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);
}
}
public void ConsoleChromatogramExportTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
string outPath = testFilesDir.GetTestPath("Exported_chromatograms.csv");
// Import the first RAW file (or mzML for international)
string rawFile = "ah_20101011y_BSA_MS-MS_only_5-2" + ExtensionTestContext.ExtThermoRaw;
string rawPath = testFilesDir.GetTestPath(rawFile);
const string replicate = "Single";
//Attach replicate
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
ProgressStatus status;
doc = CommandLine.ImportResults(doc, docPath, replicate, MsDataFileUri.Parse(rawPath), null, null, out status);
Assert.IsNull(status);
//First, programmatically generate the report
var chromFiles = new[] { rawFile };
var chromExporter = new ChromatogramExporter(doc);
var chromExtractors = new[] { ChromExtractor.summed, ChromExtractor.base_peak };
var chromSources = new[] { ChromSource.ms1, ChromSource.fragment };
var chromBuffer = new StringBuilder();
using (var chromWriter = new StringWriter(chromBuffer))
{
chromExporter.Export(chromWriter, null, chromFiles, LocalizationHelper.CurrentCulture, chromExtractors,
chromSources);
}
doc.Settings.MeasuredResults.ReadStreams.ForEach(s => s.CloseStream());
string programmaticReport = chromBuffer.ToString();
RunCommand("--in=" + docPath,
"--import-file=" + rawPath,
"--import-replicate-name=" + replicate,
"--chromatogram-file=" + outPath,
"--chromatogram-precursors",
"--chromatogram-products",
"--chromatogram-base-peaks",
"--chromatogram-tics");
string chromLines = File.ReadAllText(outPath);
AssertEx.NoDiff(chromLines, programmaticReport);
}
public void WriteChromatograms(string filePath,
IProgressMonitor progressMonitor,
IList<string> filesToExport,
CultureInfo cultureInfo,
IList<ChromExtractor> chromExtractors,
IList<ChromSource> chromSources)
{
var chromExporter = new ChromatogramExporter(Document);
using (var saver = new FileSaver(filePath))
using (var writer = new StreamWriter(saver.SafeName))
{
chromExporter.Export(writer, progressMonitor, filesToExport, cultureInfo, chromExtractors, chromSources);
writer.Close();
saver.Commit();
}
}
private static void SaveChrom(SrmDocument docResults,
string fileToSave,
IList<string> fileNames,
CultureInfo cultureInfo,
IList<ChromExtractor> extractors,
IList<ChromSource> sources)
{
var chromExporter = new ChromatogramExporter(docResults);
using (var saver = new FileSaver(fileToSave))
using (var writer = new StreamWriter(saver.SafeName))
{
chromExporter.Export(writer, null, fileNames, cultureInfo, extractors, sources);
writer.Flush();
writer.Close();
saver.Commit();
}
}
