separation of jmol script command generation from jmol binding
authorjprocter <Jim Procter>
Thu, 5 May 2011 13:56:53 +0000 (13:56 +0000)
committerjprocter <Jim Procter>
Thu, 5 May 2011 13:56:53 +0000 (13:56 +0000)
src/jalview/ext/jmol/JalviewJmolBinding.java
src/jalview/ext/jmol/JmolCommands.java [new file with mode: 0644]

index 8ea1c5d..8e1ede4 100644 (file)
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * 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.
- * 
- * 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/>.
- */
-package jalview.ext.jmol;
-
-import java.io.File;
-import java.net.URL;
-import java.util.*;
-import java.applet.Applet;
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.JPanel;
-
-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 org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-import org.jmol.viewer.Viewer;
-
-import jalview.schemes.*;
-
-public abstract class JalviewJmolBinding implements StructureListener,
-        JmolStatusListener, SequenceStructureBinding,
-        JmolSelectionListener, ComponentListener
-
-{
-  /**
-   * 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;
-
-  public boolean isFinishedInit()
-  {
-    return finishedInit;
-  }
-
-  public void setFinishedInit(boolean finishedInit)
-  {
-    this.finishedInit = finishedInit;
-  }
-
-  boolean allChainsSelected = false;
-
-  /**
-   * when true, try to search the associated datamodel for sequences that are
-   * associated with any unknown structures in the Jmol view.
-   */
-  private boolean associateNewStructs = false;
-
-  Vector atomsPicked = new Vector();
-
-  public Vector chainNames;
-
-  Hashtable chainFile;
-
-  /**
-   * array of target chains for seuqences - tied to pdbentry and sequence[]
-   */
-  protected String[][] chains;
-
-  boolean colourBySequence = true;
-
-  StringBuffer eval = new StringBuffer();
-
-  public String fileLoadingError;
-
-  /**
-   * the default or current model displayed if the model cannot be identified
-   * from the selection message
-   */
-  int frameNo = 0;
-
-  protected JmolPopup jmolpopup;
-
-  String lastCommand;
-
-  String lastMessage;
-
-  boolean loadedInline;
-
-  /**
-   * current set of model filenames loaded in the Jmol instance
-   */
-  String[] modelFileNames = null;
-
-  public PDBEntry[] pdbentry;
-
-  /**
-   * datasource protocol for access to PDBEntrylatest
-   */
-  String protocol = null;
-
-  StringBuffer resetLastRes = new StringBuffer();
-
-  /**
-   * sequences mapped to each pdbentry
-   */
-  public SequenceI[][] sequence;
-
-  StructureSelectionManager ssm;
-
-  public JmolViewer viewer;
-
-  public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
-          String[][] chains, String protocol)
-  {
-    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(),
-     * ap.av.applet.getCodeBase(), "", this);
-     * 
-     * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);
-     */
-  }
-
-  public JalviewJmolBinding(JmolViewer viewer2)
-  {
-    viewer = viewer2;
-    viewer.setJmolStatusListener(this);
-    viewer.addSelectionListener(this);
-  }
-
-  /**
-   * 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 || sequence[0].length < 1)
-    {
-      return ("Jalview Jmol Window");
-    }
-    // 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)
-    {
-      if (pdbentry[0].getProperty().get("method") != null)
-      {
-        title.append(" Method: ");
-        title.append(pdbentry[0].getProperty().get("method"));
-      }
-      if (pdbentry[0].getProperty().get("chains") != null)
-      {
-        title.append(" Chain:");
-        title.append(pdbentry[0].getProperty().get("chains"));
-      }
-    }
-    return title.toString();
-  }
-
-  /**
-   * 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 chainList)
-  {
-    StringBuffer cmd = new StringBuffer();
-    String lbl;
-    int mlength, p;
-    for (int i = 0, iSize = chainList.size(); i < iSize; i++)
-    {
-      mlength = 0;
-      lbl = (String) chainList.elementAt(i);
-      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((String) chainFile.get(lbl))) + " or ");
-    }
-    if (cmd.length() > 0)
-      cmd.setLength(cmd.length() - 4);
-    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());
-    // and shut down jmol
-    viewer.evalStringQuiet("zap");
-    viewer.setJmolStatusListener(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");
-  }
-
-  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);
-  }
-
-  /**
-   * 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)
-  {
-    String[] files = getPdbFile();
-    StringBuffer selectioncom = new StringBuffer();
-    assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);
-    // 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;
-      }
-      if (refStructure < -1)
-      {
-        refStructure = -1;
-      }
-      StringBuffer command = new StringBuffer();
-
-      boolean matched[] = new boolean[alignment.getWidth()];
-      for (int m = 0; m < matched.length; m++)
-      {
-
-        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
-      }
-
-      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++)
-      {
-        StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
-        if (mapping == null || mapping.length < 1)
-          continue;
-
-        int lastPos = -1;
-        for (int s = 0; s < sequence[pdbfnum].length; s++)
-        {
-          for (int sp, m = 0; m < mapping.length; m++)
-          {
-            if (mapping[m].getSequence() == sequence[pdbfnum][s]
-                    && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
-            {
-              if (refStructure == -1)
-              {
-                refStructure = pdbfnum;
-              }
-              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;
-                }
-
-                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);
-
-                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;
-            }
-          }
-        }
-      }
-      String[] selcom = new String[files.length];
-      int nmatched = 0;
-      // generate select statements to select regions to superimpose structures
-      {
-        for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-        {
-          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("}");
-          }
-          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("|");
-          }
-        }
-      }
-      // TODO: consider bailing if nmatched less than 4 because superposition
-      // not
-      // well defined.
-      // TODO: refactor superposable position search (above) from jmol selection
-      // construction (below)
-      for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-      {
-        if (pdbfnum == refStructure)
-        {
-          continue;
-        }
-        command.append("echo ");
-        command.append("\"Superposing (");
-        command.append(chainNames[pdbfnum]);
-        command.append(") against reference (");
-        command.append(chainNames[refStructure]);
-        command.append(")\";\ncompare ");
-        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(" ROTATE TRANSLATE;\n");
-      }
-      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());
-    }
-    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)
-  {
-    jmolHistory(false);
-    if (lastCommand == null || !lastCommand.equals(command))
-    {
-      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,
-          jalview.api.AlignmentViewPanel alignmentv)
-  {
-    if (!colourBySequence)
-      return;
-    if (ssm == null)
-    {
-      return;
-    }
-    String[] files = getPdbFile();
-
-    SequenceRenderer sr = getSequenceRenderer(alignmentv);
-
-    FeatureRenderer fr = null;
-    if (showFeatures)
-    {
-      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[pdbfnum].length; s++)
-      {
-        for (int sp, m = 0; m < mapping.length; m++)
-        {
-          if (mapping[m].getSequence() == sequence[pdbfnum][s]
-                  && (sp = alignment.findIndex(sequence[pdbfnum][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[pdbfnum][s], r);
-
-              if (showFeatures && fr != null)
-                col = fr.findFeatureColour(col, sequence[pdbfnum][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(command.toString());
-  }
-
-  public boolean isColourBySequence()
-  {
-    return colourBySequence;
-  }
-
-  public void setColourBySequence(boolean colourBySequence)
-  {
-    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");
-  }
-
-  public String createImage(String fileName, String type,
-          Object textOrBytes, int quality)
-  {
-    System.out.println("JMOL CREATE IMAGE");
-    return null;
-  }
-
-  public String eval(String strEval)
-  {
-    // System.out.println(strEval);
-    // "# 'eval' is implemented only for the applet.";
-    return null;
-  }
-
-  // End StructureListener
-  // //////////////////////////
-
-  public float[][] functionXY(String functionName, int x, int y)
-  {
-    return null;
-  }
-
-  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));
-  }
-
-  /**
-   * 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 -
-   * use getPdbFile to get number of unique models.
-   */
-  private int _modelFileNameMap[];
-
-  // ////////////////////////////////
-  // /StructureListener
-  public synchronized String[] getPdbFile()
-  {
-    if (viewer == null)
-    {
-      return new String[0];
-    }
-    if (modelFileNames == null)
-    {
-
-      String mset[] = new String[viewer.getModelCount()];
-      _modelFileNameMap = new int[mset.length];
-      int j = 1;
-      mset[0] = viewer.getModelFileName(0);
-      for (int i = 1; i < mset.length; i++)
-      {
-        mset[j] = viewer.getModelFileName(i);
-        _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;
-  }
-
-  /**
-   * map from string to applet
-   */
-  public Map 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)
-  {
-    jmolpopup.show(x, y);
-  }
-
-  // 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;
-    String fn;
-    // may need to adjust for URLencoding here - we don't worry about that yet.
