protected override void DoTest()
{
TestFilesZip = GetPerfTestDataURL(@"PerfNegativeIonDIA.zip");
TestFilesPersistent = new[] { "neg.mzML", "pos.mzML" }; // list of files that we'd like to unzip alongside parent zipFile, and (re)use in place
var testFilesDir = new TestFilesDir(TestContext, TestFilesZip, null, TestFilesPersistent);
RunUI(() => SkylineWindow.OpenFile(testFilesDir.GetTestPath("Test positive-negative.sky")));
WaitForDocumentLoaded();
ImportResultsFiles(TestFilesPersistent.Select(file => MsDataFileUri.Parse(testFilesDir.GetTestPath(file))));
// Verify that pos ion has a chromatogram for pos replicate, and neg ion has one for neg replicate
var doc = WaitForDocumentLoaded(400000);
var results = doc.Settings.MeasuredResults;
var negIndex = results.Chromatograms[0].Name.Equals("neg") ? 0 : 1;
var posIndex = (negIndex == 1) ? 0 : 1;
var tolerance = .005f;
foreach (var pair in doc.MoleculePrecursorPairs)
{
var index = pair.NodeGroup.PrecursorCharge < 0 ? negIndex : posIndex;
var message = "expected a chromatogram for precursor and for product in replicate \"" + results.Chromatograms[index].Name + "\"";
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(index, pair.NodePep, pair.NodeGroup, tolerance, true, out chromGroupInfo), message);
foreach (var chromGroup in chromGroupInfo)
{
Assert.AreEqual(2, chromGroup.TransitionPointSets.Count(), message);
}
}
}
public IEnumerable <DbSpectrum> GetSpectraByPrecursor(MsDataFileUri file, double precursor)
{
const double precursorTolerance = 0.001;
return(GetSpectraByFile(file).Where(spectrum =>
spectrum.HasPrecursorMatch && Math.Abs(spectrum.MatchedPrecursorMz.GetValueOrDefault() - precursor) <= precursorTolerance));
}
public SelectionInfo(int targetIndex, Target sequence, Adduct charge, MsDataFileUri filePath)
{
TargetIndex = targetIndex;
Sequence = sequence;
Charge = charge;
FilePath = filePath;
}
public void MsDataFileUriEncodingTest()
{
var fname = "test.mzML";
var pathSample = SampleHelp.EncodePath(fname, null, -1, null, true, false);
var lockmassParametersA = new LockMassParameters(1.23, 3.45, 4.56);
var lockmassParametersB = new LockMassParameters(1.23, null, 4.56);
Assert.IsTrue(lockmassParametersA.CompareTo(LockMassParameters.EMPTY) > 0);
Assert.IsTrue(lockmassParametersA.CompareTo(null) < 0);
Assert.IsTrue(lockmassParametersB.CompareTo(lockmassParametersA) < 0);
Assert.IsTrue(lockmassParametersA.CompareTo(new LockMassParameters(1.23, 3.45, 4.56)) == 0);
var c = new ChromatogramSet("test", new[] { MsDataFileUri.Parse(pathSample) });
Assert.AreEqual(fname, c.MSDataFilePaths.First().GetFilePath());
Assert.IsTrue(c.MSDataFilePaths.First().GetCentroidMs1());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs2());
pathSample = SampleHelp.EncodePath(fname, null, -1, lockmassParametersA, false, true);
c = new ChromatogramSet("test", new[] { MsDataFileUri.Parse(pathSample) });
Assert.AreEqual(lockmassParametersA, c.MSDataFilePaths.First().GetLockMassParameters());
Assert.IsTrue(c.MSDataFilePaths.First().GetCentroidMs2());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs1());
pathSample = SampleHelp.EncodePath(fname, "test_0", 1, lockmassParametersB, false, false);
c = new ChromatogramSet("test", new[] { MsDataFileUri.Parse(pathSample) });
Assert.AreEqual(lockmassParametersB, c.MSDataFilePaths.First().GetLockMassParameters());
Assert.AreEqual("test_0", c.MSDataFilePaths.First().GetSampleName());
