public BiblioSpecLiteBuilder(string name, string outputPath, IList <string> inputFiles, IList <string> targetSequences = null)
{
LibrarySpec = new BiblioSpecLiteSpec(name, outputPath);
InputFiles = inputFiles;
TargetSequences = targetSequences;
}
private SrmDocument ConnectLibrarySpecs(SrmDocument document, string documentPath)
{
string docLibFile = null;
if (!string.IsNullOrEmpty(documentPath) && document.Settings.PeptideSettings.Libraries.HasDocumentLibrary)
{
docLibFile = BiblioSpecLiteSpec.GetLibraryFileName(documentPath);
if (!File.Exists(docLibFile))
{
Assert.Fail(Resources.CommandLine_ConnectLibrarySpecs_Error__Could_not_find_the_spectral_library__0__for_this_document_, docLibFile);
}
}
var settings = document.Settings.ConnectLibrarySpecs((library, librarySpec) =>
{
string name = library != null ? library.Name : librarySpec.Name;
LibrarySpec spec;
if (Settings.Default.SpectralLibraryList.TryGetValue(name, out spec))
{
if (File.Exists(spec.FilePath))
{
return(spec);
}
}
string fileName = library != null ? library.FileNameHint : Path.GetFileName(librarySpec.FilePath);
if (fileName != null)
{
// First look for the file name in the document directory
string pathLibrary = PathEx.FindExistingRelativeFile(documentPath, fileName);
if (pathLibrary != null)
{
return(CreateLibrarySpec(library, librarySpec, pathLibrary, true));
}
// In the user's default library directory
pathLibrary = Path.Combine(Settings.Default.LibraryDirectory, fileName);
if (File.Exists(pathLibrary))
{
return(CreateLibrarySpec(library, librarySpec, pathLibrary, false));
}
}
Assert.Fail(Resources.CommandLine_ConnectLibrarySpecs_Warning__Could_not_find_the_spectral_library__0_, name);
return(CreateLibrarySpec(library, librarySpec, null, false));
}, docLibFile);
if (ReferenceEquals(settings, document.Settings))
{
return(document);
}
// If the libraries were moved to disconnected state, then avoid updating
// the document tree for this change, or it will strip all the library
// information off the document nodes.
if (settings.PeptideSettings.Libraries.DisconnectedLibraries != null)
{
return(document.ChangeSettingsNoDiff(settings));
}
return(document.ChangeSettings(settings));
}
public BiblioSpecLiteBuilder GetLibBuilder(SrmDocument doc, string docFilePath, bool includeAmbiguousMatches)
{
string outputPath = BiblioSpecLiteSpec.GetLibraryFileName(docFilePath);
// Check to see if the library is already there, and if it is,
// "Append" instead of "Create"
bool libraryExists = File.Exists(outputPath);
var libraryBuildAction = LibraryBuildAction.Create;
if (libraryExists)
{
if (doc.Settings.HasDocumentLibrary)
{
libraryBuildAction = LibraryBuildAction.Append;
}
else
{
// If the document does not have a document library, then delete the one that we have found
// CONSIDER: it may be that user is trying to re-import, in which case this file is probably in use
FileEx.SafeDelete(outputPath);
FileEx.SafeDelete(Path.ChangeExtension(outputPath, BiblioSpecLiteSpec.EXT_REDUNDANT));
}
}
string name = Path.GetFileNameWithoutExtension(docFilePath);
return(new BiblioSpecLiteBuilder(name, outputPath, SearchFilenames)
{
Action = libraryBuildAction,
KeepRedundant = true,
CutOffScore = CutoffScore,
Id = Helpers.MakeId(name),
IncludeAmbiguousMatches = includeAmbiguousMatches
});
}
public BiblioSpecLiteBuilder(string name, string outputPath, IList<string> inputFiles, IList<string> targetSequences = null)
{
LibrarySpec = new BiblioSpecLiteSpec(name, outputPath);
InputFiles = inputFiles;
TargetSequences = targetSequences;
}
private bool VerifyDocumentLibrary()
{
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(DocumentPath);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(DocumentPath);
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
return(File.Exists(docLibPath) && File.Exists(redundantDocLibPath) && librarySettings.HasDocumentLibrary);
}
public void FullScanPrecursorTransitionsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"Test\FullScanPrecursor.zip");
string docPath = testFilesDir.GetTestPath("FullScanPrecursor.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(doc, 0, 1, 4, 5, 52);
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
var mitoLibSpec = new BiblioSpecLiteSpec("mito2", testFilesDir.GetTestPath("mito2.blib"));
doc = docContainer.ChangeLibSpecs(new[] { mitoLibSpec });
