JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-neede...
[jalview.git] / src / jalview / io / HTMLOutput.java
old mode 100755 (executable)
new mode 100644 (file)
index 6c2c51e..eb44180
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.gui.*;\r
-\r
-public class HTMLOutput\r
-{\r
-  AlignViewport av;\r
-  SequenceRenderer sr;\r
-  FeatureRenderer fr;\r
-  Color color;\r
-\r
-  public HTMLOutput(AlignViewport av, SequenceRenderer sr, FeatureRenderer fr1)\r
-  {\r
-    this.av = av;\r
-    this.sr = sr;\r
-\r
-    fr = new FeatureRenderer(av);\r
-    fr.transferSettings(fr1);\r
-\r
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
-        getProperty(\r
-            "LAST_DIRECTORY"), new String[]\r
-        {"html"},\r
-        new String[]\r
-        {"HTML files"}, "HTML files");\r
-\r
-    chooser.setFileView(new JalviewFileView());\r
-    chooser.setDialogTitle("Save as HTML");\r
-    chooser.setToolTipText("Save");\r
-\r
-    int value = chooser.showSaveDialog(null);\r
-\r
-    if (value == JalviewFileChooser.APPROVE_OPTION)\r
-    {\r
-      String choice = chooser.getSelectedFile().getPath();\r
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
-                                    chooser.getSelectedFile().getParent());\r
-\r
-      try\r
-      {\r
-        PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
-            choice));\r
-        out.println("<HTML>");\r
-        out.println("<style type=\"text/css\">");\r
-        out.println("<!--");\r
-        out.print("td {font-family: \"" + av.getFont().getFamily() +\r
-                  "\", \"" + av.getFont().getName() + "\", mono; " +\r
-                  "font-size: " + av.getFont().getSize() + "px; ");\r
-\r
-        if (av.getFont().getStyle() == Font.BOLD)\r
-        {\r
-          out.print("font-weight: BOLD; ");\r
-        }\r
-\r
-        if (av.getFont().getStyle() == Font.ITALIC)\r
-        {\r
-          out.print("font-style: italic; ");\r
-        }\r
-\r
-        out.println("text-align: center; }");\r
-\r
-        out.println("-->");\r
-        out.println("</style>");\r
-        out.println("<BODY>");\r
-\r
-        if (av.getWrapAlignment())\r
-        {\r
-          drawWrappedAlignment(out);\r
-        }\r
-        else\r
-        {\r
-          drawUnwrappedAlignment(out);\r
-        }\r
-\r
-        out.println("\n</body>\n</html>");\r
-        out.close();\r
-        jalview.util.BrowserLauncher.openURL("file:///" + choice);\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        ex.printStackTrace();\r
-      }\r
-    }\r
-  }\r
-\r
-  void drawUnwrappedAlignment(PrintWriter out)\r
-  {\r
-    out.println("<table border=\"1\"><tr><td>\n");\r
-    out.println(\r
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
-    //////////////\r
-    SequenceI seq;\r
-    AlignmentI alignment = av.getAlignment();\r
-\r
-    // draws the top row, the measure rule\r
-    out.println("<tr><td colspan=\"6\"></td>");\r
-\r
-    int i = 0;\r
-\r
-    for (i = 10; i < (alignment.getWidth() - 10); i += 10)\r
-    {\r
-      out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-    }\r
-\r
-    out.println("<td colspan=\"3\"></td><td colspan=\"3\">" + i +\r
-                "<br>|</td>");\r
-    out.println("</tr>");\r
-\r
-    for (i = 0; i < alignment.getHeight(); i++)\r
-    {\r
-      seq = alignment.getSequenceAt(i);\r
-\r
-      String id = seq.getDisplayId(av.getShowJVSuffix());\r
-\r
-      out.println("<tr><td nowrap>" + id +\r
-                  "&nbsp;&nbsp;</td>");\r
-\r
-      for (int res = 0; res < seq.getLength(); res++)\r
-      {\r