Assert.AreEqual(1, c.MSDataFilePaths.First().GetSampleIndex());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs1());
Assert.IsFalse(c.MSDataFilePaths.First().GetCentroidMs2());
}
private void upOneLevelButton_Click(object sender, EventArgs e)
{
MsDataFileUri parent = null;
var dataFilePath = _currentDirectory as MsDataFilePath;
if (dataFilePath != null && !string.IsNullOrEmpty(dataFilePath.FilePath))
{
DirectoryInfo parentDirectory = Directory.GetParent(dataFilePath.FilePath);
if (parentDirectory != null)
{
parent = new MsDataFilePath(parentDirectory.FullName);
}
}
else
{
if (_previousDirectories.Any())
{
CurrentDirectory = _previousDirectories.Pop();
return;
}
}
if (null != parent && !Equals(parent, _currentDirectory))
{
_previousDirectories.Push(_currentDirectory);
CurrentDirectory = parent;
}
}
private static bool HasUnmatchedLibraryRuns(SrmDocument doc)
{
var libraries = doc.Settings.PeptideSettings.Libraries;
if (!libraries.HasLibraries || !libraries.HasDocumentLibrary)
{
return(false);
}
for (int i = 0; i < libraries.LibrarySpecs.Count; i++)
{
if (libraries.LibrarySpecs[i].IsDocumentLibrary)
{
var documentLibrary = libraries.Libraries[i];
// CONSIDER: Load the library?
if (documentLibrary == null)
{
return(false);
}
foreach (var dataFile in documentLibrary.LibraryFiles.FilePaths)
{
if (!doc.Settings.HasResults ||
doc.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(dataFile)) == null)
{
return(true);
}
}
}
}
return(false);
}
public override bool TryGetRetentionTimes(MsDataFileUri filePath, out LibraryRetentionTimes retentionTimes)
{
int j = _librarySourceFiles.IndexOf(info => Equals(filePath.ToString(), info.FilePath));
if (j != -1)
{
var source = _librarySourceFiles[j];
ILookup <Target, double[]> timesLookup = _libraryEntries.ToLookup(
entry => entry.Key.Target,
entry => entry.RetentionTimesByFileId.GetTimes(source.Id));
var timesDict = timesLookup.ToDictionary(
grouping => grouping.Key,
grouping =>
{
var array = grouping.SelectMany(values => values).ToArray();
Array.Sort(array);
return(array);
});
var nonEmptyTimesDict = timesDict
.Where(kvp => kvp.Value.Length > 0)
.ToDictionary(kvp => kvp.Key, kvp => new Tuple <TimeSource, double[]>(TimeSource.peak, kvp.Value));
retentionTimes = new LibraryRetentionTimes(filePath.ToString(), nonEmptyTimesDict);
return(true);
}
return(base.TryGetRetentionTimes(filePath, out retentionTimes));
}
public Key(SrmDocument document, ChromatogramSet chromatogramSet, MsDataFileUri filePath, IdentityPath precursorIdentityPath)
{
_documentReference = document.ReferenceId;
_chromatogramSet = chromatogramSet;
_filePath = filePath;
_precursorIdentityPath = precursorIdentityPath;
}
private FileProgressControl FindProgressControl(MsDataFileUri filePath)
{
FileProgressControl fileProgressControl;
_fileProgressControls.TryGetValue(filePath.GetLocation(), out fileProgressControl);
return(fileProgressControl);
}
public SingleFileLoadMonitor(MultiFileLoadMonitor loadMonitor, MsDataFileUri dataFile)
{
_loadMonitor = loadMonitor;
_dataFile = dataFile;
_lastCancelCheck = DateTime.UtcNow; // Said to be 117x faster than Now and this is for a delta
HasUI = loadMonitor.HasUI;
}
public override IEnumerable <double> GetRetentionTimesWithSequences(string filePath, IEnumerable <Target> peptideSequences, ref int?iFile)
{
if (!iFile.HasValue)
{
iFile = FindFileInList(MsDataFileUri.Parse(filePath), _sourceFiles);
}
if (iFile.Value < 0)
{
return(new double[0]);
}
var times = new List <double>();
