public void ExportChromatograms(string chromatogramsFile, bool precursors, bool products, bool basePeaks, bool tics)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Exporting_chromatograms_file__0____, chromatogramsFile);
var chromExtractors = new List<ChromExtractor>();
if (tics)
chromExtractors.Add(ChromExtractor.summed);
if (basePeaks)
chromExtractors.Add(ChromExtractor.base_peak);
var chromSources = new List<ChromSource>();
if (precursors)
chromSources.Add(ChromSource.ms1);
if (products)
chromSources.Add(ChromSource.fragment);
if (chromExtractors.Count == 0 && chromSources.Count == 0)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Error__At_least_one_chromatogram_type_must_be_selected);
return;
}
var filesToExport = Document.Settings.HasResults
? Document.Settings.MeasuredResults.MSDataFilePaths.Select(f => f.GetFileName()).ToList()
: new List<string>();
if (filesToExport.Count == 0)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Error__The_document_must_have_imported_results);
return;
}
try
{
var chromExporter = new ChromatogramExporter(Document);
using (var saver = new FileSaver(chromatogramsFile))
using (var writer = new StreamWriter(saver.SafeName))
{
var status = new ProgressStatus(string.Empty);
IProgressMonitor broker = new CommandProgressMonitor(_out, status);
chromExporter.Export(writer, broker, filesToExport, LocalizationHelper.CurrentCulture, chromExtractors, chromSources);
writer.Close();
broker.UpdateProgress(status.Complete());
saver.Commit();
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Chromatograms_file__0__exported_successfully_, chromatogramsFile);
}
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_ExportChromatograms_Error__Failure_attempting_to_save_chromatograms_file__0_, chromatogramsFile);
_out.WriteLine(x.Message);
}
}
private void ExportLiveReport(string reportName, string reportFile, char reportColSeparator, bool reportInvariant)
{
var viewContext = DocumentGridViewContext.CreateDocumentGridViewContext(_doc, reportInvariant
? DataSchemaLocalizer.INVARIANT
: SkylineDataSchema.GetLocalizedSchemaLocalizer());
var viewInfo = viewContext.GetViewInfo(PersistedViews.MainGroup.Id.ViewName(reportName));
if (null == viewInfo)
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__The_report__0__does_not_exist__If_it_has_spaces_in_its_name__use__double_quotes__around_the_entire_list_of_command_parameters_, reportName);
return;
}
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Exporting_report__0____, reportName);
try
{
using (var saver = new FileSaver(reportFile))
{
if (!saver.CanSave())
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__The_report__0__could_not_be_saved_to__1__, reportName, reportFile);
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Check_to_make_sure_it_is_not_read_only_);
}
var status = new ProgressStatus(string.Empty);
IProgressMonitor broker = new CommandProgressMonitor(_out, status);
using (var writer = new StreamWriter(saver.SafeName))
{
viewContext.Export(broker, ref status, viewInfo, writer,
new DsvWriter(reportInvariant ? CultureInfo.InvariantCulture : LocalizationHelper.CurrentCulture, reportColSeparator));
}
broker.UpdateProgress(status.Complete());
saver.Commit();
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Report__0__exported_successfully_to__1__, reportName, reportFile);
}
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_ExportLiveReport_Error__Failure_attempting_to_save__0__report_to__1__, reportName, reportFile);
_out.WriteLine(x.Message);
}
}