-    while (mdlNum < modelFileNames.length
-            && !pdbfile.equals(modelFileNames[mdlNum]))
-    {
-      // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);
-      mdlNum++;
-    }
-    if (mdlNum == modelFileNames.length)
-    {
-      return;
-    }
-
-    jmolHistory(false);
-    // if (!pdbfile.equals(pdbentry.getFile()))
-    // return;
-    if (resetLastRes.length() > 0)
-    {
-      viewer.evalStringQuiet(resetLastRes.toString());
-    }
-
-    eval.setLength(0);
-    eval.append("select " + pdbResNum); // +modelNum
-
-    resetLastRes.setLength(0);
-    resetLastRes.append("select " + pdbResNum); // +modelNum
-
-    eval.append(":");
-    resetLastRes.append(":");
-    if (!chain.equals(" "))
-    {
-      eval.append(chain);
-      resetLastRes.append(chain);
-    }
-    {
-      eval.append(" /" + (mdlNum + 1));
-      resetLastRes.append("/" + (mdlNum + 1));
-    }
-    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
-
-    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
-            + " and not hetero; spacefill 0;");
-
-    eval.append("spacefill 200;select none");
-
-    viewer.evalStringQuiet(eval.toString());
-    jmolHistory(true);
-
-  }
-
-  boolean debug = true;
-
-  private void jmolHistory(boolean enable)
-  {
-    viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));
-  }
-
-  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;
-
-    if (chainSeparator == -1)
-    {
-      chainSeparator = strInfo.indexOf(".");
-      if (mdlSep > -1 && mdlSep < chainSeparator)
-      {
-        chainSeparator1 = chainSeparator;
-        chainSeparator = mdlSep;
-      }
-    }
-    // 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("."));
-    else
-    {
-      chainId = " ";
-    }
-
-    String pdbfilename = modelFileNames[frameNo]; // default is first or current
-    // 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
-      {
-        // recover PDB filename for the model hovered over.
-        pdbfilename = viewer
-                .getModelFileName(new Integer(mdlId).intValue() - 1);
-      } catch (Exception e)
-      {
-      }
-      ;
-    }
-    if (lastMessage == null || !lastMessage.equals(strInfo))
-      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);
-
-    lastMessage = strInfo;
-  }
-
-  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 + ")");
-    }
-    mouseOverStructure(atomIndex, strInfo);
-  }
-
-  /*
-   * { if (history != null && strStatus != null &&
-   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);
-   * } }
-   */
-
-  public void notifyAtomPicked(int atomIndex, String strInfo, String strData)
-  {
-    /**
-     * this implements the toggle label behaviour copied from the original
-     * structure viewer, MCView
-     */
-    if (strData != null)
-    {
-      System.err.println("Ignoring additional pick data string " + strData);
-    }
-    int chainSeparator = strInfo.indexOf(":");
-    int p = 0;
-    if (chainSeparator == -1)
-      chainSeparator = strInfo.indexOf(".");
-
-    String picked = strInfo.substring(strInfo.indexOf("]") + 1,
-            chainSeparator);
-    String mdlString = "";
-    if ((p = strInfo.indexOf(":")) > -1)
-      picked += strInfo.substring(p + 1, strInfo.indexOf("."));
-
-    if ((p = strInfo.indexOf("/")) > -1)
-    {
-      mdlString += strInfo.substring(p, strInfo.indexOf(" #"));
-    }
-    picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"
-            + mdlString + "))";
-    jmolHistory(false);
-
-    if (!atomsPicked.contains(picked))
-    {
-      viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");
-      atomsPicked.addElement(picked);
-    }
-    else
-    {
-      viewer.evalString("select " + picked + ";label off");
-      atomsPicked.removeElement(picked);
-    }
-    jmolHistory(true);
-    // TODO: in application this happens
-    //
-    // if (scriptWindow != null)
-    // {
-    // scriptWindow.sendConsoleMessage(strInfo);
-    // scriptWindow.sendConsoleMessage("\n");
-    // }
-
-  }
-
-  public void notifyCallback(int type, Object[] data)
-  {
-    try
-    {
-      switch (type)
-      {
-      case JmolConstants.CALLBACK_LOADSTRUCT:
-        notifyFileLoaded((String) data[1], (String) data[2],
-                (String) data[3], (String) data[4],
-                ((Integer) data[5]).intValue());
-
-        break;
-      case JmolConstants.CALLBACK_PICK:
-        notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],
-                (String) data[0]);
-        // also highlight in alignment
-      case JmolConstants.CALLBACK_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());
-        break;
-      case JmolConstants.CALLBACK_ECHO:
-        sendConsoleEcho((String) data[1]);
-        break;
-      case JmolConstants.CALLBACK_MESSAGE:
-        sendConsoleMessage((data == null) ? ((String) null)
-                : (String) data[1]);
-        break;
-      case JmolConstants.CALLBACK_ERROR:
-        // System.err.println("Ignoring error callback.");
-        break;
-      case JmolConstants.CALLBACK_SYNC:
-      case JmolConstants.CALLBACK_RESIZE:
-        refreshGUI();
-        break;
-      case JmolConstants.CALLBACK_MEASURE:
-
-      case JmolConstants.CALLBACK_CLICK:
-      default:
-        System.err.println("Unhandled callback " + type + " "
-                + data[1].toString());
-        break;
-      }
-    } catch (Exception e)
-    {
-      System.err.println("Squashed Jmol callback handler error:");
-      e.printStackTrace();
-    }
-  }
-
-  public boolean notifyEnabled(int 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:
-      return true;
-    case JmolConstants.CALLBACK_RESIZE:
-    case JmolConstants.CALLBACK_SYNC:
-    case JmolConstants.CALLBACK_CLICK:
-    case JmolConstants.CALLBACK_ANIMFRAME:
-    case JmolConstants.CALLBACK_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;
-      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)
-    {
-      int oldm = 0;
-      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)
-        {
-          oldm++;
-        }
-      }
-      if (oldm > 0)
-      {
-        String[] oldmfn = new String[oldm];
-        oldm = 0;
-        for (int i = 0; i < oldmodels.length; i++)
-        {
-          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.
-        ssm.removeStructureViewerListener(this, oldmfn);
-      }
-    }
-    refreshPdbEntries();
-    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)
-    {
-      String fileName = modelfilenames[modelnum];
-      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 for this
-        // model
-        for (int pe = 0; pe < pdbentry.length; pe++)
-        {
-          boolean matches = false;
-          if (fileName == null)
-          {
-            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;
-            }
-          }
-          else
-          {
-            if (matches = pdbentry[pe].getFile().equals(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
-              {
-                File fl = new java.io.File(pdbentry[pe].getFile());
-                if (fl.exists())
-                {
-                  protocol = AppletFormatAdapter.FILE;
-                }
-              } catch (Exception e)
-              {
-              } catch (Error e)
-              {
-              }
-              ;
-              pdb = ssm.setMapping(sequence[pe], chains[pe],
-                      pdbentry[pe].getFile(), protocol);
-
-            }
-          }
-          if (matches)
-          {
-            pdbentry[pe].setId(pdb.id);
-            // 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, pdbentry[pe].getFile());
-              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
-    if (jmolpopup != null)
-    {
-      // potential for deadlock here:
-      // jmolpopup.updateComputedMenus();
-    }
-    if (!isLoadingFromArchive())
-    {
-      viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");
-    }
-    // register ourselves as a listener and notify the gui that it needs to
-    // update itself.
-    ssm.addStructureViewerListener(this);
-    if (notifyLoaded)
-    {
-      FeatureRenderer fr = getFeatureRenderer(null);
-      if (fr != null)
-      {
-        fr.featuresAdded();
-      }
-      refreshGUI();
-      loadNotifiesHandled++;
-    }
-    setLoadingFromArchive(false);
-  }
-
-  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
-  {
-    notifyAtomPicked(iatom, strMeasure, null);
-  }
-
-  public abstract void notifyScriptTermination(String strStatus,
-          int msWalltime);
-
-  /**
-   * display a message echoed from the jmol viewer
-   * 
-   * @param strEcho
-   */
-  public abstract void sendConsoleEcho(String strEcho); /*
-                                                         * { showConsole(true);
-                                                         * 
-                                                         * history.append("\n" +
-                                                         * strEcho); }
-                                                         */
-
-  // /End JmolStatusListener
-  // /////////////////////////////
-
-  /**
-   * @param strStatus
-   *          status message - usually the response received after a script
-   *          executed
-   */
-  public abstract void sendConsoleMessage(String strStatus);
-
-  public void setCallbackFunction(String callbackType,
-          String callbackFunction)
-  {
-    System.err.println("Ignoring set-callback request to associate "
-            + callbackType + " with function " + callbackFunction);
-
-  }
-
-  /**
-   * function to colour all structures using the given Jalview colourscheme.
-   * This disables the colourBySequence flag but does not record the
-   * colourscheme used for use later.