Assert.IsTrue(doc.IsLoaded);
// Switch to only precursor ions
var docPrecOnly = doc.ChangeSettings(doc.Settings.ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.precursor })));
// All precursors should have 3 precursor transitions (M, M+1 and M+2)
AssertEx.IsDocumentState(docPrecOnly, 3, 1, 4, 5, 15);
Assert.IsFalse(docPrecOnly.PeptideTransitions.Any(nodeTran => nodeTran.Transition.IonType != IonType.precursor));
// Use low resolution MS1 filtering
var docLowMs1 = docPrecOnly.ChangeSettings(docPrecOnly.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, 0.5, null)));
// All precursors should have one precursor transition
AssertEx.IsDocumentState(docLowMs1, 4, 1, 4, 5, 5);
// Add y-ions to low resolution filtering
var docLowMs1Y = docLowMs1.ChangeSettings(docLowMs1.Settings.ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y })));
AssertEx.IsDocumentState(docLowMs1Y, 5, 1, 4, 5, 33);
// Turn off MS1 filtering
var docNoMs1 = docPrecOnly.ChangeSettings(docPrecOnly.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.None, null, null)));
// One of the precursors should have no transitions, since its spectrum has no precursor match
AssertEx.IsDocumentState(docNoMs1, 4, 1, 4, 5, 4);
// Turn off MS/MS library matching
var docNoLibMatch = docNoMs1.ChangeSettings(docNoMs1.Settings.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.none)));
// All precursors should have a single precursor transition
AssertEx.IsDocumentState(docNoLibMatch, 5, 1, 4, 5, 5);
// Use library plus filter matching
var docLibPlusMatch = docNoMs1.ChangeSettings(docNoMs1.Settings.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.all_plus)));
// All precursors should have a single precursor transition
AssertEx.IsDocumentState(docLibPlusMatch, 5, 1, 4, 5, 5);
// Release the library stream, and dispose of the directory
docContainer.ChangeLibSpecs(new LibrarySpec[0]);
}
testFilesDir.Dispose();
}
public void TestBlibDriftTimes()
{
var testFilesDir = new TestFilesDir(TestContext, @"Test\Results\BlibDriftTimeTest.zip");
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath);
var doc = docContainer.Document;
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("BlibDriftTimeTest.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(20)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
// Import an mz5 file that needs drift info that's in the original data set,
// but preserved in the .blib file associated with a different raw source
// Without the bugfix this won't get any drift time filtering.
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714.mz5")), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(2, document.PeptidePrecursorPairs.Count());
var pair = document.PeptidePrecursorPairs.ToArray()[1];
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length);
var chromGroup = chromGroupInfo[0];
Assert.AreEqual(2, chromGroup.NumPeaks); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
Assert.AreEqual(278, maxHeight, 1); // Without DT filtering, this will be much greater - about 996
docContainer.Release();
}
private void VerifyDocumentLibraryBuilt(string path)
{
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(GetTestPath(path));
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
}
private void IncludeRedundantBlib(LibrarySpec librarySpec, ZipFileShare zip, string blibPath)
{
if (librarySpec is BiblioSpecLiteSpec)
{
var redundantBlibPath = BiblioSpecLiteSpec.GetRedundantName(blibPath);
if (File.Exists(redundantBlibPath))
{
zip.AddFile(redundantBlibPath);
}
}
}
public void FullScanPrecursorTransitionsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\FullScanPrecursor.zip");
string docPath = testFilesDir.GetTestPath("FullScanPrecursor.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(doc, 0, 1, 4, 5, 52);
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
var mitoLibSpec = new BiblioSpecLiteSpec("mito2", testFilesDir.GetTestPath("mito2.blib"));
doc = docContainer.ChangeLibSpecs(new [] { mitoLibSpec });
Assert.IsTrue(doc.IsLoaded);
// Switch to only precursor ions
var docPrecOnly = doc.ChangeSettings(doc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeIonTypes(new[] { IonType.precursor })));
// All precursors should have 3 precursor transitions (M, M+1 and M+2)
AssertEx.IsDocumentState(docPrecOnly, 3, 1, 4, 5, 15);
