X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlSvgOutput.java;h=68173ff6a6205c15929314a6d9d339772cb3eef9;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=68f99240238e4c5a76b8113f0da51a3bfe3f6cf7;hpb=81edd609f9841a84d5799d221277d45413a177cf;p=jalview.git

diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java
index 68f9924..68173ff 100644
--- a/src/jalview/io/HtmlSvgOutput.java
+++ b/src/jalview/io/HtmlSvgOutput.java
@@ -1,11 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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.AnnotationPanel;
-import jalview.gui.FeatureRenderer;
 import jalview.gui.HTMLOptions;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.OOMWarning;
 import jalview.math.AlignmentDimension;
 import jalview.util.MessageManager;
 
@@ -25,103 +48,213 @@ public class HtmlSvgOutput
   AlignViewport av;
 
   FeatureRenderer fr;
+
   AlignmentPanel ap;
 
-  AnnotationPanel annotationPanel;
+  private IProgressIndicator pIndicator;
+
+  private long pSessionId;
+
+  private boolean headless;
 
   public HtmlSvgOutput(File file, AlignmentPanel ap)
   {
-
-      this.av = ap.av;
-      this.ap = ap;
-      this.annotationPanel = ap.getAnnotationPanel();
+    this.av = ap.av;
+    this.ap = ap;
+    fr = ap.cloneFeatureRenderer();
     generateHtmlSvgOutput(file);
   }
 
   public void generateHtmlSvgOutput(File file)
   {
+    pIndicator = ap.alignFrame;
+    pSessionId = System.currentTimeMillis();
     try
     {
-      if (file == null /*
-                        * && !(System.getProperty("java.awt.headless") != null
-                        * && System
-                        * .getProperty("java.awt.headless").equals("true"))
-                        */)
+      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);
 
-      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();
-      }
+        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;
+        }
       }
+    } catch (Exception e)
+    {
+      pIndicator.setProgressBar(MessageManager.formatMessage(
+              "info.error_creating_file", "HTML"), pSessionId);
+      e.printStackTrace();
+      return;
+    }
+    final File fileX = file;
+    new Thread()
+    {
+      @Override
+      public void run()
+      {
+        try
+        {
+          setProgressMessage(null);
+          setProgressMessage(MessageManager.formatMessage(
+                  "status.exporting_alignment_as_x_file", "HTML"));
+          AlignmentDimension aDimension = ap.getAlignmentDimension();
+          SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
+                  aDimension.getHeight());
+          SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
+                  aDimension.getHeight());
 
-      AlignmentDimension aDimension = ap.getAlignmentDimension();
-      SVGGraphics2D g1 = new SVGGraphics2D(aDimension.getWidth(),
-              aDimension.getHeight());
-      SVGGraphics2D g2 = new SVGGraphics2D(aDimension.getWidth(),
-              aDimension.getHeight());
+          String renderStyle = jalview.bin.Cache.getDefault(
+                  "HTML_RENDERING", "Prompt each time");
 
-      String renderStyle = jalview.bin.Cache.getDefault("HTML_RENDERING",
-              "Prompt each time");
+          // 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")))
+          {
+            HTMLOptions svgOption = new HTMLOptions();
+            renderStyle = svgOption.getValue();
 
-      // 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")))
-      {
-        HTMLOptions svgOption = new HTMLOptions();
-        renderStyle = svgOption.getValue();
+            if (renderStyle == null || svgOption.cancelled)
+            {
+              setProgressMessage(MessageManager.formatMessage(
+                      "status.cancelled_image_export_operation", "HTML"));
+              return;
+            }
+          }
+
+          if (renderStyle.equalsIgnoreCase("Lineart"))
+          {
+            g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+                    SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+            g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
+                    SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
+          }
+          printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+                  g1, g2);
+
+          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;
+              }
 
-        if (renderStyle == null || svgOption.cancelled)
+              @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);
+          FileOutputStream out = new FileOutputStream(fileX);
+          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);
+          }
+        } catch (OutOfMemoryError err)
         {
-          return;
+          System.out.println("########################\n"
+                  + "OUT OF MEMORY " + fileX + "\n"
+                  + "########################");
+          new OOMWarning("Creating Image for " + fileX, err);
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+          pIndicator.setProgressBar(MessageManager.formatMessage(
+                  "info.error_creating_file", "HTML"), pSessionId);
         }
+        setProgressMessage(MessageManager.formatMessage(
+                "status.export_complete", "HTML"));
       }
+    }.start();
 