-   * 
-   * @param cs
-   */
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    colourBySequence = false;
-
-    if (cs == null)
-      return;
-
-    String res;
-    int index;
-    Color col;
-    jmolHistory(false);
-    // TODO: Switch between nucleotide or aa selection expressions
-    Enumeration en = ResidueProperties.aa3Hash.keys();
-    StringBuffer command = new StringBuffer("select *;color white;");
-    while (en.hasMoreElements())
-    {
-      res = en.nextElement().toString();
-      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();
-      if (index > 20)
-        continue;
-
-      col = cs.findColour(ResidueProperties.aa[index].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");
-  }
-
-  /**
-   * open the URL somehow
-   * 
-   * @param target
-   */
-  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);
-
-  /**
-   * @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)
-  {
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE.  See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
+package jalview.ext.jmol;\r
+\r
+import java.io.File;\r
+import java.net.URL;\r
+import java.util.*;\r
+import java.applet.Applet;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import javax.swing.JPanel;\r
+\r
+import jalview.api.AlignmentViewPanel;\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.api.SequenceStructureBinding;\r
+import jalview.datamodel.*;\r
+import jalview.structure.*;\r
+import jalview.io.*;\r
+\r
+import org.jmol.api.*;\r
+import org.jmol.adapter.smarter.SmarterJmolAdapter;\r
+\r
+import org.jmol.popup.*;\r
+import org.jmol.viewer.JmolConstants;\r
+import org.jmol.viewer.Viewer;\r
+\r
+import jalview.schemes.*;\r
+\r
+public abstract class JalviewJmolBinding implements StructureListener,\r
+        JmolStatusListener, SequenceStructureBinding,\r
+        JmolSelectionListener, ComponentListener\r
+\r
+{\r
+  /**\r
+   * set if Jmol state is being restored from some source - instructs binding\r
+   * not to apply default display style when structure set is updated for first\r
+   * time.\r
+   */\r
+  private boolean loadingFromArchive = false;\r
+\r
+  /**\r
+   * state flag used to check if the Jmol viewer's paint method can be called\r
+   */\r
+  private boolean finishedInit = false;\r
+\r
+  public boolean isFinishedInit()\r
+  {\r
+    return finishedInit;\r
+  }\r
+\r
+  public void setFinishedInit(boolean finishedInit)\r
+  {\r
+    this.finishedInit = finishedInit;\r
+  }\r
+\r
+  boolean allChainsSelected = false;\r
+\r
+  /**\r
+   * when true, try to search the associated datamodel for sequences that are\r
+   * associated with any unknown structures in the Jmol view.\r
+   */\r
+  private boolean associateNewStructs = false;\r
+\r
+  Vector atomsPicked = new Vector();\r
+\r
+  public Vector chainNames;\r
+\r
+  Hashtable chainFile;\r
+\r
+  /**\r
+   * array of target chains for seuqences - tied to pdbentry and sequence[]\r
+   */\r
+  protected String[][] chains;\r
+\r
+  boolean colourBySequence = true;\r
+\r
+  StringBuffer eval = new StringBuffer();\r
+\r
+  public String fileLoadingError;\r
+\r
+  /**\r
+   * the default or current model displayed if the model cannot be identified\r
+   * from the selection message\r
+   */\r
+  int frameNo = 0;\r
+\r
+  protected JmolPopup jmolpopup;\r
+\r
+  String lastCommand;\r
+\r
+  String lastMessage;\r
+\r
+  boolean loadedInline;\r
+\r
+  /**\r
+   * current set of model filenames loaded in the Jmol instance\r
+   */\r
+  String[] modelFileNames = null;\r
+\r
+  public PDBEntry[] pdbentry;\r
+\r
+  /**\r
+   * datasource protocol for access to PDBEntrylatest\r
+   */\r
+  String protocol = null;\r
+\r
+  StringBuffer resetLastRes = new StringBuffer();\r
+\r
+  /**\r
+   * sequences mapped to each pdbentry\r
+   */\r
+  public SequenceI[][] sequence;\r
+\r
+  StructureSelectionManager ssm;\r
+\r
+  public JmolViewer viewer;\r
+\r
+  public JalviewJmolBinding(PDBEntry[] pdbentry, SequenceI[][] sequenceIs,\r
+          String[][] chains, String protocol)\r
+  {\r
+    this.sequence = sequenceIs;\r
+    this.chains = chains;\r
+    this.pdbentry = pdbentry;\r
+    this.protocol = protocol;\r
+    if (chains == null)\r
+    {\r
+      this.chains = new String[pdbentry.length][];\r
+    }\r
+    /*\r
+     * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(),\r
+     * "jalviewJmol", ap.av.applet .getDocumentBase(),\r
+     * ap.av.applet.getCodeBase(), "", this);\r
+     * \r
+     * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true);\r
+     */\r
+  }\r
+\r
+  public JalviewJmolBinding(JmolViewer viewer2)\r
+  {\r
+    viewer = viewer2;\r
+    viewer.setJmolStatusListener(this);\r
+    viewer.addSelectionListener(this);\r
+  }\r
+\r
+  /**\r
+   * construct a title string for the viewer window based on the data jalview\r
+   * knows about\r
+   * \r
+   * @return\r
+   */\r
+  public String getViewerTitle()\r
+  {\r
+    if (sequence == null || pdbentry == null || sequence.length < 1\r
+            || pdbentry.length < 1 || sequence[0].length < 1)\r
+    {\r
+      return ("Jalview Jmol Window");\r
+    }\r
+    // TODO: give a more informative title when multiple structures are\r
+    // displayed.\r
+    StringBuffer title = new StringBuffer(sequence[0][0].getName() + ":"\r
+            + pdbentry[0].getId());\r
+\r
+    if (pdbentry[0].getProperty() != null)\r
+    {\r
+      if (pdbentry[0].getProperty().get("method") != null)\r
+      {\r
+        title.append(" Method: ");\r
+        title.append(pdbentry[0].getProperty().get("method"));\r
+      }\r
+      if (pdbentry[0].getProperty().get("chains") != null)\r
+      {\r
+        title.append(" Chain:");\r
+        title.append(pdbentry[0].getProperty().get("chains"));\r
+      }\r
+    }\r
+    return title.toString();\r
+  }\r
+\r
+  /**\r
+   * prepare the view for a given set of models/chains. chainList contains\r
+   * strings of the form 'pdbfilename:Chaincode'\r
+   * \r
+   * @param chainList\r
+   *          list of chains to make visible\r
+   */\r
+  public void centerViewer(Vector chainList)\r
+  {\r
+    StringBuffer cmd = new StringBuffer();\r
+    String lbl;\r
+    int mlength, p;\r
+    for (int i = 0, iSize = chainList.size(); i < iSize; i++)\r
+    {\r
+      mlength = 0;\r
+      lbl = (String) chainList.elementAt(i);\r
+      do\r
+      {\r
+        p = mlength;\r
+        mlength = lbl.indexOf(":", p);\r
+      } while (p < mlength && mlength < (lbl.length() - 2));\r
+      // TODO: lookup each pdb id and recover proper model number for it.\r
+      cmd.append(":" + lbl.substring(mlength + 1) + " /"\r
+              + (1 + getModelNum((String) chainFile.get(lbl))) + " or ");\r
+    }\r
+    if (cmd.length() > 0)\r
+      cmd.setLength(cmd.length() - 4);\r
+    evalStateCommand("select *;restrict " + cmd + ";cartoon;center " + cmd);\r
+  }\r
+\r
+  public void closeViewer()\r
+  {\r
+    viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE);\r
+    // remove listeners for all structures in viewer\r
+    StructureSelectionManager.getStructureSelectionManager()\r
+            .removeStructureViewerListener(this, this.getPdbFile());\r
+    // and shut down jmol\r
+    viewer.evalStringQuiet("zap");\r
+    viewer.setJmolStatusListener(null);\r
+    lastCommand = null;\r
+    viewer = null;\r
+    releaseUIResources();\r
+  }\r
+\r
+  /**\r
+   * called by JalviewJmolbinding after closeViewer is called - release any\r
+   * resources and references so they can be garbage collected.\r
+   */\r
+  protected abstract void releaseUIResources();\r
+\r
+  public void colourByChain()\r
+  {\r
+    colourBySequence = false;\r
+    // TODO: colour by chain should colour each chain distinctly across all\r
+    // visible models\r
+    // TODO: http://issues.jalview.org/browse/JAL-628\r
+    evalStateCommand("select *;color chain");\r
+  }\r
+\r
+  public void colourByCharge()\r
+  {\r
+    colourBySequence = false;\r
+    evalStateCommand("select *;color white;select ASP,GLU;color red;"\r
+            + "select LYS,ARG;color blue;select CYS;color yellow");\r
+  }\r
+\r
+  /**\r
+   * superpose the structures associated with sequences in the alignment\r
+   * according to their corresponding positions.\r
+   */\r
+  public void superposeStructures(AlignmentI alignment)\r
+  {\r
+    superposeStructures(alignment, -1, null);\r
+  }\r
+\r
+  /**\r
+   * superpose the structures associated with sequences in the alignment\r
+   * according to their corresponding positions. ded)\r
+   * \r
+   * @param refStructure\r
+   *          - select which pdb file to use as reference (default is -1 - the\r
+   *          first structure in the alignment)\r
+   */\r
+  public void superposeStructures(AlignmentI alignment, int refStructure)\r
+  {\r
+    superposeStructures(alignment, refStructure, null);\r
+  }\r
+\r
+  /**\r
+   * superpose the structures associated with sequences in the alignment\r
+   * according to their corresponding positions. ded)\r
+   * \r
+   * @param refStructure\r
+   *          - select which pdb file to use as reference (default is -1 - the\r