-        if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))\r
-        {\r
-          color = sr.getResidueBoxColour(seq, res);\r
-\r
-          color = fr.findFeatureColour(color, seq, res);\r
-        }\r
-        else\r
-        {\r
-          color = Color.white;\r
-        }\r
-\r
-        if (color.getRGB() < -1)\r
-        {\r
-          out.println("<td bgcolor=\"#" +\r
-                      jalview.util.Format.getHexString(color) + "\">" +\r
-                      seq.getCharAt(res) + "</td>");\r
-        }\r
-        else\r
-        {\r
-          out.println("<td>" + seq.getCharAt(res) + "</td>");\r
-        }\r
-      }\r
-\r
-      out.println("</tr>");\r
-    }\r
-\r
-    //////////////\r
-    out.println("</table>");\r
-    out.println("</td></tr></table>");\r
-  }\r
-\r
-  void drawWrappedAlignment(PrintWriter out)\r
-  {\r
-    ////////////////////////////////////\r
-    /// How many sequences and residues can we fit on a printable page?\r
-    AlignmentI al = av.getAlignment();\r
-    SequenceI seq;\r
-    String r;\r
-    String g;\r
-    String b;\r
-\r
-    out.println("<table border=\"1\"><tr><td>\n");\r
-    out.println(\r
-        "<table border=\"0\"  cellpadding=\"0\" cellspacing=\"0\">\n");\r
-\r
-    for (int startRes = 0; startRes < al.getWidth();\r
-         startRes += av.getWrappedWidth())\r
-    {\r
-      int endRes = startRes + av.getWrappedWidth();\r
-\r
-      if (endRes > al.getWidth())\r
-      {\r
-        endRes = al.getWidth();\r
-      }\r
-\r
-      if (av.getScaleAboveWrapped())\r
-      {\r
-        out.println("<tr>");\r
-\r
-        if (av.getScaleLeftWrapped())\r
-        {\r
-          out.println("<td colspan=\"7\">&nbsp;</td>");\r
-        }\r
-        else\r
-        {\r
-          out.println("<td colspan=\"6\">&nbsp;</td>");\r
-        }\r
-\r
-        for (int i = startRes + 10; i < endRes; i += 10)\r
-        {\r
-          out.println("<td colspan=\"9\">" + i + "<br>|</td><td></td>");\r
-        }\r
-\r
-        out.println("</tr>");\r
-      }\r
-\r
-      int startPos, endPos;\r
-      for (int s = 0; s < al.getHeight(); s++)\r
-      {\r
-        out.println("<tr>");\r
-        seq = al.getSequenceAt(s);\r
-\r
-        startPos = seq.findPosition(startRes);\r
-        endPos = seq.findPosition(endRes) - 1;\r
-\r
-        String id = seq.getDisplayId(av.getShowJVSuffix());\r
-\r
-        out.println("<td nowrap>" + id +\r
-                    "&nbsp;&nbsp;</td>");\r
-\r
-        if (av.getScaleLeftWrapped())\r
-        {\r
-          if (startPos > seq.getEnd() || endPos == 0)\r
-          {\r
-            out.println("<td nowrap>&nbsp;</td>");\r
-          }\r
-          else\r
-          {\r
-            out.println("<td nowrap>" + startPos +\r
-                        "&nbsp;&nbsp;</td>");\r
-          }\r
-        }\r
-\r
-        for (int res = startRes; res < endRes; res++)\r
-        {\r
-          if (!jalview.util.Comparison.isGap(seq.getCharAt(res)))\r
-          {\r
-            color = sr.getResidueBoxColour(seq, res);\r
-\r
-            color = fr.findFeatureColour(color, seq, res);\r
-          }\r
-          else\r
-          {\r
-            color = Color.white;\r
-          }\r
-\r
-          if (color.getRGB() < -1)\r
-          {\r
-            out.println("<td bgcolor=\"#" +\r
-                        jalview.util.Format.getHexString(color) + "\">" +\r
-                        seq.getCharAt(res) + "</td>");\r
-          }\r
-          else\r
-          {\r
-            out.println("<td>" + seq.getCharAt(res) + "</td>");\r
-          }\r
-\r
-        }\r
-\r
