X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=e60824a6e668112f4c8367b9933f930d48c62c9a;hb=fbc92d8f171f75002890bfa0ea1f436f7125d3b5;hp=decb06f6edd3fa49b16d8d44c3ede42cab72ed97;hpb=e950d7035158d0dca7bcc466aecfb32450d4bd52;p=jalview.git

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index decb06f..e60824a 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -20,91 +20,49 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
-import jalview.api.FeatureRenderer;
-import jalview.datamodel.AlignmentExportData;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.HTMLOptions;
-import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
 import jalview.math.AlignmentDimension;
 import jalview.util.MessageManager;
 
-import java.awt.Color;
-import java.awt.FontMetrics;
 import java.awt.Graphics;
-import java.awt.print.Printable;
 import java.awt.print.PrinterException;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.IOException;
 
 import org.jfree.graphics2d.svg.SVGGraphics2D;
 import org.jfree.graphics2d.svg.SVGHints;
 
-public class HtmlSvgOutput
+public class HtmlSvgOutput extends HTMLOutput
 {
-  AlignViewport av;
 
-  FeatureRenderer fr;
+  private File generatedFile;
 
-  AlignmentPanel ap;
-
-  private IProgressIndicator pIndicator;
-
-  private long pSessionId;
-
-  private boolean headless;
-
-  public HtmlSvgOutput(File file, AlignmentPanel ap)
+  public HtmlSvgOutput(AlignmentPanel ap)
   {
-    this.av = ap.av;
-    this.ap = ap;
-    fr = ap.cloneFeatureRenderer();
-    generateHtmlSvgOutput(file);
+    super(ap);
   }
 
-  public void generateHtmlSvgOutput(File file)
+  @Override
+  public void exportHTML(String file)
   {
-    pIndicator = ap.alignFrame;
-    pSessionId = System.currentTimeMillis();
+    exportStarted();
     try
     {
-      headless = (System.getProperty("java.awt.headless") != null && System
-              .getProperty("java.awt.headless").equals("true"));
       if (file == null)
       {
-        setProgressMessage(MessageManager.formatMessage(
-                "status.waiting_for_user_to_select_output_file", "HTML"));
-        JalviewFileChooser chooser = getHTMLChooser();
-        chooser.setFileView(new jalview.io.JalviewFileView());
-        chooser.setDialogTitle(ap.alignFrame.getTitle());
-        chooser.setToolTipText(MessageManager.getString("action.save"));
-        int value = chooser.showSaveDialog(ap.alignFrame);
-
-        if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
-        {
-          jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
-                  .getSelectedFile().getParent());
-          file = chooser.getSelectedFile();
-          ap.alignFrame.repaint();
-        }
-        else
-        {
-          setProgressMessage(MessageManager.formatMessage(
-                  "status.cancelled_image_export_operation", "HTML"));
-          return;
-        }
+        file = getOutputFile();
       }
+      generatedFile = new File(file);
     } catch (Exception e)
     {
-      pIndicator.setProgressBar(MessageManager.formatMessage(
-              "info.error_creating_file", "HTML"), pSessionId);
+      setProgressMessage(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"));
       e.printStackTrace();
       return;
     }
-    final File fileX = file;
     new Thread()
     {
       @Override
@@ -116,9 +74,11 @@ public class HtmlSvgOutput
           setProgressMessage(MessageManager.formatMessage(
                   "status.exporting_alignment_as_x_file", "HTML"));
           AlignmentDimension aDimension = ap.getAlignmentDimension();
-          SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
+          SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
+                  aDimension.getWidth(),
                   aDimension.getHeight());
-          SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
+          SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
+                  aDimension.getWidth(),
                   aDimension.getHeight());
 