Assert.IsFalse(docPrecOnly.PeptideTransitions.Any(nodeTran => nodeTran.Transition.IonType != IonType.precursor));
// Use low resolution MS1 filtering
var docLowMs1 = docPrecOnly.ChangeSettings(docPrecOnly.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, 0.5, null)));
// All precursors should have one precursor transition
AssertEx.IsDocumentState(docLowMs1, 4, 1, 4, 5, 5);
// Add y-ions to low resolution filtering
var docLowMs1Y = docLowMs1.ChangeSettings(docLowMs1.Settings.ChangeTransitionFilter(filter =>
filter.ChangeIonTypes(new[] { IonType.precursor, IonType.y })));
AssertEx.IsDocumentState(docLowMs1Y, 5, 1, 4, 5, 33);
// Turn off MS1 filtering
var docNoMs1 = docPrecOnly.ChangeSettings(docPrecOnly.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.None, null, null)));
// One of the precursors should have no transitions, since its spectrum has no precursor match
AssertEx.IsDocumentState(docNoMs1, 4, 1, 4, 5, 4);
// Turn off MS/MS library matching
var docNoLibMatch = docNoMs1.ChangeSettings(docNoMs1.Settings.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.none)));
// All precursors should have a single precursor transition
AssertEx.IsDocumentState(docNoLibMatch, 5, 1, 4, 5, 5);
// Use library plus filter matching
var docLibPlusMatch = docNoMs1.ChangeSettings(docNoMs1.Settings.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.all_plus)));
// All precursors should have a single precursor transition
AssertEx.IsDocumentState(docLibPlusMatch, 5, 1, 4, 5, 5);
// Release the library stream, and dispose of the directory
docContainer.ChangeLibSpecs(new LibrarySpec[0]);
testFilesDir.Dispose();
}
public BiblioSpecLiteBuilder(string name, string outputPath, IList <string> inputFiles, IList <Target> targetSequences = null)
{
LibrarySpec = new BiblioSpecLiteSpec(name, outputPath);
InputFiles = inputFiles;
// FUTURE(bspratt) small molecule workflows
if (targetSequences != null)
{
TargetSequences = targetSequences.Where(t => t.IsProteomic).Select(t => t.Sequence).ToList();
}
}
public void TestBlibDriftTimes()
{
var testFilesDir = new TestFilesDir(TestContext, @"Test\Results\BlibDriftTimeTest.zip");
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath);
var doc = docContainer.Document;
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("BlibDriftTimeTest.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(20)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
// Import an mz5 file that needs drift info that's in the original data set,
// but preserved in the .blib file associated with a different raw source
// Without the bugfix this won't get any drift time filtering.
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714.mz5")), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(2, document.PeptidePrecursorPairs.Count());
var pair = document.PeptidePrecursorPairs.ToArray()[1];
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length);
var chromGroup = chromGroupInfo[0];
Assert.AreEqual(2 , chromGroup.NumPeaks); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
Assert.AreEqual(278 , maxHeight, 1); // Without DT filtering, this will be much greater - about 996
docContainer.Release();
}
public PrositLibraryBuilder(SrmDocument doc, string name, string outPath, Func <bool> replaceLibrary,
IrtStandard irtStandard, IList <PeptideDocNode> peptides, IList <TransitionGroupDocNode> precursors, int nce)
{
_prositClient = PrositPredictionClient.Current;
_intensityModel = PrositIntensityModel.Instance;
_rtModel = PrositRetentionTimeModel.Instance;
_peptides = peptides;
_precursors = precursors;
_document = doc;
LibrarySpec = new BiblioSpecLiteSpec(name, outPath); // Needs to be created before building
_replaceLibrary = replaceLibrary;
IrtStandard = irtStandard;
_nce = nce;
}
/// <summary>
/// Added to show <see cref="SpectrumLibraryInfoDlg"/>
/// </summary>
private void TestLibraryInfo()
{
var libspec = new BiblioSpecLiteSpec("ManageLibraryRunsTestScores", TestFilesDir.GetTestPath("ManageLibraryRunsTestScores.blib"));
var newLib = BiblioSpecLiteLibrary.Load(libspec, new DefaultFileLoadMonitor(new SilentProgressMonitor()));
AddLibrary(libspec, newLib);
WaitForDocumentLoaded();
var libExplore = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
var specLibInfoDlg = ShowDialog <SpectrumLibraryInfoDlg>(libExplore.ShowLibDetails);
IList <SpectrumSourceFileDetails> datafiles = specLibInfoDlg.GetGridView();
