public void AgilentFileTypeTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string extRaw = ExtensionTestContext.ExtAgilentRaw;
// Do file type check
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("081809_100fmol-MichromMix-05" + extRaw)))
{
Assert.IsTrue(msData.IsAgilentFile);
}
}
public ChromatogramDataProvider(MsDataFileImpl dataFile,
ChromFileInfo fileInfo,
ProgressStatus status,
int startPercent,
int endPercent,
IProgressMonitor loader)
: base(fileInfo, status, startPercent, endPercent, loader)
{
_dataFile = dataFile;
if (_dataFile.IsThermoFile)
{
_readMaxMinutes = 4;
}
int len = dataFile.ChromatogramCount;
_chromIndices = new int[len];
bool fixCEOptForShimadzu = dataFile.IsShimadzuFile;
int indexPrecursor = -1;
double lastPrecursor = 0;
for (int i = 0; i < len; i++)
{
int index;
string id = dataFile.GetChromatogramId(i, out index);
if (!ChromKey.IsKeyId(id))
continue;
var chromKey = ChromKey.FromId(id, fixCEOptForShimadzu);
if (chromKey.Precursor != lastPrecursor)
{
lastPrecursor = chromKey.Precursor;
indexPrecursor++;
}
var ki = new KeyValuePair<ChromKey, int>(chromKey, index);
_chromIndices[index] = indexPrecursor;
_chromIds.Add(ki);
}
// Shimadzu can't do the necessary product m/z stepping for itself.
// So, they provide the CE values in their IDs and we need to adjust
// product m/z values for them to support CE optimization.
if (fixCEOptForShimadzu)
FixCEOptForShimadzu();
if (_chromIds.Count == 0)
throw new NoSrmDataException(dataFile.FilePath);
SetPercentComplete(50);
}
private static void VerifyInstrumentInfo(string path, string model, string ionization, string analyzer, string detector)
{
using (var msDataFile = new MsDataFileImpl(path))
{
var instrumentInfoList = msDataFile.GetInstrumentConfigInfoList().ToList();
Assert.AreEqual(1, instrumentInfoList.Count);
var instrument = instrumentInfoList[0];
Assert.IsFalse(instrument.IsEmpty);
Assert.AreEqual(model, instrument.Model);
Assert.AreEqual(ionization, instrument.Ionization);
Assert.AreEqual(analyzer, instrument.Analyzer);
Assert.AreEqual(detector, instrument.Detector);
}
}
public void FileTypeTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string extWiff = ExtensionTestContext.ExtAbWiff;
string suffix = ExtensionTestContext.CanImportAbWiff ? "" : "-test";
// Do file type checks
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion" + suffix + extWiff)))
{
Assert.IsTrue(msData.IsABFile);
}
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")))
{
Assert.IsTrue(msData.IsABFile);
Assert.IsTrue(msData.IsMzWiffXml);
}
}
public static bool HasSpectrumData(MsDataFileImpl dataFile)
{
return dataFile.SpectrumCount > 0;
}
/// <summary>
/// Releases and returns the data file associated with this instance, ending any asynchronous processing
/// </summary>
public MsDataFileImpl Detach()
{
MsDataFileImpl dataFile;
lock (_dataFileLock)
{
dataFile = _dataFile;
_dataFile = null;
}
if (_runningAsync)
{
// Just in case the Read thread is waiting to add a spectrum to a full pening list
SpectrumInfo info;
_pendingInfoList.TryTake(out info);
}
return dataFile;
}
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 void Redisplay()
{
if (!IsHandleCreated)
{
return;
}
if (_inRedisplay)
{
return;
}
try
{
_inRedisplay = true;
tbxMinCharge.Text = MinCharge.ToString();
tbxMaxCharge.Text = MaxCharge.ToString();
tbxPeptideSequence.Text = PeptideSequence;
cbxShowPeptideMzs.Enabled = !string.IsNullOrEmpty(PeptideSequence);
tbxMassAccuracy.Text = MassAccuracy.ToString();
TurnoverCalculator turnoverCalculator = null;
if (!string.IsNullOrEmpty(PeptideSequence))
{
turnoverCalculator = new TurnoverCalculator(Workspace, PeptideSequence);
}
msGraphControlEx1.GraphPane.GraphObjList.Clear();
msGraphControlEx1.GraphPane.CurveList.Clear();