foreach (var entry in LibraryEntriesWithSequences(peptideSequences))
{
FileData fileData;
if (entry.FileDatas.TryGetValue(iFile.Value, out fileData))
{
if (fileData.ApexTime.HasValue)
{
times.Add(fileData.ApexTime.Value);
}
}
}
return(times);
}
public override bool TryGetRetentionTimes(LibKey key, MsDataFileUri filePath, out double[] retentionTimes)
{
retentionTimes = null;
DbSpectrum[] spectra;
if (!key.IsPrecursorKey)
{
spectra = GetSpectraByPeptide(filePath, key).ToArray();
}
else
{
spectra = GetSpectraByPrecursor(filePath, key.PrecursorMz.GetValueOrDefault()).ToArray();
var keyRt = key.RetentionTime;
if (keyRt.HasValue)
{
spectra = spectra.Where(s => Equals(keyRt.Value, s.RetentionTime)).ToArray();
}
}
if (!spectra.Any())
{
return(false);
}
retentionTimes = spectra.Select(s => s.RetentionTime).ToArray();
return(true);
}
public override bool TryGetRetentionTimes(LibKey key, MsDataFileUri filePath, out double[] retentionTimes)
{
retentionTimes = null;
int i = FindEntry(key);
if (i < 0)
{
return(false);
}
int fileId = FindFileInList(filePath, _sourceFiles);
if (fileId < 0)
{
return(false);
}
var entry = _libraryEntries[i];
FileData fileData;
if (!entry.FileDatas.TryGetValue(fileId, out fileData))
{
return(false);
}
if (!fileData.ApexTime.HasValue)
{
return(false);
}
retentionTimes = new[] { fileData.ApexTime.Value };
return(true);
}
public override ExplicitPeakBounds GetExplicitPeakBounds(MsDataFileUri filePath, IEnumerable <Target> peptideSequences)
{
int fileId = FindFileInList(filePath, _sourceFiles);
if (fileId < 0)
{
return(null);
}
bool anyMatch = false;
foreach (var entry in LibraryEntriesWithSequences(peptideSequences))
{
FileData fileData;
if (entry.FileDatas.TryGetValue(fileId, out fileData))
{
return(fileData.PeakBounds);
}
if (entry.FileDatas.Any())
{
anyMatch = true;
}
}
if (anyMatch)
{
return(ExplicitPeakBounds.EMPTY);
}
return(null);
}
public override IEnumerable <RemoteItem> ListContents(MsDataFileUri parentUrl)
{
var unifiUrl = (UnifiUrl)parentUrl;
ImmutableList <UnifiFolderObject> folders;
if (TryGetData(GetRootContentsUrl(), out folders))
{
foreach (var folderObject in folders)
{
if (folderObject.ParentId == unifiUrl.Id)
{
var childUrl = unifiUrl.ChangeId(folderObject.Id)
.ChangePathParts(unifiUrl.GetPathParts().Concat(new[] { folderObject.Name }));
yield return(new RemoteItem(childUrl, folderObject.Name, DataSourceUtil.FOLDER_TYPE, null, 0));
}
}
}
ImmutableList <UnifiFileObject> files;
if (TryGetData(GetFileContentsUrl(unifiUrl), out files))
{
foreach (var fileObject in files)
{
var childUrl = unifiUrl.ChangeId(fileObject.Id)
.ChangePathParts(unifiUrl.GetPathParts().Concat(new[] { fileObject.Name }))
.ChangeModifiedTime(fileObject.ModifiedAt);
yield return(new RemoteItem(childUrl, fileObject.Name, DataSourceUtil.TYPE_WATERS_RAW, fileObject.ModifiedAt, 0));
}
}
}
public static void MatchChromatograms(ResultsTestDocumentContainer docContainer,
MsDataFileUri path1, MsDataFileUri path2, int delta, int missing,
LockMassParameters lockMassParameters = null)
{
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
foreach (var path in new[] { path1, path2 })
{
var setAdd = FindChromatogramSet(doc, path);
if (setAdd == null)
{
string addName = (path.GetFileName() ?? "").Replace('.', '_');
addName = Helpers.GetUniqueName(addName, n => listChromatograms.All(set => n != set.Name));
setAdd = new ChromatogramSet(addName, new[] { path });
}
listChromatograms.Add(setAdd);
}