-        if (av.getScaleRightWrapped() &&\r
-            endRes < startRes + av.getWrappedWidth())\r
-        {\r
-          out.println("<td colspan=\"" +\r
-                      (startRes + av.getWrappedWidth() - endRes) + "\">"\r
-                      + "&nbsp;&nbsp;</td>");\r
-        }\r
-\r
-        if (av.getScaleRightWrapped() && startPos < endPos)\r
-        {\r
-          out.println("<td nowrap>&nbsp;" + endPos +\r
-                      "&nbsp;&nbsp;</td>");\r
-        }\r
-\r
-        out.println("</tr>");\r
-      }\r
-\r
-      if (endRes < al.getWidth())\r
-      {\r
-        out.println("<tr><td height=\"5\"></td></tr>");\r
-      }\r
-    }\r
-\r
-    out.println("</table>");\r
-    out.println("</table>");\r
-  }\r
-\r
-  public static String getImageMapHTML()\r
-  {\r
-    return new String(\r
-        "<html>\n"\r
-        + "<head>\n"\r
-        + "<script language=\"JavaScript\">\n"\r
-        + "var ns4 = document.layers;\n"\r
-        + "var ns6 = document.getElementById && !document.all;\n"\r
-        + "var ie4 = document.all;\n"\r
-        + "offsetX = 0;\n"\r
-        + "offsetY = 20;\n"\r
-        + "var toolTipSTYLE=\"\";\n"\r
-        + "function initToolTips()\n"\r
-        + "{\n"\r
-        + "  if(ns4||ns6||ie4)\n"\r
-        + "  {\n"\r
-        + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"\r
-        + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"\r
-        + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"\r
-        + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"\r
-        + "    else\n"\r
-        + "    {\n"\r
-        + "      toolTipSTYLE.visibility = \"visible\";\n"\r
-        + "      toolTipSTYLE.display = \"none\";\n"\r
-        + "    }\n"\r
-        + "    document.onmousemove = moveToMouseLoc;\n"\r
-        + "  }\n"\r
-        + "}\n"\r
-        + "function toolTip(msg, fg, bg)\n"\r
-        + "{\n"\r
-        + "  if(toolTip.arguments.length < 1) // hide\n"\r
-        + "  {\n"\r
-        + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"\r
-        + "    else toolTipSTYLE.display = \"none\";\n"\r
-        + "  }\n"\r
-        + "  else // show\n"\r
-        + "  {\n"\r
-        + "    if(!fg) fg = \"#555555\";\n"\r
-        + "    if(!bg) bg = \"#FFFFFF\";\n"\r
-        + "    var content =\n"\r
-        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"\r
-        + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"\r
-        +\r
-        "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"\r
-        + "    '\" size=\"-2\">&nbsp;' + msg +\n"\r
-        + "    '&nbsp;</font></td></table></td></table>';\n"\r
-        + "    if(ns4)\n"\r
-        + "    {\n"\r
-        + "      toolTipSTYLE.document.write(content);\n"\r
-        + "      toolTipSTYLE.document.close();\n"\r
-        + "      toolTipSTYLE.visibility = \"visible\";\n"\r
-        + "    }\n"\r
-        + "    if(ns6)\n"\r
-        + "    {\n"\r
-        +\r
-        "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"\r
-        + "      toolTipSTYLE.display='block'\n"\r
-        + "    }\n"\r
-        + "    if(ie4)\n"\r
-        + "    {\n"\r
-        + "      document.all(\"toolTipLayer\").innerHTML=content;\n"\r
-        + "      toolTipSTYLE.display='block'\n"\r
-        + "    }\n"\r
-        + "  }\n"\r
-        + "}\n"\r
-        + "function moveToMouseLoc(e)\n"\r
-        + "{\n"\r
-        + "  if(ns4||ns6)\n"\r
-        + "  {\n"\r
-        + "    x = e.pageX;\n"\r
-        + "    y = e.pageY;\n"\r
-        + "  }\n"\r
-        + "  else\n"\r
-        + "  {\n"\r
