improved javascript callback execution thread and provided 'large string' asynchronou...
authorjprocter <Jim Procter>
Thu, 5 May 2011 14:01:26 +0000 (14:01 +0000)
committerjprocter <Jim Procter>
Thu, 5 May 2011 14:01:26 +0000 (14:01 +0000)
src/jalview/bin/JalviewLite.java
src/jalview/javascript/JSFunctionExec.java
src/jalview/javascript/MouseOverStructureListener.java

index 1801eb1..8e22a1a 100755 (executable)
-/*
- * 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.bin;
-
-import jalview.appletgui.AlignFrame;
-import jalview.appletgui.EmbmenuFrame;
-import jalview.appletgui.FeatureSettings;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.AnnotationFile;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.FileParse;
-import jalview.io.IdentifyFile;
-import jalview.io.JnetAnnotationMaker;
-import jalview.javascript.JSFunctionExec;
-import jalview.javascript.JsCallBack;
-import jalview.structure.SelectionListener;
-import jalview.structure.StructureSelectionManager;
-
-import java.applet.Applet;
-import java.awt.Button;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Font;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import netscape.javascript.JSObject;
-
-/**
- * Jalview Applet. Runs in Java 1.18 runtime
- * 
- * @author $author$
- * @version $Revision$
- */
-public class JalviewLite extends Applet
-{
-
-  // /////////////////////////////////////////
-  // The following public methods maybe called
-  // externally, eg via javascript in HTML page
-  /**
-   * @return String list of selected sequence IDs, each terminated by the
-   *         'boolean not' character (""+0x00AC) or (&#172;)
-   */
-  public String getSelectedSequences()
-  {
-    return getSelectedSequencesFrom(getDefaultTargetFrame());
-  }
-
-  /**
-   * @param sep
-   *          separator string or null for default
-   * @return String list of selected sequence IDs, each terminated by given
-   *         separator string
-   */
-  public String getSelectedSequences(String sep)
-  {
-    return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
-  }
-
-  /**
-   * @param alf
-   *          alignframe containing selection
-   * @return String list of selected sequence IDs, each terminated by current
-   *         default separator sequence
-   * 
-   */
-  public String getSelectedSequencesFrom(AlignFrame alf)
-  {
-    return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
-  }
-
-  /**
-   * get list of selected sequence IDs separated by given separator
-   * 
-   * @param alf
-   *          window containing selection
-   * @param sep
-   *          separator string to use - default is 'boolean not'
-   * @return String list of selected sequence IDs, each terminated by the given
-   *         separator
-   */
-  public String getSelectedSequencesFrom(AlignFrame alf, String sep)
-  {
-    StringBuffer result = new StringBuffer("");
-    if (sep == null || sep.length() == 0)
-    {
-      sep = separator; // "+0x00AC;
-    }
-    if (alf.viewport.getSelectionGroup() != null)
-    {
-      SequenceI[] seqs = alf.viewport.getSelectionGroup()
-              .getSequencesInOrder(alf.viewport.getAlignment());
-
-      for (int i = 0; i < seqs.length; i++)
-      {
-        result.append(seqs[i].getName());
-        result.append(sep);
-      }
-    }
-
-    return result.toString();
-  }
-
-  /**
-   * 
-   * @param sequenceId
-   *          id of sequence to highlight
-   * @param position
-   *          integer position [ tobe implemented or range ] on sequence
-   * @param alignedPosition
-   *          true/false/empty string - indicate if position is an alignment
-   *          column or unaligned sequence position
-   */
-  public void highlight(String sequenceId, String position,
-          String alignedPosition)
-  {
-    highlightIn(getDefaultTargetFrame(), sequenceId, position,
-            alignedPosition);
-  }
-
-  /**
-   * 
-   * @param sequenceId
-   *          id of sequence to highlight
-   * @param position
-   *          integer position [ tobe implemented or range ] on sequence
-   * @param alignedPosition
-   *          false, blank or something else - indicate if position is an
-   *          alignment column or unaligned sequence position
-   */
-  public void highlightIn(AlignFrame alf, String sequenceId,
-          String position, String alignedPosition)
-  {
-    // TODO: could try to highlight in all alignments if alf==null
-    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
-            alf.viewport.getAlignment().getSequencesArray());
-    SequenceI sq = matcher.findIdMatch(sequenceId);
-    if (sq != null)
-    {
-      int pos, apos = -1;
-      try
-      {
-        apos = new Integer(position).intValue();
-        apos--;
-      } catch (NumberFormatException ex)
-      {
-        return;
-      }
-      // use vamsas listener to broadcast to all listeners in scope
-      if (alignedPosition != null
-              && (alignedPosition.trim().length() == 0 || alignedPosition
-                      .toLowerCase().indexOf("false") > -1))
-      {
-        StructureSelectionManager.getStructureSelectionManager()
-                .mouseOverVamsasSequence(sq, sq.findIndex(apos), null);
-      }
-      else
-      {
-        StructureSelectionManager.getStructureSelectionManager()
-                .mouseOverVamsasSequence(sq, apos, null);
-      }
-
-    }
-  }
-
-  /**
-   * select regions of the currrent alignment frame
-   * 
-   * @param sequenceIds
-   *          String separated list of sequence ids or empty string
-   * @param columns
-   *          String separated list { column range or column, ..} or empty
-   *          string
-   */
-  public void select(String sequenceIds, String columns)
-  {
-    selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
-  }
-
-  /**
-   * select regions of the currrent alignment frame
-   * 
-   * @param toselect
-   *          String separated list { column range, seq1...seqn sequence ids }
-   * @param sep
-   *          separator between toselect fields
-   */
-  public void select(String sequenceIds, String columns, String sep)
-  {
-    selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
-  }
-
-  /**
-   * select regions of the given alignment frame
-   * 
-   * @param alf
-   * @param toselect
-   *          String separated list { column range, seq1...seqn sequence ids }
-   * @param sep
-   *          separator between toselect fields
-   */
-  public void selectIn(AlignFrame alf, String sequenceIds, String columns)
-  {
-    selectIn(alf, sequenceIds, columns, separator);
-  }
-
-  /**
-   * select regions of the given alignment frame
-   * 
-   * @param alf
-   * @param toselect
-   *          String separated list { column range, seq1...seqn sequence ids }
-   * @param sep
-   *          separator between toselect fields
-   */
-  public void selectIn(AlignFrame alf, String sequenceIds, String columns,
-          String sep)
-  {
-    if (sep == null || sep.length() == 0)
-    {
-      sep = separator;
-    }
-    else
-    {
-      if (debug)
-      {
-        System.err.println("Selecting region using separator string '"
-                + separator + "'");
-      }
-    }
-    // deparse fields
-    String[] ids = separatorListToArray(sequenceIds, sep);
-    String[] cols = separatorListToArray(columns, sep);
-    SequenceGroup sel = new SequenceGroup();
-    ColumnSelection csel = new ColumnSelection();
-    AlignmentI al = alf.viewport.getAlignment();
-    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
-            alf.viewport.getAlignment().getSequencesArray());
-    int start = 0, end = al.getWidth(), alw = al.getWidth();
-    boolean seqsfound = true;
-    if (ids != null && ids.length > 0)
-    {
-      seqsfound = false;
-      for (int i = 0; i < ids.length; i++)
-      {
-        if (ids[i].trim().length() == 0)
-        {
-          continue;
-        }
-        SequenceI sq = matcher.findIdMatch(ids[i]);
-        if (sq != null)
-        {
-          seqsfound = true;
-          sel.addSequence(sq, false);
-        }
-      }
-    }
-    boolean inseqpos = false;
-    if (cols != null && cols.length > 0)
-    {
-      boolean seset = false;
-      for (int i = 0; i < cols.length; i++)
-      {
-        String cl = cols[i].trim();
-        if (cl.length() == 0)
-        {
-          continue;
-        }
-        int p;
-        if ((p = cl.indexOf("-")) > -1)
-        {
-          int from = -1, to = -1;
-          try
-          {
-            from = new Integer(cl.substring(0, p)).intValue();
-            from--;
-          } catch (NumberFormatException ex)
-          {
-            System.err
-                    .println("ERROR: Couldn't parse first integer in range element column selection string '"
-                            + cl + "' - format is 'from-to'");
-            return;
-          }
-          try
-          {
-            to = new Integer(cl.substring(p + 1)).intValue();
-            to--;
-          } catch (NumberFormatException ex)
-          {
-            System.err
-                    .println("ERROR: Couldn't parse second integer in range element column selection string '"
-                            + cl + "' - format is 'from-to'");
-            return;
-          }
-          if (from >= 0 && to >= 0)
-          {
-            // valid range
-            if (from < to)
-            {
-              int t = to;
-              to = from;
-              to = t;
-            }
-            if (!seset)
-            {
-              start = from;
-              end = to;
-              seset = true;
-            }
-            else
-            {
-              // comment to prevent range extension
-              if (start > from)
-              {
-                start = from;
-              }
-              if (end < to)
-              {
-                end = to;
-              }
-            }
-            for (int r = from; r <= to; r++)
-            {
-              if (r >= 0 && r < alw)
-              {
-                csel.addElement(r);
-              }
-            }
-            if (debug)
-            {
-              System.err.println("Range '" + cl + "' deparsed as [" + from
-                      + "," + to + "]");
-            }
-          }
-          else
-          {
-            System.err.println("ERROR: Invalid Range '" + cl
-                    + "' deparsed as [" + from + "," + to + "]");
-          }
-        }
-        else
-        {
-          int r = -1;
-          try
-          {
-            r = new Integer(cl).intValue();
-            r--;
-          } catch (NumberFormatException ex)
-          {
-            if (cl.toLowerCase().equals("sequence"))
-            {
-              // we are in the dataset sequence's coordinate frame.
-              inseqpos = true;
-            }
-            else
-            {
-              System.err
-                      .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
-                              + cl + "'");
-              return;
-            }
-          }
-          if (r >= 0 && r <= alw)
-          {
-            if (!seset)
-            {
-              start = r;
-              end = r;
-              seset = true;
-            }
-            else
-            {
-              // comment to prevent range extension
-              if (start > r)
-              {
-                start = r;
-              }
-              if (end < r)
-              {
-                end = r;
-              }
-            }
-            csel.addElement(r);
-            if (debug)
-            {
-              System.err.println("Point selection '" + cl
-                      + "' deparsed as [" + r + "]");
-            }
-          }
-          else
-          {
-            System.err.println("ERROR: Invalid Point selection '" + cl
-                    + "' deparsed as [" + r + "]");
-          }
-        }
-      }
-    }
-    if (seqsfound)
-    {
-      // we only propagate the selection when it was the null selection, or the
-      // given sequences were found in the alignment.
-      if (inseqpos && sel.getSize() > 0)
-      {
-        // assume first sequence provides reference frame ?
-        SequenceI rs = sel.getSequenceAt(0);
-        start = rs.findIndex(start);
-        end = rs.findIndex(end);
-        if (csel != null)
-        {
-          Vector cs = csel.getSelected();
-          csel.clear();
-          for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
-          {
-            csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
-                    .intValue()));
-          }
-        }
-      }
-      sel.setStartRes(start);
-      sel.setEndRes(end);
-      alf.select(sel, csel);
-    }
-  }
-
-  /**
-   * get sequences selected in current alignFrame and return their alignment in
-   * format 'format' either with or without suffix
-   * 
-   * @param alf
-   *          - where selection is
-   * @param format
-   *          - format of alignment file
-   * @param suffix
-   *          - "true" to append /start-end string to each sequence ID
-   * @return selected sequences as flat file or empty string if there was no
-   *         current selection
-   */
-  public String getSelectedSequencesAsAlignment(String format, String suffix)
-  {
-    return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
-            format, suffix);
-  }
-
-  /**
-   * get sequences selected in alf and return their alignment in format 'format'
-   * either with or without suffix
-   * 
-   * @param alf
-   *          - where selection is
-   * @param format
-   *          - format of alignment file
-   * @param suffix
-   *          - "true" to append /start-end string to each sequence ID
-   * @return selected sequences as flat file or empty string if there was no
-   *         current selection
-   */
-  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
-          String format, String suffix)
-  {
-    try
-    {
-      boolean seqlimits = suffix.equalsIgnoreCase("true");
-      if (alf.viewport.getSelectionGroup() != null)
-      {
-        String reply = new AppletFormatAdapter().formatSequences(format,
-                new Alignment(alf.viewport.getSelectionAsNewSequence()),
-                seqlimits);
-        return reply;
-      }
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-      return "Error retrieving alignment in " + format + " format. ";
-    }
-    return "";
-  }
-
-  public String getAlignmentOrder()
-  {
-    return getAlignmentOrderFrom(getDefaultTargetFrame());
-  }
-
-  public String getAlignmentOrderFrom(AlignFrame alf)
-  {
-    return getAlignmentOrderFrom(alf, separator);
-  }
-
-  public String getAlignmentOrderFrom(AlignFrame alf, String sep)
-  {
-    AlignmentI alorder = alf.getAlignViewport().getAlignment();
-    String[] order = new String[alorder.getHeight()];
-    for (int i = 0; i < order.length; i++)
-    {
-      order[i] = alorder.getSequenceAt(i).getName();
-    }
-    return arrayToSeparatorList(order);
-  }
-
-  public String orderBy(String order, String undoName)
-  {
-    return orderBy(order, undoName, separator);
-  }
-
-  public String orderBy(String order, String undoName, String sep)
-  {
-    return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
-  }
-
-  public String orderAlignmentBy(AlignFrame alf, String order,
-          String undoName, String sep)
-  {
-    String[] ids = separatorListToArray(order, sep);
-    SequenceI[] sqs = null;
-    if (ids != null && ids.length > 0)
-    {
-      jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
-              alf.viewport.getAlignment().getSequencesArray());
-      int s = 0;
-      sqs = new SequenceI[ids.length];
-      for (int i = 0; i < ids.length; i++)
-      {
-        if (ids[i].trim().length() == 0)
-        {
-          continue;
-        }
-        SequenceI sq = matcher.findIdMatch(ids[i]);
-        if (sq != null)
-        {
-          sqs[s++] = sq;
-        }
-      }
-      if (s > 0)
-      {
-        SequenceI[] sqq = new SequenceI[s];
-        System.arraycopy(sqs, 0, sqq, 0, s);
-        sqs = sqq;
-      }
-      else
-      {
-        sqs = null;
-      }
-    }
-    if (sqs == null)
-    {
-      return "";
-    }
-    ;
-    AlignmentOrder aorder = new AlignmentOrder(sqs);
-
-    if (undoName != null && undoName.trim().length() == 0)
-    {
-      undoName = null;
-    }
-
-    return alf.sortBy(aorder, undoName) ? "true" : "";
-  }
-
-  public String getAlignment(String format)
-  {
-    return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
-  }
-
-  public String getAlignmentFrom(AlignFrame alf, String format)
-  {
-    return getAlignmentFrom(alf, format, "true");
-  }
-
-  public String getAlignment(String format, String suffix)
-  {
-    return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
-  }
-
-  public String getAlignmentFrom(AlignFrame alf, String format,
-          String suffix)
-  {
-    try
-    {
-      boolean seqlimits = suffix.equalsIgnoreCase("true");
-
-      String reply = new AppletFormatAdapter().formatSequences(format,
-              alf.viewport.getAlignment(), seqlimits);
-      return reply;
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-      return "Error retrieving alignment in " + format + " format. ";
-    }
-  }
-
-  public void loadAnnotation(String annotation)
-  {
-    loadAnnotationFrom(getDefaultTargetFrame(), annotation);
-  }
-
-  public void loadAnnotationFrom(AlignFrame alf, String annotation)
-  {
-    if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
-            .getAlignment(), annotation, AppletFormatAdapter.PASTE))
-    {
-      alf.alignPanel.fontChanged();
-      alf.alignPanel.setScrollValues(0, 0);
-    }
-    else
-    {
-      alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
-    }
-  }
-
-  public String getFeatures(String format)
-  {
-    return getFeaturesFrom(getDefaultTargetFrame(), format);
-  }
-
-  public String getFeaturesFrom(AlignFrame alf, String format)
-  {
-    return alf.outputFeatures(false, format);
-  }
-
-  public String getAnnotation()
-  {
-    return getAnnotationFrom(getDefaultTargetFrame());
-  }
-
-  public String getAnnotationFrom(AlignFrame alf)
-  {
-    return alf.outputAnnotations(false);
-  }
-
-  public AlignFrame newView()
-  {
-    return newViewFrom(getDefaultTargetFrame());
-  }
-
-  public AlignFrame newView(String name)
-  {
-    return newViewFrom(getDefaultTargetFrame(), name);
-  }
-
-  public AlignFrame newViewFrom(AlignFrame alf)
-  {
-    return alf.newView(null);
-  }
-
-  public AlignFrame newViewFrom(AlignFrame alf, String name)
-  {
-    return alf.newView(name);
-  }
-
-  /**
-   * 
-   * @param text
-   *          alignment file as a string
-   * @param title
-   *          window title
-   * @return null or new alignment frame
-   */
-  public AlignFrame loadAlignment(String text, String title)
-  {
-    Alignment al = null;
-
-    String format = new IdentifyFile().Identify(text,
-            AppletFormatAdapter.PASTE);
-    try
-    {
-      al = new AppletFormatAdapter().readFile(text,
-              AppletFormatAdapter.PASTE, format);
-      if (al.getHeight() > 0)
-      {
-        return new AlignFrame(al, this, title, false);
-      }
-    } catch (java.io.IOException ex)
-    {
-      ex.printStackTrace();
-    }
-    return null;
-  }
-
-  public void setMouseoverListener(String listener)
-  {
-    setMouseoverListener(currentAlignFrame, listener);
-  }