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
MatchChromatograms(docResults, 0, 1, delta, missing);
}
public RemoteItem(MsDataFileUri msDataFileUri, string label, string type, DateTime?lastModified, long fileSizeBytes)
{
MsDataFileUri = msDataFileUri;
Label = label;
Type = type;
LastModified = lastModified;
FileSize = (ulong)fileSizeBytes;
}
public IEnumerable <DbSpectrum> GetSpectraByRetentionTime(MsDataFileUri file, double precursor, double rtMin, double rtMax)
{
var min = rtMin - RT_TOLERANCE;
var max = rtMax + RT_TOLERANCE;
return(GetSpectraByPrecursor(file, precursor).Where(spectrum =>
min <= spectrum.RetentionTime && spectrum.RetentionTime <= max));
}
public bool Matches(MsDataFileUri msDataFilePath)
{
if (null != FilePath && !FilePath.Equals(msDataFilePath))
{
return(false);
}
return(Name.Equals(GetName(msDataFilePath)));
}
public void DoAgilentMseChromatogramTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
System.Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
TestSmallMolecules = false; // We have an explicit test for that here
string docPath;
SrmDocument document = InitAgilentMseDocument(testFilesDir, out docPath);
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var refine = new RefinementSettings();
document = refine.ConvertToSmallMolecules(document, asSmallMolecules);
}
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
var path = MsDataFileUri.Parse(@"AgilentMse\BSA-AI-0-10-25-41_first_100_scans.mzML");
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var results = document.Settings.MeasuredResults;
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length);
}
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assert.AreEqual(0.2462, (double)nodePep.GetMeasuredRetentionTime(0), .0001, "averaged retention time differs in node " + nodePep.RawTextId);
Assert.AreEqual(0.3333, (double)nodePep.GetPeakCountRatio(0), 0.0001);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
}
testFilesDir.Dispose();
}
/// <summary>
/// Display chromatogram data.
/// </summary>
/// <param name="status"></param>
public void UpdateStatus(ChromatogramLoadingStatus status)
{
// Update progress bars and progress labels.
var fileCount = Math.Max(1, status.SegmentCount - 1);
// Update file label.
if (status.Segment == status.SegmentCount - 1)
{
lblFileName.Visible = false;
progressBarFile.Visible = false;
lblFileCount.Text = Resources.AllChromatogramsGraph_UpdateStatus_Joining_chromatograms___;
}
else
{
progressBarFile.Value = status.ZoomedPercentComplete;
// Clear graph when a new file starts loading.
if (null != status.FilePath && _currentFilePath != status.FilePath)
{
_currentFilePath = status.FilePath;
// LOG.Info("Showing " + _currentFilePath); // Not L10N
lblFileName.Text = status.FilePath.GetFileName() + status.FilePath.GetSampleName();
asyncGraph.ClearGraph(status);
}
lblFileCount.Text = string.Format(Resources.AllChromatogramsGraph_UpdateStatus__0__of__1__files, status.Segment + 1, fileCount);
}
// Show multi-file progress bar if we have more than one file to import.
if (fileCount != 1)
{
if (Visible && !panelMultifileProgress.Visible)
{
panelMultifileProgress.Visible = true;
panelFileProgress.Top -= _adjustLayoutForMultifile;
panelGraph.Height -= _adjustLayoutForMultifile;
// TODO: uncomment this when single file cancellation works
//btnCancelFile.Visible = true;
}
progressBarAllFiles.Value = status.PercentComplete;
}
// Show warning message if necessary.
