public MsxDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
_isoMapper = new MsxIsolationWindowMapper();
}
public OverlapDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
_isoMapper = new OverlapIsolationWindowMapper();
_overlapRegionsInApprox = 7;
}
public OverlapDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
_isoMapper = new OverlapIsolationWindowMapper();
_overlapRegionsInApprox = 7;
}
public MsxTypeDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
}
/// <summary>
/// Process a list of spectra - typically of length one,
/// but possibly a set of drift bins all with same retention time,
/// or a set of Agilent ramped-CE Mse scans to be averaged
/// </summary>
private void ProcessSpectrumList(MsDataSpectrum[] spectra,
ChromDataCollectorSet chromMap,
double rt,
SpectrumFilter filter,
string scanId)
{
lock (_blockWriter)
{
foreach (var spectrum in filter.Extract(rt, spectra))
{
if (_loader.IsCanceled)
throw new LoadCanceledException(Status);
chromMap.ProcessExtractedSpectrum((float) rt, _collectors, GetScanIdIndex(scanId), spectrum, AddChromCollector);
}
}
}
public LookaheadContext(SpectrumFilter filter, MsDataFileImpl dataFile)
{
_lookAheadIndex = 0;
_lookAheadDataSpectrum = null;
_filter = filter;
_dataFile = dataFile;
_rt = null;
_previousDriftTime = 0;
_lenSpectra = dataFile.SpectrumCount;
}
public SpectraChromDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
SrmDocument document,
IRetentionTimePredictor retentionTimePredictor,
string cachePath, // We'll write tempfiles in this directory
ProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_document = document;
_filePath = dataFile.FilePath;
_cachePath = cachePath;
// If no SRM spectra, then full-scan filtering must be enabled
_isSrm = dataFile.HasSrmSpectra;
if (!_isSrm)
{
if (!document.Settings.TransitionSettings.FullScan.IsEnabled)
throw new NoFullScanFilteringException(dataFile.FilePath);
// Only use the retention time predictor on non-SRM data, and only when
// there are enough transitions to cause performance issues with extracting
// full-gradient in a single pass, and then trimming.
if (_document.Settings.TransitionSettings.FullScan.RetentionTimeFilterType == RetentionTimeFilterType.scheduling_windows &&
_document.MoleculeTransitionCount > MAX_FULL_GRADIENT_TRANSITIONS)
{
_retentionTimePredictor = retentionTimePredictor;
}
}
// Only mzXML from mzWiff requires the introduction of zero values
// during interpolation.
_isProcessedScans = dataFile.IsMzWiffXml;
UpdatePercentComplete();
// Create the filter responsible for chromatogram extraction
bool firstPass = (_retentionTimePredictor != null);
_filter = new SpectrumFilter(_document, FileInfo.FilePath, new DataFileInstrumentInfo(dataFile),
_retentionTimePredictor, firstPass);
if (!_isSrm && (_filter.EnabledMs || _filter.EnabledMsMs))
{
// Full-scan filtering should always match a single precursor
// m/z value to a single precursor node in the document tree,
// because that is the way the filters are constructed in the
// first place.
_isSingleMzMatch = true;
}
// Get data object used to graph all of the chromatograms.
if (_loader.HasUI)
_allChromData = LoadingStatus.Transitions;
try
{
InitSpectrumReader(dataFile);
InitChromatogramExtraction();
}
catch(Exception)
{
// If exception thrown before construction is complete than Dispose will not be called.
if (_spectra == null)
dataFile.Dispose();
else
_spectra.Dispose();
throw;
}
}
public override bool CompleteFirstPass()
{
// Ignore this notification, if there is no retention time predictor
if (_retentionTimePredictor == null)
return false;
ExtractionComplete();
var dataFile = _spectra.Detach();
// Start the second pass
_filter = new SpectrumFilter(_document, FileInfo.FilePath, _filter, _retentionTimePredictor);
_spectra = null;
_isSrm = false;
InitSpectrumReader(dataFile);
InitChromatogramExtraction();
return true;
}
protected override void DoTest()
{
string chorusRequestOutputDirectory;
if (null != TestContext.TestResultsDirectory)
{
chorusRequestOutputDirectory = Path.Combine(TestContext.TestResultsDirectory, "chorusrequests");
Directory.CreateDirectory(chorusRequestOutputDirectory);
}
else
{
// When running unit tests under resharper, we have no TestResultsDirectory, so we only send
// the output to Console.Out.
