package jalview.io;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
{
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());
+JSONFile.FILE_DESC,
+ ap.getAlignViewport(), exportSettings);
if (exportData.getSettings().isCancelled())
{
return;