Assert.AreEqual(datafiles.Count, 5);
foreach (var file in datafiles)
{
Assert.AreEqual(0, file.BestSpectrum);
Assert.AreEqual(0, file.MatchedSpectrum);
Assert.AreEqual(file.CutoffScores.Count, 0);
}
OkDialog(specLibInfoDlg, specLibInfoDlg.OkDialog);
var modDlg = ShowDialog <AddModificationsDlg>(() => libExplore.ChangeSelectedLibrary("ManageLibraryRunsTestScores"));
OkDialog(modDlg, modDlg.OkDialog);
WaitForConditionUI(() => libExplore.HasSelectedLibrary);
specLibInfoDlg = ShowDialog <SpectrumLibraryInfoDlg>(libExplore.ShowLibDetails);
datafiles = specLibInfoDlg.GetGridView();
Assert.AreEqual(datafiles.Count, 4);
Assert.AreEqual(datafiles[0].CutoffScores.Count, 1);
Assert.AreEqual(datafiles[0].MatchedSpectrum, 1);
Assert.AreEqual(datafiles[0].BestSpectrum, 1);
Assert.AreEqual(datafiles[1].CutoffScores.Count, 1);
Assert.AreEqual(datafiles[1].MatchedSpectrum, 10);
Assert.AreEqual(datafiles[1].BestSpectrum, 9);
Assert.AreEqual(datafiles[1].CutoffScores.Count, 1);
Assert.AreEqual(datafiles[2].MatchedSpectrum, 3);
Assert.AreEqual(datafiles[2].BestSpectrum, 3);
Assert.AreEqual(datafiles[3].MatchedSpectrum, 1);
Assert.AreEqual(datafiles[3].BestSpectrum, 1);
OkDialog(specLibInfoDlg, specLibInfoDlg.OkDialog);
OkDialog(libExplore, libExplore.CancelDialog);
}
private static double driftTimeMax = 13.799765403988133; // Known max drift time for this file - use to mimic resolving power logic for test purposes
private static SrmDocument InitWatersImsMseDocument(TestFilesDir testFilesDir,
IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType driftPeakWidthCalcType,
bool withDriftTimeFilter, bool withDriftTimePredictor,
out string docPath)
{
var skyFile = withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky";
docPath = testFilesDir.GetTestPath(skyFile);
var cmdline = new CommandLine();
Assert.IsTrue(cmdline.OpenSkyFile(docPath)); // Handles any path shifts in database files, like our .imdb file
SrmDocument doc = cmdline.Document;
// Cause library load and subsequent document update
using (var docContainer = new ResultsTestDocumentContainer(null, docPath))
{
docContainer.SetDocument(doc, null, true);
docContainer.AssertComplete();
doc = docContainer.Document;
double resolvingPower = 100; // Test was originally written with resolving power 100
double widthAtDtMax = 2 * driftTimeMax / resolvingPower;
var driftTimeWindowWidthCalculator = new IonMobilityWindowWidthCalculator(driftPeakWidthCalcType, resolvingPower, 0, widthAtDtMax);
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("waters-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesWindowWidthCalculator(driftTimeWindowWidthCalculator)).
ChangePeptidePrediction(p => p.ChangeUseLibraryIonMobilityValues(true))
);
}
else if (withDriftTimeFilter)
{
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideSettings(ps => ps.ChangePrediction(
ps.Prediction.ChangeDriftTimePredictor(ps.Prediction.IonMobilityPredictor.ChangeDriftTimeWindowWidthCalculator(driftTimeWindowWidthCalculator)))));
}
}
return(doc);
}
public void ExportSpectralLibrary(string path, IProgressMonitor progressMonitor)
{
const string name = "exported";
var spectra = new Dictionary <LibKey, SpectrumMzInfo>();
foreach (var nodePepGroup in Document.MoleculeGroups)
{
foreach (var nodePep in nodePepGroup.Molecules)
{
foreach (var nodeTranGroup in nodePep.TransitionGroups)
{
for (var i = 0; i < Document.Settings.MeasuredResults.Chromatograms.Count; i++)
{
ProcessTransitionGroup(spectra, nodePepGroup, nodePep, nodeTranGroup, i);
}
}
}
}
var rCalcIrt = Document.Settings.HasRTPrediction
? Document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator as RCalcIrt
: null;
IProgressStatus status = new ProgressStatus();
if (rCalcIrt != null && progressMonitor != null)
{
progressMonitor.UpdateProgress(status = status.ChangeSegments(0, 2));
}
using (var blibDb = BlibDb.CreateBlibDb(path))
{
var libSpec = new BiblioSpecLiteSpec(name, path);
blibDb.CreateLibraryFromSpectra(libSpec, spectra.Values.ToList(), name, progressMonitor, ref status);
}
if (rCalcIrt != null)
{
IrtDb.CreateIrtDb(path).AddPeptides(progressMonitor, rCalcIrt.GetDbIrtPeptides().ToList(), ref status);
}
}
/// <summary>
/// Minimizes all libraries in a document to produce a new document with
/// just the library information necessary for the spectra referenced by
/// the nodes in the document.
