package jalview.io;
+import jalview.api.AlignExportSettingI;
import jalview.api.FeatureRenderer;
import jalview.datamodel.AlignmentExportData;
import jalview.datamodel.SequenceI;
.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
if (isEmbbedBioJSON)
{
- AlignmentExportData exportData = ap.alignFrame.getAlignmentForExport(
- JSONFile.FILE_DESC, av);
- if (exportData.getSettings().isCancelled())
- {
- return;
- }
+ 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, av,
+ exportSettings);
jsonData = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(JSONFile.FILE_DESC, exportData
.getAlignment(), exportData.getOmitHidden(),
- exportData.getStartEndPostions(), ap
- .getAlignViewport().getColumnSelection());
+ exportData.getStartEndPostions(),
+ av.getColumnSelection());
}
String htmlData = getHtml(titleSvgData, alignSvgData, jsonData);
FileOutputStream out = new FileOutputStream(file);