           String renderStyle = jalview.bin.Cache.getDefault(
@@ -127,8 +87,7 @@ public class HtmlSvgOutput
           // If we need to prompt, and if the GUI is visible then
           // Prompt for rendering style
           if (renderStyle.equalsIgnoreCase("Prompt each time")
-                  && !(System.getProperty("java.awt.headless") != null && System
-                          .getProperty("java.awt.headless").equals("true")))
+                  && !isHeadless())
           {
             HTMLOptions svgOption = new HTMLOptions();
             renderStyle = svgOption.getValue();
@@ -143,100 +102,44 @@ public class HtmlSvgOutput
 
           if (renderStyle.equalsIgnoreCase("Lineart"))
           {
-            g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+            idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
-            g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+            alignPanelGraphics.setRenderingHint(
+                    SVGHints.KEY_DRAW_STRING_TYPE,
                     SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
           }
-          if (av.getWrapAlignment())
+          if (ap.av.getWrapAlignment())
           {
             printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
-                    g1, g2);
+                    alignPanelGraphics);
           }
           else
           {
           printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
-                  g1, g2);
+ idPanelGraphics, alignPanelGraphics);
           }
 
-          String titleSvgData = g1.getSVGDocument();
-          String alignSvgData = g2.getSVGDocument();
-          String jsonData = null;
-          boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
-                  .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
-          if (isEmbbedBioJSON)
-          {
-            AlignExportSettingI exportSettings = new AlignExportSettingI()
-            {
-              @Override
-              public boolean isExportHiddenSequences()
-              {
-                return true;
-              }
-
-              @Override
-              public boolean isExportHiddenColumns()
-              {
-                return true;
-              }
-
-              @Override
-              public boolean isExportAnnotations()
-              {
-                return true;
-              }
-
-              @Override
-              public boolean isExportFeatures()
-              {
-                return true;
-              }
-
-              @Override
-              public boolean isExportGroups()
-              {
-                return true;
-              }
-
-              @Override
-              public boolean isCancelled()
-              {
-                return false;
-              }
-
-            };
-            AlignmentExportData exportData = jalview.gui.AlignFrame
-                    .getAlignmentForExport(JSONFile.FILE_DESC, av,
-                            exportSettings);
-            jsonData = new FormatAdapter(ap, exportData.getSettings())
-                    .formatSequences(JSONFile.FILE_DESC,
-                            exportData.getAlignment(),
-                            exportData.getOmitHidden(),
-                            exportData.getStartEndPostions(),
-                            av.getColumnSelection());
-          }
-          String htmlData = getHtml(titleSvgData, alignSvgData, jsonData,
-                  av.getWrapAlignment());
-          FileOutputStream out = new FileOutputStream(fileX);
+          String idPanelSvgData = idPanelGraphics.getSVGDocument();
+          String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
+          String jsonData = getBioJSONData();
+          String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
+ ap.av.getWrapAlignment());
+          FileOutputStream out = new FileOutputStream(generatedFile);
           out.write(htmlData.getBytes());
           out.flush();
           out.close();
-          if (!(System.getProperty("java.awt.headless") != null && System
-                  .getProperty("java.awt.headless").equals("true")))
-          {
-            jalview.util.BrowserLauncher.openURL("file:///" + fileX);
-          }
+          exportCompleted();
         } catch (OutOfMemoryError err)
         {
           System.out.println("########################\n"
-                  + "OUT OF MEMORY " + fileX + "\n"
+                  + "OUT OF MEMORY " + generatedFile + "\n"
                   + "########################");
-          new OOMWarning("Creating Image for " + fileX, err);
+          new OOMWarning("Creating Image for " + generatedFile, err);
         } catch (Exception e)
         {
           e.printStackTrace();
-          pIndicator.setProgressBar(MessageManager.formatMessage(
-                  "info.error_creating_file", "HTML"), pSessionId);
+          setProgressMessage(MessageManager.formatMessage(
+                  "info.error_creating_file", "HTML"));
         }
         setProgressMessage(MessageManager.formatMessage(
                 "status.export_complete", "HTML"));
@@ -245,17 +148,6 @@ public class HtmlSvgOutput
 