/// </summary>
/// <param name="document">Document for which to minimize library information</param>
/// <param name="pathDirectory">Directory into which new minimized libraries are built</param>
/// <param name="nameModifier">A name modifier to append to existing names for
/// full libraries to create new library names</param>
/// <param name="progressMonitor">Broker to communicate status and progress</param>
/// <returns>A new document instance with minimized libraries</returns>
public static SrmDocument MinimizeLibraries(SrmDocument document,
string pathDirectory, string nameModifier, IProgressMonitor progressMonitor)
{
var settings = document.Settings;
var pepLibraries = settings.PeptideSettings.Libraries;
if (!pepLibraries.HasLibraries)
return document;
if (!pepLibraries.IsLoaded)
throw new InvalidOperationException(Resources.BlibDb_MinimizeLibraries_Libraries_must_be_fully_loaded_before_they_can_be_minimzed);
// Separate group nodes by the libraries to which they refer
var setUsedLibrarySpecs = new HashSet<LibrarySpec>();
foreach (var librarySpec in pepLibraries.LibrarySpecs)
{
string libraryName = librarySpec.Name;
if (document.MoleculeTransitionGroups.Contains(nodeGroup =>
nodeGroup.HasLibInfo && Equals(nodeGroup.LibInfo.LibraryName, libraryName)))
{
setUsedLibrarySpecs.Add(librarySpec);
}
}
var listLibraries = new List<Library>();
var listLibrarySpecs = new List<LibrarySpec>();
var dictOldNameToNew = new Dictionary<string, string>();
if (setUsedLibrarySpecs.Count > 0)
{
Directory.CreateDirectory(pathDirectory);
var usedNames = new HashSet<string>();
for (int i = 0; i < pepLibraries.LibrarySpecs.Count; i++)
{
var librarySpec = pepLibraries.LibrarySpecs[i];
if (!setUsedLibrarySpecs.Contains(librarySpec))
continue;
string baseName = Path.GetFileNameWithoutExtension(librarySpec.FilePath);
string fileName = GetUniqueName(baseName, usedNames) + BiblioSpecLiteSpec.EXT;
using (var blibDb = CreateBlibDb(Path.Combine(pathDirectory, fileName)))
{
blibDb.ProgressMonitor = progressMonitor;
var librarySpecMin = librarySpec as BiblioSpecLiteSpec;
if (librarySpecMin == null || !librarySpecMin.IsDocumentLibrary)
{
string nameMin = librarySpec.Name;
// Avoid adding the modifier a second time, if it has
// already been done once.