-
-  private Vector javascriptListeners = new Vector();
-
-  public void setMouseoverListener(AlignFrame af, String listener)
-  {
-    if (listener != null)
-    {
-      listener = listener.trim();
-      if (listener.length() == 0)
-      {
-        System.err
-                .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
-        return;
-      }
-    }
-    jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
-            this, af, listener);
-    javascriptListeners.addElement(mol);
-    StructureSelectionManager.getStructureSelectionManager()
-            .addStructureViewerListener(mol);
-    if (debug)
-    {
-      System.err.println("Added a mouseover listener for "
-              + ((af == null) ? "All frames" : "Just views for "
-                      + af.getAlignViewport().getSequenceSetId()));
-      System.err.println("There are now " + javascriptListeners.size()
-              + " listeners in total.");
-    }
-  }
-
-  public void setSelectionListener(String listener)
-  {
-    setSelectionListener(null, listener);
-  }
-
-  public void setSelectionListener(AlignFrame af, String listener)
-  {
-    if (listener != null)
-    {
-      listener = listener.trim();
-      if (listener.length() == 0)
-      {
-        System.err
-                .println("jalview Javascript error: Ignoring empty function for selection listener.");
-        return;
-      }
-    }
-    jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
-            this, af, listener);
-    javascriptListeners.addElement(mol);
-    StructureSelectionManager.getStructureSelectionManager()
-            .addSelectionListener(mol);
-    if (debug)
-    {
-      System.err.println("Added a selection listener for "
-              + ((af == null) ? "All frames" : "Just views for "
-                      + af.getAlignViewport().getSequenceSetId()));
-      System.err.println("There are now " + javascriptListeners.size()
-              + " listeners in total.");
-    }
-  }
-
-  public void setStructureListener(String listener)
-  {
-    if (listener != null)
-    {
-      listener = listener.trim();
-      if (listener.length() == 0)
-      {
-        System.err
-                .println("jalview Javascript error: Ignoring empty function for selection listener.");
-        return;
-      }
-    }
-    jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(this, listener);
-    javascriptListeners.addElement(mol);
-    StructureSelectionManager.getStructureSelectionManager()
-            .addStructureViewerListener(mol);
-    if (debug)
-    {
-      System.err.println("Added a javascript structure viewer listener '"+listener+"'");
-      System.err.println("There are now " + javascriptListeners.size()
-              + " listeners in total.");
-    }
-  }
-  /**
-   * remove any callback using the given listener function and associated with
-   * the given alignFrame (or null for all callbacks)
-   * 
-   * @param af
-   *          (may be null)
-   * @param listener
-   *          (may be null)
-   */
-  public void removeJavascriptListener(AlignFrame af, String listener)
-  {
-    if (listener != null)
-    {
-      listener = listener.trim();
-      if (listener.length() == 0)
-      {
-        listener = null;
-      }
-    }
-    boolean rprt = false;
-    for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
-    {
-      Object lstn = javascriptListeners.elementAt(ms);
-      JsCallBack lstner = (JsCallBack) lstn;
-      if ((af == null || lstner.getAlignFrame() == af)
-              && (listener == null || lstner.getListenerFunction().equals(
-                      listener)))
-      {
-        javascriptListeners.removeElement(lstner);
-        msSize--;
-        if (lstner instanceof SelectionListener)
-        {
-          StructureSelectionManager.getStructureSelectionManager()
-                  .removeSelectionListener((SelectionListener) lstner);
-        }
-        else
-        {
-          StructureSelectionManager.getStructureSelectionManager()
-                  .removeStructureViewerListener(lstner, null);
-        }
-        rprt = debug;
-        if (debug)
-        {
-          System.err.println("Removed listener '" + listener + "'");
-        }
-      }
-      else
-      {
-        ms++;
-      }
-    }
-    if (rprt)
-    {
-      System.err.println("There are now " + javascriptListeners.size()
-              + " listeners in total.");
-    }
-  }
-
-  public void stop()
-  {
-    if (javascriptListeners != null)
-    {
-      while (javascriptListeners.size() > 0)
-      {
-        Object mol = javascriptListeners.elementAt(0);
-        javascriptListeners.removeElement(mol);
-        if (mol instanceof SelectionListener)
-        {
-          StructureSelectionManager.getStructureSelectionManager()
-                  .removeSelectionListener((SelectionListener) mol);
-        }
-        else
-        {
-          StructureSelectionManager.getStructureSelectionManager()
-                  .removeStructureViewerListener(mol, null);
-        }
-      }
-    }
-    jalview.javascript.JSFunctionExec.stopQueue();
-  }
-
-  /**
-   * send a mouseover message to all the alignment windows associated with the
-   * given residue in the pdbfile
-   * 
-   * @param pdbResNum
-   * @param chain
-   * @param pdbfile
-   */
-  public void mouseOverStructure(String pdbResNum, String chain, String pdbfile)
-  {
-    try {
-    StructureSelectionManager.getStructureSelectionManager()
-            .mouseOverStructure(new Integer(pdbResNum).intValue(), chain, pdbfile);
-    if (debug)
-    {
-      System.err.println("mouseOver for '"+pdbResNum+"' in chain '"+chain+"' in structure '"+pdbfile+"'");
-    }
-    } catch (NumberFormatException e)
-    {
-        System.err.println("Ignoring invalid residue number string '"+pdbResNum+"'");
-    }
-  }
-
-  // //////////////////////////////////////////////
-  // //////////////////////////////////////////////
-
-  public static int lastFrameX = 200;
-
-  public static int lastFrameY = 200;
-
-  boolean fileFound = true;
-
-  String file = "No file";
-
-  Button launcher = new Button("Start Jalview");
-
-  /**
-   * The currentAlignFrame is static, it will change if and when the user
-   * selects a new window. Note that it will *never* point back to the embedded
-   * AlignFrame if the applet is started as embedded on the page and then
-   * afterwards a new view is created.
-   */
-  public AlignFrame currentAlignFrame = null;
-
-  /**
-   * This is the first frame to be displayed, and does not change. API calls
-   * will default to this instance if currentAlignFrame is null.
-   */
-  AlignFrame initialAlignFrame = null;
-
-  boolean embedded = false;
-
-  private boolean checkForJmol = true;
-
-  private boolean checkedForJmol = false; // ensure we don't check for jmol
-
-  // every time the app is re-inited
-
-  public boolean jmolAvailable = false;
-
-  private boolean alignPdbStructures = false;
-
-  /**
-   * use an external structure viewer exclusively (no jmols or MCViews will be opened by JalviewLite itself)
-   */
-  public boolean useXtrnalSviewer=false;
-
-  public static boolean debug = false;
-
-  static String builddate = null, version = null;
-
-  private static void initBuildDetails()
-  {
-    if (builddate == null)
-    {
-      builddate = "unknown";
-      version = "test";
-      java.net.URL url = JalviewLite.class
-              .getResource("/.build_properties");
-      if (url != null)
-      {
-        try
-        {
-          BufferedReader reader = new BufferedReader(new InputStreamReader(
-                  url.openStream()));
-          String line;
-          while ((line = reader.readLine()) != null)
-          {
-            if (line.indexOf("VERSION") > -1)
-            {
-              version = line.substring(line.indexOf("=") + 1);
-            }
-            if (line.indexOf("BUILD_DATE") > -1)
-            {
-              builddate = line.substring(line.indexOf("=") + 1);
-            }
-          }
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-    }
-  }
-
-  public static String getBuildDate()
-  {
-    initBuildDetails();
-    return builddate;
-  }
-
-  public static String getVersion()
-  {
-    initBuildDetails();
-    return version;
-  }
-
-  // public JSObject scriptObject = null;
-
-  /**
-   * init method for Jalview Applet
-   */
-  public void init()
-  {
-    // remove any handlers that might be hanging around from an earlier instance
-    try
-    {
-      if (debug)
-      {
-        System.err.println("Applet context is '"
-                + getAppletContext().getClass().toString() + "'");
-      }
-      JSObject scriptObject = JSObject.getWindow(this);
-      if (debug && scriptObject != null)
-      {
-        System.err.println("Applet has Javascript callback support.");
-      }
-
-    } catch (Exception ex)
-    {
-      System.err
-              .println("Warning: No JalviewLite javascript callbacks available.");
-      if (debug)
-      {
-        ex.printStackTrace();
-      }
-    }
-    /**
-     * turn on extra applet debugging
-     */
-    String dbg = getParameter("debug");
-    if (dbg != null)
-    {
-      debug = dbg.toLowerCase().equals("true");
-    }
-    if (debug)
-    {
-
-      System.err.println("JalviewLite Version " + getVersion());
-      System.err.println("Build Date : " + getBuildDate());
-
-    }
-    String externalsviewer = getParameter("externalstructureviewer");
-    if (externalsviewer!=null)
-    {
-      useXtrnalSviewer=externalsviewer.trim().toLowerCase().equals("true");
-    }
-    /**
-     * if true disable the check for jmol
-     */
-    String chkforJmol = getParameter("nojmol");
-    if (chkforJmol != null)
-    {
-      checkForJmol = !chkforJmol.equals("true");
-    }
-    /**
-     * get the separator parameter if present
-     */
-    String sep = getParameter("separator");
-    if (sep != null)
-    {
-      if (sep.length() > 0)
-      {
-        separator = sep;
-        if (debug)
-        {
-          System.err.println("Separator set to '" + separator + "'");
-        }
-      }
-      else
-      {
-        throw new Error(
-                "Invalid separator parameter - must be non-zero length");
-      }
-    }
-    int r = 255;
-    int g = 255;
-    int b = 255;
-    String param = getParameter("RGB");
-
-    if (param != null)
-    {
-      try
-      {
-        r = Integer.parseInt(param.substring(0, 2), 16);
-        g = Integer.parseInt(param.substring(2, 4), 16);
-        b = Integer.parseInt(param.substring(4, 6), 16);
-      } catch (Exception ex)
-      {
-        r = 255;
-        g = 255;
-        b = 255;
-      }
-    }
-    param = getParameter("label");
-    if (param != null)
-    {
-      launcher.setLabel(param);
-    }
-
-    setBackground(new Color(r, g, b));
-
-    file = getParameter("file");
-
-    if (file == null)
-    {
-      // Maybe the sequences are added as parameters
-      StringBuffer data = new StringBuffer("PASTE");
-      int i = 1;
-      while ((file = getParameter("sequence" + i)) != null)
-      {
-        data.append(file.toString() + "\n");
-        i++;
-      }
-      if (data.length() > 5)
-      {
-        file = data.toString();
-      }
-    }
-
-    final JalviewLite jvapplet = this;
-    if (getParameter("embedded") != null
-            && getParameter("embedded").equalsIgnoreCase("true"))
-    {
-      // Launch as embedded applet in page
-      embedded = true;
-      LoadingThread loader = new LoadingThread(file, jvapplet);
-      loader.start();
-    }
-    else if (file != null)
-    {
-      if (getParameter("showbutton") == null
-              || !getParameter("showbutton").equalsIgnoreCase("false"))
-      {
-        // Add the JalviewLite 'Button' to the page
-        add(launcher);
-        launcher.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            LoadingThread loader = new LoadingThread(file, jvapplet);
-            loader.start();
-          }
-        });
-      }
-      else
-      {
-        // Open jalviewLite immediately.
-        LoadingThread loader = new LoadingThread(file, jvapplet);
-        loader.start();
-      }
-    }
-    else
-    {
-      // jalview initialisation with no alignment. loadAlignment() method can
-      // still be called to open new alignments.
-      file = "NO FILE";
-      fileFound = false;
-      // callInitCallback();
-    }
-  }
-
-  private void callInitCallback()
-  {
-    String initjscallback = getParameter("oninit");
-    if (initjscallback == null)
-    {
-      return;
-    }
-    initjscallback = initjscallback.trim();
-    if (initjscallback.length() > 0)
-    {
-      JSObject scriptObject = null;
-      try
-      {
-        scriptObject = JSObject.getWindow(this);
-      } catch (Exception ex)
-      {
-      }
-      ;
-      if (scriptObject != null)
-      {
-        try
-        {
-          // do onInit with the JS executor thread
-          new JSFunctionExec(this).executeJavascriptFunction(true,
-                  initjscallback, null, "Calling oninit callback '"
-                          + initjscallback + "'.");
-        } catch (Exception e)
-        {
-          System.err.println("Exception when executing _oninit callback '"
-                  + initjscallback + "'.");
-          e.printStackTrace();
-        }
-      }
-      else
-      {
-        System.err.println("Not executing _oninit callback '"
-                + initjscallback + "' - no scripting allowed.");
-      }
-    }
-  }
-
-  /**
-   * Initialises and displays a new java.awt.Frame
-   * 
-   * @param frame
-   *          java.awt.Frame to be displayed
-   * @param title
-   *          title of new frame
-   * @param width
-   *          width if new frame
-   * @param height
-   *          height of new frame
-   */
-  public static void addFrame(final Frame frame, String title, int width,
-          int height)
-  {
-    frame.setLocation(lastFrameX, lastFrameY);
-    lastFrameX += 40;
-    lastFrameY += 40;
-    frame.setSize(width, height);
-    frame.setTitle(title);
-    frame.addWindowListener(new WindowAdapter()
-    {
-      public void windowClosing(WindowEvent e)
-      {
-        if (frame instanceof AlignFrame)
-        {
-          ((AlignFrame) frame).closeMenuItem_actionPerformed();
-          if (((AlignFrame) frame).viewport.applet.currentAlignFrame == frame)
-          {
-            ((AlignFrame) frame).viewport.applet.currentAlignFrame = null;
-          }
-        }
-        lastFrameX -= 40;
-        lastFrameY -= 40;
-        if (frame instanceof EmbmenuFrame)
-        {
-          ((EmbmenuFrame) frame).destroyMenus();
-        }
-        frame.setMenuBar(null);
-        frame.dispose();
-      }
-
-      public void windowActivated(WindowEvent e)
-      {
-        if (frame instanceof AlignFrame)
-        {
-          ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
-          if (debug)
-          {
-            System.err.println("Activated window " + frame);
-          }
-        }
-        // be good.
-        super.windowActivated(e);
-      }
-      /*
-       * Probably not necessary to do this - see TODO above. (non-Javadoc)
-       * 
-       * @see
-       * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
-       * )
-       * 
-       * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
-       * frame) { currentAlignFrame = null; if (debug) {
-       * System.err.println("Deactivated window "+frame); } }
-       * super.windowDeactivated(e); }
-       */
-    });
-    frame.setVisible(true);
-  }
-
-  /**
-   * This paints the background surrounding the "Launch Jalview button" <br>
-   * <br>
-   * If file given in parameter not found, displays error message
-   * 
-   * @param g
-   *          graphics context
-   */
-  public void paint(Graphics g)
-  {
-    if (!fileFound)
-    {
-      g.setColor(new Color(200, 200, 200));
-      g.setColor(Color.cyan);
-      g.fillRect(0, 0, getSize().width, getSize().height);
-      g.setColor(Color.red);
-      g.drawString("Jalview can't open file", 5, 15);
-      g.drawString("\"" + file + "\"", 5, 30);
-    }
-    else if (embedded)
-    {
-      g.setColor(Color.black);
-      g.setFont(new Font("Arial", Font.BOLD, 24));
-      g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);
-      g.drawString("Loading Data...", 50, getSize().height / 2);
-    }
-  }
-
-  /**
-   * get all components associated with the applet of the given type
-   * 
-   * @param class1
-   * @return
-   */
-  public Vector getAppletWindow(Class class1)
-  {
-    Vector wnds = new Vector();
-    Component[] cmp = getComponents();
-    if (cmp != null)
-    {
-      for (int i = 0; i < cmp.length; i++)
-      {
-        if (class1.isAssignableFrom(cmp[i].getClass()))
-        {
-          wnds.addElement(cmp);
-        }
-      }
-    }
-    return wnds;
-  }
-
-  class LoadJmolThread extends Thread
-  {
-    private boolean running = false;
-
-    public void run()
-    {
-      if (running || checkedForJmol)
-      {
-        return;
-      }
-      running = true;
-      if (checkForJmol)
-      {
-        try
-        {
-          if (!System.getProperty("java.version").startsWith("1.1"))
-          {
-            Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
-            jmolAvailable = true;
-          }
-          if (!jmolAvailable)
-          {
-            System.out
-                    .println("Jmol not available - Using MCview for structures");
-          }
-        } catch (java.lang.ClassNotFoundException ex)
-        {
-        }
-      }
-      else
-      {
-        jmolAvailable = false;
-        if (debug)
-        {
-          System.err
-                  .println("Skipping Jmol check. Will use MCView (probably)");
-        }
-      }
-      checkedForJmol = true;
-      running = false;
-    }
-
-    public boolean notFinished()
-    {
-      return running || !checkedForJmol;
-    }
-  }
-
-  class LoadingThread extends Thread
-  {
-    /**
-     * State variable: File source
-     */
-    String file;
-
-    /**
-     * State variable: protocol for access to file source
-     */
-    String protocol;
-
-    /**
-     * State variable: format of file source
-     */
-    String format;
-
-    String _file;
-
-    JalviewLite applet;
-
-    private void dbgMsg(String msg)
-    {
-      if (applet.debug)
-      {
-        System.err.println(msg);
-      }
-    }
-
-    /**
-     * update the protocol state variable for accessing the datasource located
-     * by file.
-     * 
-     * @param file
-     * @return possibly updated datasource string
-     */
-    public String setProtocolState(String file)
-    {
-      if (file.startsWith("PASTE"))
-      {
-        file = file.substring(5);
-        protocol = AppletFormatAdapter.PASTE;
-      }
-      else if (inArchive(file))
-      {
-        protocol = AppletFormatAdapter.CLASSLOADER;
-      }
-      else
-      {
-        file = addProtocol(file);
-        protocol = AppletFormatAdapter.URL;
-      }
-      dbgMsg("Protocol identified as '" + protocol + "'");
-      return file;
-    }
-
-    public LoadingThread(String _file, JalviewLite _applet)
-    {
-      this._file = _file;
-      applet = _applet;
-    }
-
-    public void run()
-    {
-      LoadJmolThread jmolchecker = new LoadJmolThread();
-      jmolchecker.start();
-      while (jmolchecker.notFinished())
-      {
-        // wait around until the Jmol check is complete.