if (_spectrumData == null || comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
if (comboChromatogram.SelectedIndex >= 0 && null == _chromatogramDatas[comboChromatogram.SelectedIndex])
{
string chromatogramName;
float[] timeArray;
float[] intensityArray;
msDataFileImpl.GetChromatogram(comboChromatogram.SelectedIndex, out chromatogramName, out timeArray, out intensityArray);
_chromatogramDatas[comboChromatogram.SelectedIndex] = new ChromatogramData(chromatogramName, timeArray, intensityArray);
}
_spectrumData = _spectrumData ?? new SpectrumData(msDataFileImpl, ScanIndex);
}
}
ChromatogramData chromatogram = null;
if (comboChromatogram.SelectedIndex >= 0)
{
chromatogram = _chromatogramDatas[comboChromatogram.SelectedIndex];
}
tbxMsLevel.Text = _spectrumData.MsLevel.ToString();
tbxTime.Text = _spectrumData.Time.ToString();
if (chromatogram != null && ScanIndex < chromatogram.TimeArray.Length)
{
tbxChromatogramRetentionTime.Text = chromatogram.TimeArray[ScanIndex].ToString();
tbxChromatogramIonCurrent.Text = chromatogram.IntensityArray[ScanIndex].ToString(NumberFormat);
}
else
{
tbxChromatogramRetentionTime.Text = tbxChromatogramIonCurrent.Text = @"N/A";
}
if (cbxShowProfile.Checked && _spectrumData.ProfileMzs != null)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, new SpectrumGraphItem()
{
Points =
new PointPairList(_spectrumData.ProfileMzs,
_spectrumData.ProfileIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.line,
Color = Color.Blue,
});
}
if (_spectrumData.ProfileIntensities != null)
{
tbxSumOfProfileIntensities.Text = _spectrumData.ProfileIntensities.Sum().ToString(NumberFormat);
}
else
{
tbxSumOfProfileIntensities.Text = "";
}
tbxCentroidIntensitySum.Text = _spectrumData.CentroidIntensities.Sum().ToString(NumberFormat);
var spectrum = new SpectrumGraphItem
{
Points = new PointPairList(_spectrumData.CentroidMzs, _spectrumData.CentroidIntensities),
GraphItemDrawMethod = MSGraphItemDrawMethod.stick,
Color = Color.Black
};
if (turnoverCalculator != null)
{
var mzRanges = new Dictionary<MzRange, String>();
double monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideSequence);
double peptideIntensity = 0.0;
for (int charge = MinCharge; charge <= MaxCharge; charge ++)
{
foreach (var mzRange in turnoverCalculator.GetMzs(charge))
{
double mass = (mzRange.Center - AminoAcidFormulas.ProtonMass)* charge;
double massDifference = mass - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
mzRanges.Add(mzRange, label);
var chromatogramPoint = MsDataFileUtil.GetPoint(mzRange, _spectrumData.CentroidMzs, _spectrumData.CentroidIntensities);
peptideIntensity += chromatogramPoint.GetIntensity(mzRange, MassAccuracy);
}
}
spectrum.MassAccuracy = MassAccuracy;
spectrum.MzRanges = mzRanges;
tbxPeptideIntensity.Text = peptideIntensity.ToString(NumberFormat);
}
if (cbxShowCentroids.Checked)
{
msGraphControlEx1.AddGraphItem(msGraphControlEx1.GraphPane, spectrum);
}
if (turnoverCalculator != null && cbxShowPeptideMzs.Checked)
{
double massAccuracy = MassAccuracy;
for (int charge = MinCharge; charge <= MaxCharge; charge++)
{
var mzs = turnoverCalculator.GetMzs(charge);
var height = int.MaxValue;
foreach (var mzRange in mzs)
{
double min = mzRange.MinWithMassAccuracy(massAccuracy);
double max = mzRange.MaxWithMassAccuracy(massAccuracy);
msGraphControlEx1.GraphPane.GraphObjList.Add(new BoxObj(min, height, max - min, height, Color.Goldenrod, Color.Goldenrod)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.F_BehindGrid
});
}
}
}
msGraphControlEx1.Invalidate();
}
finally
{
_inRedisplay = false;
}
}
private MsDataFileImpl GetDataFile()
{
if (_dataFile == null)
{
string dataFilePath = FindDataFilePath();
var lockMassParameters = DataFilePath.GetLockMassParameters();