+   *          first structure in the alignment)\r
+   * @param hiddenCols\r
+   *          TODO\r
+   */\r
+  public void superposeStructures(AlignmentI alignment, int refStructure,\r
+          ColumnSelection hiddenCols)\r
+  {\r
+    superposeStructures(new AlignmentI[]\r
+    { alignment }, new int[]\r
+    { refStructure }, new ColumnSelection[]\r
+    { hiddenCols });\r
+  }\r
+\r
+  public void superposeStructures(AlignmentI[] _alignment,\r
+          int[] _refStructure, ColumnSelection[] _hiddenCols)\r
+  {\r
+    String[] files = getPdbFile();\r
+    StringBuffer selectioncom = new StringBuffer();\r
+    assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length);\r
+    // union of all aligned positions are collected together.\r
+    for (int a = 0; a < _alignment.length; a++)\r
+    {\r
+      int refStructure = _refStructure[a];\r
+      AlignmentI alignment = _alignment[a];\r
+      ColumnSelection hiddenCols = _hiddenCols[a];\r
+      if (a > 0\r
+              && selectioncom.length() > 0\r
+              && !selectioncom.substring(selectioncom.length() - 1).equals(\r
+                      "|"))\r
+      {\r
+        selectioncom.append("|");\r
+      }\r
+      // process this alignment\r
+      if (refStructure >= files.length)\r
+      {\r
+        System.err.println("Invalid reference structure value "\r
+                + refStructure);\r
+        refStructure = -1;\r
+      }\r
+      if (refStructure < -1)\r
+      {\r
+        refStructure = -1;\r
+      }\r
+      StringBuffer command = new StringBuffer();\r
+\r
+      boolean matched[] = new boolean[alignment.getWidth()];\r
+      for (int m = 0; m < matched.length; m++)\r
+      {\r
+\r
+        matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;\r
+      }\r
+\r
+      int commonrpositions[][] = new int[files.length][alignment.getWidth()];\r
+      String isel[] = new String[files.length];\r
+      // reference structure - all others are superposed in it\r
+      String[] targetC = new String[files.length];\r
+      String[] chainNames = new String[files.length];\r
+      for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+      {\r
+        StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
+\r
+        if (mapping == null || mapping.length < 1)\r
+          continue;\r
+\r
+        int lastPos = -1;\r
+        for (int s = 0; s < sequence[pdbfnum].length; s++)\r
+        {\r
+          for (int sp, m = 0; m < mapping.length; m++)\r
+          {\r
+            if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
+                    && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
+            {\r
+              if (refStructure == -1)\r
+              {\r
+                refStructure = pdbfnum;\r
+              }\r
+              SequenceI asp = alignment.getSequenceAt(sp);\r
+              for (int r = 0; r < matched.length; r++)\r
+              {\r
+                if (!matched[r])\r
+                {\r
+                  continue;\r
+                }\r
+                matched[r] = false; // assume this is not a good site\r
+                if (r >= asp.getLength())\r
+                {\r
+                  continue;\r
+                }\r
+\r
+                if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
+                {\r
+                  // no mapping to gaps in sequence\r
+                  continue;\r
+                }\r
+                int t = asp.findPosition(r); // sequence position\r
+                int apos = mapping[m].getAtomNum(t);\r
+                int pos = mapping[m].getPDBResNum(t);\r
+\r
+                if (pos < 1 || pos == lastPos)\r
+                {\r
+                  // can't align unmapped sequence\r
+                  continue;\r
+                }\r
+                matched[r] = true; // this is a good ite\r
+                lastPos = pos;\r
+                // just record this residue position\r
+                commonrpositions[pdbfnum][r] = pos;\r
+              }\r
+              // create model selection suffix\r
+              isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1";\r
+              if (mapping[m].getChain() == null\r
+                      || mapping[m].getChain().trim().length() == 0)\r
+              {\r
+                targetC[pdbfnum] = "";\r
+              }\r
+              else\r
+              {\r
+                targetC[pdbfnum] = ":" + mapping[m].getChain();\r
+              }\r
+              chainNames[pdbfnum] = mapping[m].getPdbId()\r
+                      + targetC[pdbfnum];\r
+              // move on to next pdb file\r
+              s = sequence[pdbfnum].length;\r
+              break;\r
+            }\r
+          }\r
+        }\r
+      }\r
+      String[] selcom = new String[files.length];\r
+      int nmatched = 0;\r
+      // generate select statements to select regions to superimpose structures\r
+      {\r
+        for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+        {\r
+          String chainCd = targetC[pdbfnum];\r
+          int lpos = -1;\r
+          boolean run = false;\r
+          StringBuffer molsel = new StringBuffer();\r
+          molsel.append("{");\r
+          for (int r = 0; r < matched.length; r++)\r
+          {\r
+            if (matched[r])\r
+            {\r
+              if (pdbfnum == 0)\r
+              {\r
+                nmatched++;\r
+              }\r
+              if (lpos != commonrpositions[pdbfnum][r] - 1)\r
+              {\r
+                // discontinuity\r
+                if (lpos != -1)\r
+                {\r
+                  molsel.append(lpos);\r
+                  molsel.append(chainCd);\r
+                  // molsel.append("} {");\r
+                  molsel.append("|");\r
+                }\r
+              }\r
+              else\r
+              {\r
+                // continuous run - and lpos >-1\r
+                if (!run)\r
+                {\r
+                  // at the beginning, so add dash\r
+                  molsel.append(lpos);\r
+                  molsel.append("-");\r
+                }\r
+                run = true;\r
+              }\r
+              lpos = commonrpositions[pdbfnum][r];\r
+              // molsel.append(lpos);\r
+            }\r
+          }\r
+          // add final selection phrase\r
+          if (lpos != -1)\r
+          {\r
+            molsel.append(lpos);\r
+            molsel.append(chainCd);\r
+            molsel.append("}");\r
+          }\r
+          selcom[pdbfnum] = molsel.toString();\r
+          selectioncom.append("((");\r
+          selectioncom.append(selcom[pdbfnum].substring(1,\r
+                  selcom[pdbfnum].length() - 1));\r
+          selectioncom.append(" )& ");\r
+          selectioncom.append(pdbfnum + 1);\r
+          selectioncom.append(".1)");\r
+          if (pdbfnum < files.length - 1)\r
+          {\r
+            selectioncom.append("|");\r
+          }\r
+        }\r
+      }\r
+      // TODO: consider bailing if nmatched less than 4 because superposition\r
+      // not\r
+      // well defined.\r
+      // TODO: refactor superposable position search (above) from jmol selection\r
+      // construction (below)\r
+      for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+      {\r
+        if (pdbfnum == refStructure)\r
+        {\r
+          continue;\r
+        }\r
+        command.append("echo ");\r
+        command.append("\"Superposing (");\r
+        command.append(chainNames[pdbfnum]);\r
+        command.append(") against reference (");\r
+        command.append(chainNames[refStructure]);\r
+        command.append(")\";\ncompare ");\r
+        command.append("{");\r
+        command.append(1 + pdbfnum);\r
+        command.append(".1} {");\r
+        command.append(1 + refStructure);\r
+        command.append(".1} SUBSET {*.CA | *.P} ATOMS ");\r
+\r
+        // form the matched pair strings\r
+        String sep = "";\r
+        for (int s = 0; s < 2; s++)\r
+        {\r
+          command.append(selcom[(s == 0 ? pdbfnum : refStructure)]);\r
+        }\r
+        command.append(" ROTATE TRANSLATE;\n");\r
+      }\r
+      System.out.println("Select regions:\n" + selectioncom.toString());\r
+      evalStateCommand("select *; cartoons off; backbone; select ("\r
+              + selectioncom.toString() + "); cartoons; ");\r
+      // selcom.append("; ribbons; ");\r
+      System.out.println("Superimpose command(s):\n" + command.toString());\r
+\r
+      evalStateCommand(command.toString());\r
+    }\r
+    if (selectioncom.length() > 0)\r
+    {// finally, mark all regions that were superposed.\r
+      if (selectioncom.substring(selectioncom.length() - 1).equals("|"))\r
+      {\r
+        selectioncom.setLength(selectioncom.length() - 1);\r
+      }\r
+      System.out.println("Select regions:\n" + selectioncom.toString());\r
+      evalStateCommand("select *; cartoons off; backbone; select ("\r
+              + selectioncom.toString() + "); cartoons; ");\r
+      // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());\r
+    }\r