-        + "    x = event.x + document.body.scrollLeft;\n"\r
-        + "    y = event.y + document.body.scrollTop;\n"\r
-        + "  }\n"\r
-        + "  toolTipSTYLE.left = x + offsetX;\n"\r
-        + "  toolTipSTYLE.top = y + offsetY;\n"\r
-        + "  return true;\n"\r
-        + "}\n"\r
-        + "</script>\n"\r
-        + "</head>\n"\r
-        + "<body>\n"\r
-        + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"\r
-        + "<script language=\"JavaScript\"><!--\n"\r
-        + "initToolTips(); //--></script>\n");\r
-\r
-  }\r
-}\r
+/*
+ * 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 java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+import java.util.Objects;
+
+import jalview.api.AlignExportSettingsI;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignExportSettingsAdapter;
+import jalview.datamodel.AlignmentExportData;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.IProgressIndicator;
+import jalview.util.MessageManager;
+
+public abstract class HTMLOutput implements Runnable
+{
+  protected AlignmentPanel ap;
+
+  /*
+   * key for progress or status messages
+   */
+  protected long pSessionId;
+
+  /*
+   * (optional) place to write progress messages to
+   */
+  protected IProgressIndicator pIndicator;
+
+  protected File generatedFile;
+
+  String _bioJson = null;
+
+  private String description;
+
+  /**
+   * Constructor given an alignment panel (which should not be null)
+   * 
+   * @param ap
+   * @param desc
+   */
+  public HTMLOutput(AlignmentPanel ap, String desc)
+  {
+    this.ap = ap;
+    this.pIndicator = ap.alignFrame;
+    this.description = desc;
+    this.pSessionId = System.currentTimeMillis();
+  }
+
+  /**
+   * Gets the BioJSON data as a string, with lazy evaluation (first time called
+   * only). If the output format is configured not to embed BioJSON, returns
+   * null.
+   * 
+   * @return
+   */
+  public String getBioJSONData()
+  {
+    if (!isEmbedData())
+    {
+      return null;
+    }
+    if (_bioJson == null)
+    {
+      AlignExportSettingsI options = new AlignExportSettingsAdapter(true);
+      AlignmentExportData exportData = ap.getAlignViewport()
+              .getAlignExportData(options);
+      _bioJson = new FormatAdapter(ap, options).formatSequences(
+              FileFormat.Json, exportData.getAlignment(),
+              exportData.getOmitHidden(), exportData.getStartEndPostions(),
+              ap.getAlignViewport().getAlignment().getHiddenColumns());
+    }
+
+    return _bioJson;
+  }
+
+  /**
+   * Read a template file content as string
+   * 
+   * @param file
+   *          - the file to be read
+   * @return File content as String
+   * @throws IOException
+   */
+  public static String readFileAsString(File file) throws IOException
+  {
+    InputStreamReader isReader = null;
+    BufferedReader buffReader = null;
+    StringBuilder sb = new StringBuilder();
+    Objects.requireNonNull(file, "File must not be null!");
+    @SuppressWarnings("deprecation")
+    URL url = file.toURL();
+    if (url != null)
+    {
+      try
+      {
+        isReader = new InputStreamReader(url.openStream());
+        buffReader = new BufferedReader(isReader);
+        String line;
+        String lineSeparator = System.getProperty("line.separator");
+        while ((line = buffReader.readLine()) != null)
+        {
+          sb.append(line).append(lineSeparator);
+        }
+
+      } catch (Exception ex)
+      {
+        ex.printStackTrace();
+      } finally
+      {
+        if (isReader != null)
+        {
+          isReader.close();
+        }
+