-        try
-        {
-          Thread.sleep(2);
-        } catch (Exception e)
-        {
-        }
-        ;
-      }
-      startLoading();
-      // applet.callInitCallback();
-    }
-
-    private void startLoading()
-    {
-      AlignFrame newAlignFrame;
-      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
-      file = setProtocolState(_file);
-
-      format = new jalview.io.IdentifyFile().Identify(file, protocol);
-      dbgMsg("File identified as '" + format + "'");
-      dbgMsg("Loading started.");
-      Alignment al = null;
-      try
-      {
-        al = new AppletFormatAdapter().readFile(file, protocol, format);
-      } catch (java.io.IOException ex)
-      {
-        dbgMsg("File load exception.");
-        ex.printStackTrace();
-        if (debug)
-        {
-          try
-          {
-            FileParse fp = new FileParse(file, protocol);
-            String ln = null;
-            dbgMsg(">>>Dumping contents of '" + file + "' " + "("
-                    + protocol + ")");
-            while ((ln = fp.nextLine()) != null)
-            {
-              dbgMsg(ln);
-            }
-            dbgMsg(">>>Dump finished.");
-          } catch (Exception e)
-          {
-            System.err
-                    .println("Exception when trying to dump the content of the file parameter.");
-            e.printStackTrace();
-          }
-        }
-      }
-      if ((al != null) && (al.getHeight() > 0))
-      {
-        dbgMsg("Successfully loaded file.");
-        newAlignFrame = new AlignFrame(al, applet, file, embedded);
-        if (initialAlignFrame == null)
-        {
-          initialAlignFrame = newAlignFrame;
-        }
-        // update the focus.
-        currentAlignFrame = newAlignFrame;
-
-        if (protocol == jalview.io.AppletFormatAdapter.PASTE)
-        {
-          newAlignFrame.setTitle("Sequences from "
-                  + applet.getDocumentBase());
-        }
-
-        newAlignFrame.statusBar.setText("Successfully loaded file " + file);
-
-        String treeFile = applet.getParameter("tree");
-        if (treeFile == null)
-        {
-          treeFile = applet.getParameter("treeFile");
-        }
-
-        if (treeFile != null)
-        {
-          try
-          {
-            treeFile = setProtocolState(treeFile);
-            /*
-             * if (inArchive(treeFile)) { protocol =
-             * AppletFormatAdapter.CLASSLOADER; } else { protocol =
-             * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
-             */
-            jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
-                    protocol);
-
-            fin.parse();
-
-            if (fin.getTree() != null)
-            {
-              newAlignFrame.loadTree(fin, treeFile);
-              dbgMsg("Successfuly imported tree.");
-            }
-            else
-            {
-              dbgMsg("Tree parameter did not resolve to a valid tree.");
-            }
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-        }
-
-        String param = applet.getParameter("features");
-        if (param != null)
-        {
-          param = setProtocolState(param);
-
-          newAlignFrame.parseFeaturesFile(param, protocol);
-        }
-
-        param = applet.getParameter("showFeatureSettings");
-        if (param != null && param.equalsIgnoreCase("true"))
-        {
-          newAlignFrame.viewport.showSequenceFeatures(true);
-          new FeatureSettings(newAlignFrame.alignPanel);
-        }
-
-        param = applet.getParameter("annotations");
-        if (param != null)
-        {
-          param = setProtocolState(param);
-
-          if (new AnnotationFile().readAnnotationFile(
-                  newAlignFrame.viewport.getAlignment(), param, protocol))
-          {
-            newAlignFrame.alignPanel.fontChanged();
-            newAlignFrame.alignPanel.setScrollValues(0, 0);
-          }
-          else
-          {
-            System.err
-                    .println("Annotations were not added from annotation file '"
-                            + param + "'");
-          }
-
-        }
-
-        param = applet.getParameter("jnetfile");
-        if (param != null)
-        {
-          try
-          {
-            param = setProtocolState(param);
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                    param, protocol);
-            JnetAnnotationMaker.add_annotation(predictions,
-                    newAlignFrame.viewport.getAlignment(), 0, false); // false==do
-            // not
-            // add
-            // sequence
-            // profile
-            // from
-            // concise
-            // output
-            newAlignFrame.alignPanel.fontChanged();
-            newAlignFrame.alignPanel.setScrollValues(0, 0);
-          } catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-        }
-        /*
-         * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
-         * - related to JAL-434
-         */
-        applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
-                false));
-        /*
-         * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
-         * PDB|1GAQ|1GAQ|C">
-         * 
-         * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
-         * 
-         * <param name="PDBfile3" value="1q0o Q45135_9MICO">
-         */
-
-        int pdbFileCount = 0;
-        // Accumulate pdbs here if they are heading for the same view (if
-        // alignPdbStructures is true)
-        Vector pdbs = new Vector();
-        // create a lazy matcher if we're asked to
-        jalview.analysis.SequenceIdMatcher matcher = (applet.getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
-                newAlignFrame.getAlignViewport().getAlignment().getSequencesArray()) : null;
-
-        do
-        {
-          if (pdbFileCount > 0)
-            param = applet.getParameter("PDBFILE" + pdbFileCount);
-          else
-            param = applet.getParameter("PDBFILE");
-
-          if (param != null)
-          {
-            PDBEntry pdb = new PDBEntry();
-
-            String seqstring;
-            SequenceI[] seqs = null;
-            String[] chains = null;
-
-            StringTokenizer st = new StringTokenizer(param, " ");
-
-            if (st.countTokens() < 2)
-            {
-              String sequence = applet.getParameter("PDBSEQ");
-              if (sequence != null)
-                seqs = new SequenceI[]
-                { matcher==null ? (Sequence) newAlignFrame.getAlignViewport()
-                        .getAlignment().findName(sequence) : matcher.findIdMatch(sequence) };
-
-            }
-            else
-            {
-              param = st.nextToken();
-              Vector tmp = new Vector();
-              Vector tmp2 = new Vector();
-
-              while (st.hasMoreTokens())
-              {
-                seqstring = st.nextToken();
-                StringTokenizer st2 = new StringTokenizer(seqstring, "=");
-                if (st2.countTokens() > 1)
-                {
-                  // This is the chain
-                  tmp2.addElement(st2.nextToken());
-                  seqstring = st2.nextToken();
-                }
-                tmp.addElement(matcher==null ? (Sequence) newAlignFrame.getAlignViewport()
-                        .getAlignment().findName(seqstring) : matcher.findIdMatch(seqstring));
-              }
-
-              seqs = new SequenceI[tmp.size()];
-              tmp.copyInto(seqs);
-              if (tmp2.size() == tmp.size())
-              {
-                chains = new String[tmp2.size()];
-                tmp2.copyInto(chains);
-              }
-            }
-            param = setProtocolState(param);
-
-            if (// !jmolAvailable
-            // &&
-            protocol == AppletFormatAdapter.CLASSLOADER)
-            {
-              // TODO: verify this Re:
-              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
-              // This exception preserves the current behaviour where, even if
-              // the local pdb file was identified in the class loader
-              protocol = AppletFormatAdapter.URL; // this is probably NOT
-              // CORRECT!
-              param = addProtocol(param); //
-            }
-
-            pdb.setFile(param);
-
-            if (seqs != null)
-            {
-              for (int i = 0; i < seqs.length; i++)
-              {
-                if (seqs[i] != null)
-                {
-                  ((Sequence) seqs[i]).addPDBId(pdb);
-                }
-                else
-                {
-                  if (JalviewLite.debug)
-                  {
-                    // this may not really be a problem but we give a warning
-                    // anyway
-                    System.err
-                            .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
-                                    + i + ")");
-                  }
-                }
-              }
-
-              if (!alignPdbStructures)
-              {
-                newAlignFrame.newStructureView(applet, pdb, seqs, chains,
-                        protocol);
-              }
-              else
-              {
-                pdbs.addElement(new Object[]
-                { pdb, seqs, chains, new String(protocol) });
-              }
-            }
-          }
-
-          pdbFileCount++;
-        } while (pdbFileCount < 10);
-        if (pdbs.size() > 0)
-        {
-          SequenceI[][] seqs = new SequenceI[pdbs.size()][];
-          PDBEntry[] pdb = new PDBEntry[pdbs.size()];
-          String[][] chains = new String[pdbs.size()][];
-          String[] protocols = new String[pdbs.size()];
-          for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
-          {
-            Object[] o = (Object[]) pdbs.elementAt(pdbsi);
-            pdb[pdbsi] = (PDBEntry) o[0];
-            seqs[pdbsi] = (SequenceI[]) o[1];
-            chains[pdbsi] = (String[]) o[2];
-            protocols[pdbsi] = (String) o[3];
-          }
-          newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
-                  protocols);
-
-        }
-        // ///////////////////////////
-        // modify display of features
-        //
-        // hide specific groups
-        param = applet.getParameter("hidefeaturegroups");
-        if (param != null)
-        {
-          applet.setFeatureGroupStateOn(newAlignFrame, param, false);
-        }
-        // show specific groups
-        param = applet.getParameter("showfeaturegroups");
-        if (param != null)
-        {
-          applet.setFeatureGroupStateOn(newAlignFrame, param, true);
-        }
-      }
-      else
-      {
-        fileFound = false;
-        applet.remove(launcher);
-        applet.repaint();
-      }
-    }
-
-    /**
-     * Discovers whether the given file is in the Applet Archive
-     * 
-     * @param file
-     *          String
-     * @return boolean
-     */
-    boolean inArchive(String file)
-    {
-      // This might throw a security exception in certain browsers
-      // Netscape Communicator for instance.
-      try
-      {
-        boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
-        if (debug)
-        {
-          System.err.println("Resource '" + file + "' was "
-                  + (rtn ? "" : "not") + " located by classloader.");
-        }
-        return rtn;
-      } catch (Exception ex)
-      {
-        System.out.println("Exception checking resources: " + file + " "
-                + ex);
-        return false;
-      }
-    }
-
-    String addProtocol(String file)
-    {
-      if (file.indexOf("://") == -1)
-      {
-        file = applet.getCodeBase() + file;
-        if (debug)
-        {
-          System.err.println("Prepended codebase for resource: '" + file
-                  + "'");
-        }
-      }
-
-      return file;
-    }
-  }
-
-  /**
-   * @return the default alignFrame acted on by the public applet methods. May
-   *         return null with an error message on System.err indicating the
-   *         fact.
-   */
-  public AlignFrame getDefaultTargetFrame()
-  {
-    if (currentAlignFrame != null)
-    {
-      return currentAlignFrame;
-    }
-    if (initialAlignFrame != null)
-    {
-      return initialAlignFrame;
-    }
-    System.err
-            .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
-    return null;
-  }
-
-  /**
-   * separator used for separatorList
-   */
-  protected String separator = "" + ((char) 0x00AC); // the default used to be
-                                                     // '|' but many sequence
-                                                     // IDS include pipes.
-
-  /**
-   * parse the string into a list
-   * 
-   * @param list
-   * @return elements separated by separator
-   */
-  public String[] separatorListToArray(String list)
-  {
-    return separatorListToArray(list, separator);
-  }
-
-  /**
-   * parse the string into a list
-   * 
-   * @param list
-   * @param separator
-   * @return elements separated by separator
-   */
-  public String[] separatorListToArray(String list, String separator)
-  {
-    // note separator local variable intentionally masks object field
-    int seplen = separator.length();
-    if (list == null || list.equals("") || list.equals(separator))
-      return null;
-    java.util.Vector jv = new Vector();
-    int cp = 0, pos;
-    while ((pos = list.indexOf(separator, cp)) > cp)
-    {
-      jv.addElement(list.substring(cp, pos));
-      cp = pos + seplen;
-    }
-    if (cp < list.length())
-    {
-      String c = list.substring(cp);
-      if (!c.equals(separator))
-      {
-        jv.addElement(c);
-      }
-    }
-    if (jv.size() > 0)
-    {
-      String[] v = new String[jv.size()];
-      for (int i = 0; i < v.length; i++)
-      {
-        v[i] = (String) jv.elementAt(i);
-      }
-      jv.removeAllElements();
-      if (debug)
-      {
-        System.err.println("Array from '" + separator
-                + "' separated List:\n" + v.length);
-        for (int i = 0; i < v.length; i++)
-        {
-          System.err.println("item " + i + " '" + v[i] + "'");
-        }
-      }
-      return v;
-    }
-    if (debug)
-    {
-      System.err.println("Empty Array from '" + separator
-              + "' separated List");
-    }
-    return null;
-  }
-
-  /**
-   * concatenate the list with separator
-   * 
-   * @param list
-   * @return concatenated string
-   */
-  public String arrayToSeparatorList(String[] list)
-  {
-    return arrayToSeparatorList(list, separator);
-  }
-
-  /**
-   * concatenate the list with separator
-   * 
-   * @param list
-   * @param separator
-   * @return concatenated string
-   */
-  public String arrayToSeparatorList(String[] list, String separator)
-  {
-    StringBuffer v = new StringBuffer();
-    if (list != null && list.length > 0)
-    {
-      for (int i = 0, iSize = list.length; i < iSize; i++)
-      {
-        if (list[i] != null)
-        {
-          if (i > 0)
-          {
-            v.append(separator);
-          }
-          v.append(list[i]);
-        }
-      }
-      if (debug)
-      {
-        System.err.println("Returning '" + separator
-                + "' separated List:\n");
-        System.err.println(v);
-      }
-      return v.toString();
-    }
-    if (debug)
-    {
-      System.err.println("Returning empty '" + separator
-              + "' separated List\n");
-    }
-    return "" + separator;
-  }
-
-  /**
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroups()
-   */
-  public String getFeatureGroups()
-  {
-    String lst = arrayToSeparatorList(getDefaultTargetFrame()
-            .getFeatureGroups());
-    return lst;
-  }
-
-  /**
-   * @param alf
-   *          alignframe to get feature groups on
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroups()
-   */
-  public String getFeatureGroupsOn(AlignFrame alf)
-  {
-    String lst = arrayToSeparatorList(alf.getFeatureGroups());
-    return lst;
-  }
-
-  /**
-   * @param visible
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
-   */
-  public String getFeatureGroupsOfState(boolean visible)
-  {
-    return arrayToSeparatorList(getDefaultTargetFrame()
-            .getFeatureGroupsOfState(visible));
-  }
-
-  /**
-   * @param alf
-   *          align frame to get groups of state visible
-   * @param visible
-   * @return
-   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)
-   */
-  public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
-  {
-    return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
-  }
-
-  /**
-   * @param groups
-   *          tab separated list of group names
-   * @param state
-   *          true or false
-   * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],
-   *      boolean)
-   */
-  public void setFeatureGroupStateOn(AlignFrame alf, String groups,
-          boolean state)
-  {
-    boolean st = state;// !(state==null || state.equals("") ||
-    // state.toLowerCase().equals("false"));
-    alf.setFeatureGroupState(separatorListToArray(groups), st);
-  }
-
-  public void setFeatureGroupState(String groups, boolean state)
-  {
-    setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
-  }
-
-  /**
-   * List separator string
-   * 
-   * @return the separator
-   */
-  public String getSeparator()
-  {
-    return separator;
-  }
-
-  /**
-   * List separator string
-   * 
-   * @param separator
-   *          the separator to set. empty string will reset separator to default
-   */
-  public void setSeparator(String separator)
-  {
-    if (separator == null || separator.length() < 1)
-    {
-      // reset to default
-      separator = "" + ((char) 0x00AC);
-    }
-    this.separator = separator;
-    if (debug)
-    {
-      System.err.println("Default Separator now: '" + separator + "'");
-    }
-  }
-
-  /**
-   * get boolean value of applet parameter 'name' and return default if
-   * parameter is not set
-   * 
-   * @param name
-   *          name of paremeter
-   * @param def
-   *          the value to return otherwise
-   * @return true or false
-   */
-  public boolean getDefaultParameter(String name, boolean def)
-  {
-    String stn;
-    if ((stn = getParameter(name)) == null)
-    {
-      return def;
-    }
-    if (stn.toLowerCase().equals("true"))
-    {
-      return true;
-    }
-    return false;
-  }
-
-  /**
-   * bind a pdb file to a sequence in the given alignFrame.
-   * 
-   * @param alFrame
-   *          - null or specific alignFrame. This specifies the dataset that
-   *          will be searched for a seuqence called sequenceId
-   * @param sequenceId
-   *          - sequenceId within the dataset.
-   * @param pdbEntryString
-   *          - the short name for the PDB file
-   * @param pdbFile
-   *          - pdb file - either a URL or a valid PDB file.
-   * @return true if binding was as success TODO: consider making an exception
-   *         structure for indicating when PDB parsing or seqeunceId location
-   *         fails.