if (dataFilePath == null)
throw new FileNotFoundException(string.Format(Resources.ScanProvider_GetScans_The_data_file__0__could_not_be_found__either_at_its_original_location_or_in_the_document_or_document_parent_folder_, DataFilePath));
int sampleIndex = SampleHelp.GetPathSampleIndexPart(dataFilePath);
if (sampleIndex == -1)
sampleIndex = 0;
// Full-scan extraction always uses SIM as spectra
_dataFile = new MsDataFileImpl(dataFilePath, sampleIndex, lockMassParameters, true,
requireVendorCentroidedMS1: DataFilePath.GetCentroidMs1(), requireVendorCentroidedMS2: DataFilePath.GetCentroidMs2());
}
return _dataFile;
}
public OverlapDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
_isoMapper = new OverlapIsolationWindowMapper();
_overlapRegionsInApprox = 7;
}
public MsxTypeDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
}
private static void TestOverlapIsolationWindowMapper(AbstractIsoWindowMapper isoMapper, MsDataFileImpl file)
{
// ReSharper disable once CollectionNeverQueried.Local
var isoWinList = new List<IsoWin>(); // Useful for debugging
Assert.AreEqual(40,isoMapper.NumWindows);
Assert.AreEqual(41,isoMapper.NumDeconvRegions);
// Check that each isolation window has two overlap regions with mz values that are contained in it
for (int isoIndex = 0; isoIndex < isoMapper.NumWindows; ++isoIndex)
{
IsoWin isoWin = isoMapper.GetIsolationWindow(isoIndex);
isoWinList.Add(isoWin);
Assert.AreEqual(2, isoWin.DeconvRegions.Count);
for (int i = 0; i < isoWin.DeconvRegions.Count; ++i)
{
// Check self-consistency of each deconvRegion in the isolation window
var deconvRegion = isoWin.DeconvRegions[i];
var deconvIndex = deconvRegion.Id;
Assert.AreEqual(deconvRegion.Start, isoMapper.GetDeconvRegion(deconvIndex).Start);
Assert.AreEqual(deconvRegion.Stop, isoMapper.GetDeconvRegion(deconvIndex).Stop);
Assert.AreEqual(deconvRegion.Id, isoMapper.GetDeconvRegion(deconvIndex).Id);
Assert.IsTrue(isoWin.Contains(deconvRegion));
Assert.IsTrue(isoWin.Start <= deconvRegion.Start && isoWin.Stop >= deconvRegion.Stop);
double deconvRegionCenter = (deconvRegion.StartMz + deconvRegion.StopMz) / 2.0;
int newDeconvIndex;
isoMapper.TryGetDeconvFromMz(deconvRegionCenter, out newDeconvIndex);
Assert.AreEqual(deconvIndex, newDeconvIndex);
int[] isosForDeconv;
isoMapper.TryGetIsosForDeconv(deconvIndex, out isosForDeconv);
// 2 isolation windows cover this deconv region, unless it's at beginning or end
int deconvInIsos = deconvRegion.Id == 0 || deconvRegion.Id == isoMapper.NumDeconvRegions - 1 ? 1 : 2;
Assert.IsTrue(isosForDeconv.Length == deconvInIsos);
foreach (var isoForDeconv in isosForDeconv)
{
IsoWin isoWindow = isoMapper.GetIsolationWindow(isoForDeconv);
Assert.IsTrue(isoWindow.Contains(deconvRegion));
}
}
}
}
private static void TestSpectrumProcessor(TransitionBinner transBinner,AbstractIsoWindowMapper isoMapper,
MsDataFileImpl file, int testSpectrumNum)
{
int lastSpectrum = testSpectrumNum + 60;
int firstSpectrum = testSpectrumNum - 60;
var spectrumProcessor = new SpectrumProcessor(lastSpectrum + 1, isoMapper, transBinner);
// Make a new spectrum processor using the testing constructor that takes in
// a TransitionBinner, which will be the one used for overlap
// Add the spectra to the cache +/- 60 from the spectrum of interest
for (int i = firstSpectrum; i <= lastSpectrum; ++i)
{
var spectrum = file.GetSpectrum(i);
spectrumProcessor.AddSpectrum(i, spectrum);
}
// Check that the caching worked correctly
for (int spectrumIndex = firstSpectrum; spectrumIndex <= lastSpectrum; ++spectrumIndex)
{
ScanCached specData;
Assert.IsTrue(spectrumProcessor.TryGetSpectrum(spectrumIndex, out specData));
// Check that the cached processing results match the output of