+        if (buffReader != null)
+        {
+          buffReader.close();
+        }
+      }
+    }
+    return sb.toString();
+  }
+
+  public static String getImageMapHTML()
+  {
+    return new String("<html>\n" + "<head>\n"
+            + "<script language=\"JavaScript\">\n"
+            + "var ns4 = document.layers;\n"
+            + "var ns6 = document.getElementById && !document.all;\n"
+            + "var ie4 = document.all;\n" + "offsetX = 0;\n"
+            + "offsetY = 20;\n" + "var toolTipSTYLE=\"\";\n"
+            + "function initToolTips()\n" + "{\n" + "  if(ns4||ns6||ie4)\n"
+            + "  {\n"
+            + "    if(ns4) toolTipSTYLE = document.toolTipLayer;\n"
+            + "    else if(ns6) toolTipSTYLE = document.getElementById(\"toolTipLayer\").style;\n"
+            + "    else if(ie4) toolTipSTYLE = document.all.toolTipLayer.style;\n"
+            + "    if(ns4) document.captureEvents(Event.MOUSEMOVE);\n"
+            + "    else\n" + "    {\n"
+            + "      toolTipSTYLE.visibility = \"visible\";\n"
+            + "      toolTipSTYLE.display = \"none\";\n" + "    }\n"
+            + "    document.onmousemove = moveToMouseLoc;\n" + "  }\n"
+            + "}\n" + "function toolTip(msg, fg, bg)\n" + "{\n"
+            + "  if(toolTip.arguments.length < 1) // hide\n" + "  {\n"
+            + "    if(ns4) toolTipSTYLE.visibility = \"hidden\";\n"
+            + "    else toolTipSTYLE.display = \"none\";\n" + "  }\n"
+            + "  else // show\n" + "  {\n"
+            + "    if(!fg) fg = \"#555555\";\n"
+            + "    if(!bg) bg = \"#FFFFFF\";\n" + "    var content =\n"
+            + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + fg + '\"><td>' +\n"
+            + "    '<table border=\"0\" cellspacing=\"0\" cellpadding=\"1\" bgcolor=\"' + bg + \n"
+            + "    '\"><td align=\"center\"><font face=\"sans-serif\" color=\"' + fg +\n"
+            + "    '\" size=\"-2\">&nbsp;' + msg +\n"
+            + "    '&nbsp;</font></td></table></td></table>';\n"
+            + "    if(ns4)\n" + "    {\n"
+            + "      toolTipSTYLE.document.write(content);\n"
+            + "      toolTipSTYLE.document.close();\n"
+            + "      toolTipSTYLE.visibility = \"visible\";\n" + "    }\n"
+            + "    if(ns6)\n" + "    {\n"
+            + "      document.getElementById(\"toolTipLayer\").innerHTML = content;\n"
+            + "      toolTipSTYLE.display='block'\n" + "    }\n"
+            + "    if(ie4)\n" + "    {\n"
+            + "      document.all(\"toolTipLayer\").innerHTML=content;\n"
+            + "      toolTipSTYLE.display='block'\n" + "    }\n" + "  }\n"
+            + "}\n" + "function moveToMouseLoc(e)\n" + "{\n"
+            + "  if(ns4||ns6)\n" + "  {\n" + "    x = e.pageX;\n"
+            + "    y = e.pageY;\n" + "  }\n" + "  else\n" + "  {\n"
+            + "    x = event.x + document.body.scrollLeft;\n"
+            + "    y = event.y + document.body.scrollTop;\n" + "  }\n"
+            + "  toolTipSTYLE.left = x + offsetX;\n"
+            + "  toolTipSTYLE.top = y + offsetY;\n" + "  return true;\n"
+            + "}\n" + "</script>\n" + "</head>\n" + "<body>\n"
+            + "<div id=\"toolTipLayer\" style=\"position:absolute; visibility: hidden\"></div>\n"
+            + "<script language=\"JavaScript\"><!--\n"
+            + "initToolTips(); //--></script>\n");
+
+  }
+
+  /**
+   * Prompts the user to choose an output file and returns the file path, or
+   * null on Cancel
+   * 
+   * @return
+   */
+  public String getOutputFile()
+  {
+    String selectedFile = null;
+