-   */
-  public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
-          String pdbEntryString, String pdbFile)
-  {
-    return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
-  }
-
-  protected void setAlignPdbStructures(boolean alignPdbStructures)
-  {
-    this.alignPdbStructures = alignPdbStructures;
-  }
-
-  public boolean isAlignPdbStructures()
-  {
-    return alignPdbStructures;
-  }
-
-  public void start()
-  {
-    callInitCallback();
-  }
-
-  /**
-   * bind structures in a viewer to any matching sequences in an alignFrame (use
-   * sequenceIds to limit scope of search to specific sequences)
-   * 
-   * @param alFrame
-   * @param viewer
-   * @param sequenceIds
-   * @return TODO: consider making an exception structure for indicating when
-   *         binding fails public SequenceStructureBinding
-   *         addStructureViewInstance( AlignFrame alFrame, Object viewer, String
-   *         sequenceIds) {
-   * 
-   *         if (sequenceIds != null && sequenceIds.length() > 0) { return
-   *         alFrame.addStructureViewInstance(viewer,
-   *         separatorListToArray(sequenceIds)); } else { return
-   *         alFrame.addStructureViewInstance(viewer, null); } // return null; }
-   */
-}
+/*\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.bin;\r
+\r
+import jalview.appletgui.AlignFrame;\r
+import jalview.appletgui.EmbmenuFrame;\r
+import jalview.appletgui.FeatureSettings;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FileParse;\r
+import jalview.io.IdentifyFile;\r
+import jalview.io.JnetAnnotationMaker;\r
+import jalview.javascript.JSFunctionExec;\r
+import jalview.javascript.JsCallBack;\r
+import jalview.structure.SelectionListener;\r
+import jalview.structure.StructureSelectionManager;\r
+\r
+import java.applet.Applet;\r
+import java.awt.Button;\r
+import java.awt.Color;\r
+import java.awt.Component;\r
+import java.awt.Font;\r
+import java.awt.Frame;\r
+import java.awt.Graphics;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.BufferedReader;\r
+import java.io.InputStreamReader;\r
+import java.util.Hashtable;\r
+import java.util.StringTokenizer;\r
+import java.util.Vector;\r
+\r
+import netscape.javascript.JSObject;\r
+\r
+/**\r
+ * Jalview Applet. Runs in Java 1.18 runtime\r
+ * \r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class JalviewLite extends Applet\r
+{\r
+\r
+  // /////////////////////////////////////////\r
+  // The following public methods maybe called\r
+  // externally, eg via javascript in HTML page\r
+  /**\r
+   * @return String list of selected sequence IDs, each terminated by the\r
+   *         'boolean not' character (""+0x00AC) or (&#172;)\r
+   */\r
+  public String getSelectedSequences()\r
+  {\r
+    return getSelectedSequencesFrom(getDefaultTargetFrame());\r
+  }\r
+\r
+  /**\r
+   * @param sep\r
+   *          separator string or null for default\r
+   * @return String list of selected sequence IDs, each terminated by given\r
+   *         separator string\r
+   */\r
+  public String getSelectedSequences(String sep)\r
+  {\r
+    return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);\r
+  }\r
+\r
+  /**\r
+   * @param alf\r
+   *          alignframe containing selection\r
+   * @return String list of selected sequence IDs, each terminated by current\r
+   *         default separator sequence\r
+   * \r
+   */\r
+  public String getSelectedSequencesFrom(AlignFrame alf)\r
+  {\r
+    return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);\r
+  }\r
+\r
+  /**\r
+   * get list of selected sequence IDs separated by given separator\r
+   * \r
+   * @param alf\r
+   *          window containing selection\r
+   * @param sep\r
+   *          separator string to use - default is 'boolean not'\r
+   * @return String list of selected sequence IDs, each terminated by the given\r
+   *         separator\r
+   */\r
+  public String getSelectedSequencesFrom(AlignFrame alf, String sep)\r
+  {\r
+    StringBuffer result = new StringBuffer("");\r
+    if (sep == null || sep.length() == 0)\r
+    {\r
+      sep = separator; // "+0x00AC;\r
+    }\r
+    if (alf.viewport.getSelectionGroup() != null)\r
+    {\r
+      SequenceI[] seqs = alf.viewport.getSelectionGroup()\r
+              .getSequencesInOrder(alf.viewport.getAlignment());\r
+\r
+      for (int i = 0; i < seqs.length; i++)\r
+      {\r
+        result.append(seqs[i].getName());\r
+        result.append(sep);\r
+      }\r
+    }\r
+\r
+    return result.toString();\r
+  }\r
+\r
+  /**\r
+   * \r
+   * @param sequenceId\r
+   *          id of sequence to highlight\r
+   * @param position\r
+   *          integer position [ tobe implemented or range ] on sequence\r
+   * @param alignedPosition\r
+   *          true/false/empty string - indicate if position is an alignment\r
+   *          column or unaligned sequence position\r
+   */\r
+  public void highlight(String sequenceId, String position,\r
+          String alignedPosition)\r
+  {\r
+    highlightIn(getDefaultTargetFrame(), sequenceId, position,\r
+            alignedPosition);\r
+  }\r
+\r
+  /**\r
+   * \r
+   * @param sequenceId\r
+   *          id of sequence to highlight\r
+   * @param position\r
+   *          integer position [ tobe implemented or range ] on sequence\r
+   * @param alignedPosition\r
+   *          false, blank or something else - indicate if position is an\r
+   *          alignment column or unaligned sequence position\r
+   */\r
+  public void highlightIn(AlignFrame alf, String sequenceId,\r
+          String position, String alignedPosition)\r
+  {\r
+    // TODO: could try to highlight in all alignments if alf==null\r
+    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+            alf.viewport.getAlignment().getSequencesArray());\r
+    SequenceI sq = matcher.findIdMatch(sequenceId);\r
+    if (sq != null)\r
+    {\r
+      int pos, apos = -1;\r
+      try\r
+      {\r
+        apos = new Integer(position).intValue();\r
+        apos--;\r
+      } catch (NumberFormatException ex)\r
+      {\r
+        return;\r
+      }\r
+      // use vamsas listener to broadcast to all listeners in scope\r
+      if (alignedPosition != null\r
+              && (alignedPosition.trim().length() == 0 || alignedPosition\r
+                      .toLowerCase().indexOf("false") > -1))\r
+      {\r
+        StructureSelectionManager.getStructureSelectionManager()\r
+                .mouseOverVamsasSequence(sq, sq.findIndex(apos), null);\r
+      }\r
+      else\r
+      {\r
+        StructureSelectionManager.getStructureSelectionManager()\r
+                .mouseOverVamsasSequence(sq, apos, null);\r
+      }\r
+\r
+    }\r
+  }\r
+\r
+  /**\r
+   * select regions of the currrent alignment frame\r
+   * \r
+   * @param sequenceIds\r
+   *          String separated list of sequence ids or empty string\r
+   * @param columns\r
+   *          String separated list { column range or column, ..} or empty\r
+   *          string\r
+   */\r
+  public void select(String sequenceIds, String columns)\r
+  {\r
+    selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);\r
+  }\r
+\r
+  /**\r
+   * select regions of the currrent alignment frame\r
+   * \r
+   * @param toselect\r
+   *          String separated list { column range, seq1...seqn sequence ids }\r
+   * @param sep\r
+   *          separator between toselect fields\r
+   */\r
+  public void select(String sequenceIds, String columns, String sep)\r
+  {\r
+    selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);\r
+  }\r
+\r
+  /**\r
+   * select regions of the given alignment frame\r
+   * \r
+   * @param alf\r
+   * @param toselect\r
+   *          String separated list { column range, seq1...seqn sequence ids }\r
+   * @param sep\r
+   *          separator between toselect fields\r
+   */\r
+  public void selectIn(AlignFrame alf, String sequenceIds, String columns)\r
+  {\r
+    selectIn(alf, sequenceIds, columns, separator);\r
+  }\r
+\r
+  /**\r
+   * select regions of the given alignment frame\r
+   * \r
+   * @param alf\r
+   * @param toselect\r
+   *          String separated list { column range, seq1...seqn sequence ids }\r
+   * @param sep\r
+   *          separator between toselect fields\r
+   */\r
+  public void selectIn(AlignFrame alf, String sequenceIds, String columns,\r
+          String sep)\r
+  {\r
+    if (sep == null || sep.length() == 0)\r
+    {\r
+      sep = separator;\r
+    }\r
+    else\r
+    {\r
+      if (debug)\r
+      {\r
+        System.err.println("Selecting region using separator string '"\r
+                + separator + "'");\r
+      }\r
+    }\r
+    // deparse fields\r
+    String[] ids = separatorListToArray(sequenceIds, sep);\r
+    String[] cols = separatorListToArray(columns, sep);\r
+    SequenceGroup sel = new SequenceGroup();\r
+    ColumnSelection csel = new ColumnSelection();\r
+    AlignmentI al = alf.viewport.getAlignment();\r
+    jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+            alf.viewport.getAlignment().getSequencesArray());\r
+    int start = 0, end = al.getWidth(), alw = al.getWidth();\r
+    boolean seqsfound = true;\r
+    if (ids != null && ids.length > 0)\r
+    {\r
+      seqsfound = false;\r
+      for (int i = 0; i < ids.length; i++)\r
+      {\r
+        if (ids[i].trim().length() == 0)\r
+        {\r
+          continue;\r
+        }\r
+        SequenceI sq = matcher.findIdMatch(ids[i]);\r
+        if (sq != null)\r
+        {\r
+          seqsfound = true;\r
+          sel.addSequence(sq, false);\r
+        }\r
+      }\r
+    }\r
+    boolean inseqpos = false;\r
+    if (cols != null && cols.length > 0)\r
+    {\r
+      boolean seset = false;\r
+      for (int i = 0; i < cols.length; i++)\r
+      {\r
+        String cl = cols[i].trim();\r
+        if (cl.length() == 0)\r
+        {\r
+          continue;\r
+        }\r
+        int p;\r
+        if ((p = cl.indexOf("-")) > -1)\r
+        {\r
+          int from = -1, to = -1;\r
+          try\r
+          {\r
+            from = new Integer(cl.substring(0, p)).intValue();\r
+            from--;\r
+          } catch (NumberFormatException ex)\r
+          {\r
+            System.err\r
+                    .println("ERROR: Couldn't parse first integer in range element column selection string '"\r
+                            + cl + "' - format is 'from-to'");\r
+            return;\r
+          }\r
+          try\r
+          {\r
+            to = new Integer(cl.substring(p + 1)).intValue();\r
+            to--;\r
+          } catch (NumberFormatException ex)\r
+          {\r
+            System.err\r
+                    .println("ERROR: Couldn't parse second integer in range element column selection string '"\r
+                            + cl + "' - format is 'from-to'");\r
+            return;\r
+          }\r
+          if (from >= 0 && to >= 0)\r
+          {\r
+            // valid range\r
+            if (from < to)\r
+            {\r
+              int t = to;\r
+              to = from;\r
+              to = t;\r
+            }\r
+            if (!seset)\r
+            {\r
+              start = from;\r
+              end = to;\r
+              seset = true;\r
+            }\r
+            else\r
+            {\r
+              // comment to prevent range extension\r
+              if (start > from)\r
+              {\r
+                start = from;\r
+              }\r
+              if (end < to)\r
+              {\r
+                end = to;\r
+              }\r
+            }\r
+            for (int r = from; r <= to; r++)\r
+            {\r
+              if (r >= 0 && r < alw)\r
+              {\r
+                csel.addElement(r);\r
+              }\r
+            }\r
+            if (debug)\r
+            {\r
+              System.err.println("Range '" + cl + "' deparsed as [" + from\r
+                      + "," + to + "]");\r
+            }\r
+          }\r
+          else\r
+          {\r
+            System.err.println("ERROR: Invalid Range '" + cl\r
+                    + "' deparsed as [" + from + "," + to + "]");\r
+          }\r
+        }\r
+        else\r
+        {\r
+          int r = -1;\r
+          try\r
+          {\r
+            r = new Integer(cl).intValue();\r
+            r--;\r
+          } catch (NumberFormatException ex)\r
+          {\r
+            if (cl.toLowerCase().equals("sequence"))\r
+            {\r
+              // we are in the dataset sequence's coordinate frame.\r
+              inseqpos = true;\r
+            }\r
+            else\r
+            {\r
+              System.err\r
+                      .println("ERROR: Couldn't parse integer from point selection element of column selection string '"\r
+                              + cl + "'");\r
+              return;\r
+            }\r
+          }\r
+          if (r >= 0 && r <= alw)\r
+          {\r
+            if (!seset)\r
+            {\r
+              start = r;\r
+              end = r;\r
+              seset = true;\r
+            }\r
+            else\r
+            {\r
+              // comment to prevent range extension\r
+              if (start > r)\r
+              {\r
+                start = r;\r
+              }\r
+              if (end < r)\r
+              {\r
+                end = r;\r
+              }\r
+            }\r
+            csel.addElement(r);\r
+            if (debug)\r
+            {\r
+              System.err.println("Point selection '" + cl\r
+                      + "' deparsed as [" + r + "]");\r
+            }\r
+          }\r
+          else\r
+          {\r
+            System.err.println("ERROR: Invalid Point selection '" + cl\r
+                    + "' deparsed as [" + r + "]");\r
+          }\r
+        }\r
+      }\r
+    }\r
+    if (seqsfound)\r
+    {\r
+      // we only propagate the selection when it was the null selection, or the\r
+      // given sequences were found in the alignment.\r
+      if (inseqpos && sel.getSize() > 0)\r
+      {\r
+        // assume first sequence provides reference frame ?\r
+        SequenceI rs = sel.getSequenceAt(0);\r
+        start = rs.findIndex(start);\r
+        end = rs.findIndex(end);\r
+        if (csel != null)\r
+        {\r
+          Vector cs = csel.getSelected();\r
+          csel.clear();\r
+          for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)\r
+          {\r
+            csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))\r
+                    .intValue()));\r
+          }\r
+        }\r
+      }\r
+      sel.setStartRes(start);\r
+      sel.setEndRes(end);\r
+      alf.select(sel, csel);\r
+    }\r
+  }\r
+\r
+  /**\r
+   * get sequences selected in current alignFrame and return their alignment in\r
+   * format 'format' either with or without suffix\r
+   * \r
+   * @param alf\r
+   *          - where selection is\r
+   * @param format\r
+   *          - format of alignment file\r
+   * @param suffix\r
+   *          - "true" to append /start-end string to each sequence ID\r
+   * @return selected sequences as flat file or empty string if there was no\r
+   *         current selection\r
+   */\r
+  public String getSelectedSequencesAsAlignment(String format, String suffix)\r
+  {\r
+    return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),\r
+            format, suffix);\r
+  }\r
+\r
+  /**\r
+   * get sequences selected in alf and return their alignment in format 'format'\r
+   * either with or without suffix\r
+   * \r
+   * @param alf\r
+   *          - where selection is\r
+   * @param format\r
+   *          - format of alignment file\r
+   * @param suffix\r
+   *          - "true" to append /start-end string to each sequence ID\r
+   * @return selected sequences as flat file or empty string if there was no\r
+   *         current selection\r
+   */\r
+  public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,\r
+          String format, String suffix)\r
+  {\r
+    try\r
+    {\r
+      boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+      if (alf.viewport.getSelectionGroup() != null)\r
+      {\r
+        String reply = new AppletFormatAdapter().formatSequences(format,\r
+                new Alignment(alf.viewport.getSelectionAsNewSequence()),\r
+                seqlimits);\r
+        return reply;\r
+      }\r
+    } catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+      return "Error retrieving alignment in " + format + " format. ";\r
+    }\r
+    return "";\r
+  }\r
+\r
+  public String getAlignmentOrder()\r
+  {\r
+    return getAlignmentOrderFrom(getDefaultTargetFrame());\r
+  }\r
+\r
+  public String getAlignmentOrderFrom(AlignFrame alf)\r
+  {\r
+    return getAlignmentOrderFrom(alf, separator);\r
+  }\r
+\r
+  public String getAlignmentOrderFrom(AlignFrame alf, String sep)\r
+  {\r
+    AlignmentI alorder = alf.getAlignViewport().getAlignment();\r
+    String[] order = new String[alorder.getHeight()];\r
+    for (int i = 0; i < order.length; i++)\r
+    {\r
+      order[i] = alorder.getSequenceAt(i).getName();\r
+    }\r
+    return arrayToSeparatorList(order);\r
+  }\r
+\r
+  public String orderBy(String order, String undoName)\r
+  {\r
+    return orderBy(order, undoName, separator);\r
+  }\r
+\r
+  public String orderBy(String order, String undoName, String sep)\r
+  {\r
+    return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);\r
+  }\r
+\r
+  public String orderAlignmentBy(AlignFrame alf, String order,\r
+          String undoName, String sep)\r
+  {\r
+    String[] ids = separatorListToArray(order, sep);\r
+    SequenceI[] sqs = null;\r
+    if (ids != null && ids.length > 0)\r
+    {\r
+      jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(\r
+              alf.viewport.getAlignment().getSequencesArray());\r
+      int s = 0;\r
+      sqs = new SequenceI[ids.length];\r
+      for (int i = 0; i < ids.length; i++)\r
+      {\r
+        if (ids[i].trim().length() == 0)\r
+        {\r
+          continue;\r
+        }\r
+        SequenceI sq = matcher.findIdMatch(ids[i]);\r
+        if (sq != null)\r
+        {\r
+          sqs[s++] = sq;\r
+        }\r
+      }\r
+      if (s > 0)\r
+      {\r
+        SequenceI[] sqq = new SequenceI[s];\r