// redoing the processing manually by extracting the spectrum from
// the file again and using transBinner to bin the data
var testSpectrum = file.GetSpectrum(spectrumIndex);
double[] expectedBinnedData = new double[transBinner.NumBins];
transBinner.BinData(testSpectrum.Mzs, testSpectrum.Intensities, ref expectedBinnedData);
ScanCached testSpecData;
spectrumProcessor.TryGetSpectrum(spectrumIndex, out testSpecData);
var seenBinnedData = testSpecData.Data;
Assert.AreEqual(expectedBinnedData.Length, seenBinnedData.Length);
for (int i = 0; i < expectedBinnedData.Length; ++i)
{
Assert.AreEqual(expectedBinnedData[i], seenBinnedData[i], 0.0001);
}
}
}
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);
}
}
private static void TestIsolationWindowMapper(AbstractIsoWindowMapper isoMapper, MsDataFileImpl file, double width)
{
// Check the first five spectra in the file
for (int checkIndex = 0 ; checkIndex < 5; ++checkIndex)
{
var spectrum = file.GetSpectrum(checkIndex);
var precursors = spectrum.Precursors;
List<int> isoIndices = new List<int>();
// Make sure that each precursor read from the file is included in the isolation
// window mapper
foreach (var precursor in precursors)
{
int index;
Assert.IsTrue(precursor.IsolationMz.HasValue);
Assert.IsTrue(isoMapper.TryGetWindowIndex(precursor.IsolationMz.Value, out index));
isoIndices.Add(index);
}
int[] isoIndicesFromMapper;
int[] overlapIndicesFromMapper;
double[] mask = new double[isoMapper.NumWindows];
// Make sure the isolation windows called from GetWindowMask match those
// extracted from the spectrum manually above using TryGetWindowIndex
isoMapper.GetWindowMask(spectrum, out isoIndicesFromMapper, out overlapIndicesFromMapper, ref mask);
Assert.AreEqual(isoIndices.Count,isoIndicesFromMapper.Length);
foreach (int index in isoIndicesFromMapper)
{
Assert.IsTrue(isoIndices.Contains(index));
}
// Make sure the overlapIndicesFromMapper matches the mask
for (int i = 0; i < mask.Length; ++i)
{
if (mask[i] < 0.5)
Assert.AreEqual(0.0, mask[i]);
else
{
Assert.AreEqual(1.0, mask[i]);
Assert.IsTrue(overlapIndicesFromMapper.Contains(i));
}
}
}
var testMzs = new[] {553.49, 623.7, 859, 658.55, 768.7, 621.52};
// For each test m/z, get the matching isolation window from isoMapper and
// make sure the m/z does indeed fall within the window
foreach (var checkMz in testMzs)
{
int windowIndex;
Assert.IsTrue(isoMapper.TryGetWindowFromMz(checkMz, out windowIndex));
var matchWindowCenterMz = isoMapper.GetPrecursor(windowIndex);
Assert.IsTrue(matchWindowCenterMz.IsolationMz.HasValue);
// Check that mz is within window (width/2 )
Assert.IsTrue(Math.Abs(matchWindowCenterMz.IsolationMz.Value - checkMz) < width/2);
}
// Test out of range precursors
int dummyIndex;
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(315.25, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
Assert.IsFalse(isoMapper.TryGetDeconvFromMz(1005.2, out dummyIndex));
Assert.AreEqual(-1, dummyIndex);
}
public override bool IsWatersLockmassCorrectionCandidate()
{
string filePath = GetFilePath();
// Has to be a Waters .raw file, not just an mzML translation of one
if (String.IsNullOrEmpty(filePath))
return false; // Not even a file
if (!GetFilePath().ToLowerInvariant().EndsWith(".raw")) // Not L10N
return false; // Return without even opening the file
if (!Directory.Exists(filePath))
return false; // Thermo .raw is a file, Waters .raw is actually a directory
try
{
using (var f = new MsDataFileImpl(filePath))
return f.IsWatersLockmassCorrectionCandidate;
}
catch (Exception)
{
return false; // whatever that was, it wasn't a Waters lockmass file
}
}
protected void TestUsePredictedTime()
{
const double FILTER_LENGTH = 2.7;
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("RetentionTimeFilterTest.sky")));
