import jalview.analysis.Dna;
import jalview.analysis.ParseProperties;
import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.AlignViewportI;
return false;
}
- AlignmentExportData exportData = getAlignmentForExport(format, viewport);
+ AlignmentExportData exportData = getAlignmentForExport(format,
+ viewport, null);
if (exportData.getSettings().isCancelled())
{
return false;
{
AlignmentExportData exportData = getAlignmentForExport(
- e.getActionCommand(), viewport);
+ e.getActionCommand(), viewport, null);
if (exportData.getSettings().isCancelled())
{
return;
}
public static AlignmentExportData getAlignmentForExport(String exportFormat,
- AlignViewportI viewport)
+ AlignViewportI viewport,
+ AlignExportSettingI exportSettings)
{
AlignmentI alignmentToExport = null;
+ AlignExportSettingI settings = exportSettings;
String[] omitHidden = null;
int[] alignmentStartEnd = new int[2];
{ 0, alignmentToExport.getWidth() - 1 };
boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
- AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
+ if (settings == null)
+ {
+ settings = new AlignExportSettings(hasHiddenSeqs,
viewport.hasHiddenColumns(), exportFormat);
- settings.isExportAnnotations();
+ }
+ // settings.isExportAnnotations();
if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
{