+        System.arraycopy(sqs, 0, sqq, 0, s);\r
+        sqs = sqq;\r
+      }\r
+      else\r
+      {\r
+        sqs = null;\r
+      }\r
+    }\r
+    if (sqs == null)\r
+    {\r
+      return "";\r
+    }\r
+    ;\r
+    AlignmentOrder aorder = new AlignmentOrder(sqs);\r
+\r
+    if (undoName != null && undoName.trim().length() == 0)\r
+    {\r
+      undoName = null;\r
+    }\r
+\r
+    return alf.sortBy(aorder, undoName) ? "true" : "";\r
+  }\r
+\r
+  public String getAlignment(String format)\r
+  {\r
+    return getAlignmentFrom(getDefaultTargetFrame(), format, "true");\r
+  }\r
+\r
+  public String getAlignmentFrom(AlignFrame alf, String format)\r
+  {\r
+    return getAlignmentFrom(alf, format, "true");\r
+  }\r
+\r
+  public String getAlignment(String format, String suffix)\r
+  {\r
+    return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);\r
+  }\r
+\r
+  public String getAlignmentFrom(AlignFrame alf, String format,\r
+          String suffix)\r
+  {\r
+    try\r
+    {\r
+      boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+      String reply = new AppletFormatAdapter().formatSequences(format,\r
+              alf.viewport.getAlignment(), seqlimits);\r
+      return reply;\r
+    } catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+      return "Error retrieving alignment in " + format + " format. ";\r
+    }\r
+  }\r
+\r
+  public void loadAnnotation(String annotation)\r
+  {\r
+    loadAnnotationFrom(getDefaultTargetFrame(), annotation);\r
+  }\r
+\r
+  public void loadAnnotationFrom(AlignFrame alf, String annotation)\r
+  {\r
+    if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()\r
+            .getAlignment(), annotation, AppletFormatAdapter.PASTE))\r
+    {\r
+      alf.alignPanel.fontChanged();\r
+      alf.alignPanel.setScrollValues(0, 0);\r
+    }\r
+    else\r
+    {\r
+      alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);\r
+    }\r
+  }\r
+\r
+  public String getFeatures(String format)\r
+  {\r
+    return getFeaturesFrom(getDefaultTargetFrame(), format);\r
+  }\r
+\r
+  public String getFeaturesFrom(AlignFrame alf, String format)\r
+  {\r
+    return alf.outputFeatures(false, format);\r
+  }\r
+\r
+  public String getAnnotation()\r
+  {\r
+    return getAnnotationFrom(getDefaultTargetFrame());\r
+  }\r
+\r
+  public String getAnnotationFrom(AlignFrame alf)\r
+  {\r
+    return alf.outputAnnotations(false);\r
+  }\r
+\r
+  public AlignFrame newView()\r
+  {\r
+    return newViewFrom(getDefaultTargetFrame());\r
+  }\r
+\r
+  public AlignFrame newView(String name)\r
+  {\r
+    return newViewFrom(getDefaultTargetFrame(), name);\r
+  }\r
+\r
+  public AlignFrame newViewFrom(AlignFrame alf)\r
+  {\r
+    return alf.newView(null);\r
+  }\r
+\r
+  public AlignFrame newViewFrom(AlignFrame alf, String name)\r
+  {\r
+    return alf.newView(name);\r
+  }\r
+\r
+  /**\r
+   * \r
+   * @param text\r
+   *          alignment file as a string\r
+   * @param title\r
+   *          window title\r
+   * @return null or new alignment frame\r
+   */\r
+  public AlignFrame loadAlignment(String text, String title)\r
+  {\r
+    Alignment al = null;\r
+\r
+    String format = new IdentifyFile().Identify(text,\r
+            AppletFormatAdapter.PASTE);\r
+    try\r
+    {\r
+      al = new AppletFormatAdapter().readFile(text,\r
+              AppletFormatAdapter.PASTE, format);\r
+      if (al.getHeight() > 0)\r
+      {\r
+        return new AlignFrame(al, this, title, false);\r
+      }\r
+    } catch (java.io.IOException ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
+    return null;\r
+  }\r
+\r
+  public void setMouseoverListener(String listener)\r
+  {\r
+    setMouseoverListener(currentAlignFrame, listener);\r
+  }\r
+\r
+  private Vector javascriptListeners = new Vector();\r
+\r
+  public void setMouseoverListener(AlignFrame af, String listener)\r
+  {\r
+    if (listener != null)\r
+    {\r
+      listener = listener.trim();\r
+      if (listener.length() == 0)\r
+      {\r
+        System.err\r
+                .println("jalview Javascript error: Ignoring empty function for mouseover listener.");\r
+        return;\r
+      }\r
+    }\r
+    jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(\r
+            this, af, listener);\r
+    javascriptListeners.addElement(mol);\r
+    StructureSelectionManager.getStructureSelectionManager()\r
+            .addStructureViewerListener(mol);\r
+    if (debug)\r
+    {\r
+      System.err.println("Added a mouseover listener for "\r
+              + ((af == null) ? "All frames" : "Just views for "\r
+                      + af.getAlignViewport().getSequenceSetId()));\r
+      System.err.println("There are now " + javascriptListeners.size()\r
+              + " listeners in total.");\r
+    }\r
+  }\r
+\r
+  public void setSelectionListener(String listener)\r
+  {\r
+    setSelectionListener(null, listener);\r
+  }\r
+\r
+  public void setSelectionListener(AlignFrame af, String listener)\r
+  {\r
+    if (listener != null)\r
+    {\r
+      listener = listener.trim();\r
+      if (listener.length() == 0)\r
+      {\r
+        System.err\r
+                .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+        return;\r
+      }\r
+    }\r
+    jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(\r
+            this, af, listener);\r
+    javascriptListeners.addElement(mol);\r
+    StructureSelectionManager.getStructureSelectionManager()\r
+            .addSelectionListener(mol);\r
+    if (debug)\r
+    {\r
+      System.err.println("Added a selection listener for "\r
+              + ((af == null) ? "All frames" : "Just views for "\r
+                      + af.getAlignViewport().getSequenceSetId()));\r
+      System.err.println("There are now " + javascriptListeners.size()\r
+              + " listeners in total.");\r
+    }\r
+  }\r
+\r
+  public void setStructureListener(String listener, String modelSet)\r
+  {\r
+    if (listener != null)\r
+    {\r
+      listener = listener.trim();\r
+      if (listener.length() == 0)\r
+      {\r
+        System.err\r
+                .println("jalview Javascript error: Ignoring empty function for selection listener.");\r
+        return;\r
+      }\r
+    }\r
+    jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(\r
+            this, listener, separatorListToArray(modelSet));\r
+    javascriptListeners.addElement(mol);\r
+    StructureSelectionManager.getStructureSelectionManager()\r
+            .addStructureViewerListener(mol);\r
+    if (debug)\r
+    {\r
+      System.err.println("Added a javascript structure viewer listener '"\r
+              + listener + "'");\r
+      System.err.println("There are now " + javascriptListeners.size()\r
+              + " listeners in total.");\r
+    }\r
+  }\r
+\r
+  /**\r
+   * remove any callback using the given listener function and associated with\r
+   * the given alignFrame (or null for all callbacks)\r
+   * \r
+   * @param af\r
+   *          (may be null)\r
+   * @param listener\r
+   *          (may be null)\r
+   */\r
+  public void removeJavascriptListener(AlignFrame af, String listener)\r
+  {\r
+    if (listener != null)\r
+    {\r
+      listener = listener.trim();\r
+      if (listener.length() == 0)\r
+      {\r
+        listener = null;\r
+      }\r
+    }\r
+    boolean rprt = false;\r
+    for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)\r
+    {\r
+      Object lstn = javascriptListeners.elementAt(ms);\r
+      JsCallBack lstner = (JsCallBack) lstn;\r
+      if ((af == null || lstner.getAlignFrame() == af)\r
+              && (listener == null || lstner.getListenerFunction().equals(\r
+                      listener)))\r
+      {\r
+        javascriptListeners.removeElement(lstner);\r
+        msSize--;\r
+        if (lstner instanceof SelectionListener)\r
+        {\r
+          StructureSelectionManager.getStructureSelectionManager()\r
+                  .removeSelectionListener((SelectionListener) lstner);\r
+        }\r
+        else\r
+        {\r
+          StructureSelectionManager.getStructureSelectionManager()\r
+                  .removeStructureViewerListener(lstner, null);\r
+        }\r
+        rprt = debug;\r
+        if (debug)\r
+        {\r
+          System.err.println("Removed listener '" + listener + "'");\r
+        }\r
+      }\r
+      else\r
+      {\r
+        ms++;\r
+      }\r
+    }\r
+    if (rprt)\r
+    {\r
+      System.err.println("There are now " + javascriptListeners.size()\r
+              + " listeners in total.");\r
+    }\r
+  }\r
+\r
+  public void stop()\r
+  {\r
+    if (javascriptListeners != null)\r
+    {\r
+      while (javascriptListeners.size() > 0)\r
+      {\r
+        Object mol = javascriptListeners.elementAt(0);\r
+        javascriptListeners.removeElement(mol);\r
+        if (mol instanceof SelectionListener)\r
+        {\r
+          StructureSelectionManager.getStructureSelectionManager()\r
+                  .removeSelectionListener((SelectionListener) mol);\r
+        }\r
+        else\r
+        {\r
+          StructureSelectionManager.getStructureSelectionManager()\r
+                  .removeStructureViewerListener(mol, null);\r
+        }\r
+      }\r
+    }\r
+    jsFunctionExec.stopQueue();\r
+  }\r
+  private jalview.javascript.JSFunctionExec jsFunctionExec;\r
+  /**\r
+   * send a mouseover message to all the alignment windows associated with the\r
+   * given residue in the pdbfile\r
+   * \r
+   * @param pdbResNum\r
+   * @param chain\r
+   * @param pdbfile\r
+   */\r
+  public void mouseOverStructure(String pdbResNum, String chain,\r
+          String pdbfile)\r
+  {\r
+    try\r
+    {\r
+      StructureSelectionManager.getStructureSelectionManager()\r
+              .mouseOverStructure(new Integer(pdbResNum).intValue(), chain,\r
+                      pdbfile);\r
+      if (debug)\r
+      {\r
+        System.err.println("mouseOver for '" + pdbResNum + "' in chain '"\r
+                + chain + "' in structure '" + pdbfile + "'");\r
+      }\r
+    } catch (NumberFormatException e)\r
+    {\r
+      System.err.println("Ignoring invalid residue number string '"\r
+              + pdbResNum + "'");\r
+    }\r
+  }\r
+\r
+  // //////////////////////////////////////////////\r
+  // //////////////////////////////////////////////\r
+\r
+  public static int lastFrameX = 200;\r
+\r
+  public static int lastFrameY = 200;\r
+\r
+  boolean fileFound = true;\r
+\r
+  String file = "No file";\r
+\r
+  Button launcher = new Button("Start Jalview");\r
+\r
+  /**\r
+   * The currentAlignFrame is static, it will change if and when the user\r
+   * selects a new window. Note that it will *never* point back to the embedded\r
+   * AlignFrame if the applet is started as embedded on the page and then\r
+   * afterwards a new view is created.\r
+   */\r
+  public AlignFrame currentAlignFrame = null;\r
+\r
+  /**\r
+   * This is the first frame to be displayed, and does not change. API calls\r
+   * will default to this instance if currentAlignFrame is null.\r
+   */\r
+  AlignFrame initialAlignFrame = null;\r
+\r
+  boolean embedded = false;\r
+\r
+  private boolean checkForJmol = true;\r
+\r
+  private boolean checkedForJmol = false; // ensure we don't check for jmol\r
+\r
+  // every time the app is re-inited\r
+\r
+  public boolean jmolAvailable = false;\r
+\r
+  private boolean alignPdbStructures = false;\r
+\r
+  /**\r
+   * use an external structure viewer exclusively (no jmols or MCViews will be\r
+   * opened by JalviewLite itself)\r
+   */\r
+  public boolean useXtrnalSviewer = false;\r
+\r
+  public static boolean debug = false;\r
+\r
+  static String builddate = null, version = null;\r
+\r
+  private static void initBuildDetails()\r
+  {\r
+    if (builddate == null)\r
+    {\r
+      builddate = "unknown";\r
+      version = "test";\r
+      java.net.URL url = JalviewLite.class\r
+              .getResource("/.build_properties");\r
+      if (url != null)\r
+      {\r
+        try\r
+        {\r
+          BufferedReader reader = new BufferedReader(new InputStreamReader(\r
+                  url.openStream()));\r
+          String line;\r
+          while ((line = reader.readLine()) != null)\r
+          {\r
+            if (line.indexOf("VERSION") > -1)\r
+            {\r
+              version = line.substring(line.indexOf("=") + 1);\r
+            }\r
+            if (line.indexOf("BUILD_DATE") > -1)\r
+            {\r
+              builddate = line.substring(line.indexOf("=") + 1);\r
+            }\r
+          }\r
+        } catch (Exception ex)\r
+        {\r
+          ex.printStackTrace();\r
+        }\r
+      }\r
+    }\r
+  }\r
+\r
+  public static String getBuildDate()\r
+  {\r
+    initBuildDetails();\r
+    return builddate;\r
+  }\r
+\r
+  public static String getVersion()\r
+  {\r
+    initBuildDetails();\r
+    return version;\r
+  }\r
+\r
+  // public JSObject scriptObject = null;\r
+\r
+  /**\r
+   * init method for Jalview Applet\r
+   */\r
+  public void init()\r
+  {\r
+    // remove any handlers that might be hanging around from an earlier instance\r
+    try\r
+    {\r
+      if (debug)\r
+      {\r
+        System.err.println("Applet context is '"\r
+                + getAppletContext().getClass().toString() + "'");\r
+      }\r
+      JSObject scriptObject = JSObject.getWindow(this);\r
+      if (debug && scriptObject != null)\r
+      {\r
+        System.err.println("Applet has Javascript callback support.");\r
+      }\r
+\r
+    } catch (Exception ex)\r
+    {\r
+      System.err\r
+              .println("Warning: No JalviewLite javascript callbacks available.");\r
+      if (debug)\r
+      {\r
+        ex.printStackTrace();\r
+      }\r
+    }\r
+    /**\r
+     * turn on extra applet debugging\r
+     */\r
+    String dbg = getParameter("debug");\r
+    if (dbg != null)\r
+    {\r
+      debug = dbg.toLowerCase().equals("true");\r
+    }\r
+    if (debug)\r
+    {\r
+\r
+      System.err.println("JalviewLite Version " + getVersion());\r
+      System.err.println("Build Date : " + getBuildDate());\r
+\r
+    }\r
+    String externalsviewer = getParameter("externalstructureviewer");\r
+    if (externalsviewer != null)\r
+    {\r
+      useXtrnalSviewer = externalsviewer.trim().toLowerCase()\r
+              .equals("true");\r
+    }\r
+    /**\r
+     * if true disable the check for jmol\r
+     */\r
+    String chkforJmol = getParameter("nojmol");\r
+    if (chkforJmol != null)\r
+    {\r
+      checkForJmol = !chkforJmol.equals("true");\r
+    }\r
+    /**\r
+     * get the separator parameter if present\r
+     */\r
+    String sep = getParameter("separator");\r
+    if (sep != null)\r
+    {\r
+      if (sep.length() > 0)\r
+      {\r
+        separator = sep;\r
+        if (debug)\r
+        {\r
+          System.err.println("Separator set to '" + separator + "'");\r
+        }\r
+      }\r
+      else\r
+      {\r
+        throw new Error(\r
+                "Invalid separator parameter - must be non-zero length");\r
+      }\r
+    }\r
+    int r = 255;\r
+    int g = 255;\r
+    int b = 255;\r
+    String param = getParameter("RGB");\r
+\r
+    if (param != null)\r
+    {\r
+      try\r
+      {\r
+        r = Integer.parseInt(param.substring(0, 2), 16);\r
+        g = Integer.parseInt(param.substring(2, 4), 16);\r
+        b = Integer.parseInt(param.substring(4, 6), 16);\r
+      } catch (Exception ex)\r
+      {\r
+        r = 255;\r
+        g = 255;\r
+        b = 255;\r
+      }\r
+    }\r
+    param = getParameter("label");\r
+    if (param != null)\r
+    {\r
+      launcher.setLabel(param);\r
+    }\r
+\r
+    setBackground(new Color(r, g, b));\r
+\r
+    file = getParameter("file");\r
+\r
+    if (file == null)\r
+    {\r
+      // Maybe the sequences are added as parameters\r
+      StringBuffer data = new StringBuffer("PASTE");\r
+      int i = 1;\r
+      while ((file = getParameter("sequence" + i)) != null)\r
+      {\r
+        data.append(file.toString() + "\n");\r
+        i++;\r
+      }\r
+      if (data.length() > 5)\r
+      {\r
+        file = data.toString();\r
+      }\r
+    }\r
+\r
+    final JalviewLite jvapplet = this;\r
+    if (getParameter("embedded") != null\r
+            && getParameter("embedded").equalsIgnoreCase("true"))\r
+    {\r
+      // Launch as embedded applet in page\r
+      embedded = true;\r
+      LoadingThread loader = new LoadingThread(file, jvapplet);\r
+      loader.start();\r
+    }\r
+    else if (file != null)\r
+    {\r
+      if (getParameter("showbutton") == null\r
+              || !getParameter("showbutton").equalsIgnoreCase("false"))\r
+      {\r
+        // Add the JalviewLite 'Button' to the page\r
+        add(launcher);\r
+        launcher.addActionListener(new java.awt.event.ActionListener()\r
+        {\r
+          public void actionPerformed(ActionEvent e)\r
+          {\r
+            LoadingThread loader = new LoadingThread(file, jvapplet);\r
+            loader.start();\r
+          }\r
+        });\r
+      }\r
+      else\r
+      {\r
+        // Open jalviewLite immediately.\r
+        LoadingThread loader = new LoadingThread(file, jvapplet);\r
+        loader.start();\r
+      }\r
+    }\r
+    else\r
+    {\r
+      // jalview initialisation with no alignment. loadAlignment() method can\r
+      // still be called to open new alignments.\r
+      file = "NO FILE";\r
+      fileFound = false;\r
+      // callInitCallback();\r
+    }\r
+  }\r
+\r
+  private void callInitCallback()\r
+  {\r
+    String initjscallback = getParameter("oninit");\r
+    if (initjscallback == null)\r
+    {\r
+      return;\r
+    }\r
+    initjscallback = initjscallback.trim();\r
+    if (initjscallback.length() > 0)\r
+    {\r
+      JSObject scriptObject = null;\r
+      try\r
+      {\r
+        scriptObject = JSObject.getWindow(this);\r
+      } catch (Exception ex)\r
+      {\r
+      }\r
+      ;\r
+      if (scriptObject != null)\r
+      {\r
+        try\r
+        {\r
+          // do onInit with the JS executor thread\r
+          new JSFunctionExec(this).executeJavascriptFunction(true,\r
+                  initjscallback, null, "Calling oninit callback '"\r