if (status.WarningMessage != null)
{
lblWarning.Text = status.WarningMessage;
lblWarning.Visible = true;
asyncGraph.Height = lblWarning.Top - 7;
}
else
{
lblWarning.Visible = false;
asyncGraph.Height = panelFileProgress.Top - 7;
}
lblDuration.Text = _stopwatch.Elapsed.ToString(@"hh\:mm\:ss"); // Not L10N
}
private void OpenFolder(MsDataFileUri uri)
{
if (_currentDirectory != null)
{
_previousDirectories.Push(_currentDirectory);
}
CurrentDirectory = uri;
_abortPopulateList = true;
}
private void RunMultiplePeptidesSameMz(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
TestDirectoryName = asSmallMolecules.ToString();
}
TestSmallMolecules = false; // Don't need the magic test node, we have an explicit test
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument document = InitMultiplePeptidesSameMzDocument(testFilesDir, out docPath);
document = (new RefinementSettings()).ConvertToSmallMolecules(document, asSmallMolecules);
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
var path = MsDataFileUri.Parse(@"AMultiplePeptidesSameMz\ljz_20131201k_Newvariant_standards_braf.mzML");
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var results = document.Settings.MeasuredResults;
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length); // without the fix, only the first pair will have a chromatogram
}
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null))
{
// expecting three peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assert.AreEqual(34.2441024780273, (double)nodePep.GetMeasuredRetentionTime(0), .0001);
nPeptides++;
}
}
Assert.AreEqual(3, nPeptides); // without the fix this will give just one result
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
}
/// <summary>
/// If the passed in MsDataFileUri is a multi-sample wiff file, then return a list of
/// MsDataFileUri's representing the samples, otherwise, return the MsDataFileUri itself.
/// </summary>
public static IEnumerable <MsDataFileUri> ListSubPaths(MsDataFileUri msDataFileUri)
{
var msDataFilePath = msDataFileUri as MsDataFilePath;
if (msDataFilePath == null || !IsWiffFile(msDataFilePath.FilePath))
{
return(new[] { msDataFileUri });
}
return(GetWiffSubPaths(msDataFilePath.FilePath));
}
public IProgressStatus GetStatus(MsDataFileUri filePath)
{
foreach (var loadingStatus in ProgressList)
{
if (loadingStatus.FilePath.Equals(filePath))
{
return(loadingStatus);
}
}
return(null);
}
private static IDictionary <Target, double> GetFirstRetentionTimes(
SrmSettings settings, RetentionTimeSource retentionTimeSource)
{
var libraryRetentionTimes = settings.GetRetentionTimes(MsDataFileUri.Parse(retentionTimeSource.Name));
if (null == libraryRetentionTimes)
{
return(new Dictionary <Target, double>());
}
return(libraryRetentionTimes.GetFirstRetentionTimes());
}
public SpectrumDisplayInfo(SpectrumInfo spectrumInfo, string replicateName,
MsDataFileUri filePath, int fileOrder, double?retentionTime, bool isBest)
{
_spectrumInfo = spectrumInfo;
ReplicateName = replicateName;
FilePath = filePath;
FileOrder = fileOrder;
RetentionTime = retentionTime;
IsBest = isBest;
}
private ChromatogramLoadingStatus FindStatus(MultiProgressStatus status, MsDataFileUri filePath)
{
foreach (ChromatogramLoadingStatus loadingStatus in status.ProgressList)
{
if (loadingStatus.FilePath.Equals(filePath))
{
return(loadingStatus);
}
}
return(null);
}
public void ClearFile(MsDataFileUri filePath)
{
lock (this)
{
_loadingPaths.Remove(filePath);
if (_loadingPaths.Count == 0)
{
ResetStatus();
}
}
}
private FileProgressControl FindProgressControl(MsDataFileUri filePath)
{
foreach (FileProgressControl fileProgressControl in flowFileStatus.Controls)
{
if (fileProgressControl.FilePath.Equals(filePath))
{
return(fileProgressControl);
}
}
return(null);
}