   }
 
-  private void setProgressMessage(String message)
-  {
-    if (pIndicator != null && !headless)
-    {
-      pIndicator.setProgressBar(message, pSessionId);
-    }
-    else
-    {
-      System.out.println(message);
-    }
-  }
 
   static JalviewFileChooser getHTMLChooser()
   {
@@ -269,138 +161,13 @@ public class HtmlSvgOutput
   public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
           throws PrinterException
   {
-    int idWidth = ap.getVisibleIdWidth(false);
-    FontMetrics fm = ap.getFontMetrics(av.getFont());
-    int scaleHeight = av.getCharHeight() + fm.getDescent();
-
-    pg[0].setColor(Color.white);
-    pg[0].fillRect(0, 0, pwidth, pheight);
-    pg[0].setFont(av.getFont());
-
-    // //////////////////////////////////
-    // / How many sequences and residues can we fit on a printable page?
-    int totalRes = (pwidth - idWidth) / av.getCharWidth();
-    int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
-    int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
-
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int startRes;
-
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int endRes;
-
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int startSeq;
-
-    // ///////////////////////////
-    // / Only print these sequences and residues on this page
-    int endSeq;
-    startRes = (pi % pagesWide) * totalRes;
-    endRes = (startRes + totalRes) - 1;
-
-    if (endRes > (av.getAlignment().getWidth() - 1))
-    {
-      endRes = av.getAlignment().getWidth() - 1;
-    }
-    startSeq = (pi / pagesWide) * totalSeq;
-    endSeq = startSeq + totalSeq;
-    if (endSeq > av.getAlignment().getHeight())
-    {
-      endSeq = av.getAlignment().getHeight();
-    }
-    int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
-            * pheight;
-    if (av.isShowAnnotation())
-    {
-      pagesHigh += ap.getAnnotationPanel().adjustPanelHeight() + 3;
-    }
-    pagesHigh /= pheight;
-    if (pi >= (pagesWide * pagesHigh))
-    {
-      return Printable.NO_SUCH_PAGE;
-    }
-
-    // draw Scale
-    pg[1].translate(0, 0);
-    ap.getScalePanel().drawScale(pg[1], startRes, endRes, pwidth - idWidth,
-            scaleHeight);
-    pg[1].translate(-idWidth, scaleHeight);
-
-    // //////////////
-    // Draw the ids
-    Color currentColor = null;
-    Color currentTextColor = null;
-    pg[0].translate(0, scaleHeight);
-    pg[0].setFont(ap.getIdPanel().getIdCanvas().getIdfont());
-    SequenceI seq;
-    for (int i = startSeq; i < endSeq; i++)
-    {
-      seq = av.getAlignment().getSequenceAt(i);
-      if ((av.getSelectionGroup() != null)
-              && av.getSelectionGroup().getSequences(null).contains(seq))
-      {
-        currentColor = Color.gray;
-        currentTextColor = Color.black;
-      }
-      else
-      {
-        currentColor = av.getSequenceColour(seq);
-        currentTextColor = Color.black;
-      }
-      pg[0].setColor(currentColor);
-      pg[0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
-              av.getCharHeight());
-      pg[0].setColor(currentTextColor);
-      int xPos = 0;
-      if (av.isRightAlignIds())
-      {
-        fm = pg[0].getFontMetrics();
-        xPos = idWidth
-                - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
-                - 4;
-      }
-      pg[0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
-              (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
-                      - (av.getCharHeight() / 5));
-    }
-    pg[0].setFont(av.getFont());
-    pg[0].translate(idWidth, 0);
-
-    // draw main sequence panel
-    pg[1].translate(idWidth, 0);
-    ap.getSeqPanel().seqCanvas.drawPanel(pg[1], startRes, endRes, startSeq,
-            endSeq, 0);
-    if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
-    {
-      // draw annotation label - need to offset for current scroll position
-      int offset = -ap.getAlabels().getScrollOffset();
-      pg[0].translate(0, offset);
-      pg[0].translate(-idWidth - 3,
-              (endSeq - startSeq) * av.getCharHeight() + 3);
-      ap.getAlabels().drawComponent(pg[0], idWidth);
-      pg[0].translate(idWidth + 3, 0);
-      pg[0].translate(0, -offset);
-
-      // draw annotation - need to offset for current scroll position
-      pg[1].translate(0, offset);
-      pg[1].translate(-idWidth - 3,
-              (endSeq - startSeq) * av.getCharHeight() + 3);
-      pg[1].translate(idWidth + 3, 0);
-      ap.getAnnotationPanel().renderer.drawComponent(
-              ap.getAnnotationPanel(), av, pg[1], -1, startRes, endRes + 1);
-      pg[1].translate(0, -offset);
-    }
-
-    return Printable.PAGE_EXISTS;
+    return ap.printUnwrapped(pwidth, pheight, pi, pg);
   }
 