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("TestUsePredictedTime.sky")));
SetUiDocument(ChangeFullScanSettings(SkylineWindow.Document, SkylineWindow.Document.Settings.TransitionSettings.FullScan
.ChangeRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, FILTER_LENGTH)));
Assert.IsNull(SkylineWindow.Document.Settings.PeptideSettings.Prediction.RetentionTime);
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Prediction.UseMeasuredRTs);
// When we try to import a file, we should get an error about not having a peptide prediction algorithm
var messageDlg = ShowDialog<MessageDlg>(() => SkylineWindow.ImportResults());
RunUI(() =>
{
Assert.AreEqual(Resources.SkylineWindow_CheckRetentionTimeFilter_NoPredictionAlgorithm, messageDlg.Message);
messageDlg.Close();
});
var ssrCalcRegression = new RetentionTimeRegression("SSRCALC_FOR_RtFilterTest",
new RetentionScoreCalculator(RetentionTimeRegression.SSRCALC_100_A), .63,
5.8, 1.4, new MeasuredRetentionTime[0]);
// Now give the document a prediction algorithm
SetUiDocument(ChangePeptidePrediction(SkylineWindow.Document, SkylineWindow.Document.Settings.PeptideSettings.
Prediction.ChangeRetentionTime(ssrCalcRegression)));
// Now import two result files
{
var importResultsDlg = ShowDialog<ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog<OpenDataSourceDialog>(importResultsDlg.OkDialog);
RunUI(() =>
{
openDataSourceDialog.SelectFile("200fmol" + extension);
openDataSourceDialog.SelectFile("20fmol" + extension);
});
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
WaitForResultsImport();
{
var document = WaitForDocumentLoaded();
foreach (var chromatogramSet in document.Settings.MeasuredResults.Chromatograms)
{
foreach (var tuple in LoadAllChromatograms(document, chromatogramSet))
{
var peptide = tuple.Item1;
if (!peptide.IsProteomic)
continue;
var transitionGroup = tuple.Item2;
var predictedRetentionTime = ssrCalcRegression.GetRetentionTime(
document.Settings.GetModifiedSequence(peptide.Peptide.Sequence,
transitionGroup.TransitionGroup.LabelType, peptide.ExplicitMods)).Value;
AssertChromatogramWindow(document, chromatogramSet,
predictedRetentionTime - FILTER_LENGTH,
predictedRetentionTime + FILTER_LENGTH, tuple.Item3);
}
}
}
ChromatogramSet chromSetForScheduling = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[1];
// Create a SrmDocument with just the one ChromatogramSet that we are going to use for scheduling, so that
// we can assert later that the chromatogram windows are where this document says they should be.
SrmDocument documentForScheduling =
SkylineWindow.Document.ChangeMeasuredResults(
SkylineWindow.Document.Settings.MeasuredResults.ChangeChromatograms(new[] {chromSetForScheduling}));
SetUiDocument(ChangePeptidePrediction(SkylineWindow.Document, SkylineWindow.Document.Settings.PeptideSettings
.Prediction.ChangeUseMeasuredRTs(true).ChangeRetentionTime(null)));
{
var chooseSchedulingReplicatesDlg = ShowDialog<ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
// Choose a scheduling replicate (the one saved above)
RunUI(() => Assert.IsTrue(chooseSchedulingReplicatesDlg.TrySetReplicateChecked(
chromSetForScheduling, true)));
var importResultsDlg = ShowDialog<ImportResultsDlg>(chooseSchedulingReplicatesDlg.OkDialog);
var openDataSourceDialog = ShowDialog<OpenDataSourceDialog>(importResultsDlg.OkDialog);
RunUI(()=>openDataSourceDialog.SelectFile("40fmol" + extension));
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
WaitForResultsImport();
{
var document = WaitForDocumentLoaded();
var chromatogramSet = document.Settings.MeasuredResults.Chromatograms.First(cs => cs.Name == "40fmol");
int countNull = 0;
foreach (var tuple in LoadAllChromatograms(document, chromatogramSet))
{