chorusRequestOutputDirectory = null;
}
var xmlSerializer = new XmlSerializer(typeof(pwiz.Skyline.Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
foreach (var chorusDataSet in ChorusDataSets)
{
TestFilesDir testFilesDir = TestFilesDirForUrl(chorusDataSet.SkyZipUrl);
string skyFileName = Path.GetFileName(testFilesDir.FullPath);
Assert.IsNotNull(skyFileName, "skyFileName != null");
StringAssert.EndsWith(skyFileName, ".sky");
skyFileName = Uri.UnescapeDataString(skyFileName);
string skyFilePath = Path.Combine(testFilesDir.FullPath, skyFileName);
RunUI(()=>SkylineWindow.OpenFile(skyFilePath));
WaitForDocumentLoaded();
SrmDocument document = null;
RunUI(()=> { document = SkylineWindow.DocumentUI; });
Assert.IsNotNull(document);
SpectrumFilter spectrumFilterData = new SpectrumFilter(document, MsDataFileUri.Parse(""), null);
var chorusRequestDocument = spectrumFilterData.ToChromatogramRequestDocument();
Console.Out.WriteLine("***BEGIN {0}.chorusrequest.xml***", chorusDataSet.Name);
using (var xmlWriter = XmlWriter.Create(Console.Out, new XmlWriterSettings {Encoding = Encoding.UTF8}))
{
xmlSerializer.Serialize(xmlWriter, chorusRequestDocument);
}
Console.Out.WriteLine("***END {0}.chorusrequest.xml***", chorusDataSet.Name);
if (null != chorusRequestOutputDirectory)
{
string outputFile = Path.Combine(chorusRequestOutputDirectory,
chorusDataSet.Name + ".chorusrequest.xml");
using (var stream = new FileStream(outputFile, FileMode.Create))
{
xmlSerializer.Serialize(stream, chorusRequestDocument);
}
}
}
}
public Spectra(SrmDocument document, SpectrumFilter filter, ChromatogramLoadingStatus.TransitionData allChromData, MsDataFileImpl dataFile)
{
_document = document;
_filter = filter;
_dataFile = dataFile;
_allChromData = allChromData;
_lookaheadContext = new LookaheadContext(_filter, _dataFile);
_countSpectra = dataFile.SpectrumCount;
HasSrmSpectra = dataFile.HasSrmSpectra;
// If possible, find the maximum retention time in order to scale the chromatogram graph.
if (_allChromData != null && (_filter.EnabledMsMs || _filter.EnabledMs))
{
var retentionTime = _dataFile.GetStartTime(_countSpectra - 1);
if (retentionTime.HasValue)
{
_allChromData.MaxRetentionTime = (float)retentionTime.Value;
_allChromData.MaxRetentionTimeKnown = true;
_allChromData.Progressive = true;
}
}
}
public void TestMsx(SrmDocument doc, string dataPath)
{
// Load the file and check MsDataFileImpl
using (var file = new MsDataFileImpl(dataPath))
{
var filter = new SpectrumFilter(doc, null, null);
Assert.IsTrue(filter.EnabledMsMs);
var demultiplexer = new MsxDemultiplexer(file, filter);
demultiplexer.ForceInitializeFile();
// Check that the demultiplexer found the correct multiplexing parameters
Assert.AreEqual(5, demultiplexer.IsoWindowsPerScan);
Assert.AreEqual(100, demultiplexer.NumIsoWindows);
Assert.AreEqual(20, demultiplexer.DutyCycleLength);
var isoMapper = demultiplexer.IsoMapperTest;
Assert.AreEqual(100, isoMapper.NumWindows);
// Check the isolation window mapper responsible for mapping each unique isolation
// window detected in the file to a unique index
TestIsolationWindowMapper(isoMapper, file, 4.00182);
var transBinner = new TransitionBinner(filter, isoMapper);
// Test creation of a transition binner from a spectrum filter
TestTransitionBinnerFromFilter(transBinner, isoMapper);
var testSpectrum = file.GetSpectrum(TEST_SPECTRUM);
// Generate a transition binner containing a lot of tough cases with
// overlapping transitions and test
double[] binnedExpected =
{
0.0, 25160.11261, 18254.06375, 18254.06375, 18254.06375,
11090.00577, 19780.18628, 19780.18628
};
var transBinnerOverlap = TestTransitionBinnerOverlap(testSpectrum, isoMapper, binnedExpected);
TestSpectrumProcessor(transBinnerOverlap, isoMapper, file, TEST_SPECTRUM);