+  }\r
+\r
+  public void evalStateCommand(String command)\r
+  {\r
+    jmolHistory(false);\r
+    if (lastCommand == null || !lastCommand.equals(command))\r
+    {\r
+      viewer.evalStringQuiet(command + "\n");\r
+    }\r
+    jmolHistory(true);\r
+    lastCommand = command;\r
+  }\r
+\r
+  /**\r
+   * colour any structures associated with sequences in the given alignment\r
+   * using the getFeatureRenderer() and getSequenceRenderer() renderers but only\r
+   * if colourBySequence is enabled.\r
+   */\r
+  public void colourBySequence(boolean showFeatures,\r
+          jalview.api.AlignmentViewPanel alignmentv)\r
+  {\r
+    if (!colourBySequence)\r
+      return;\r
+    if (ssm == null)\r
+    {\r
+      return;\r
+    }\r
+    String[] files = getPdbFile();\r
+\r
+    SequenceRenderer sr = getSequenceRenderer(alignmentv);\r
+\r
+    FeatureRenderer fr = null;\r
+    if (showFeatures)\r
+    {\r
+      fr = getFeatureRenderer(alignmentv);\r
+    }\r
+    AlignmentI alignment = alignmentv.getAlignment();\r
+\r
+    for (String cbyseq : JmolCommands.getColourBySequenceCommand(ssm, files, sequence, sr, fr, alignment)) {\r
+      evalStateCommand(cbyseq);\r
+    }\r
+  }\r
+  \r
+  public boolean isColourBySequence()\r
+  {\r
+    return colourBySequence;\r
+  }\r
+\r
+  public void setColourBySequence(boolean colourBySequence)\r
+  {\r
+    this.colourBySequence = colourBySequence;\r
+  }\r
+\r
+  public void createImage(String file, String type, int quality)\r
+  {\r
+    System.out.println("JMOL CREATE IMAGE");\r
+  }\r
+\r
+  public String createImage(String fileName, String type,\r
+          Object textOrBytes, int quality)\r
+  {\r
+    System.out.println("JMOL CREATE IMAGE");\r
+    return null;\r
+  }\r
+\r
+  public String eval(String strEval)\r
+  {\r
+    // System.out.println(strEval);\r
+    // "# 'eval' is implemented only for the applet.";\r
+    return null;\r
+  }\r
+\r
+  // End StructureListener\r
+  // //////////////////////////\r
+\r
+  public float[][] functionXY(String functionName, int x, int y)\r
+  {\r
+    return null;\r
+  }\r
+\r
+  public float[][][] functionXYZ(String functionName, int nx, int ny, int nz)\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return null;\r
+  }\r
+\r
+  public Color getColour(int atomIndex, int pdbResNum, String chain,\r
+          String pdbfile)\r
+  {\r
+    if (getModelNum(pdbfile) < 0)\r
+      return null;\r
+    // TODO: verify atomIndex is selecting correct model.\r
+    return new Color(viewer.getAtomArgb(atomIndex));\r
+  }\r
+\r
+  /**\r
+   * returns the current featureRenderer that should be used to colour the\r
+   * structures\r
+   * \r
+   * @param alignment\r
+   * \r
+   * @return\r
+   */\r
+  public abstract FeatureRenderer getFeatureRenderer(\r
+          AlignmentViewPanel alignment);\r
+\r
+  /**\r
+   * instruct the Jalview binding to update the pdbentries vector if necessary\r
+   * prior to matching the jmol view's contents to the list of structure files\r
+   * Jalview knows about.\r
+   */\r
+  public abstract void refreshPdbEntries();\r
+\r
+  private int getModelNum(String modelFileName)\r
+  {\r
+    String[] mfn = getPdbFile();\r
+    if (mfn == null)\r
+    {\r
+      return -1;\r
+    }\r
+    for (int i = 0; i < mfn.length; i++)\r
+    {\r
+      if (mfn[i].equalsIgnoreCase(modelFileName))\r
+        return i;\r
+    }\r
+    return -1;\r
+  }\r
+\r
+  /**\r
+   * map between index of model filename returned from getPdbFile and the first\r
+   * index of models from this file in the viewer. Note - this is not trimmed -\r
+   * use getPdbFile to get number of unique models.\r
+   */\r
+  private int _modelFileNameMap[];\r
+\r
+  // ////////////////////////////////\r
+  // /StructureListener\r
+  public synchronized String[] getPdbFile()\r
+  {\r
+    if (viewer == null)\r
+    {\r
+      return new String[0];\r
+    }\r
+    if (modelFileNames == null)\r
+    {\r
+\r
+      String mset[] = new String[viewer.getModelCount()];\r
+      _modelFileNameMap = new int[mset.length];\r
+      int j = 1;\r
+      mset[0] = viewer.getModelFileName(0);\r
+      for (int i = 1; i < mset.length; i++)\r
+      {\r
+        mset[j] = viewer.getModelFileName(i);\r
+        _modelFileNameMap[j] = i; // record the model index for the filename\r
+        // skip any additional models in the same file (NMR structures)\r
+        if ((mset[j] == null ? mset[j] != mset[j - 1]\r
+                : (mset[j - 1] == null || !mset[j].equals(mset[j - 1]))))\r
+        {\r
+          j++;\r
+        }\r
+      }\r
+      modelFileNames = new String[j];\r
+      System.arraycopy(mset, 0, modelFileNames, 0, j);\r
+    }\r
+    return modelFileNames;\r
+  }\r
+\r
+  /**\r
+   * map from string to applet\r
+   */\r
+  public Map getRegistryInfo()\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return null;\r
+  }\r
+\r
+  /**\r
+   * returns the current sequenceRenderer that should be used to colour the\r
+   * structures\r
+   * \r
+   * @param alignment\r
+   * \r
+   * @return\r
+   */\r
+  public abstract SequenceRenderer getSequenceRenderer(\r
+          AlignmentViewPanel alignment);\r
+\r
+  // ///////////////////////////////\r
+  // JmolStatusListener\r
+\r
+  public void handlePopupMenu(int x, int y)\r
+  {\r
+    jmolpopup.show(x, y);\r
+  }\r
+\r
+  // jmol/ssm only\r
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,\r
+          String pdbfile)\r
+  {\r
+    if (modelFileNames == null)\r
+    {\r
+      return;\r
+    }\r
+\r
+    // look up file model number for this pdbfile\r
+    int mdlNum = 0;\r
+    String fn;\r
+    // may need to adjust for URLencoding here - we don't worry about that yet.\r
+    while (mdlNum < modelFileNames.length\r
+            && !pdbfile.equals(modelFileNames[mdlNum]))\r
+    {\r
+      // System.out.println("nomatch:"+pdbfile+"\nmodelfn:"+fn);\r
+      mdlNum++;\r
+    }\r
+    if (mdlNum == modelFileNames.length)\r
+    {\r
+      return;\r
+    }\r
+\r
+    jmolHistory(false);\r
+    // if (!pdbfile.equals(pdbentry.getFile()))\r
+    // return;\r
+    if (resetLastRes.length() > 0)\r
+    {\r
+      viewer.evalStringQuiet(resetLastRes.toString());\r
+    }\r
+\r
+    eval.setLength(0);\r
+    eval.append("select " + pdbResNum); // +modelNum\r
+\r
+    resetLastRes.setLength(0);\r
+    resetLastRes.append("select " + pdbResNum); // +modelNum\r
+\r
+    eval.append(":");\r
+    resetLastRes.append(":");\r
+    if (!chain.equals(" "))\r
+    {\r
+      eval.append(chain);\r
+      resetLastRes.append(chain);\r
+    }\r
+    {\r
+      eval.append(" /" + (mdlNum + 1));\r
+      resetLastRes.append("/" + (mdlNum + 1));\r
+    }\r
+    eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");\r
+\r
+    resetLastRes.append(";wireframe 0;" + resetLastRes.toString()\r
+            + " and not hetero; spacefill 0;");\r
+\r
+    eval.append("spacefill 200;select none");\r
+\r
+    viewer.evalStringQuiet(eval.toString());\r
+    jmolHistory(true);\r
+\r
+  }\r
+\r
+  boolean debug = true;\r
+\r
+  private void jmolHistory(boolean enable)\r
+  {\r
+    viewer.evalStringQuiet("History " + ((debug || enable) ? "on" : "off"));\r
+  }\r
+\r
+  public void loadInline(String string)\r
+  {\r
+    loadedInline = true;\r
+    // TODO: re JAL-623\r
+    // viewer.loadInline(strModel, isAppend);\r
+    // could do this:\r
+    // construct fake fullPathName and fileName so we can identify the file\r
+    // later.\r
+    // Then, construct pass a reader for the string to Jmol.\r
+    // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName,\r
+    // fileName, null, reader, false, null, null, 0);\r
+    viewer.openStringInline(string);\r
+  }\r
+\r
+  public void mouseOverStructure(int atomIndex, String strInfo)\r
+  {\r
+    int pdbResNum;\r
+    int alocsep = strInfo.indexOf("^");\r
+    int mdlSep = strInfo.indexOf("/");\r
+    int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1;\r
+\r
+    if (chainSeparator == -1)\r
+    {\r
+      chainSeparator = strInfo.indexOf(".");\r
+      if (mdlSep > -1 && mdlSep < chainSeparator)\r
+      {\r
+        chainSeparator1 = chainSeparator;\r
+        chainSeparator = mdlSep;\r
+      }\r
+    }\r
+    // handle insertion codes\r
+    if (alocsep != -1)\r
+    {\r
+      pdbResNum = Integer.parseInt(strInfo.substring(\r
+              strInfo.indexOf("]") + 1, alocsep));\r
+\r
+    }\r
+    else\r
+    {\r
+      pdbResNum = Integer.parseInt(strInfo.substring(\r
+              strInfo.indexOf("]") + 1, chainSeparator));\r
+    }\r
+    String chainId;\r
+\r
+    if (strInfo.indexOf(":") > -1)\r
+      chainId = strInfo.substring(strInfo.indexOf(":") + 1,\r
+              strInfo.indexOf("."));\r
+    else\r
+    {\r
+      chainId = " ";\r
+    }\r
+\r
+    String pdbfilename = modelFileNames[frameNo]; // default is first or current\r
+    // model\r
+    if (mdlSep > -1)\r
+    {\r
+      if (chainSeparator1 == -1)\r
+      {\r
+        chainSeparator1 = strInfo.indexOf(".", mdlSep);\r
+      }\r
+      String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1,\r
