
    */
   public abstract void showConsole(boolean show);
 
+  public static Viewer getJmolData(JmolParser jmolParser) {
+    return (Viewer) JmolViewer.allocateViewer(null, null, null, null, null, "-x -o -n", jmolParser);
+  }
+
   /**
+   * 
+   * 
+   * 
    * @param renderPanel
-   * @param jmolfileio
-   *          - when true will initialise jmol's file IO system (should be false
-   *          in applet context)
+   * @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);
+  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 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
+   * @param consolePanel   - panel to contain Jmol console
+   * @param buttonsToShow  - buttons to show on the console, in order
    */
-  public void allocateViewer(Container renderPanel, boolean jmolfileio,
-          String htmlName, URL documentBase, URL codeBase,
-          String commandOptions, final Container consolePanel,
-          String buttonsToShow)
-  {
-    if (commandOptions == null)
-    {
+  public void allocateViewer(Container renderPanel, boolean jmolfileio, String htmlName, URL documentBase, URL codeBase,
+      String commandOptions, final Container consolePanel, String buttonsToShow) {
+
+    System.err.println("Allocating Jmol Viewer: " + commandOptions);
+
+    if (commandOptions == null) {
       commandOptions = "";
     }
-    viewer = (Viewer) JmolViewer.allocateViewer(renderPanel,
-            (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
-                    + ((Object) this).toString(), documentBase, codeBase,
-            commandOptions, this);
+    jmolViewer = (Viewer) JmolViewer.allocateViewer(renderPanel, (jmolfileio ? new SmarterJmolAdapter() : null),
+        htmlName + ((Object) this).toString(), documentBase, codeBase, commandOptions, this);
 
-    viewer.setJmolStatusListener(this); // extends JmolCallbackListener
+    jmolViewer.setJmolStatusListener(this); // extends JmolCallbackListener
 
-    console = createJmolConsole(consolePanel, buttonsToShow);
-    if (consolePanel != null)
-    {
+    try {
+      console = createJmolConsole(consolePanel, buttonsToShow);
+    } catch (Throwable e) {
+      System.err.println("Could not create Jmol application console. " + e.getMessage());
+      e.printStackTrace();
+    }
+    if (consolePanel != null) {
       consolePanel.addComponentListener(this);
 
     }
 
   }
 
-  protected abstract JmolAppConsoleInterface createJmolConsole(
-          Container consolePanel, String buttonsToShow);
+  protected abstract JmolAppConsoleInterface createJmolConsole(Container consolePanel, String buttonsToShow);
 
-  protected org.jmol.api.JmolAppConsoleInterface console = null;
+  // BH 2018 -- Jmol console is not working due to problems with styled
+  // documents.
 
-  public void setBackgroundColour(java.awt.Color col)
-  {
-    jmolHistory(false);
-    viewer.evalStringQuiet("background [" + col.getRed() + ","
-            + col.getGreen() + "," + col.getBlue() + "];");
-    jmolHistory(true);
-  }
+  protected org.jmol.api.JmolAppConsoleInterface console = null;
 
   @Override
-  public Dimension resizeInnerPanel(String data)
-  {
+  public int[] resizeInnerPanel(String data) {
     // Jalview doesn't honour resize panel requests
     return null;
   }
@@ -1404,17 +785,12 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   /**
    * 
    */
-  protected void closeConsole()
-  {
-    if (console != null)
-    {
-      try
-      {
+  protected void closeConsole() {
+    if (console != null) {
+      try {
         console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
+      } catch (Error e) {
+      } catch (Exception x) {
       }
       ;
       console = null;
@@ -1425,24 +801,21 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * ComponentListener method
    */
   @Override
-  public void componentMoved(ComponentEvent e)
-  {
+  public void componentMoved(ComponentEvent e) {
   }
 
   /**
    * ComponentListener method
    */
   @Override
-  public void componentResized(ComponentEvent e)
-  {
+  public void componentResized(ComponentEvent e) {
   }
 
   /**
    * ComponentListener method
    */
   @Override
-  public void componentShown(ComponentEvent e)
-  {
+  public void componentShown(ComponentEvent e) {
     showConsole(true);
   }
 
@@ -1450,8 +823,57 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    * ComponentListener method
    */
   @Override
-  public void componentHidden(ComponentEvent e)
-  {
+  public void componentHidden(ComponentEvent e) {
     showConsole(false);
   }
+
+  @Override
+  protected String getModelIdForFile(String pdbFile) {
+    if (modelFileNames == null) {
+      return "";
+    }
+    for (int i = 0; i < modelFileNames.length; i++) {
+      if (modelFileNames[i].equalsIgnoreCase(pdbFile)) {
+        return String.valueOf(i + 1);
+      }
+    }
+    return "";
+  }
+
+  @Override
+  protected ViewerType getViewerType() {
+    return ViewerType.JMOL;
+  }
+
+  @Override
+  protected String getModelId(int pdbfnum, String file) {
+    return String.valueOf(pdbfnum + 1);
+  }
+
+  /**
+   * Returns ".spt" - the Jmol session file extension
+   * 
+   * @return
+   * @see https://chemapps.stolaf.edu/jmol/docs/#writemodel
+   */
+  @Override
+  public String getSessionFileExtension() {
+    return ".spt";
+  }
+
+  @Override
+  public void selectionChanged(BS arg0) {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp) {
+    return new jalview.gui.SequenceRenderer(avp.getAlignViewport());
+  }
+
+  @Override
+  public String getHelpURL() {
+    return "http://wiki.jmol.org"; // BH 2018
+  }
 }