   public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)
           throws PrinterException
   {
-    return ap.printWrappedAlignment(pg[1], pwidth, pheight, pi);
+    return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
   }
 
   private String getHtml(String titleSvg, String alignmentSvg,
@@ -506,266 +273,37 @@ public class HtmlSvgOutput
     // jquery facebox for displaying raw BioJSON data");
     if (jsonData != null)
     {
-      htmlSvg.append("/* Facebox (for jQuery)\n");
-      htmlSvg.append("* version: 1.3\n");
-      htmlSvg.append(" * @requires jQuery v1.2 or later\n");
-      htmlSvg.append(" * @homepage https://github.com/defunkt/facebox\n");
-      htmlSvg.append(" * Licensed under the MIT:\n");
-      htmlSvg.append(" *   http://www.opensource.org/licenses/mit-license.php\n");
-      htmlSvg.append(" * Copyright Forever Chris Wanstrath, Kyle Neath\n");
-      htmlSvg.append(" * Usage:\n");
-      htmlSvg.append(" *  jQuery(document).ready(function() {\n");
-      htmlSvg.append(" *    jQuery('a[rel*=facebox]').facebox()\n");
-      htmlSvg.append(" *  })\n");
-      htmlSvg.append(" *  <a href=\"#terms\" rel=\"facebox\">Terms</a>\n");
-      htmlSvg.append(" *    Loads the #terms div in the box\n");
-      htmlSvg.append(" *  <a href=\"terms.html\" rel=\"facebox\">Terms</a>\n");
-      htmlSvg.append(" *    Loads the terms.html page in the box\n");
-      htmlSvg.append(" *  <a href=\"terms.png\" rel=\"facebox\">Terms</a>\n");
-      htmlSvg.append(" *    Loads the terms.png image in the box\n");
-      htmlSvg.append(" *  You can also use it programmatically:\n");
-      htmlSvg.append(" *    jQuery.facebox('some html')\n");
-      htmlSvg.append(" *    jQuery.facebox('some html', 'my-groovy-style')\n");
-      htmlSvg.append(" *  The above will open a facebox with \"some html\" as the content.\n");
-      htmlSvg.append(" *    jQuery.facebox(function($) {\n");
-      htmlSvg.append(" *      $.get('blah.html', function(data) { $.facebox(data) })\n");
-      htmlSvg.append(" *    })\n");
-      htmlSvg.append(" *  The above will show a loading screen before the passed function is called,\n");
-      htmlSvg.append(" *  allowing for a better ajaxy experience.\n");
-      htmlSvg.append(" *  The facebox function can also display an ajax page, an image, or the contents of a div:\n");
-      htmlSvg.append(" *    jQuery.facebox({ ajax: 'remote.html' })\n");
-      htmlSvg.append(" *    jQuery.facebox({ ajax: 'remote.html' }, 'my-groovy-style')\n");
-      htmlSvg.append(" *    jQuery.facebox({ image: 'stairs.jpg' })\n");
-      htmlSvg.append(" *    jQuery.facebox({ image: 'stairs.jpg' }, 'my-groovy-style')\n");
-      htmlSvg.append(" *    jQuery.facebox({ div: '#box' })\n");
-      htmlSvg.append(" *    jQuery.facebox({ div: '#box' }, 'my-groovy-style')\n");
-      htmlSvg.append(" *    Want to close the facebox?  Trigger the 'close.facebox' document event:\n");
-      htmlSvg.append(" *    jQuery(document).trigger('close.facebox')\n");
-      htmlSvg.append(" *  Facebox also has a bunch of other hooks:\n");
-      htmlSvg.append(" *    loading.facebox\n");
-      htmlSvg.append(" *    beforeReveal.facebox\n");
-      htmlSvg.append(" *    reveal.facebox (aliased as 'afterReveal.facebox')\n");
-      htmlSvg.append(" *    init.facebox\n");
-      htmlSvg.append(" *    afterClose.facebox\n");