var prediction = new PeptidePrediction(null, null, true, 1, false, 0);
double windowRtIgnored;
var schedulingPeptide =
documentForScheduling.Molecules.First(pep => ReferenceEquals(pep.Peptide, tuple.Item1.Peptide));
var schedulingTransitionGroup = (TransitionGroupDocNode) schedulingPeptide.FindNode(tuple.Item2.TransitionGroup);
double? predictedRt = prediction.PredictRetentionTime(documentForScheduling,
schedulingPeptide,
schedulingTransitionGroup,
null, ExportSchedulingAlgorithm.Average, true, out windowRtIgnored);
if (!predictedRt.HasValue)
{
countNull++;
continue;
}
AssertChromatogramWindow(document, chromatogramSet, predictedRt.Value - FILTER_LENGTH, predictedRt.Value + FILTER_LENGTH, tuple.Item3);
}
Assert.AreEqual((TestSmallMolecules ? 1 : 0), countNull);
}
// Test using iRT with auto-calculated regression
{
const string calcName = "TestCalculator";
const string regressionName = "TestCalculatorAutoCalcRegression";
var peptideSettingsDlg = ShowDialog<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editIrtDlg = ShowDialog<EditIrtCalcDlg>(peptideSettingsDlg.AddCalculator);
RunUI(() =>
{
editIrtDlg.OpenDatabase(TestFilesDir.GetTestPath("RetentionTimeFilterTest.irtdb"));
editIrtDlg.CalcName = calcName;
});
SkylineWindow.BeginInvoke(new Action(editIrtDlg.OkDialog));
var multiButtonMsgDlg = WaitForOpenForm<MultiButtonMsgDlg>();
OkDialog(multiButtonMsgDlg, ()=>multiButtonMsgDlg.DialogResult = DialogResult.Yes);
var editRtDlg = ShowDialog<EditRTDlg>(peptideSettingsDlg.AddRTRegression);
RunUI(() =>
{
editRtDlg.ChooseCalculator(calcName);
editRtDlg.SetAutoCalcRegression(true);
editRtDlg.SetRegressionName(regressionName);
editRtDlg.SetTimeWindow(1.0);
});
OkDialog(editRtDlg, editRtDlg.OkDialog);
RunUI(() =>
{
peptideSettingsDlg.ChooseRegression(regressionName);
peptideSettingsDlg.UseMeasuredRT(false);
});
OkDialog(peptideSettingsDlg, peptideSettingsDlg.OkDialog);
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Prediction.UseMeasuredRTs);
var importResultsDlg = ShowDialog<ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog<OpenDataSourceDialog>(importResultsDlg.OkDialog);
RunUI(() => openDataSourceDialog.SelectFile("8fmol" + extension));
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
WaitForResultsImport();
var document = WaitForDocumentLoaded();
var chromatogramSet = document.Settings.MeasuredResults.Chromatograms.First(cs => cs.Name == "8fmol");
var regressionLine =
document.Settings.PeptideSettings.Prediction.RetentionTime.GetConversion(
chromatogramSet.MSDataFileInfos.First().FileId);
var calculator = document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator;
double fullGradientStartTime;
double fullGradientEndTime;
using (var msDataFile = new MsDataFileImpl(TestFilesDir.GetTestPath("8fmol" + extension)))
{
fullGradientStartTime = msDataFile.GetSpectrum(0).RetentionTime.Value;
fullGradientEndTime = msDataFile.GetSpectrum(msDataFile.SpectrumCount - 1).RetentionTime.Value;
}
foreach (var tuple in LoadAllChromatograms(document, chromatogramSet))
{
if (tuple.Item1.GlobalStandardType != PeptideDocNode.STANDARD_TYPE_IRT)
{
double? score =
calculator.ScoreSequence(document.Settings.GetModifiedSequence(tuple.Item1.Peptide.Sequence,
tuple.Item2.TransitionGroup.LabelType, tuple.Item1.ExplicitMods));
if (score.HasValue)
{
double? predictedRt = regressionLine.GetY(score.Value);
AssertChromatogramWindow(document, chromatogramSet, predictedRt.Value - FILTER_LENGTH,
predictedRt.Value + FILTER_LENGTH, tuple.Item3);
}
}
else
{
// IRT Standards get extracted for the full gradient
AssertChromatogramWindow(document, chromatogramSet, fullGradientStartTime, fullGradientEndTime, tuple.Item3);
}
}
}
}
public bool Adopt(IScanProvider other)
{