-      if (renderStyle.equalsIgnoreCase("lineart"))
-      {
-        g1.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
-                SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
-        g2.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
-                SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
-      }
-      printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, g1,
-              g2);
-      FileOutputStream out = new FileOutputStream(file);
-
-      String titleSvgData = g1.getSVGDocument();
-      String alignSvgData = g2.getSVGDocument();
-      String htmlData = getHtml(titleSvgData, alignSvgData);
-
-      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:///" + file);
-      }
-    } catch (Exception e)
+  }
+
+  private void setProgressMessage(String message)
+  {
+    if (pIndicator != null && !headless)
     {
-      e.printStackTrace();
+      pIndicator.setProgressBar(message, pSessionId);
+    }
+    else
+    {
+      System.out.println(message);
     }
   }
-  
+
   static JalviewFileChooser getHTMLChooser()
   {
     return new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
-            { "html" }, new String[]
-            { "Hypertext Markup Language" }, "Hypertext Markup Language");
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            new String[] { "html" },
+            new String[] { "Hypertext Markup Language" },
+            "Hypertext Markup Language");
   }
 
   public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg)
@@ -220,9 +353,7 @@ public class HtmlSvgOutput
                 - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
                 - 4;
       }
-      pg[0].drawString(
-              seq.getDisplayId(av.getShowJVSuffix()),
-              xPos,
+      pg[0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
               (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
                       - (av.getCharHeight() / 5));
     }
@@ -256,19 +387,360 @@ public class HtmlSvgOutput
 