-      htmlSvg.append(" *  Simply bind a function to any of these hooks:\n");
-      htmlSvg.append(" *   $(document).bind('reveal.facebox', function() { ...stuff to do after the facebox and contents are revealed... })\n");
-      htmlSvg.append(" *\n");
-      htmlSvg.append(" */\n");
-      htmlSvg.append("(function($) {\n");
-      htmlSvg.append("  $.facebox = function(data, klass) {\n");
-      htmlSvg.append("    $.facebox.loading()\n");
-      htmlSvg.append("    if (data.ajax) fillFaceboxFromAjax(data.ajax, klass)\n");
-      htmlSvg.append("    else if (data.image) fillFaceboxFromImage(data.image, klass)\n");
-      htmlSvg.append("    else if (data.div) fillFaceboxFromHref(data.div, klass)\n");
-      htmlSvg.append("    else if ($.isFunction(data)) data.call($)\n");
-      htmlSvg.append("    else $.facebox.reveal(data, klass)\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  $.extend($.facebox, {\n");
-      htmlSvg.append("    settings: {\n");
-      htmlSvg.append("      opacity      : 0.2,\n");
-      htmlSvg.append("      overlay      : true,\n");
-      htmlSvg.append("      loadingImage : 'https://raw.githubusercontent.com/jalview/biojson/gh-pages/images/loading.gif',\n");
-      htmlSvg.append("      closeImage   : 'https://raw.githubusercontent.com/jalview/biojson/gh-pages/images/cancel.png',\n");
-      htmlSvg.append("      imageTypes   : [ 'png', 'jpg', 'jpeg', 'gif' ],\n");
-      htmlSvg.append("      faceboxHtml  : '<div  id=\"facebox\" style=\"display:none; width: 95%; height: 85%; overflow: auto;\"> ");
-      htmlSvg.append("      <div class=\"popup\"> ");
-      htmlSvg.append("        <div class=\"content\"> ");
-      htmlSvg.append("        </div> ");
-      htmlSvg.append("        <a href=\"#\" class=\"close\"></a> ");
-      htmlSvg.append("      </div> ");
-      htmlSvg.append("    </div>'\n");
-      htmlSvg.append("    },      \n");
-      htmlSvg.append("    loading: function() {\n");
-      htmlSvg.append("      init()\n");
-      htmlSvg.append("      if ($('#facebox .loading').length == 1) return true\n");
-      htmlSvg.append("      showOverlay()      \n");
-      htmlSvg.append("      $('#facebox .content').empty().\n");
-      htmlSvg.append("        append('<div class=\"loading\"><img src=\"'+$.facebox.settings.loadingImage+'\"/></div>')\n");
-      htmlSvg.append("      $('#facebox').show().css({\n");
-      htmlSvg.append("        top:    getPageScroll()[1] + (getPageHeight() / 10),\n");
-      htmlSvg.append("        left:    $(window).width() / 2 - ($('#facebox .popup').outerWidth() / 2)\n");
-      htmlSvg.append("      })      \n");
-      htmlSvg.append("      $(document).bind('keydown.facebox', function(e) {\n");
-      htmlSvg.append("       if (e.keyCode == 27) $.facebox.close()\n");
-      htmlSvg.append("        return true\n");
-      htmlSvg.append("      })\n");
-      htmlSvg.append("      $(document).trigger('loading.facebox')\n");
-      htmlSvg.append("    },\n");
-      htmlSvg.append("    reveal: function(data, klass) {\n");
-      htmlSvg.append("      $(document).trigger('beforeReveal.facebox')\n");
-      htmlSvg.append("      if (klass) $('#facebox .content').addClass(klass)\n");
-      htmlSvg.append("      $('#facebox .content').empty().append('<pre><code>'+JSON.stringify(JSON.parse(data),null,4)+'</pre></code>')\n");
-      htmlSvg.append("      $('#facebox .popup').children().fadeIn('normal')\n");
