package jalview.io;
import jalview.api.AlignExportSettingI;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentExportData;
import jalview.exceptions.NoFileSelectedException;
import jalview.gui.AlignmentPanel;
String bioJSON = new FormatAdapter(ap, exportData.getSettings())
.formatSequences(FileFormat.Json, exportData.getAlignment(),
exportData.getOmitHidden(), exportData
- .getStartEndPostions(), ap.getAlignViewport()
- .getColumnSelection());
+.getStartEndPostions(), ap.getAlignViewport()
+ .getAlignment().getHiddenColumns());
return bioJSON;
}
pSessionId);
}
- JalviewFileChooser jvFileChooser = new JalviewFileChooser(
- Cache.getProperty("LAST_DIRECTORY"), "html", "HTML files");
+ JalviewFileChooser jvFileChooser = new JalviewFileChooser("html",
+ "HTML files");
jvFileChooser.setFileView(new JalviewFileView());
jvFileChooser.setDialogTitle(MessageManager