+              chainSeparator1) : strInfo.substring(mdlSep + 1);\r
+      try\r
+      {\r
+        // recover PDB filename for the model hovered over.\r
+        pdbfilename = viewer\r
+                .getModelFileName(new Integer(mdlId).intValue() - 1);\r
+      } catch (Exception e)\r
+      {\r
+      }\r
+      ;\r
+    }\r
+    if (lastMessage == null || !lastMessage.equals(strInfo))\r
+      ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename);\r
+\r
+    lastMessage = strInfo;\r
+  }\r
+\r
+  public void notifyAtomHovered(int atomIndex, String strInfo, String data)\r
+  {\r
+    if (data != null)\r
+    {\r
+      System.err.println("Ignoring additional hover info: " + data\r
+              + " (other info: '" + strInfo + "' pos " + atomIndex + ")");\r
+    }\r
+    mouseOverStructure(atomIndex, strInfo);\r
+  }\r
+\r
+  /*\r
+   * { if (history != null && strStatus != null &&\r
+   * !strStatus.equals("Script completed")) { history.append("\n" + strStatus);\r
+   * } }\r
+   */\r
+\r
+  public void notifyAtomPicked(int atomIndex, String strInfo, String strData)\r
+  {\r
+    /**\r
+     * this implements the toggle label behaviour copied from the original\r
+     * structure viewer, MCView\r
+     */\r
+    if (strData != null)\r
+    {\r
+      System.err.println("Ignoring additional pick data string " + strData);\r
+    }\r
+    int chainSeparator = strInfo.indexOf(":");\r
+    int p = 0;\r
+    if (chainSeparator == -1)\r
+      chainSeparator = strInfo.indexOf(".");\r
+\r
+    String picked = strInfo.substring(strInfo.indexOf("]") + 1,\r
+            chainSeparator);\r
+    String mdlString = "";\r
+    if ((p = strInfo.indexOf(":")) > -1)\r
+      picked += strInfo.substring(p + 1, strInfo.indexOf("."));\r
+\r
+    if ((p = strInfo.indexOf("/")) > -1)\r
+    {\r
+      mdlString += strInfo.substring(p, strInfo.indexOf(" #"));\r
+    }\r
+    picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P"\r
+            + mdlString + "))";\r
+    jmolHistory(false);\r
+\r
+    if (!atomsPicked.contains(picked))\r
+    {\r
+      viewer.evalStringQuiet("select " + picked + ";label %n %r:%c");\r
+      atomsPicked.addElement(picked);\r
+    }\r
+    else\r
+    {\r
+      viewer.evalString("select " + picked + ";label off");\r
+      atomsPicked.removeElement(picked);\r
+    }\r
+    jmolHistory(true);\r
+    // TODO: in application this happens\r
+    //\r
+    // if (scriptWindow != null)\r
+    // {\r
+    // scriptWindow.sendConsoleMessage(strInfo);\r
+    // scriptWindow.sendConsoleMessage("\n");\r
+    // }\r
+\r
+  }\r
+\r
+  public void notifyCallback(int type, Object[] data)\r
+  {\r
+    try\r
+    {\r
+      switch (type)\r
+      {\r
+      case JmolConstants.CALLBACK_LOADSTRUCT:\r
+        notifyFileLoaded((String) data[1], (String) data[2],\r
+                (String) data[3], (String) data[4],\r
+                ((Integer) data[5]).intValue());\r
+\r
+        break;\r
+      case JmolConstants.CALLBACK_PICK:\r
+        notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1],\r
+                (String) data[0]);\r
+        // also highlight in alignment\r
+      case JmolConstants.CALLBACK_HOVER:\r
+        notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1],\r
+                (String) data[0]);\r
+        break;\r
+      case JmolConstants.CALLBACK_SCRIPT:\r
+        notifyScriptTermination((String) data[2],\r
+                ((Integer) data[3]).intValue());\r
+        break;\r
+      case JmolConstants.CALLBACK_ECHO:\r
+        sendConsoleEcho((String) data[1]);\r
+        break;\r
+      case JmolConstants.CALLBACK_MESSAGE:\r
+        sendConsoleMessage((data == null) ? ((String) null)\r
+                : (String) data[1]);\r
+        break;\r
+      case JmolConstants.CALLBACK_ERROR:\r
+        // System.err.println("Ignoring error callback.");\r
+        break;\r
+      case JmolConstants.CALLBACK_SYNC:\r
+      case JmolConstants.CALLBACK_RESIZE:\r
+        refreshGUI();\r
+        break;\r
+      case JmolConstants.CALLBACK_MEASURE:\r
+\r
+      case JmolConstants.CALLBACK_CLICK:\r
+      default:\r
+        System.err.println("Unhandled callback " + type + " "\r
+                + data[1].toString());\r
+        break;\r
+      }\r
+    } catch (Exception e)\r
+    {\r
+      System.err.println("Squashed Jmol callback handler error:");\r
+      e.printStackTrace();\r
+    }\r
+  }\r
+\r
+  public boolean notifyEnabled(int callbackPick)\r
+  {\r
+    switch (callbackPick)\r
+    {\r
+    case JmolConstants.CALLBACK_ECHO:\r
+    case JmolConstants.CALLBACK_LOADSTRUCT:\r
+    case JmolConstants.CALLBACK_MEASURE:\r
+    case JmolConstants.CALLBACK_MESSAGE:\r
+    case JmolConstants.CALLBACK_PICK:\r
+    case JmolConstants.CALLBACK_SCRIPT:\r
+    case JmolConstants.CALLBACK_HOVER:\r
+    case JmolConstants.CALLBACK_ERROR:\r
+      return true;\r
+    case JmolConstants.CALLBACK_RESIZE:\r
+    case JmolConstants.CALLBACK_SYNC:\r
+    case JmolConstants.CALLBACK_CLICK:\r
+    case JmolConstants.CALLBACK_ANIMFRAME:\r
+    case JmolConstants.CALLBACK_MINIMIZATION:\r
+    }\r
+    return false;\r
+  }\r
+\r
+  // incremented every time a load notification is successfully handled -\r
+  // lightweight mechanism for other threads to detect when they can start\r
+  // referrring to new structures.\r
+  private long loadNotifiesHandled = 0;\r
+\r
+  public long getLoadNotifiesHandled()\r
+  {\r
+    return loadNotifiesHandled;\r
+  }\r
+\r
+  public void notifyFileLoaded(String fullPathName, String fileName2,\r
+          String modelName, String errorMsg, int modelParts)\r
+  {\r
+    if (errorMsg != null)\r
+    {\r
+      fileLoadingError = errorMsg;\r
+      refreshGUI();\r
+      return;\r
+    }\r
+    // TODO: deal sensibly with models loaded inLine:\r
+    // modelName will be null, as will fullPathName.\r
+\r
+    // the rest of this routine ignores the arguments, and simply interrogates\r
+    // the Jmol view to find out what structures it contains, and adds them to\r
+    // the structure selection manager.\r
+    fileLoadingError = null;\r
+    String[] oldmodels = modelFileNames;\r
+    modelFileNames = null;\r
+    chainNames = new Vector();\r
+    chainFile = new Hashtable();\r
+    boolean notifyLoaded = false;\r
+    String[] modelfilenames = getPdbFile();\r
+    ssm = StructureSelectionManager.getStructureSelectionManager();\r
+    // first check if we've lost any structures\r
+    if (oldmodels != null && oldmodels.length > 0)\r
+    {\r
+      int oldm = 0;\r
+      for (int i = 0; i < oldmodels.length; i++)\r
+      {\r
+        for (int n = 0; n < modelfilenames.length; n++)\r
+        {\r
+          if (modelfilenames[n] == oldmodels[i])\r
+          {\r
+            oldmodels[i] = null;\r
+            break;\r
+          }\r
+        }\r
+        if (oldmodels[i] != null)\r
+        {\r
+          oldm++;\r
+        }\r
+      }\r
+      if (oldm > 0)\r
+      {\r
+        String[] oldmfn = new String[oldm];\r
+        oldm = 0;\r
+        for (int i = 0; i < oldmodels.length; i++)\r
+        {\r
+          if (oldmodels[i] != null)\r
+          {\r
+            oldmfn[oldm++] = oldmodels[i];\r
+          }\r
+        }\r
+        // deregister the Jmol instance for these structures - we'll add\r
+        // ourselves again at the end for the current structure set.\r
+        ssm.removeStructureViewerListener(this, oldmfn);\r
+      }\r
+    }\r
+    refreshPdbEntries();\r
+    for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++)\r
+    {\r
+      String fileName = modelfilenames[modelnum];\r
+      boolean foundEntry = false;\r
+      MCview.PDBfile pdb = null;\r
+      String pdbfile = null, pdbfhash = null;\r
+      // model was probably loaded inline - so check the pdb file hashcode\r
+      if (loadedInline)\r
+      {\r
+        // calculate essential attributes for the pdb data imported inline.\r
+        // prolly need to resolve modelnumber properly - for now just use our\r
+        // 'best guess'\r
+        pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])\r
+                + ".0", "PDB");\r
+        pdbfhash = "" + pdbfile.hashCode();\r
+      }\r
+      if (pdbentry != null)\r
+      {\r
+        // search pdbentries and sequences to find correct pdbentry for this\r
+        // model\r
+        for (int pe = 0; pe < pdbentry.length; pe++)\r
+        {\r
+          boolean matches = false;\r
+          if (fileName == null)\r
+          {\r
+            if (false)\r
+            // see JAL-623 - need method of matching pasted data up\r
+            {\r
+              pdb = ssm.setMapping(sequence[pe], chains[pe], pdbfile,\r
+                      AppletFormatAdapter.PASTE);\r
+              pdbentry[modelnum].setFile("INLINE" + pdb.id);\r
+              matches = true;\r
+              foundEntry = true;\r
+            }\r
+          }\r
+          else\r
+          {\r
+            if (matches = pdbentry[pe].getFile().equals(fileName))\r
+            {\r
+              foundEntry = true;\r
+              // TODO: Jmol can in principle retrieve from CLASSLOADER but\r