+    // TODO: JAL-3048 generate html rendered view (requires SvgGraphics and/or
+    // Jalview HTML rendering system- probably not required for Jalview-JS)
+    JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
+            "HTML files");
+    jvFileChooser.setFileView(new JalviewFileView());
+
+    jvFileChooser
+            .setDialogTitle(MessageManager.getString("label.save_as_html"));
+    jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
+
+    int fileChooserOpt = jvFileChooser.showSaveDialog(null);
+    if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
+    {
+      Cache.setProperty("LAST_DIRECTORY",
+              jvFileChooser.getSelectedFile().getParent());
+      selectedFile = jvFileChooser.getSelectedFile().getPath();
+    }
+
+    return selectedFile;
+  }
+
+  protected void setProgressMessage(String message)
+  {
+    if (pIndicator != null && !isHeadless())
+    {
+      pIndicator.setProgressBar(message, pSessionId);
+    }
+    else
+    {
+      System.out.println(message);
+    }
+  }
+
+  /**
+   * Answers true if HTML export is invoke in headless mode or false otherwise
+   * 
+   * @return
+   */
+  protected boolean isHeadless()
+  {
+    return System.getProperty("java.awt.headless") != null
+            && System.getProperty("java.awt.headless").equals("true");
+  }
+
+  /**
+   * This method provides implementation of consistent behaviour which should
+   * occur after a HTML file export. It MUST be called at the end of the
+   * exportHTML() method implementation.
+   */
+  protected void exportCompleted()
+  {
+    if (isLaunchInBrowserAfterExport() && !isHeadless())
+    {
+      /*
+      try
+      {
+      */
+      jalview.util.BrowserLauncher.openURL("file:///" + getExportedFile());
+      /*
+      } catch (IOException e)
+      {
+        e.printStackTrace();
+      }
+      */
+    }
+  }
+
+  /**
+   * if this answers true then BioJSON data will be embedded to the exported
+   * HTML file otherwise it won't be embedded.
+   * 
+   * @return
+   */
+  public abstract boolean isEmbedData();
+
+  /**
+   * if this answers true then the generated HTML file is opened for viewing in
+   * a browser after its generation otherwise it won't be opened in a browser
+   * 
+   * @return
+   */
+  public abstract boolean isLaunchInBrowserAfterExport();
+
+  /**
+   * handle to the generated HTML file
+   * 
+   * @return
+   */
+  public File getExportedFile()
+  {
+    return generatedFile;
+  }
+
+  public void exportHTML(String outputFile)
+  {
+    setProgressMessage(MessageManager.formatMessage(
+            "status.exporting_alignment_as_x_file", getDescription()));
+    try
+    {
+      if (outputFile == null)
+      {
+        /*
+         * prompt for output file
+         */
+        outputFile = getOutputFile();
+        if (outputFile == null)
+        {
+          setProgressMessage(MessageManager.formatMessage(
+                  "status.cancelled_image_export_operation",
+                  getDescription()));
+          return;
+        }
+      }
+      generatedFile = new File(outputFile);
+    } catch (Exception e)
+    {
+      setProgressMessage(MessageManager
+              .formatMessage("info.error_creating_file", getDescription()));
+      e.printStackTrace();
+      return;
+    }
+    new Thread(this).start();
+
+  }
+
+  /**
+   * Answers a short description of the image format suitable for display in
+   * messages
+   * 
+   * @return
+   */
+  protected final String getDescription()
+  {
+    return description;
+  }
+}
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