-      htmlSvg.append("      $('#facebox').css('left', $(window).width() / 2 - ($('#facebox .popup').outerWidth() / 2))\n");
-      htmlSvg.append("      $(document).trigger('reveal.facebox').trigger('afterReveal.facebox')\n");
-      htmlSvg.append("    },      \n");
-      htmlSvg.append("    close: function() {\n");
-      htmlSvg.append("      $(document).trigger('close.facebox')\n");
-      htmlSvg.append("      return false\n");
-      htmlSvg.append("    }\n");
-      htmlSvg.append("  })\n");
-      htmlSvg.append("  $.fn.facebox = function(settings) {\n");
-      htmlSvg.append("    if ($(this).length == 0) return    \n");
-      htmlSvg.append("    init(settings)      \n");
-      htmlSvg.append("    function clickHandler() {\n");
-      htmlSvg.append("      $.facebox.loading(true)      \n");
-      htmlSvg.append("      // support for rel=\"facebox.inline_popup\" syntax, to add a class\n");
-      htmlSvg.append("      // also supports deprecated \"facebox[.inline_popup]\" syntax\n");
-      htmlSvg.append("      var klass = this.rel.match(/facebox\\[?\\.(\\w+)\\]?/)\n");
-      htmlSvg.append("      if (klass) klass = klass[1]\n");
-      htmlSvg.append("      fillFaceboxFromHref(this.href, klass)\n");
-      htmlSvg.append("      return false\n");
-      htmlSvg.append("    }      \n");
-      htmlSvg.append("    return this.bind('click.facebox', clickHandler)\n");
-      htmlSvg.append("  }\n");
-      htmlSvg.append("  // called one time to setup facebox on this page\n");
-      htmlSvg.append("  function init(settings) {\n");
-      htmlSvg.append("    if ($.facebox.settings.inited) return true\n");
-      htmlSvg.append("    else $.facebox.settings.inited = true\n");
-      htmlSvg.append("    $(document).trigger('init.facebox')\n");
-      htmlSvg.append("    makeCompatible()\n");
-      htmlSvg.append("    var imageTypes = $.facebox.settings.imageTypes.join('|')\n");
-      htmlSvg.append("    $.facebox.settings.imageTypesRegexp = new RegExp('\\\\.(' + imageTypes + ')(\\\\?.*)?$', 'i')\n");
-
-      htmlSvg.append("    if (settings) $.extend($.facebox.settings, settings)\n");
-      htmlSvg.append("    $('body').append($.facebox.settings.faceboxHtml)\n");
-
-      htmlSvg.append("    var preload = [ new Image(), new Image() ]\n");
-      htmlSvg.append("    preload[0].src = $.facebox.settings.closeImage\n");
-      htmlSvg.append("    preload[1].src = $.facebox.settings.loadingImage\n");
-
-      htmlSvg.append("    $('#facebox').find('.b:first, .bl').each(function() {\n");
-      htmlSvg.append("      preload.push(new Image())\n");
-      htmlSvg.append("      preload.slice(-1).src = $(this).css('background-image').replace(/url\\((.+)\\)/, '$1')\n");
-      htmlSvg.append("    })\n");
-
-      htmlSvg.append("    $('#facebox .close')\n");
-      htmlSvg.append("      .click($.facebox.close)\n");
-      htmlSvg.append("      .append('<img src=\"'\n");
-      htmlSvg.append("              + $.facebox.settings.closeImage\n");
-      htmlSvg.append("              + '\" class=\"close_image\" title=\"close\">')\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  // getPageScroll() by quirksmode.com\n");
-      htmlSvg.append("  function getPageScroll() {\n");
-      htmlSvg.append("    var xScroll, yScroll;\n");
-      htmlSvg.append("    if (self.pageYOffset) {\n");
-      htmlSvg.append("      yScroll = self.pageYOffset;\n");