+                          + initjscallback + "'.");\r
+        } catch (Exception e)\r
+        {\r
+          System.err.println("Exception when executing _oninit callback '"\r
+                  + initjscallback + "'.");\r
+          e.printStackTrace();\r
+        }\r
+      }\r
+      else\r
+      {\r
+        System.err.println("Not executing _oninit callback '"\r
+                + initjscallback + "' - no scripting allowed.");\r
+      }\r
+    }\r
+  }\r
+\r
+  /**\r
+   * Initialises and displays a new java.awt.Frame\r
+   * \r
+   * @param frame\r
+   *          java.awt.Frame to be displayed\r
+   * @param title\r
+   *          title of new frame\r
+   * @param width\r
+   *          width if new frame\r
+   * @param height\r
+   *          height of new frame\r
+   */\r
+  public static void addFrame(final Frame frame, String title, int width,\r
+          int height)\r
+  {\r
+    frame.setLocation(lastFrameX, lastFrameY);\r
+    lastFrameX += 40;\r
+    lastFrameY += 40;\r
+    frame.setSize(width, height);\r
+    frame.setTitle(title);\r
+    frame.addWindowListener(new WindowAdapter()\r
+    {\r
+      public void windowClosing(WindowEvent e)\r
+      {\r
+        if (frame instanceof AlignFrame)\r
+        {\r
+          ((AlignFrame) frame).closeMenuItem_actionPerformed();\r
+          if (((AlignFrame) frame).viewport.applet.currentAlignFrame == frame)\r
+          {\r
+            ((AlignFrame) frame).viewport.applet.currentAlignFrame = null;\r
+          }\r
+        }\r
+        lastFrameX -= 40;\r
+        lastFrameY -= 40;\r
+        if (frame instanceof EmbmenuFrame)\r
+        {\r
+          ((EmbmenuFrame) frame).destroyMenus();\r
+        }\r
+        frame.setMenuBar(null);\r
+        frame.dispose();\r
+      }\r
+\r
+      public void windowActivated(WindowEvent e)\r
+      {\r
+        if (frame instanceof AlignFrame)\r
+        {\r
+          ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;\r
+          if (debug)\r
+          {\r
+            System.err.println("Activated window " + frame);\r
+          }\r
+        }\r
+        // be good.\r
+        super.windowActivated(e);\r
+      }\r
+      /*\r
+       * Probably not necessary to do this - see TODO above. (non-Javadoc)\r
+       * \r
+       * @see\r
+       * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent\r
+       * )\r
+       * \r
+       * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==\r
+       * frame) { currentAlignFrame = null; if (debug) {\r
+       * System.err.println("Deactivated window "+frame); } }\r
+       * super.windowDeactivated(e); }\r
+       */\r
+    });\r
+    frame.setVisible(true);\r
+  }\r
+\r
+  /**\r
+   * This paints the background surrounding the "Launch Jalview button" <br>\r
+   * <br>\r
+   * If file given in parameter not found, displays error message\r
+   * \r
+   * @param g\r
+   *          graphics context\r
+   */\r
+  public void paint(Graphics g)\r
+  {\r
+    if (!fileFound)\r
+    {\r
+      g.setColor(new Color(200, 200, 200));\r
+      g.setColor(Color.cyan);\r
+      g.fillRect(0, 0, getSize().width, getSize().height);\r
+      g.setColor(Color.red);\r
+      g.drawString("Jalview can't open file", 5, 15);\r
+      g.drawString("\"" + file + "\"", 5, 30);\r
+    }\r
+    else if (embedded)\r
+    {\r
+      g.setColor(Color.black);\r
+      g.setFont(new Font("Arial", Font.BOLD, 24));\r
+      g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);\r
+      g.drawString("Loading Data...", 50, getSize().height / 2);\r
+    }\r
+  }\r
+\r
+  /**\r
+   * get all components associated with the applet of the given type\r
+   * \r
+   * @param class1\r
+   * @return\r
+   */\r
+  public Vector getAppletWindow(Class class1)\r
+  {\r
+    Vector wnds = new Vector();\r
+    Component[] cmp = getComponents();\r
+    if (cmp != null)\r
+    {\r
+      for (int i = 0; i < cmp.length; i++)\r
+      {\r
+        if (class1.isAssignableFrom(cmp[i].getClass()))\r
+        {\r
+          wnds.addElement(cmp);\r
+        }\r
+      }\r
+    }\r
+    return wnds;\r
+  }\r
+\r
+  class LoadJmolThread extends Thread\r
+  {\r
+    private boolean running = false;\r
+\r
+    public void run()\r
+    {\r
+      if (running || checkedForJmol)\r
+      {\r
+        return;\r
+      }\r
+      running = true;\r
+      if (checkForJmol)\r
+      {\r
+        try\r
+        {\r
+          if (!System.getProperty("java.version").startsWith("1.1"))\r
+          {\r
+            Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");\r
+            jmolAvailable = true;\r
+          }\r
+          if (!jmolAvailable)\r
+          {\r
+            System.out\r
+                    .println("Jmol not available - Using MCview for structures");\r
+          }\r
+        } catch (java.lang.ClassNotFoundException ex)\r
+        {\r
+        }\r
+      }\r
+      else\r
+      {\r
+        jmolAvailable = false;\r
+        if (debug)\r
+        {\r
+          System.err\r
+                  .println("Skipping Jmol check. Will use MCView (probably)");\r
+        }\r
+      }\r
+      checkedForJmol = true;\r
+      running = false;\r
+    }\r
+\r
+    public boolean notFinished()\r
+    {\r
+      return running || !checkedForJmol;\r
+    }\r
+  }\r
+\r
+  class LoadingThread extends Thread\r
+  {\r
+    /**\r
+     * State variable: File source\r
+     */\r
+    String file;\r
+\r
+    /**\r
+     * State variable: protocol for access to file source\r
+     */\r
+    String protocol;\r
+\r
+    /**\r
+     * State variable: format of file source\r
+     */\r
+    String format;\r
+\r
+    String _file;\r
+\r
+    JalviewLite applet;\r
+\r
+    private void dbgMsg(String msg)\r
+    {\r
+      if (applet.debug)\r
+      {\r
+        System.err.println(msg);\r
+      }\r
+    }\r
+\r
+    /**\r
+     * update the protocol state variable for accessing the datasource located\r
+     * by file.\r
+     * \r
+     * @param file\r
+     * @return possibly updated datasource string\r
+     */\r
+    public String setProtocolState(String file)\r
+    {\r
+      if (file.startsWith("PASTE"))\r
+      {\r
+        file = file.substring(5);\r
+        protocol = AppletFormatAdapter.PASTE;\r
+      }\r
+      else if (inArchive(file))\r
+      {\r
+        protocol = AppletFormatAdapter.CLASSLOADER;\r
+      }\r
+      else\r
+      {\r
+        file = addProtocol(file);\r
+        protocol = AppletFormatAdapter.URL;\r
+      }\r
+      dbgMsg("Protocol identified as '" + protocol + "'");\r
+      return file;\r
+    }\r
+\r
+    public LoadingThread(String _file, JalviewLite _applet)\r
+    {\r
+      this._file = _file;\r
+      applet = _applet;\r
+    }\r
+\r
+    public void run()\r
+    {\r
+      LoadJmolThread jmolchecker = new LoadJmolThread();\r
+      jmolchecker.start();\r
+      while (jmolchecker.notFinished())\r
+      {\r
+        // wait around until the Jmol check is complete.\r
+        try\r
+        {\r
+          Thread.sleep(2);\r
+        } catch (Exception e)\r
+        {\r
+        }\r
+        ;\r
+      }\r
+      startLoading();\r
+      // applet.callInitCallback();\r
+    }\r
+\r
+    private void startLoading()\r
+    {\r
+      AlignFrame newAlignFrame;\r
+      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");\r
+      file = setProtocolState(_file);\r
+\r
+      format = new jalview.io.IdentifyFile().Identify(file, protocol);\r
+      dbgMsg("File identified as '" + format + "'");\r
+      dbgMsg("Loading started.");\r
+      Alignment al = null;\r
+      try\r
+      {\r
+        al = new AppletFormatAdapter().readFile(file, protocol, format);\r
+      } catch (java.io.IOException ex)\r
+      {\r
+        dbgMsg("File load exception.");\r
+        ex.printStackTrace();\r
+        if (debug)\r
+        {\r
+          try\r
+          {\r
+            FileParse fp = new FileParse(file, protocol);\r
+            String ln = null;\r
+            dbgMsg(">>>Dumping contents of '" + file + "' " + "("\r
+                    + protocol + ")");\r
+            while ((ln = fp.nextLine()) != null)\r
+            {\r
+              dbgMsg(ln);\r
+            }\r
+            dbgMsg(">>>Dump finished.");\r
+          } catch (Exception e)\r
+          {\r
+            System.err\r
+                    .println("Exception when trying to dump the content of the file parameter.");\r
+            e.printStackTrace();\r
+          }\r
+        }\r
+      }\r
+      if ((al != null) && (al.getHeight() > 0))\r
+      {\r
+        dbgMsg("Successfully loaded file.");\r
+        newAlignFrame = new AlignFrame(al, applet, file, embedded);\r
+        if (initialAlignFrame == null)\r
+        {\r
+          initialAlignFrame = newAlignFrame;\r
+        }\r
+        // update the focus.\r
+        currentAlignFrame = newAlignFrame;\r
+\r
+        if (protocol == jalview.io.AppletFormatAdapter.PASTE)\r
+        {\r
+          newAlignFrame.setTitle("Sequences from "\r
+                  + applet.getDocumentBase());\r
+        }\r
+\r
+        newAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
+\r
+        String treeFile = applet.getParameter("tree");\r
+        if (treeFile == null)\r
+        {\r
+          treeFile = applet.getParameter("treeFile");\r
+        }\r
+\r
+        if (treeFile != null)\r
+        {\r
+          try\r
+          {\r
+            treeFile = setProtocolState(treeFile);\r
+            /*\r
+             * if (inArchive(treeFile)) { protocol =\r
+             * AppletFormatAdapter.CLASSLOADER; } else { protocol =\r
+             * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }\r
+             */\r
+            jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,\r
+                    protocol);\r
+\r
+            fin.parse();\r
+\r
+            if (fin.getTree() != null)\r
+            {\r
+              newAlignFrame.loadTree(fin, treeFile);\r
+              dbgMsg("Successfuly imported tree.");\r
+            }\r
+            else\r
+            {\r
+              dbgMsg("Tree parameter did not resolve to a valid tree.");\r
+            }\r
+          } catch (Exception ex)\r
+          {\r
+            ex.printStackTrace();\r
+          }\r
+        }\r
+\r
+        String param = applet.getParameter("features");\r
+        if (param != null)\r
+        {\r
+          param = setProtocolState(param);\r
+\r
+          newAlignFrame.parseFeaturesFile(param, protocol);\r
+        }\r
+\r
+        param = applet.getParameter("showFeatureSettings");\r
+        if (param != null && param.equalsIgnoreCase("true"))\r
+        {\r
+          newAlignFrame.viewport.showSequenceFeatures(true);\r
+          new FeatureSettings(newAlignFrame.alignPanel);\r
+        }\r
+\r
+        param = applet.getParameter("annotations");\r
+        if (param != null)\r
+        {\r
+          param = setProtocolState(param);\r
+\r
+          if (new AnnotationFile().readAnnotationFile(\r
+                  newAlignFrame.viewport.getAlignment(), param, protocol))\r
+          {\r
+            newAlignFrame.alignPanel.fontChanged();\r
+            newAlignFrame.alignPanel.setScrollValues(0, 0);\r
+          }\r
+          else\r
+          {\r
+            System.err\r
+                    .println("Annotations were not added from annotation file '"\r
+                            + param + "'");\r
+          }\r
+\r
+        }\r
+\r
+        param = applet.getParameter("jnetfile");\r
+        if (param != null)\r
+        {\r
+          try\r
+          {\r
+            param = setProtocolState(param);\r
+            jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+                    param, protocol);\r
+            JnetAnnotationMaker.add_annotation(predictions,\r
+                    newAlignFrame.viewport.getAlignment(), 0, false); // false==do\r
+            // not\r
+            // add\r
+            // sequence\r
+            // profile\r
+            // from\r
+            // concise\r
+            // output\r
+            newAlignFrame.alignPanel.fontChanged();\r
+            newAlignFrame.alignPanel.setScrollValues(0, 0);\r
+          } catch (Exception ex)\r
+          {\r
+            ex.printStackTrace();\r
+          }\r
+        }\r
+        /*\r
+         * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6\r
+         * - related to JAL-434\r
+         */\r
+        applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",\r
+                false));\r
+        /*\r
+         * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B\r
+         * PDB|1GAQ|1GAQ|C">\r
+         * \r
+         * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">\r
+         * \r
+         * <param name="PDBfile3" value="1q0o Q45135_9MICO">\r
+         */\r
+\r
+        int pdbFileCount = 0;\r
+        // Accumulate pdbs here if they are heading for the same view (if\r
+        // alignPdbStructures is true)\r
+        Vector pdbs = new Vector();\r
+        // create a lazy matcher if we're asked to\r
+        jalview.analysis.SequenceIdMatcher matcher = (applet\r
+                .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(\r
+                newAlignFrame.getAlignViewport().getAlignment()\r
+                        .getSequencesArray()) : null;\r
+\r
+        do\r
+        {\r
+          if (pdbFileCount > 0)\r
+          {\r
+            param = applet.getParameter("PDBFILE" + pdbFileCount);\r
+          }\r
+          else\r
+          {\r
+            param = applet.getParameter("PDBFILE");\r
+          }\r
+\r
+          if (param != null)\r
+          {\r
+            PDBEntry pdb = new PDBEntry();\r
+\r
+            String seqstring;\r
+            SequenceI[] seqs = null;\r
+            String[] chains = null;\r
+\r
+            StringTokenizer st = new StringTokenizer(param, " ");\r
+\r
+            if (st.countTokens() < 2)\r
+            {\r
+              String sequence = applet.getParameter("PDBSEQ");\r
+              if (sequence != null)\r
+                seqs = new SequenceI[]\r
+                { matcher == null ? (Sequence) newAlignFrame\r
+                        .getAlignViewport().getAlignment()\r
+                        .findName(sequence) : matcher.findIdMatch(sequence) };\r
+\r
+            }\r
+            else\r
+            {\r
+              param = st.nextToken();\r
+              Vector tmp = new Vector();\r
+              Vector tmp2 = new Vector();\r
+\r
+              while (st.hasMoreTokens())\r
+              {\r
+                seqstring = st.nextToken();\r
+                StringTokenizer st2 = new StringTokenizer(seqstring, "=");\r
+                if (st2.countTokens() > 1)\r
+                {\r
+                  // This is the chain\r
+                  tmp2.addElement(st2.nextToken());\r
+                  seqstring = st2.nextToken();\r
+                }\r
+                tmp.addElement(matcher == null ? (Sequence) newAlignFrame\r
+                        .getAlignViewport().getAlignment()\r
+                        .findName(seqstring) : matcher\r
+                        .findIdMatch(seqstring));\r
+              }\r
+\r
+              seqs = new SequenceI[tmp.size()];\r
+              tmp.copyInto(seqs);\r
+              if (tmp2.size() == tmp.size())\r
+              {\r
+                chains = new String[tmp2.size()];\r
+                tmp2.copyInto(chains);\r
+              }\r
+            }\r
+            param = setProtocolState(param);\r
+\r
+            if (// !jmolAvailable\r
+            // &&\r
+            protocol == AppletFormatAdapter.CLASSLOADER\r
+                    && !useXtrnalSviewer)\r
+            {\r
+              // Re: JAL-357 : the bug isn't a problem if we are using an\r
+              // external viewer!\r
+              // TODO: verify this Re:\r
+              // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605\r
+              // This exception preserves the current behaviour where, even if\r
+              // the local pdb file was identified in the class loader\r
+              protocol = AppletFormatAdapter.URL; // this is probably NOT\r
+              // CORRECT!\r
+              param = addProtocol(param); //\r
+            }\r
+\r
+            pdb.setFile(param);\r
+\r
+            if (seqs != null)\r
+            {\r
+              for (int i = 0; i < seqs.length; i++)\r
+              {\r
+                if (seqs[i] != null)\r
+                {\r
+                  ((Sequence) seqs[i]).addPDBId(pdb);\r
+                }\r
+                else\r
+                {\r
+                  if (JalviewLite.debug)\r
+                  {\r
+                    // this may not really be a problem but we give a warning\r
+                    // anyway\r
+                    System.err\r
+                            .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "\r
+                                    + i + ")");\r
+                  }\r
+                }\r
+              }\r
+\r
+              if (!alignPdbStructures)\r
+              {\r
+                newAlignFrame.newStructureView(applet, pdb, seqs, chains,\r
+                        protocol);\r
+              }\r
+              else\r
+              {\r
+                pdbs.addElement(new Object[]\r
+                { pdb, seqs, chains, new String(protocol) });\r
+              }\r
+            }\r
+          }\r
+\r
+          pdbFileCount++;\r
+        } while (param != null || pdbFileCount < 10);\r
+        if (pdbs.size() > 0)\r
+        {\r
+          SequenceI[][] seqs = new SequenceI[pdbs.size()][];\r
+          PDBEntry[] pdb = new PDBEntry[pdbs.size()];\r
+          String[][] chains = new String[pdbs.size()][];\r
+          String[] protocols = new String[pdbs.size()];\r
+          for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)\r
+          {\r
+            Object[] o = (Object[]) pdbs.elementAt(pdbsi);\r
+            pdb[pdbsi] = (PDBEntry) o[0];\r
+            seqs[pdbsi] = (SequenceI[]) o[1];\r
+            chains[pdbsi] = (String[]) o[2];\r
+            protocols[pdbsi] = (String) o[3];\r
+          }\r
+          newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,\r