if (!Equals(DocFilePath, other.DocFilePath) || !Equals(DataFilePath, other.DataFilePath))
return false;
var scanProvider = other as ScanProvider;
if (scanProvider == null)
return false;
_dataFile = scanProvider._dataFile;
_msDataFileScanIds = scanProvider._msDataFileScanIds;
_getMsDataFileScanIds = scanProvider._getMsDataFileScanIds;
scanProvider._dataFile = null;
return true;
}
private void InitSpectrumReader(MsDataFileImpl dataFile)
{
// Create the spectra object responsible for delivering spectra for extraction
_spectra = new Spectra(_document, _filter, _allChromData, dataFile);
// Determine what type of demultiplexer, if any, to use based on settings in the
// IsolationScheme menu
_demultiplexer = _spectra.CreateDemultiplexer();
if (_demultiplexer == null)
{
_spectra.RunAsync();
}
}
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 LookaheadContext(SpectrumFilter filter, MsDataFileImpl dataFile)
{
_lookAheadIndex = 0;
_lookAheadDataSpectrum = null;
_filter = filter;
_dataFile = dataFile;
_rt = null;
_previousDriftTime = 0;
_lenSpectra = dataFile.SpectrumCount;
}
private bool MoveToNextScan(int direction, bool onlyMs1)
{
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
int scanIndex = Math.Min(msDataFileImpl.SpectrumCount - 1, Math.Max(0, ScanIndex));
if (scanIndex < 0)
{
return false;
}
while (true)
{
scanIndex += direction;
if (scanIndex < 0 || scanIndex >= msDataFileImpl.SpectrumCount)
{
return false;
}
if (!onlyMs1 || msDataFileImpl.GetMsLevel(scanIndex) == 1)
{
break;
}
}
ScanIndex = scanIndex;
return true;
}
}
private void GenerateChromatograms(ChromatogramTask chromatogramTask)
{
int totalAnalyses = chromatogramTask.AnalysisChromatograms.Count;
if (totalAnalyses == 0)
{
return;
}
if (!UpdateProgress(chromatogramTask, 0))
{
return;
}
var msDataFile = chromatogramTask.MsDataFile;
MsDataFileUtil.InitMsDataFile(chromatogramTask.Workspace, msDataFile);
var analyses = new List<AnalysisChromatograms>(chromatogramTask.AnalysisChromatograms);
MsDataFileImpl pwizMsDataFileImpl;
var path = _workspace.GetDataFilePath(msDataFile.Name);
try
{
pwizMsDataFileImpl = new MsDataFileImpl(path);
}
catch (Exception exception)
{
ErrorHandler.LogException("Chromatogram Generator", "Error opening " + path, exception);
_workspace.RejectMsDataFile(msDataFile);
return;
}
using (pwizMsDataFileImpl)
{
var completeAnalyses = new List<AnalysisChromatograms>();
int totalScanCount = pwizMsDataFileImpl.SpectrumCount;
var lastTimeInDataFile =
chromatogramTask.MsDataFile.GetTime(chromatogramTask.MsDataFile.GetSpectrumCount() - 1);
double minTime = lastTimeInDataFile;
double maxTime = msDataFile.GetTime(0);
foreach (var analysis in analyses)
{
minTime = Math.Min(minTime, analysis.FirstTime);
maxTime = Math.Max(maxTime, analysis.LastTime);
}
int firstScan = msDataFile.FindScanIndex(minTime);
for (int iScan = firstScan; analyses.Count > 0 && iScan < totalScanCount; iScan++)
{
double time = msDataFile.GetTime(iScan);
int progress = (int)(100 * (time - minTime) / (maxTime - minTime));
progress = Math.Min(progress, 100);
progress = Math.Max(progress, 0);
if (!UpdateProgress(chromatogramTask, progress))
{
return;
}
List<AnalysisChromatograms> activeAnalyses = new List<AnalysisChromatograms>();
double nextTime = Double.MaxValue;
if (msDataFile.GetMsLevel(iScan, pwizMsDataFileImpl) != 1)
{
continue;
}
foreach (var analysis in analyses)
{
nextTime = Math.Min(nextTime, analysis.FirstTime);
if (analysis.FirstTime <= time)
{
activeAnalyses.Add(analysis);
}
}
if (activeAnalyses.Count == 0)
{
int nextScan = msDataFile.FindScanIndex(nextTime);
iScan = Math.Max(iScan, nextScan - 1);
continue;
}
bool lowMemory = IsLowOnMemory();
// If we have exceeded the number of analyses we should be working on at once,
// throw out any that we haven't started.