-      htmlSvg.append("      xScroll = self.pageXOffset;\n");
-      htmlSvg.append("    } else if (document.documentElement && document.documentElement.scrollTop) {     // Explorer 6 Strict\n");
-      htmlSvg.append("      yScroll = document.documentElement.scrollTop;\n");
-      htmlSvg.append("      xScroll = document.documentElement.scrollLeft;\n");
-      htmlSvg.append("    } else if (document.body) {// all other Explorers\n");
-      htmlSvg.append("      yScroll = document.body.scrollTop;\n");
-      htmlSvg.append("      xScroll = document.body.scrollLeft;\n");
-      htmlSvg.append("    }\n");
-      htmlSvg.append("    return new Array(xScroll,yScroll)\n");
-      htmlSvg.append("  }\n");
-
-      // Adapted from getPageSize() by quirksmode.com");
-      htmlSvg.append("  function getPageHeight() {\n");
-      htmlSvg.append("    var windowHeight\n");
-      htmlSvg.append("    if (self.innerHeight) {    // all except Explorer\n");
-      htmlSvg.append("      windowHeight = self.innerHeight;\n");
-      htmlSvg.append("    } else if (document.documentElement && document.documentElement.clientHeight) { // Explorer 6 Strict Mode\n");
-      htmlSvg.append("      windowHeight = document.documentElement.clientHeight;\n");
-      htmlSvg.append("    } else if (document.body) { // other Explorers\n");
-      htmlSvg.append("      windowHeight = document.body.clientHeight;\n");
-      htmlSvg.append("    }\n");
-      htmlSvg.append("    return windowHeight\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  // Backwards compatibility\n");
-      htmlSvg.append("  function makeCompatible() {\n");
-      htmlSvg.append("    var $s = $.facebox.settings      \n");
-      htmlSvg.append("    $s.loadingImage = $s.loading_image || $s.loadingImage\n");
-      htmlSvg.append("    $s.closeImage = $s.close_image || $s.closeImage\n");
-      htmlSvg.append("    $s.imageTypes = $s.image_types || $s.imageTypes\n");
-      htmlSvg.append("    $s.faceboxHtml = $s.facebox_html || $s.faceboxHtml\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  // Figures out what you want to display and displays it\n");
-      htmlSvg.append("  // formats are:\n");
-      htmlSvg.append("  //     div: #id\n");
-      htmlSvg.append("  //   image: blah.extension\n");
-      htmlSvg.append("  //    ajax: anything else\n");
-      htmlSvg.append("  function fillFaceboxFromHref(href, klass) {\n");
-      htmlSvg.append("    // div\n");
-      htmlSvg.append("    if (href.match(/#/)) {\n");
-      htmlSvg.append("      var url    = window.location.href.split('#')[0]\n");
-      htmlSvg.append("      var target = href.replace(url,'')\n");
-      htmlSvg.append("      if (target == '#') return\n");
-      htmlSvg.append("      $.facebox.reveal($(target).html(), klass)\n");
-
-      htmlSvg.append("    // image\n");
-      htmlSvg.append("    } else if (href.match($.facebox.settings.imageTypesRegexp)) {\n");
-      htmlSvg.append("      fillFaceboxFromImage(href, klass)\n");
-      htmlSvg.append("    // ajax\n");
-      htmlSvg.append("    } else {\n");
-      htmlSvg.append("      fillFaceboxFromAjax(href, klass)\n");
-      htmlSvg.append("    }\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  function fillFaceboxFromImage(href, klass) {\n");
-      htmlSvg.append("    var image = new Image()\n");
-      htmlSvg.append("    image.onload = function() {\n");