     return Printable.PAGE_EXISTS;
   }
-  
-  private String getHtml(String titleSvg, String alignmentSvg)
+
+  private String getHtml(String titleSvg, String alignmentSvg,
+          String jsonData)
   {
     StringBuilder htmlSvg = new StringBuilder();
-    htmlSvg.append("<html><style type=\"text/css\">" + "div.title {"
-            + "height: 100%;" + "width: 9%;" + "float: left;" + "}"
-            + "div.align {" + "height: 100%;" + "width: 91%;"
-            + "overflow: scroll;" + "float: right;" + "}" + "</style>"
-            + "<div style=\"width:100%; height:100%; overflow: hidden\">"
-            + "<div class=\"title\">");
+    htmlSvg.append("<html>\n");
+    if (jsonData != null)
+    {
+      htmlSvg.append("<button onclick=\"javascipt:openJalviewUsingCurrentUrl();\">Launch in Jalview</button> &nbsp;");
+      htmlSvg.append("<input type=\"submit\" value=\"View raw BioJSON Data\" onclick=\"jQuery.facebox({ div:'#seqData' }); return false;\" />");
+      htmlSvg.append("<div style=\"display: none;\" name=\"seqData\" id=\"seqData\" >"
+              + jsonData + "</div>");
+      htmlSvg.append("<br/>&nbsp;");
+    }
+    htmlSvg.append("\n<style type=\"text/css\"> "
+            + "div.parent{ width:100%;<!-- overflow: auto; -->}\n"
+            + "div.titlex{ width:11%; float: left; }\n"
+            + "div.align{ width:89%; float: right; }\n"
+            + "div.main-container{ border: 2px solid blue; border: 2px solid blue; width: 99%;   min-height: 99%; }\n"
+            + ".sub-category-container {overflow-y: scroll; overflow-x: hidden; width: 100%; height: 100%;}\n"
+            + "object {pointer-events: none;}");
+    if (jsonData != null)
+    {
+      // facebox style sheet for displaying raw BioJSON data
+      htmlSvg.append("#facebox { position: absolute;  top: 0;   left: 0; z-index: 100; text-align: left; }\n"
+              + "#facebox .popup{ position:relative; border:3px solid rgba(0,0,0,0); -webkit-border-radius:5px;"
+              + "-moz-border-radius:5px; border-radius:5px; -webkit-box-shadow:0 0 18px rgba(0,0,0,0.4); -moz-box-shadow:0 0 18px rgba(0,0,0,0.4);"
+              + "box-shadow:0 0 18px rgba(0,0,0,0.4); }\n"
+              + "#facebox .content { display:table; width: 98%; padding: 10px; background: #fff; -webkit-border-radius:4px; -moz-border-radius:4px;"
+              + " border-radius:4px; }\n"
+              + "#facebox .content > p:first-child{ margin-top:0; }\n"
+              + "#facebox .content > p:last-child{ margin-bottom:0; }\n"
+              + "#facebox .close{ position:absolute; top:5px; right:5px; padding:2px; background:#fff; }\n"
+              + "#facebox .close img{ opacity:0.3; }\n"
+              + "#facebox .close:hover img{ opacity:1.0; }\n"
+              + "#facebox .loading { text-align: center; }\n"
+              + "#facebox .image { text-align: center;}\n"
+              + "#facebox img { border: 0;  margin: 0; }\n"
+              + "#facebox_overlay { position: fixed; top: 0px; left: 0px; height:100%; width:100%; }\n"
+              + ".facebox_hide { z-index:-100; }\n"
+              + ".facebox_overlayBG { background-color: #000;  z-index: 99;  }");
+    }
+
+    htmlSvg.append("</style>");
+    htmlSvg.append("<div class=\"main-container\" \n>");
+    htmlSvg.append("<div class=\"titlex\">\n");
+    htmlSvg.append("<div class=\"sub-category-container\"> \n");
     htmlSvg.append(titleSvg);
-    htmlSvg.append("</div><div class=\"align\">").append(alignmentSvg);
     htmlSvg.append("</div>");
+    htmlSvg.append("</div>\n\n<!-- ========================================================================================== -->\n\n");
+    htmlSvg.append("<div class=\"align\" >");
+    htmlSvg.append(
+            "<div class=\"sub-category-container\"> <div style=\"overflow-x: scroll;\">")
+            .append(alignmentSvg).append("</div></div>").append("</div>");
+    htmlSvg.append("</div>");
+
+    htmlSvg.append("<script language=\"JavaScript\" type=\"text/javascript\" src=\"http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js\"></script>\n"
+            + "<script language=\"JavaScript\" type=\"text/javascript\"  src=\"http://ajax.googleapis.com/ajax/libs/jqueryui/1.11.2/jquery-ui.min.js\"></script>\n"
+            + "<script>\n"
+            + "var subCatContainer = $(\".sub-category-container\");\n"
+            + "subCatContainer.scroll(\nfunction() {\n"
+            + "subCatContainer.scrollTop($(this).scrollTop());\n});\n");
+
+    htmlSvg.append("</script>\n");
+
+    // javascript for launching file in Jalview
+
+    htmlSvg.append("<script language=\"JavaScript\">\n");
+    htmlSvg.append("function openJalviewUsingCurrentUrl(){\n");
+    htmlSvg.append("    var json = JSON.parse(document.getElementById(\"seqData\").innerHTML);\n");
+    htmlSvg.append("    var jalviewVersion = json['appSettings'].version;\n");
+    htmlSvg.append("    var url = json['appSettings'].webStartUrl;\n");
+    htmlSvg.append("    var myForm = document.createElement(\"form\");\n\n");
+    htmlSvg.append("    var heap = document.createElement(\"input\");\n");
+    htmlSvg.append("    heap.setAttribute(\"name\", \"jvm-max-heap\") ;\n");
+    htmlSvg.append("    heap.setAttribute(\"value\", \"2G\");\n\n");
+    htmlSvg.append("    var target = document.createElement(\"input\");\n");
+    htmlSvg.append("    target.setAttribute(\"name\", \"open\");\n");
+    htmlSvg.append("    target.setAttribute(\"value\", document.URL);\n\n");
+    htmlSvg.append("    var jvVersion = document.createElement(\"input\");\n");
+    htmlSvg.append("    jvVersion.setAttribute(\"name\", \"version\") ;\n");
+    htmlSvg.append("    jvVersion.setAttribute(\"value\", jalviewVersion);\n\n");
+    htmlSvg.append("    myForm.action = url;\n");
+    htmlSvg.append("    myForm.appendChild(heap);\n");
+    htmlSvg.append("    myForm.appendChild(target);\n");
+    htmlSvg.append("    myForm.appendChild(jvVersion);\n");
+    htmlSvg.append("    document.body.appendChild(myForm);\n");
+    htmlSvg.append("    myForm.submit() ;\n");
+    htmlSvg.append("    document.body.removeChild(myForm);\n");
+    htmlSvg.append("}\n");
+
+    // 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");
+
+    }
+
+    htmlSvg.append("</script>\n");
+    htmlSvg.append("</html>");
     return htmlSvg.toString();
   }
 }