TestPeakIntensityCorrection(testSpectrum, isoMapper,
demultiplexer);
int[] intensityIndices = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 290, 291, 292, 293, 294, 295, 296 };
double[] intensityValues =
{
0.0, 0.0, 0.0, 0.0, 142.95, 349.75,
542.87, 511.77, 248.4, 0.0, 49.28,
1033.65, 278.56, 0.0, 0.0, 0.0,
0.0, 0.0
};
// Test demultiplexing of a real spectrum
TestSpectrumDemultiplex(demultiplexer, TEST_SPECTRUM, testSpectrum, intensityIndices, intensityValues, 0);
}
}
public void TestOverlap(SrmDocument doc, string dataPath)
{
// Load the file and check MsDataFileImpl
using (var file = new MsDataFileImpl(dataPath))
{
var filter = new SpectrumFilter(doc, null, null);
Assert.IsTrue(filter.EnabledMsMs);
var demultiplexer = new OverlapDemultiplexer(file, filter);
demultiplexer.ForceInitializeFile();
// Check that the demultiplexer found the correct multiplexing parameters
Assert.AreEqual(1, demultiplexer.IsoWindowsPerScan);
Assert.AreEqual(40, demultiplexer.NumIsoWindows);
Assert.AreEqual(41, demultiplexer.NumDeconvRegions);
var isoMapper = demultiplexer.IsoMapperTest;
// Basic checks of IsolationWindowMapper
TestIsolationWindowMapper(isoMapper, file, 20.009);
// Checks of overlap-specific functionality in IsolationWindowMapper
TestOverlapIsolationWindowMapper(isoMapper, file);
var transBinner = new TransitionBinner(filter, isoMapper);
// Test creation of a transition binner from a spectrum filter
TestTransitionBinnerFromFilter(transBinner, isoMapper);
var testSpectrum = file.GetSpectrum(TEST_SPECTRUM_OVERLAP);
// Generate a transition binner containing a lot of tough cases with
// overlapping transitions and test
double[] binnedExpected =
{
0.0, 0.0, 0.0, 0.0, 0.0,
0.0, 0.0, 0.0
};
var transBinnerOverlap = TestTransitionBinnerOverlap(testSpectrum, isoMapper, binnedExpected);
TestSpectrumProcessor(transBinnerOverlap, isoMapper, file, TEST_SPECTRUM_OVERLAP);
int[] intensityIndices = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 290, 291, 292, 293, 294, 295, 296};
double[] intensityValues =
{
0.0, 0.0, 0.0, 0.0, 4545.85, 15660.49,
35050.01, 56321.66, 62715.75, 43598.31, 23179.42,
2745.94, 3870.54, 4060.16, 3148.17, 1656.38,
0.0, 0.0
};
// Test demultiplexing of a real spectrum
TestSpectrumDemultiplex(demultiplexer, TEST_SPECTRUM_OVERLAP, testSpectrum, intensityIndices,
intensityValues, 0);
}
}
public MsxOverlapDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
_isoMapper = new OverlapIsolationWindowMapper();
}
public MsxTypeDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
}
private void btnExport_Click(object sender, EventArgs e)
{
string strReferenceFile = (string) comboBoxReferenceFile.SelectedItem;
string strSaveFileName = string.Empty;
if (!string.IsNullOrEmpty(_documentFilePath))
{
strSaveFileName = Path.GetFileNameWithoutExtension(_documentFilePath);
}
if (!string.IsNullOrEmpty(strReferenceFile))
{
strSaveFileName += Path.GetFileNameWithoutExtension(strReferenceFile);
}
strSaveFileName += ".ChorusRequest.xml"; // Not L10N
strSaveFileName = strSaveFileName.Replace(' ', '_');
using (var saveFileDialog = new SaveFileDialog { FileName = strSaveFileName})
{
if (saveFileDialog.ShowDialog(this) != DialogResult.OK || string.IsNullOrEmpty(saveFileDialog.FileName))
{
return;
}
SpectrumFilter spectrumFilterData = new SpectrumFilter(Document, MsDataFileUri.Parse(strReferenceFile), null);
using (var saver = new FileSaver(saveFileDialog.FileName))
{
if (!saver.CanSave(this))
{
return;
}
using (var stream = new StreamWriter(saver.SafeName))
{
var xmlSerializer = new XmlSerializer(typeof(Model.Results.RemoteApi.GeneratedCode.ChromatogramRequestDocument));
xmlSerializer.Serialize(stream, spectrumFilterData.ToChromatogramRequestDocument());
}
saver.Commit();
}
}
Close();
}