+                  protocols);\r
+\r
+        }\r
+        // ///////////////////////////\r
+        // modify display of features\r
+        //\r
+        // hide specific groups\r
+        param = applet.getParameter("hidefeaturegroups");\r
+        if (param != null)\r
+        {\r
+          applet.setFeatureGroupStateOn(newAlignFrame, param, false);\r
+        }\r
+        // show specific groups\r
+        param = applet.getParameter("showfeaturegroups");\r
+        if (param != null)\r
+        {\r
+          applet.setFeatureGroupStateOn(newAlignFrame, param, true);\r
+        }\r
+      }\r
+      else\r
+      {\r
+        fileFound = false;\r
+        applet.remove(launcher);\r
+        applet.repaint();\r
+      }\r
+    }\r
+\r
+    /**\r
+     * Discovers whether the given file is in the Applet Archive\r
+     * \r
+     * @param file\r
+     *          String\r
+     * @return boolean\r
+     */\r
+    boolean inArchive(String file)\r
+    {\r
+      // This might throw a security exception in certain browsers\r
+      // Netscape Communicator for instance.\r
+      try\r
+      {\r
+        boolean rtn = (getClass().getResourceAsStream("/" + file) != null);\r
+        if (debug)\r
+        {\r
+          System.err.println("Resource '" + file + "' was "\r
+                  + (rtn ? "" : "not") + " located by classloader.");\r
+        }\r
+        return rtn;\r
+      } catch (Exception ex)\r
+      {\r
+        System.out.println("Exception checking resources: " + file + " "\r
+                + ex);\r
+        return false;\r
+      }\r
+    }\r
+\r
+    String addProtocol(String file)\r
+    {\r
+      if (file.indexOf("://") == -1)\r
+      {\r
+        String fl = applet.getDocumentBase() + file;\r
+        try\r
+        {\r
+          if (new java.net.URL(fl).openStream() != null)\r
+          {\r
+            if (debug)\r
+            {\r
+              System.err.println("Prepended document base for resource: '"\r
+                      + file + "'");\r
+            }\r
+            return fl;\r
+          }\r
+        } catch (Exception x)\r
+        {\r
+        }\r
+        ;\r
+        fl = applet.getCodeBase() + file;\r
+        try\r
+        {\r
+          if (new java.net.URL(fl).openStream() != null)\r
+          {\r
+            if (debug)\r
+            {\r
+              if (debug)\r
+              {\r
+                System.err.println("Prepended codebase for resource: '"\r
+                        + file + "'");\r
+              }\r
+              return fl;\r
+            }\r
+          }\r
+        } catch (Exception x)\r
+        {\r
+        }\r
+        ;\r
+\r
+      }\r
+\r
+      return file;\r
+    }\r
+  }\r
+\r
+  /**\r
+   * @return the default alignFrame acted on by the public applet methods. May\r
+   *         return null with an error message on System.err indicating the\r
+   *         fact.\r
+   */\r
+  public AlignFrame getDefaultTargetFrame()\r
+  {\r
+    if (currentAlignFrame != null)\r
+    {\r
+      return currentAlignFrame;\r
+    }\r
+    if (initialAlignFrame != null)\r
+    {\r
+      return initialAlignFrame;\r
+    }\r
+    System.err\r
+            .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");\r
+    return null;\r
+  }\r
+\r
+  /**\r
+   * separator used for separatorList\r
+   */\r
+  protected String separator = "" + ((char) 0x00AC); // the default used to be\r
+                                                     // '|' but many sequence\r
+                                                     // IDS include pipes.\r
+\r
+  /**\r
+   * set to enable the URL based javascript execution mechanism \r
+   */\r
+  public boolean jsfallbackEnabled=false;\r
+\r
+  /**\r
+   * parse the string into a list\r
+   * \r
+   * @param list\r
+   * @return elements separated by separator\r
+   */\r
+  public String[] separatorListToArray(String list)\r
+  {\r
+    return separatorListToArray(list, separator);\r
+  }\r
+\r
+  /**\r
+   * parse the string into a list\r
+   * \r
+   * @param list\r
+   * @param separator\r
+   * @return elements separated by separator\r
+   */\r
+  public String[] separatorListToArray(String list, String separator)\r
+  {\r
+    // note separator local variable intentionally masks object field\r
+    int seplen = separator.length();\r
+    if (list == null || list.equals("") || list.equals(separator))\r
+      return null;\r
+    java.util.Vector jv = new Vector();\r
+    int cp = 0, pos;\r
+    while ((pos = list.indexOf(separator, cp)) > cp)\r
+    {\r
+      jv.addElement(list.substring(cp, pos));\r
+      cp = pos + seplen;\r
+    }\r
+    if (cp < list.length())\r
+    {\r
+      String c = list.substring(cp);\r
+      if (!c.equals(separator))\r
+      {\r
+        jv.addElement(c);\r
+      }\r
+    }\r
+    if (jv.size() > 0)\r
+    {\r
+      String[] v = new String[jv.size()];\r
+      for (int i = 0; i < v.length; i++)\r
+      {\r
+        v[i] = (String) jv.elementAt(i);\r
+      }\r
+      jv.removeAllElements();\r
+      if (debug)\r
+      {\r
+        System.err.println("Array from '" + separator\r
+                + "' separated List:\n" + v.length);\r
+        for (int i = 0; i < v.length; i++)\r
+        {\r
+          System.err.println("item " + i + " '" + v[i] + "'");\r
+        }\r
+      }\r
+      return v;\r
+    }\r
+    if (debug)\r
+    {\r
+      System.err.println("Empty Array from '" + separator\r
+              + "' separated List");\r
+    }\r
+    return null;\r
+  }\r
+\r
+  /**\r
+   * concatenate the list with separator\r
+   * \r
+   * @param list\r
+   * @return concatenated string\r
+   */\r
+  public String arrayToSeparatorList(String[] list)\r
+  {\r
+    return arrayToSeparatorList(list, separator);\r
+  }\r
+\r
+  /**\r
+   * concatenate the list with separator\r
+   * \r
+   * @param list\r
+   * @param separator\r
+   * @return concatenated string\r
+   */\r
+  public String arrayToSeparatorList(String[] list, String separator)\r
+  {\r
+    StringBuffer v = new StringBuffer();\r
+    if (list != null && list.length > 0)\r
+    {\r
+      for (int i = 0, iSize = list.length; i < iSize; i++)\r
+      {\r
+        if (list[i] != null)\r
+        {\r
+          if (i > 0)\r
+          {\r
+            v.append(separator);\r
+          }\r
+          v.append(list[i]);\r
+        }\r
+      }\r
+      if (debug)\r
+      {\r
+        System.err.println("Returning '" + separator\r
+                + "' separated List:\n");\r
+        System.err.println(v);\r
+      }\r
+      return v.toString();\r
+    }\r
+    if (debug)\r
+    {\r
+      System.err.println("Returning empty '" + separator\r
+              + "' separated List\n");\r
+    }\r
+    return "" + separator;\r
+  }\r
+\r
+  /**\r
+   * @return\r
+   * @see jalview.appletgui.AlignFrame#getFeatureGroups()\r
+   */\r
+  public String getFeatureGroups()\r
+  {\r
+    String lst = arrayToSeparatorList(getDefaultTargetFrame()\r
+            .getFeatureGroups());\r
+    return lst;\r
+  }\r
+\r
+  /**\r
+   * @param alf\r
+   *          alignframe to get feature groups on\r
+   * @return\r
+   * @see jalview.appletgui.AlignFrame#getFeatureGroups()\r
+   */\r
+  public String getFeatureGroupsOn(AlignFrame alf)\r
+  {\r
+    String lst = arrayToSeparatorList(alf.getFeatureGroups());\r
+    return lst;\r
+  }\r
+\r
+  /**\r
+   * @param visible\r
+   * @return\r
+   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)\r
+   */\r
+  public String getFeatureGroupsOfState(boolean visible)\r
+  {\r
+    return arrayToSeparatorList(getDefaultTargetFrame()\r
+            .getFeatureGroupsOfState(visible));\r
+  }\r
+\r
+  /**\r
+   * @param alf\r
+   *          align frame to get groups of state visible\r
+   * @param visible\r
+   * @return\r
+   * @see jalview.appletgui.AlignFrame#getFeatureGroupsOfState(boolean)\r
+   */\r
+  public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)\r
+  {\r
+    return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));\r
+  }\r
+\r
+  /**\r
+   * @param groups\r
+   *          tab separated list of group names\r
+   * @param state\r
+   *          true or false\r
+   * @see jalview.appletgui.AlignFrame#setFeatureGroupState(java.lang.String[],\r
+   *      boolean)\r
+   */\r
+  public void setFeatureGroupStateOn(AlignFrame alf, String groups,\r
+          boolean state)\r
+  {\r
+    boolean st = state;// !(state==null || state.equals("") ||\r
+    // state.toLowerCase().equals("false"));\r
+    alf.setFeatureGroupState(separatorListToArray(groups), st);\r
+  }\r
+\r
+  public void setFeatureGroupState(String groups, boolean state)\r
+  {\r
+    setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);\r
+  }\r
+\r
+  /**\r
+   * List separator string\r
+   * \r
+   * @return the separator\r
+   */\r
+  public String getSeparator()\r
+  {\r
+    return separator;\r
+  }\r
+\r
+  /**\r
+   * List separator string\r
+   * \r
+   * @param separator\r
+   *          the separator to set. empty string will reset separator to default\r
+   */\r
+  public void setSeparator(String separator)\r
+  {\r
+    if (separator == null || separator.length() < 1)\r
+    {\r
+      // reset to default\r
+      separator = "" + ((char) 0x00AC);\r
+    }\r
+    this.separator = separator;\r
+    if (debug)\r
+    {\r
+      System.err.println("Default Separator now: '" + separator + "'");\r
+    }\r
+  }\r
+\r
+  /**\r
+   * get boolean value of applet parameter 'name' and return default if\r
+   * parameter is not set\r
+   * \r
+   * @param name\r
+   *          name of paremeter\r
+   * @param def\r
+   *          the value to return otherwise\r
+   * @return true or false\r
+   */\r
+  public boolean getDefaultParameter(String name, boolean def)\r
+  {\r
+    String stn;\r
+    if ((stn = getParameter(name)) == null)\r
+    {\r
+      return def;\r
+    }\r
+    if (stn.toLowerCase().equals("true"))\r
+    {\r
+      return true;\r
+    }\r
+    return false;\r
+  }\r
+\r
+  /**\r
+   * bind a pdb file to a sequence in the given alignFrame.\r
+   * \r
+   * @param alFrame\r
+   *          - null or specific alignFrame. This specifies the dataset that\r
+   *          will be searched for a seuqence called sequenceId\r
+   * @param sequenceId\r
+   *          - sequenceId within the dataset.\r
+   * @param pdbEntryString\r
+   *          - the short name for the PDB file\r
+   * @param pdbFile\r
+   *          - pdb file - either a URL or a valid PDB file.\r
+   * @return true if binding was as success TODO: consider making an exception\r
+   *         structure for indicating when PDB parsing or sequenceId location\r
+   *         fails.\r
+   */\r
+  public boolean addPdbFile(AlignFrame alFrame, String sequenceId,\r
+          String pdbEntryString, String pdbFile)\r
+  {\r
+    return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);\r
+  }\r
+\r
+  protected void setAlignPdbStructures(boolean alignPdbStructures)\r
+  {\r
+    this.alignPdbStructures = alignPdbStructures;\r
+  }\r
+\r
+  public boolean isAlignPdbStructures()\r
+  {\r
+    return alignPdbStructures;\r
+  }\r
+\r
+  public void start()\r
+  {\r
+    callInitCallback();\r
+  }\r
+  private Hashtable<String,long[]> jshashes=new Hashtable<String,long[]>();\r
+  private Hashtable<String,Hashtable<String,String[]>> jsmessages=new Hashtable<String,Hashtable<String,String[]>>();\r
+  public void setJsMessageSet(String messageclass, String viewId,\r
+          String[] colcommands)\r
+  {\r
+    Hashtable<String,String[]> msgset = jsmessages.get(messageclass);\r
+    if (msgset==null)\r
+    {\r
+      msgset=new Hashtable<String,String[]>();\r
+      jsmessages.put(messageclass, msgset);\r
+    }\r
+    msgset.put(viewId, colcommands);\r
+    long[] l = new long[colcommands.length];\r
+    for (int i=0;i<colcommands.length;i++) { l[i] = colcommands[i].hashCode();}\r
+    jshashes.put(messageclass+"|"+viewId,l);\r
+  }\r
+  public String getJsMessage(String messageclass, String viewId)\r
+  {\r
+    Hashtable<String,String[]> msgset = jsmessages.get(messageclass);\r
+    if (msgset!=null)\r
+    {\r
+      String[] msgs = msgset.get(viewId);\r
+      if (msgs!=null)\r
+      {\r
+        for (int i=0;i<msgs.length;i++) {\r
+          if (msgs[i]!=null) {\r
+            String m = msgs[i];\r
+            msgs[i]=null;\r
+            return m;\r
+          }\r
+        }\r
+      }\r
+    }\r
+    return "";\r
+  }\r
+\r
+  public boolean isJsMessageSetChanged(String string, String string2,\r
+          String[] colcommands)\r
+  {\r
+    long[] l=jshashes.get(string+"|"+string2);\r
+    if (l==null && colcommands!=null)\r
+    {\r
+      return true;\r
+    }\r
+    for (int i=0;i<colcommands.length;i++) { if (l[i] != colcommands[i].hashCode()) { return true; }}\r
+    return false;\r
+  }\r
+\r
+  private Vector jsExecQueue=new Vector();\r
+  public Vector getJsExecQueue()\r
+  {\r
+    return jsExecQueue;\r
+  }\r
+\r
+  public void setExecutor(JSFunctionExec jsFunctionExec2)\r
+  {\r
+    jsFunctionExec=jsFunctionExec2;\r
+  }\r
+\r
+  /**\r
+   * bind structures in a viewer to any matching sequences in an alignFrame (use\r
+   * sequenceIds to limit scope of search to specific sequences)\r
+   * \r
+   * @param alFrame\r
+   * @param viewer\r
+   * @param sequenceIds\r
+   * @return TODO: consider making an exception structure for indicating when\r
+   *         binding fails public SequenceStructureBinding\r
+   *         addStructureViewInstance( AlignFrame alFrame, Object viewer, String\r
+   *         sequenceIds) {\r
+   * \r
+   *         if (sequenceIds != null && sequenceIds.length() > 0) { return\r
+   *         alFrame.addStructureViewInstance(viewer,\r
+   *         separatorListToArray(sequenceIds)); } else { return\r
+   *         alFrame.addStructureViewInstance(viewer, null); } // return null; }\r
+   */\r
+}\r
index 6ab0865..8eb0bd9 100644 (file)
-package jalview.javascript;
-
-import java.net.URL;
-import java.util.Vector;
-
-import netscape.javascript.JSException;
-import netscape.javascript.JSObject;
-import jalview.bin.JalviewLite;
-
-public class JSFunctionExec implements Runnable
-{
-  JalviewLite jvlite;
-
-  public JSFunctionExec(JalviewLite applet)
-  {
-    jvlite = applet;
-  }
-
-  private static Vector jsExecQueue;
-
-  private static Thread executor = null;
-
-  public static void stopQueue()
-  {
-    if (jsExecQueue != null)
-    {
-      synchronized (jsExecQueue)
-      {
-        Vector q = jsExecQueue;
-        q.removeAllElements();
-        jsExecQueue = null;
-        synchronized (q)
-        {
-          q.notifyAll();
-        }
-      }
-      executor = null;
-    }
-  }
-
-  public void run()
-  {
-    while (jsExecQueue != null)
-    {
-      if (jsExecQueue.size() > 0)
-      {
-        Runnable r = (Runnable) jsExecQueue.elementAt(0);
-        jsExecQueue.removeElementAt(0);
-        try
-        {
-          r.run();
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        } catch (Error ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      else
-      {
-        try
-        {
-          synchronized (jsExecQueue)
-          {
-            jsExecQueue.wait(1000);
-          }
-        } catch (Exception ex)
-        {
-        }
-        ;
-      }
-    }
-
-  }
-
-  /**
-   * execute a javascript callback asynchronously
-   * 
-   * @param _listener
-   * @param objects
-   * @throws Exception
-   */
-  public void executeJavascriptFunction(final String _listener,
-          final Object[] objects) throws Exception
-  {
-    executeJavascriptFunction(false, _listener, objects);
-  }
-
-  /**
-   * execute a javascript callback synchronously or asynchronously
-   * 
-   * @param async
-   *          - true to execute asynchronously (do this for gui events)
-   * @param _listener
-   *          - javascript function
-   * @param objects
-   *          - arguments
-   * @throws Exception
-   *           - only if call is synchronous
-   */
-  public void executeJavascriptFunction(final boolean async,
-          final String _listener, Object[] arguments) throws Exception
-  {
-
-    executeJavascriptFunction(async, _listener, arguments, null);
-
-  }
-
-  public void executeJavascriptFunction(final boolean async,
-          final String _listener, Object[] arguments, final String dbgMsg)
-          throws Exception
-  {
-    final Object[] objects = new Object[arguments != null ? arguments.length
-            : 0];
-    if (arguments != null)
-    {
-      System.arraycopy(arguments, 0, objects, 0, arguments.length);
-    }
-    final Exception[] jsex = new Exception[1];
-    Runnable exec = new Runnable()
-    {
-      public void run()
-      {
-        try
-        {
-          JSObject scriptObject = null;
-          try
-          {
-            scriptObject = JSObject.getWindow(jvlite);
-          } catch (Exception ex)
-          {
-          }
-          ;
-          if (scriptObject != null)
-          {
-            if (jvlite.debug && dbgMsg != null)
-            {
-              System.err.println(dbgMsg);
-            }
-            scriptObject.call(_listener, objects);
-          }
-        } catch (Exception jex)
-        {
-          // squash any malformedURLExceptions thrown by windows/safari
-          if (!(jex instanceof java.net.MalformedURLException))
-          {
-            if (jvlite.debug)
-            {
-              System.err.println(jex);
-            }
-            if (jex instanceof netscape.javascript.JSException)
-            {
-              jsex[0] = (netscape.javascript.JSException) jex;
-              if (jvlite.debug)
-              {
-                System.err.println("Falling back to javascript: url call");
-              }
-              StringBuffer sb = new StringBuffer("javascript:" + _listener
-                      + "(");
-              for (int i = 0; objects != null && i < objects.length; i++)
-              {
-                if (i > 0)
-                {
-                  sb.append(",");
-                }
-                sb.append("\"");
-                // strip out nulls and complex objects that we can't pass this
-                // way.
