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 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();
+ .replaceAll("#sequenceData#", bioJSON).toString();
PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
outputFile));