+              // this\r
+              // needs\r
+              // to be tested. See mantis bug\r
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605\r
+              String protocol = AppletFormatAdapter.URL;\r
+              try\r
+              {\r
+                File fl = new java.io.File(pdbentry[pe].getFile());\r
+                if (fl.exists())\r
+                {\r
+                  protocol = AppletFormatAdapter.FILE;\r
+                }\r
+              } catch (Exception e)\r
+              {\r
+              } catch (Error e)\r
+              {\r
+              }\r
+              ;\r
+              pdb = ssm.setMapping(sequence[pe], chains[pe],\r
+                      pdbentry[pe].getFile(), protocol);\r
+\r
+            }\r
+          }\r
+          if (matches)\r
+          {\r
+            pdbentry[pe].setId(pdb.id);\r
+            // add an entry for every chain in the model\r
+            for (int i = 0; i < pdb.chains.size(); i++)\r
+            {\r
+              String chid = new String(pdb.id + ":"\r
+                      + ((MCview.PDBChain) pdb.chains.elementAt(i)).id);\r
+              chainFile.put(chid, pdbentry[pe].getFile());\r
+              chainNames.addElement(chid);\r
+            }\r
+            notifyLoaded = true;\r
+          }\r
+        }\r
+      }\r
+      if (!foundEntry && associateNewStructs)\r
+      {\r
+        // this is a foreign pdb file that jalview doesn't know about - add\r
+        // it to the dataset and try to find a home - either on a matching\r
+        // sequence or as a new sequence.\r
+        String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1",\r
+                "PDB");\r
+        // parse pdb file into a chain, etc.\r
+        // locate best match for pdb in associated views and add mapping to\r
+        // ssm\r
+        // if properly registered then\r
+        notifyLoaded = true;\r
+\r
+      }\r
+    }\r
+    // FILE LOADED OK\r
+    // so finally, update the jmol bits and pieces\r
+    if (jmolpopup != null)\r
+    {\r
+      // potential for deadlock here:\r
+      // jmolpopup.updateComputedMenus();\r
+    }\r
+    if (!isLoadingFromArchive())\r
+    {\r
+      viewer.evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off");\r
+    }\r
+    // register ourselves as a listener and notify the gui that it needs to\r
+    // update itself.\r
+    ssm.addStructureViewerListener(this);\r
+    if (notifyLoaded)\r
+    {\r
+      FeatureRenderer fr = getFeatureRenderer(null);\r
+      if (fr != null)\r
+      {\r
+        fr.featuresAdded();\r
+      }\r
+      refreshGUI();\r
+      loadNotifiesHandled++;\r
+    }\r
+    setLoadingFromArchive(false);\r
+  }\r
+\r
+  public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)\r
+  {\r
+    notifyAtomPicked(iatom, strMeasure, null);\r
+  }\r
+\r
+  public abstract void notifyScriptTermination(String strStatus,\r
+          int msWalltime);\r
+\r
+  /**\r
+   * display a message echoed from the jmol viewer\r
+   * \r
+   * @param strEcho\r
+   */\r
+  public abstract void sendConsoleEcho(String strEcho); /*\r
+                                                         * { showConsole(true);\r
+                                                         * \r
+                                                         * history.append("\n" +\r
+                                                         * strEcho); }\r
+                                                         */\r
+\r
+  // /End JmolStatusListener\r
+  // /////////////////////////////\r
+\r
+  /**\r
+   * @param strStatus\r
+   *          status message - usually the response received after a script\r
+   *          executed\r
+   */\r
+  public abstract void sendConsoleMessage(String strStatus);\r
+\r
+  public void setCallbackFunction(String callbackType,\r
+          String callbackFunction)\r
+  {\r
+    System.err.println("Ignoring set-callback request to associate "\r
+            + callbackType + " with function " + callbackFunction);\r
+\r
+  }\r
+\r
+  public void setJalviewColourScheme(ColourSchemeI cs)\r
+  {\r
+    colourBySequence = false;\r
+\r
+    if (cs == null)\r
+      return;\r
+\r
+    String res;\r
+    int index;\r
+    Color col;\r
+    jmolHistory(false);\r
+    // TODO: Switch between nucleotide or aa selection expressions\r
+    Enumeration en = ResidueProperties.aa3Hash.keys();\r
+    StringBuffer command = new StringBuffer("select *;color white;");\r
+    while (en.hasMoreElements())\r
+    {\r
+      res = en.nextElement().toString();\r
+      index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue();\r
+      if (index > 20)\r
+        continue;\r
+\r
+      col = cs.findColour(ResidueProperties.aa[index].charAt(0));\r
+\r
+      command.append("select " + res + ";color[" + col.getRed() + ","\r
+              + col.getGreen() + "," + col.getBlue() + "];");\r
+    }\r
+\r
+    evalStateCommand(command.toString());\r
+    jmolHistory(true);\r
+  }\r
+\r
+  public void showHelp()\r
+  {\r
+    showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp");\r
+  }\r
+\r
+  /**\r
+   * open the URL somehow\r
+   * \r
+   * @param target\r
+   */\r
+  public abstract void showUrl(String url, String target);\r
+\r
+  /**\r
+   * called when the binding thinks the UI needs to be refreshed after a Jmol\r
+   * state change. this could be because structures were loaded, or because an\r
+   * error has occured.\r
+   */\r
+  public abstract void refreshGUI();\r
+\r
+  /**\r
+   * called to show or hide the associated console window container.\r
+   * \r
+   * @param show\r
+   */\r
+  public abstract void showConsole(boolean show);\r
+\r
+  /**\r
+   * @param renderPanel\r
+   * @param jmolfileio\r
+   *          - when true will initialise jmol's file IO system (should be false\r
+   *          in applet context)\r
+   * @param htmlName\r
+   * @param documentBase\r
+   * @param codeBase\r
+   * @param commandOptions\r
+   */\r
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,\r
+          String htmlName, URL documentBase, URL codeBase,\r
+          String commandOptions)\r
+  {\r
+    allocateViewer(renderPanel, jmolfileio, htmlName, documentBase,\r
+            codeBase, commandOptions, null, null);\r
+  }\r
+\r
+  /**\r
+   * \r
+   * @param renderPanel\r
+   * @param jmolfileio\r
+   *          - when true will initialise jmol's file IO system (should be false\r
+   *          in applet context)\r
+   * @param htmlName\r
+   * @param documentBase\r
+   * @param codeBase\r
+   * @param commandOptions\r
+   * @param consolePanel\r
+   *          - panel to contain Jmol console\r
+   * @param buttonsToShow\r
+   *          - buttons to show on the console, in ordr\r
+   */\r
+  public void allocateViewer(Container renderPanel, boolean jmolfileio,\r
+          String htmlName, URL documentBase, URL codeBase,\r
+          String commandOptions, final Container consolePanel,\r
+          String buttonsToShow)\r
+  {\r
     if (commandOptions==null) {
       commandOptions="";
     }
-    viewer = JmolViewer.allocateViewer(renderPanel,
-            (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
-                    + ((Object) this).toString(), documentBase, codeBase,
-            commandOptions, this);
-
-    console = createJmolConsole(viewer, consolePanel, buttonsToShow);
-    if (consolePanel != null)
-    {
-      consolePanel.addComponentListener(this);
-
-    }
-
-  }
-
-  protected abstract JmolAppConsoleInterface createJmolConsole(
-          JmolViewer viewer2, Container consolePanel, String buttonsToShow);
-
-  protected org.jmol.api.JmolAppConsoleInterface console = null;
-
-  public void componentResized(ComponentEvent e)
-  {
-
-  }
-
-  public void componentMoved(ComponentEvent e)
-  {
-
-  }
-
-  public void componentShown(ComponentEvent e)
-  {
-    showConsole(true);
-  }
-
-  public void componentHidden(ComponentEvent e)
-  {
-    showConsole(false);
-  }
-
-  public void setLoadingFromArchive(boolean loadingFromArchive)
-  {
-    this.loadingFromArchive = loadingFromArchive;
-  }
-
-  public boolean isLoadingFromArchive()
-  {
-    return loadingFromArchive;
-  }
-
-  public void setBackgroundColour(java.awt.Color col)
-  {
-    jmolHistory(false);
-    viewer.evalStringQuiet("background [" + col.getRed() + ","
-            + 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(
-              "Implementation error - no corresponding pdbentry (for index "
-                      + pe + ") to add sequences mappings to");
-    }
-    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;
-    }
-  }
-}
+    viewer = JmolViewer.allocateViewer(renderPanel,\r
+            (jmolfileio ? new SmarterJmolAdapter() : null), htmlName\r
+                    + ((Object) this).toString(), documentBase, codeBase,\r
+            commandOptions, this);\r
+\r
+    console = createJmolConsole(viewer, consolePanel, buttonsToShow);\r
+    if (consolePanel != null)\r
+    {\r
+      consolePanel.addComponentListener(this);\r
+\r
+    }\r
+\r
+  }\r
+\r