for (int iAnalysis = activeAnalyses.Count - 1; iAnalysis >= 0
&& (activeAnalyses.Count > _maxConcurrentAnalyses || lowMemory); iAnalysis--)
{
var analysis = activeAnalyses[iAnalysis];
if (analysis.Times.Count > 0)
{
continue;
}
activeAnalyses.RemoveAt(iAnalysis);
analyses.Remove(analysis);
}
double[] mzArray, intensityArray;
pwizMsDataFileImpl.GetSpectrum(iScan, out mzArray, out intensityArray);
if (!pwizMsDataFileImpl.IsCentroided(iScan))
{
var centroider = new Centroider(mzArray, intensityArray);
centroider.GetCentroidedData(out mzArray, out intensityArray);
}
foreach (var analysis in activeAnalyses)
{
var points = new List<ChromatogramPoint>();
foreach (var chromatogram in analysis.Chromatograms)
{
points.Add(MsDataFileUtil.GetPoint(chromatogram.MzRange, mzArray, intensityArray));
}
analysis.AddPoints(iScan, time, points);
}
var incompleteAnalyses = new List<AnalysisChromatograms>();
foreach (var analysis in analyses)
{
if (analysis.LastTime <= time)
{
completeAnalyses.Add(analysis);
}
else
{
incompleteAnalyses.Add(analysis);
}
}
SaveChromatograms(chromatogramTask, completeAnalyses, false);
completeAnalyses.Clear();
analyses = incompleteAnalyses;
}
completeAnalyses.AddRange(analyses);
SaveChromatograms(chromatogramTask, completeAnalyses, true);
}
}
public void ThermoFileTypeTest()
{
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string extRaw = ExtensionTestContext.ExtThermoRaw;
// Do file type checks
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_03" + extRaw)))
{
Assert.IsTrue(msData.IsThermoFile);
}
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_03.mzXML")))
{
Assert.IsTrue(msData.IsThermoFile);
}
using (var msData = new MsDataFileImpl(testFilesDir.GetTestPath("Site20_STUDY9P_PHASEII_QC_05" + extRaw)))
{
Assert.IsTrue(msData.IsThermoFile);
}
}
public MsxDemultiplexer(MsDataFileImpl file, SpectrumFilter filter)
: base(file, filter)
{
_isoMapper = new MsxIsolationWindowMapper();
}
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;
}
}
}
private void ComboChromatogramOnDropDown(object sender, EventArgs e)
{
if (_chromatogramDatas != null)
{
return;
}
comboChromatogram.Items.Clear();
using (var msDataFileImpl = new MsDataFileImpl(Workspace.GetDataFilePath(MsDataFile.Name)))
{
_chromatogramDatas = new ChromatogramData[msDataFileImpl.ChromatogramCount];
for (int i = 0; i < _chromatogramDatas.Length; i++)
{
int indexId;
comboChromatogram.Items.Add(msDataFileImpl.GetChromatogramId(i, out indexId));
}
}
}
public void Dispose()
{
lock (this)
{
if (_dataFile != null)
{
_dataFile.Dispose();
_dataFile = null;
}
}
}
public SpectrumData(MsDataFileImpl msDataFileImpl, int scanIndex)
{
ScanIndex = scanIndex;
var spectrum = msDataFileImpl.GetSpectrum(scanIndex);
if (spectrum.Centroided)
{
CentroidMzs = spectrum.Mzs;
CentroidIntensities = spectrum.Intensities;
}
else
{
ProfileMzs = spectrum.Mzs;
ProfileIntensities = spectrum.Intensities;
var centroider = new Centroider(ProfileMzs, ProfileIntensities);
double[] centroidMzs, centroidIntensities;
centroider.GetCentroidedData(out centroidMzs, out centroidIntensities);
CentroidMzs = centroidMzs;
CentroidIntensities = centroidIntensities;
}
Time = spectrum.RetentionTime;
MsLevel = spectrum.Level;
}
public DataFileInstrumentInfo(MsDataFileImpl dataFile)
{
_dataFile = dataFile;
}