-      htmlSvg.append("      $.facebox.reveal('<div class=\"image\"><img src=\"' + image.src + '\" /></div>', klass)\n");
-      htmlSvg.append("    }\n");
-      htmlSvg.append("    image.src = href\n");
-      htmlSvg.append("   }\n");
-
-      htmlSvg.append("  function fillFaceboxFromAjax(href, klass) {\n");
-      htmlSvg.append("    $.facebox.jqxhr = $.get(href, function(data) { $.facebox.reveal(data, klass) })\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  function skipOverlay() {\n");
-      htmlSvg.append("    return $.facebox.settings.overlay == false || $.facebox.settings.opacity === null\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  function showOverlay() {\n");
-      htmlSvg.append("    if (skipOverlay()) return\n");
-
-      htmlSvg.append("    if ($('#facebox_overlay').length == 0)\n");
-      htmlSvg.append("      $(\"body\").append('<div id=\"facebox_overlay\" class=\"facebox_hide\"></div>')\n");
-
-      htmlSvg.append("    $('#facebox_overlay').hide().addClass(\"facebox_overlayBG\")\n");
-      htmlSvg.append("      .css('opacity', $.facebox.settings.opacity)\n");
-      htmlSvg.append("      .click(function() { $(document).trigger('close.facebox') })\n");
-      htmlSvg.append("       .fadeIn(200)\n");
-      htmlSvg.append("    return false\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  function hideOverlay() {\n");
-      htmlSvg.append("    if (skipOverlay()) return      \n");
-      htmlSvg.append("    $('#facebox_overlay').fadeOut(200, function(){\n");
-      htmlSvg.append("      $(\"#facebox_overlay\").removeClass(\"facebox_overlayBG\")\n");
-      htmlSvg.append("      $(\"#facebox_overlay\").addClass(\"facebox_hide\")\n");
-      htmlSvg.append("      $(\"#facebox_overlay\").remove()\n");
-      htmlSvg.append("    })      \n");
-      htmlSvg.append("    return false\n");
-      htmlSvg.append("  }\n");
-
-      htmlSvg.append("  $(document).bind('close.facebox', function() {\n");
-      htmlSvg.append("    if ($.facebox.jqxhr) {\n");
-      htmlSvg.append("      $.facebox.jqxhr.abort()\n");
-      htmlSvg.append("      $.facebox.jqxhr = null\n");
-      htmlSvg.append("    }\n");
-      htmlSvg.append("    $(document).unbind('keydown.facebox')\n");
-      htmlSvg.append("    $('#facebox').fadeOut(function() {\n");
-      htmlSvg.append("      $('#facebox .content').removeClass().addClass('content')\n");
-      htmlSvg.append("      $('#facebox .loading').remove()\n");
-      htmlSvg.append("      $(document).trigger('afterClose.facebox')\n");
-      htmlSvg.append("    })\n");
-      htmlSvg.append("    hideOverlay()\n");
-      htmlSvg.append("  })\n");
-
-      htmlSvg.append("})(jQuery);\n");
-
+      File faceBoxJsFile = new File("examples/javascript/facebox-1.3.js");
+      try
+      {
+        htmlSvg.append(HTMLOutput.readFileAsString(faceBoxJsFile));
+      } catch (IOException e)
+      {
+        e.printStackTrace();
+      }
     }
 
     htmlSvg.append("</script>\n");
     htmlSvg.append("</html>");
     return htmlSvg.toString();
   }
+
+  @Override
+  public boolean isEmbedData()
+  {
+    return Boolean.valueOf(jalview.bin.Cache.getDefault(
+            "EXPORT_EMBBED_BIOJSON", "true"));
+  }
+
+  @Override
+  public boolean isLaunchInBrowserAfterExport()
+  {
+    return true;
+  }
+
+  @Override
+  public File getExportedFile()
+  {
+    return generatedFile;
+  }
 }