+  protected abstract JmolAppConsoleInterface createJmolConsole(\r
+          JmolViewer viewer2, Container consolePanel, String buttonsToShow);\r
+\r
+  protected org.jmol.api.JmolAppConsoleInterface console = null;\r
+\r
+  public void componentResized(ComponentEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void componentMoved(ComponentEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void componentShown(ComponentEvent e)\r
+  {\r
+    showConsole(true);\r
+  }\r
+\r
+  public void componentHidden(ComponentEvent e)\r
+  {\r
+    showConsole(false);\r
+  }\r
+\r
+  public void setLoadingFromArchive(boolean loadingFromArchive)\r
+  {\r
+    this.loadingFromArchive = loadingFromArchive;\r
+  }\r
+\r
+  public boolean isLoadingFromArchive()\r
+  {\r
+    return loadingFromArchive;\r
+  }\r
+\r
+  public void setBackgroundColour(java.awt.Color col)\r
+  {\r
+    jmolHistory(false);\r
+    viewer.evalStringQuiet("background [" + col.getRed() + ","\r
+            + col.getGreen() + "," + col.getBlue() + "];");\r
+    jmolHistory(true);\r
+  }\r
+\r
+  /**\r
+   * add structures and any known sequence associations\r
+   * \r
+   * @returns the pdb entries added to the current set.\r
+   */\r
+  public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,\r
+          SequenceI[][] seq, String[][] chns)\r
+  {\r
+    int pe = -1;\r
+    Vector v = new Vector();\r
+    Vector rtn = new Vector();\r
+    for (int i = 0; i < pdbentry.length; i++)\r
+    {\r
+      v.addElement(pdbentry[i]);\r
+    }\r
+    for (int i = 0; i < pdbe.length; i++)\r
+    {\r
+      int r = v.indexOf(pdbe[i]);\r
+      if (r == -1 || r >= pdbentry.length)\r
+      {\r
+        rtn.addElement(new int[]\r
+        { v.size(), i });\r
+        v.addElement(pdbe[i]);\r
+      }\r
+      else\r
+      {\r
+        // just make sure the sequence/chain entries are all up to date\r
+        addSequenceAndChain(r, seq[i], chns[i]);\r
+      }\r
+    }\r
+    pdbe = new PDBEntry[v.size()];\r
+    v.copyInto(pdbe);\r
+    pdbentry = pdbe;\r
+    if (rtn.size() > 0)\r
+    {\r
+      // expand the tied seuqence[] and string[] arrays\r
+      SequenceI[][] sqs = new SequenceI[pdbentry.length][];\r
+      String[][] sch = new String[pdbentry.length][];\r
+      System.arraycopy(sequence, 0, sqs, 0, sequence.length);\r
+      System.arraycopy(chains, 0, sch, 0, this.chains.length);\r
+      sequence = sqs;\r
+      chains = sch;\r
+      pdbe = new PDBEntry[rtn.size()];\r
+      for (int r = 0; r < pdbe.length; r++)\r
+      {\r
+        int[] stri = ((int[]) rtn.elementAt(r));\r
+        // record the pdb file as a new addition\r
+        pdbe[r] = pdbentry[stri[0]];\r
+        // and add the new sequence/chain entries\r
+        addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);\r
+      }\r
+    }\r
+    else\r
+    {\r
+      pdbe = null;\r
+    }\r
+    return pdbe;\r
+  }\r
+\r
+  public void addSequence(int pe, SequenceI[] seq)\r
+  {\r
+    // add sequences to the pe'th pdbentry's seuqence set.\r
+    addSequenceAndChain(pe, seq, null);\r
+  }\r
+\r
+  private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)\r
+  {\r
+    if (pe < 0 || pe >= pdbentry.length)\r
+    {\r
+      throw new Error(\r
+              "Implementation error - no corresponding pdbentry (for index "\r
+                      + pe + ") to add sequences mappings to");\r
+    }\r
+    final String nullChain = "TheNullChain";\r
+    Vector s = new Vector();\r
+    Vector c = new Vector();\r
+    if (chains == null)\r
+    {\r
+      chains = new String[pdbentry.length][];\r
+    }\r
+    if (sequence[pe] != null)\r
+    {\r
+      for (int i = 0; i < sequence[pe].length; i++)\r
+      {\r
+        s.addElement(sequence[pe][i]);\r
+        if (chains[pe] != null)\r
+        {\r
+          if (i < chains[pe].length)\r
+          {\r
+            c.addElement(chains[pe][i]);\r
+          }\r
+          else\r
+          {\r
+            c.addElement(nullChain);\r
+          }\r
+        }\r
+        else\r
+        {\r
+          if (tchain != null && tchain.length > 0)\r
+          {\r
+            c.addElement(nullChain);\r
+          }\r
+        }\r
+      }\r
+    }\r
+    for (int i = 0; i < seq.length; i++)\r
+    {\r
+      if (!s.contains(seq[i]))\r
+      {\r
+        s.addElement(seq[i]);\r
+        if (tchain != null && i < tchain.length)\r
+        {\r
+          c.addElement(tchain[i] == null ? nullChain : tchain[i]);\r
+        }\r
+      }\r
+    }\r
+    SequenceI[] tmp = new SequenceI[s.size()];\r
+    s.copyInto(tmp);\r
+    sequence[pe] = tmp;\r
+    if (c.size() > 0)\r
+    {\r
+      String[] tch = new String[c.size()];\r
+      c.copyInto(tch);\r
+      for (int i = 0; i < tch.length; i++)\r
+      {\r
+        if (tch[i] == nullChain)\r
+        {\r
+          tch[i] = null;\r
+        }\r
+      }\r
+      chains[pe] = tch;\r
+    }\r
+    else\r
+    {\r
+      chains[pe] = null;\r
+    }\r
+  }\r
+}\r
diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
new file mode 100644 (file)
index 0000000..acf27f6
--- /dev/null
@@ -0,0 +1,135 @@
+/**\r
+ * \r
+ */\r
+package jalview.ext.jmol;\r
+\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.structure.StructureMapping;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.util.Comparison;\r
+\r
+import java.awt.Color;\r
+import java.util.ArrayList;\r
+\r
+/**\r
+ * Routines for generating Jmol commands for Jalview/Jmol binding\r
+ * @author JimP\r
+ *\r
+ */\r
+public class JmolCommands\r
+{\r
+\r
+  /**\r
+   * Jmol utility which constructs the commands to colour chains by the given alignment\r
+   * \r
+   */\r
+  public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
+  {\r
+    ArrayList<String> str = new ArrayList<String>();\r
+    StringBuffer command = new StringBuffer();\r
+  \r
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)\r
+    {\r
+      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);\r
+  \r
+      if (mapping == null || mapping.length < 1)\r
+        continue;\r
+  \r
+      int lastPos = -1;\r
+      for (int s = 0; s < sequence[pdbfnum].length; s++)\r
+      {\r
+        for (int sp, m = 0; m < mapping.length; m++)\r
+        {\r
+          if (mapping[m].getSequence() == sequence[pdbfnum][s]\r
+                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)\r
+          {\r
+            SequenceI asp = alignment.getSequenceAt(sp);\r
+            for (int r = 0; r < asp.getLength(); r++)\r
+            {\r
+              // no mapping to gaps in sequence\r
+              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))\r
+              {\r
+                continue;\r
+              }\r
+              int pos = mapping[m].getPDBResNum(asp.findPosition(r));\r
+  \r
+              if (pos < 1 || pos == lastPos)\r
+                continue;\r
+  \r
+              lastPos = pos;\r
+  \r
+              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);\r
+  \r
+              if (fr != null)\r
+                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);\r
+              String newSelcom = (mapping[m].getChain() != " " ? ":"\r
+                      + mapping[m].getChain() : "")\r
+                      + "/"\r
+                      + (pdbfnum + 1)\r
+                      + ".1"\r
+                      + ";color["\r
+                      + col.getRed()\r
+                      + ","\r
+                      + col.getGreen()\r
+                      + ","\r
+                      + col.getBlue() + "]";\r
+              if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))\r
+              {\r
+                command = JmolCommands.condenseCommand(command, pos);\r
+                continue;\r
+              }\r
+              // TODO: deal with case when buffer is too large for Jmol to parse\r
+              // - execute command and flush\r
+  \r
+              command.append(";");\r
+              if (command.length()>51200)\r
+              {\r
+                // add another chunk\r
+                str.add(command.toString());\r
+                command.setLength(0);\r
+              }\r
+              command.append("select " + pos);\r
+              command.append(newSelcom);\r
+            }\r
+            break;\r
+          }\r
+        }\r
+      }\r
+    }\r
+    return str.toArray(new String[str.size()]);\r
+  }\r
+\r
+  public static StringBuffer condenseCommand(StringBuffer command, int pos)\r
+  {\r
+  \r
+    // work back to last 'select'\r
+    int p=command.length(),q=p;\r
+    do {\r
+      p-=6;\r
+      if (p<1) { p=0; };\r
+    } while ((q=command.indexOf("select",p))==-1 && p>0);\r
+    \r
+    StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r
+  \r
+    command =  command.delete(0,q+7);\r
+  \r
+    String start;\r
+  \r
+    if (command.indexOf("-") > -1)\r
+    {\r
+      start = command.substring(0, command.indexOf("-"));\r
+    }\r
+    else\r
+    {\r
+      start = command.substring(0, command.indexOf(":"));\r
+    }\r
+  \r
+    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));\r
+  \r
+    return sb;\r
+  }\r
+\r
+}\r