-                if (objects[i] != null
-                        && !(objects[i].getClass().getName()
-                                .indexOf("jalview") == 0))
-                {
-                  sb.append(objects[i].toString());
-                }
-                sb.append("\"");
-              }
-              sb.append(")");
-              if (jvlite.debug)
-              {
-                System.err.println(sb.toString());
-              }
-              // alternate
-              URL url = null;
-              try
-              {
-                url = new URL(sb.toString());
-                jvlite.getAppletContext().showDocument(url);
-                jex = null;
-              } catch (Exception uex)
-              {
-                jex = uex;
-              }
-            }
-            if (jex != null)
-            {
-              if (async)
-              {
-                jex.printStackTrace();
-              }
-              else
-              {
-                jsex[0] = jex;
-              }
-            }
-            ;
-          }
-
-        }
-      }
-    };
-    if (async)
-    {
-      if (JSFunctionExec.executor == null)
-      {
-        JSFunctionExec.jsExecQueue = new Vector();
-        JSFunctionExec.executor = new Thread(new JSFunctionExec(jvlite));
-        executor.start();
-      }
-      synchronized (jsExecQueue)
-      {
-        jsExecQueue.addElement(exec);
-        jsExecQueue.notify();
-      }
-    }
-    else
-    {
-      exec.run();
-      if (jsex[0] != null)
-      {
-        throw (jsex[0]);
-      }
-    }
-  }
-
-}
+package jalview.javascript;\r
+\r
+import java.net.URL;\r
+import java.util.Vector;\r
+\r
+import netscape.javascript.JSException;\r
+import netscape.javascript.JSObject;\r
+import jalview.bin.JalviewLite;\r
+\r
+public class JSFunctionExec implements Runnable\r
+{\r
+  JalviewLite jvlite;\r
+\r
+  public JSFunctionExec(JalviewLite applet)\r
+  {\r
+    jvlite = applet;\r
+    \r
+    jsExecQueue = jvlite.getJsExecQueue();\r
+    jvlite.setExecutor(this);\r
+  }\r
+\r
+  private Vector jsExecQueue;\r
+\r
+  private Thread executor = null;\r
+\r
+  public void stopQueue()\r
+  {\r
+    if (jsExecQueue != null)\r
+    {\r
+      synchronized (jsExecQueue)\r
+      {\r
+        Vector q = jsExecQueue;\r
+        q.removeAllElements();\r
+        jsExecQueue = null;\r
+        synchronized (q)\r
+        {\r
+          q.notifyAll();\r
+        }\r
+      }\r
+      executor = null;\r
+    }\r
+  }\r
+\r
+  public void run()\r
+  {\r
+    while (jsExecQueue != null)\r
+    {\r
+      if (jsExecQueue.size() > 0)\r
+      {\r
+        Runnable r = (Runnable) jsExecQueue.elementAt(0);\r
+        jsExecQueue.removeElementAt(0);\r
+        try\r
+        {\r
+          r.run();\r
+        } catch (Exception ex)\r
+        {\r
+          ex.printStackTrace();\r
+        } catch (Error ex)\r
+        {\r
+          ex.printStackTrace();\r
+        }\r
+      }\r
+      else\r
+      {\r
+        try\r
+        {\r
+          synchronized (jsExecQueue)\r
+          {\r
+            jsExecQueue.wait(1000);\r
+          }\r
+        } catch (Exception ex)\r
+        {\r
+        }\r
+        ;\r
+      }\r
+    }\r
+\r
+  }\r
+\r
+  /**\r
+   * execute a javascript callback synchronously\r
+   * \r
+   * @param _listener\r
+   * @param objects\r
+   * @throws Exception\r
+   */\r
+  public void executeJavascriptFunction(final String _listener,\r
+          final Object[] objects) throws Exception\r
+  {\r
+    executeJavascriptFunction(false, _listener, objects);\r
+  }\r
+\r
+  /**\r
+   * execute a javascript callback synchronously or asynchronously\r
+   * \r
+   * @param async\r
+   *          - true to execute asynchronously (do this for gui events)\r
+   * @param _listener\r
+   *          - javascript function\r
+   * @param objects\r
+   *          - arguments\r
+   * @throws Exception\r
+   *           - only if call is synchronous\r
+   */\r
+  public void executeJavascriptFunction(final boolean async,\r
+          final String _listener, Object[] arguments) throws Exception\r
+  {\r
+\r
+    executeJavascriptFunction(async, _listener, arguments, null);\r
+\r
+  }\r
+\r
+  public void executeJavascriptFunction(final boolean async,\r
+          final String _listener, Object[] arguments, final String dbgMsg)\r
+          throws Exception\r
+  {\r
+    final Object[] objects = new Object[arguments != null ? arguments.length\r
+            : 0];\r
+    if (arguments != null)\r
+    {\r
+      System.arraycopy(arguments, 0, objects, 0, arguments.length);\r
+    }\r
+    final Exception[] jsex = new Exception[1];\r
+    Runnable exec = new Runnable()\r
+    {\r
+      public void run()\r
+      {\r
+        try\r
+        {\r
+          JSObject scriptObject = null;\r
+          try\r
+          {\r
+            scriptObject = JSObject.getWindow(jvlite);\r
+          } catch (Exception ex)\r
+          {\r
+          }\r
+          ;\r
+          if (scriptObject != null)\r
+          {\r
+            if (jvlite.debug && dbgMsg != null)\r
+            {\r
+              System.err.println(dbgMsg);\r
+            }\r
+            scriptObject.call(_listener, objects);\r
+          }\r
+        } catch (Exception jex)\r
+        {\r
+          // squash any malformedURLExceptions thrown by windows/safari\r
+          if (!(jex instanceof java.net.MalformedURLException))\r
+          {\r
+            if (jvlite.debug)\r
+            {\r
+              System.err.println(jex);\r
+            }\r
+            if (jex instanceof netscape.javascript.JSException && jvlite.jsfallbackEnabled)\r
+            {\r
+              jsex[0] = (netscape.javascript.JSException) jex;\r
+              if (jvlite.debug)\r
+              {\r
+                System.err.println("Falling back to javascript: url call");\r
+              }\r
+              StringBuffer sb = new StringBuffer("javascript:" + _listener\r
+                      + "(");\r
+              for (int i = 0; objects != null && i < objects.length; i++)\r
+              {\r
+                if (i > 0)\r
+                {\r
+                  sb.append(",");\r
+                }\r
+                sb.append("\"");\r
+                // strip out nulls and complex objects that we can't pass this\r
+                // way.\r
+                if (objects[i] != null\r
+                        && !(objects[i].getClass().getName()\r
+                                .indexOf("jalview") == 0))\r
+                {\r
+                  sb.append(objects[i].toString());\r
+                }\r
+                sb.append("\"");\r
+              }\r
+              sb.append(")");\r
+              if (jvlite.debug)\r
+              {\r
+                System.err.println(sb.toString());\r
+              }\r
+              // alternate\r
+              URL url = null;\r
+              try\r
+              {\r
+                url = new URL(sb.toString());\r
+                jvlite.getAppletContext().showDocument(url);\r
+                jex = null;\r
+              } catch (Exception uex)\r
+              {\r
+                jex = uex;\r
+              }\r
+            }\r
+            if (jex != null)\r
+            {\r
+              if (async)\r
+              {\r
+                jex.printStackTrace();\r
+              }\r
+              else\r
+              {\r
+                jsex[0] = jex;\r
+              }\r
+            }\r
+            ;\r
+          }\r
+\r
+        }\r
+      }\r
+    };\r
+    if (async)\r
+    {\r
+      if (executor == null)\r
+      {\r
+        executor = new Thread(new JSFunctionExec(jvlite));\r
+        executor.start();\r
+      }\r
+      synchronized (jsExecQueue)\r
+      {\r
+        jsExecQueue.addElement(exec);\r
+        jsExecQueue.notify();\r
+      }\r
+    }\r
+    else\r
+    {\r
+      // wat for executor to notify us if it's running.\r
+      exec.run();\r
+      if (jsex[0] != null)\r
+      {\r
+        throw (jsex[0]);\r
+      }\r
+    }\r
+  }\r
+\r
+}\r
index 37d2559..2f28820 100644 (file)
-package jalview.javascript;
-
-import java.awt.Color;
-
-import jalview.appletgui.AlignFrame;
-import jalview.bin.JalviewLite;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureSelectionManager;
-
-public class MouseOverStructureListener extends JSFunctionExec implements
-        JsCallBack, StructureListener
-{
-
-  String _listenerfn;
-  public MouseOverStructureListener(JalviewLite applet, String listenerCb)
-  {
-    super(applet);
-    _listenerfn = listenerCb;
-    
-  }
-  @Override
-  public String[] getPdbFile()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public void mouseOverStructure(int atomIndex, String strInfo)
-  {
-    
-    // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex, chain, pdbfile)
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    String[] st=new String[0];
-    try {
-      executeJavascriptFunction(_listenerfn, st = new String[] { "mouseover",""+pdbId, ""+chain, ""+(pdbResNum), ""+atomIndex});
-    } catch (Exception ex)
-    {
-      System.err.println("Couldn't execute callback with "+_listenerfn+" using args { "+st[0]+", "+st[1]+", "+st[2]+","+st[3]+"\n");
-      ex.printStackTrace();
-      
-    }
-
-  }
-
-  @Override
-  public void updateColours(Object source)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  @Override
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbId)
-  {
-    return null;
-  }
-
-  @Override
-  public AlignFrame getAlignFrame()
-  {
-    // associated with all alignframes, always.
-    return null;
-  }
-
-  @Override
-  public String getListenerFunction()
-  {
-    return _listenerfn;
-  }
-  @Override
-  public void releaseReferences(Object svl)
-  {
-    // TODO Auto-generated method stub
-    
-  }
-
-}
+package jalview.javascript;\r
+\r
+import java.awt.Color;\r
+import jalview.api.AlignmentViewPanel;\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.appletgui.AlignFrame;\r
+import jalview.bin.JalviewLite;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.ext.jmol.JmolCommands;\r
+import jalview.structure.StructureListener;\r
+import jalview.structure.StructureMapping;\r
+import jalview.structure.StructureSelectionManager;\r
+\r
+public class MouseOverStructureListener extends JSFunctionExec implements\r
+        JsCallBack, StructureListener\r
+{\r
+\r
+  String _listenerfn;\r
+\r
+  String[] modelSet;\r
+\r
+  public MouseOverStructureListener(JalviewLite jalviewLite,\r
+          String listener, String[] modelList)\r
+  {\r
+    super(jalviewLite);\r
+    _listenerfn = listener;\r
+    modelSet = modelList;\r
+    if (modelSet != null)\r
+    {\r
+      for (int i = 0; i < modelSet.length; i++)\r
+      {\r
+        // resolve a real filename\r
+        try\r
+        {\r
+          if (new java.net.URL(modelSet[i]).openConnection() != null)\r
+          {\r
+            continue;\r
+          }\r
+        } catch (Exception x)\r
+        {\r
+        }\r
+        ;\r
+        try\r
+        {\r
+          String db = jvlite.getDocumentBase().toString();\r
+          db = db.substring(0, db.lastIndexOf("/"));\r
+          if (new java.net.URL(db + "/" + modelSet[i]).openConnection() != null)\r
+          {\r
+            modelSet[i] = db + "/" + modelSet[i];\r
+            continue;\r
+          }\r
+        } catch (Exception x)\r
+        {\r
+        }\r
+        ;\r
+        try\r
+        {\r
+          if (new java.net.URL(jvlite.getCodeBase() + modelSet[i])\r
+                  .openConnection() != null)\r
+          {\r
+            modelSet[i] = jvlite.getCodeBase() + modelSet[i];\r
+            continue;\r
+          }\r
+        } catch (Exception x)\r
+        {\r
+        }\r
+        ;\r
+\r
+      }\r
+    }\r
+  }\r
+\r
+  @Override\r
+  public String[] getPdbFile()\r
+  {\r
+    return modelSet;\r
+  }\r
+\r
+  @Override\r
+  public void mouseOverStructure(int atomIndex, String strInfo)\r
+  {\r
+\r
+    // StructureSelectionManager.getStructureSelectionManager().mouseOverStructure(atomIndex,\r
+    // chain, pdbfile)\r
+    // TODO Auto-generated method stub\r
+\r
+  }\r
+\r
+  @Override\r
+  public void highlightAtom(int atomIndex, int pdbResNum, String chain,\r
+          String pdbId)\r
+  {\r
+    String[] st = new String[0];\r
+    try\r
+    {\r
+      executeJavascriptFunction(_listenerfn, st = new String[]\r
+      { "mouseover", "" + pdbId, "" + chain, "" + (pdbResNum),\r
+          "" + atomIndex });\r
+    } catch (Exception ex)\r
+    {\r
+      System.err.println("Couldn't execute callback with " + _listenerfn\r
+              + " using args { " + st[0] + ", " + st[1] + ", " + st[2]\r
+              + "," + st[3] + "\n");\r
+      ex.printStackTrace();\r
+\r
+    }\r
+\r
+  }\r
+\r
+  @Override\r
+ public synchronized void updateColours(Object srce)\r
+  {\r
+    final Object source = srce;\r
+    StructureSelectionManager ssm = StructureSelectionManager\r
+            .getStructureSelectionManager();\r
+    // if (jvlite.debug)\r
+    // {\r
+    // ssm.reportMapping();\r
+    // }\r
+    if (source instanceof jalview.api.AlignmentViewPanel)\r
+    {\r
+      SequenceI[][] sequence = new SequenceI[modelSet.length][];\r
+      for (int m = 0; m < modelSet.length; m++)\r
+      {\r
+        StructureMapping[] sm = ssm.getMapping(modelSet[m]);\r
+        if (sm != null && sm.length > 0)\r
+        {\r
+          sequence[m] = new SequenceI[sm.length];\r
+          for (int i = 0; i < sm.length; i++)\r
+          {\r
+            sequence[m][i] = sm[i].getSequence();\r
+          }\r
+        }\r
+        else\r
+        {\r
+          sequence[m] = new SequenceI[0];\r
+        }\r
+        // if (jvlite.debug)\r
+        // {\r
+        // System.err.println("Mapped '" + modelSet[m] + "' to "\r
+        // + sequence[m].length + " sequences.");\r
+        // }\r
+      }\r
+\r
+      SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source)\r
+              .getSequenceRenderer();\r
+      FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av\r
+              .getShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer(\r
+              ((jalview.appletgui.AlignmentPanel) source).av) : null;\r
+      if (fr != null)\r
+      {\r
+        ((jalview.appletgui.FeatureRenderer) fr)\r
+                .transferSettings(((jalview.appletgui.AlignmentPanel) source)\r
+                        .getFeatureRenderer());\r
+      }\r
+      ;\r
+\r
+      // Form a colour command for the given alignment panel\r
+      final String[] colcommands = JmolCommands.getColourBySequenceCommand(\r
+              ssm, modelSet, sequence, sr, fr,\r
+              ((AlignmentViewPanel) source).getAlignment());\r
+      String mclass,mhandle;\r
+      if (jvlite.isJsMessageSetChanged(mclass="colourstruct",mhandle=((jalview.appletgui.AlignmentPanel) source).av\r
+              .getViewId(), colcommands)) {\r
+      jvlite.setJsMessageSet(mclass, mhandle , colcommands);\r
+      // and notify javascript handler\r
+      String st[] = new String[0];\r
+      try\r
+      {\r
+        executeJavascriptFunction(\r
+                true,\r
+                _listenerfn,\r
+                st = new String[]\r
+                {\r
+                    "colourstruct",\r
+                    ""\r
+                            + ((jalview.appletgui.AlignmentPanel) source).av\r
+                                    .getViewId(), ""+colcommands.length, "" });\r
+      } catch (Exception ex)\r
+      {\r
+        System.err.println("Couldn't execute callback with "\r
+                + _listenerfn + " using args { " + st[0] + ", "\r
+                + st[1] + ", " + st[2] + "," + st[3] + "\n");\r
+        ex.printStackTrace();\r
+\r
+      }\r
+      }\r
+/*      new Thread(new Runnable()\r
+      {\r
+        public void run()\r
+        {\r
+          // and send to javascript handler\r
+          String st[] = new String[0];\r
+          int i = 0;\r
+          for (String colcommand : colcommands)\r
+          {\r
+            // do sync execution for each chunk\r
+            try\r
+            {\r
+              executeJavascriptFunction(\r
+                      false,\r
+                      _listenerfn,\r
+                      st = new String[]\r
+                      {\r
+                          "colourstruct",\r
+                          ""\r
+                                  + ((jalview.appletgui.AlignmentPanel) source).av\r
+                                          .getViewId(), handle, "" });\r
+            } catch (Exception ex)\r
+            {\r
+              System.err.println("Couldn't execute callback with "\r
+                      + _listenerfn + " using args { " + st[0] + ", "\r
+                      + st[1] + ", " + st[2] + "," + st[3] + "\n");\r
+              ex.printStackTrace();\r
+\r
+            }\r
+          }\r
+        }\r
+      }).start();\r
+  */\r
+    }\r
+\r
+  }\r
+\r
+  @Override\r
+  public Color getColour(int atomIndex, int pdbResNum, String chain,\r
+          String pdbId)\r
+  {\r
+    return null;\r
+  }\r
+\r
+  @Override\r
+  public AlignFrame getAlignFrame()\r
+  {\r
+    // associated with all alignframes, always.\r
+    return null;\r
+  }\r
+\r
+  @Override\r
+  public String getListenerFunction()\r
+  {\r
+    return _listenerfn;\r
+  }\r
+\r
+  @Override\r
+  public void releaseReferences(Object svl)\r
+  {\r
+    // TODO Auto-generated method stub\r
+\r
+  }\r
+\r
+}\r