- 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 = HtmlFile.readFileAsString(getCurrentBJSTemplateFile());
- 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);
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "status.export_complete", "BioJS"), pSessionId);
- }
- } catch (NoFileSelectedException ex)