+ private static File currentBJSTemplateFile;
+
+ private static TreeMap<String, File> bioJsMSAVersions;
+
+ public static final String DEFAULT_DIR = System.getProperty("user.home")
+ + File.separatorChar + ".biojs_templates" + File.separatorChar;
+
+ public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
+ .getDefault("biojs_template_directory", DEFAULT_DIR);
+
+ public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
+ .getDefault(
+ "biojs_template_git_repo",
+ "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
+
+ public BioJsHTMLOutput(AlignmentViewPanel ap)
+ {
+ if (ap != null)
+ {
+ this.ap = ap;
+ }
+ }
+
+ public void exportJalviewAlignmentAsBioJsHtmlFile()
+ {
+ try
+ {
+ String outputFile = getOutputFile();
+ // String jalviewAlignmentJson = JSONFile.getJSONData(ap);
+ 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,
+ ap.getAlignViewport(), exportSettings);
+ String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+ .formatSequences(JSONFile.FILE_DESC, exportData
+ .getAlignment(), exportData.getOmitHidden(),
+ exportData.getStartEndPostions(), ap
+ .getAlignViewport().getColumnSelection());
+
+ String bioJSTemplateString = getBioJsTemplateAsString();
+ String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
+ .replaceAll("#sequenceData#", bioJSON).toString();
+
+ PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
+ outputFile));
+ out.print(generatedBioJsWithJalviewAlignmentAsJson);
+ out.flush();
+ out.close();
+ jalview.util.BrowserLauncher.openURL("file:///" + outputFile);
+ } catch (NoFileSelectedException ex)
+ {
+ // do noting if no file was selected
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ public String getOutputFile() throws NoFileSelectedException
+ {
+ String selectedFile = null;
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[] { "html" }, new String[] { "HTML files" },
+ "HTML files");
+ jvFileChooser.setFileView(new JalviewFileView());
+
+ jvFileChooser.setDialogTitle(MessageManager
+ .getString("label.save_as_biojs_html"));
+ jvFileChooser.setToolTipText(MessageManager.getString("action.save"));
+
+ int fileChooserOpt = jvFileChooser.showSaveDialog(null);
+ if (fileChooserOpt == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", jvFileChooser
+ .getSelectedFile().getParent());
+ selectedFile = jvFileChooser.getSelectedFile().getPath();
+ }
+ else
+ {
+ throw new NoFileSelectedException("No file was selected.");
+ }
+ return selectedFile;
+ }
+
+ public static String getBioJsTemplateAsString() throws IOException