if (!nameMin.EndsWith(nameModifier + ")")) // Not L10N
nameMin = string.Format("{0} ({1})", librarySpec.Name, nameModifier); // Not L10N
librarySpecMin = new BiblioSpecLiteSpec(nameMin, blibDb.FilePath);
}
listLibraries.Add(blibDb.MinimizeLibrary(librarySpecMin,
pepLibraries.Libraries[i], document));
// Terminate if user canceled
if (progressMonitor != null && progressMonitor.IsCanceled)
return document;
listLibrarySpecs.Add(librarySpecMin);
dictOldNameToNew.Add(librarySpec.Name, librarySpecMin.Name);
}
}
document = (SrmDocument) document.ChangeAll(node =>
{
var nodeGroup = node as TransitionGroupDocNode;
if (nodeGroup == null || !nodeGroup.HasLibInfo)
return node;
string libName = nodeGroup.LibInfo.LibraryName;
string libNameNew = dictOldNameToNew[libName];
if (Equals(libName, libNameNew))
return node;
var libInfo = nodeGroup.LibInfo.ChangeLibraryName(libNameNew);
return nodeGroup.ChangeLibInfo(libInfo);
},
(int) SrmDocument.Level.TransitionGroups);
}
return document.ChangeSettingsNoDiff(settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(listLibrarySpecs, listLibraries)));
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] {MATCHER.GetModifiedNode(STR_MOD_BY_NAME)})}, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList<string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList<string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.HeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List<string> { STR_MOD_BY_NAME }, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException<FormatException>(() => UpdateMatcher(new[] {OXIDATION_M_C_TERM}, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] {LABEL15_N}, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] {carbC}, null, new[] {MET_OX_ROUNDED}, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List<StaticMod> { LABEL15_N });
var peptideMods = new PeptideModifications(new List<StaticMod>(), new List<TypedModifications> { typedMod });
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList<string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList<string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add( LABEL15_N );
MATCHER.CreateMatches(settingsMultiLabel, new List<string> { STR_HEAVY_15_F }, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] {MATCHER.GetModifiedNode(STR_HEAVY_15_F)})}, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications, settingsNew);
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F});
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
{
var modMatchDocContainer = InitMatchDocContainer(testDir);
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17
&& match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx)
&& match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
/* TODO bspratt drift time libs for small molecules
*
* [TestMethod]
* public void WatersImsMsePredictedDriftTimesChromatogramTestAsSmallMolecules()
* {
* WatersImsMseChromatogramTest(DriftFilterType.predictor, true);
* }
*
* [TestMethod]
* public void WatersImsMseLibraryDriftTimesChromatogramTestAsSmallMolecules()
* {
* WatersImsMseChromatogramTest(DriftFilterType.library, true);
* }
*
*/
private void WatersImsMseChromatogramTest(DriftFilterType mode,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
TestSmallMolecules = false; // Don't need that extra magic node
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky", asSmallMolecules, out docPath);
AssertEx.IsDocumentState(document, (withDriftTimePredictor || (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)) ? 1 : 0, 1, 1, 1, 8); // Drift time lib load bumps the doc version
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var docOriginal = doc;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("mse-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(100)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
testModeStr = "with drift times from spectral library";
}
var listChromatograms = new List <ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
const string path = @"waters-mobility.mz5";
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, new MsDataFilePath(path)) ??
new ChromatogramSet(Path.GetFileName(path).Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(1, document.MoleculePrecursorPairs.Count());
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, testModeStr);
var chromGroup = chromGroupInfo[0];
var expectedPeaks = ((asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 6 : 5);
Assert.AreEqual(withDriftTimeFilter ? 3 : expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assert.AreEqual(withDriftTimeFilter? 5226 : 20075, maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// 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(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assert.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath = testFilesDir.GetTestPath(complete == 1?"share_complete.zip":"share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath, complete == 1);
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest -- sharing document",
})
{
longWaitDlg.PerformWork(null, 1000, share.Share);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
var files = share.ListEntries().ToArray();
Assert.IsTrue(files.Contains(withDriftTimePredictor ? "scaled.imdb" : "mse-mobility.filtered-scaled.blib"));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest",
})
{
longWaitDlg.PerformWork(null, 1000, share.Extract);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
using (TextReader reader = new StreamReader(share.DocumentPath))
{
XmlSerializer documentSerializer = new XmlSerializer(typeof(SrmDocument));
var document2 = (SrmDocument)documentSerializer.Deserialize(reader);
Assert.IsNotNull(document2);
var im = document.Settings.GetIonMobilities(new MsDataFilePath(path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
pep, nodeGroup, im, out windowDT);
Assert.AreEqual(3.86124, centerDriftTime.DriftTimeMsec(false) ?? 0, .0001, testModeStr);
Assert.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
}
public bool BuildLibrary(IProgressMonitor progress)
{
RetentionTimeRegression regr = null;
var standardSpectra = new List <SpectrumMzInfo>();
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY))
{
// Align Prosit iRTs with iRT standard
var standardPeptidesToAdd = SkylineWindow.ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
var original = standardIRTMap.ToDictionary(p => p.Key.ModifiedTarget, p => p.Value);
var target = IrtStandard.Peptides.ToDictionary(p => p.ModifiedTarget, p => p.Irt);
var aligned = AlignedRetentionTimes.AlignLibraryRetentionTimes(target, original, 0.0, RegressionMethodRT.linear,
CancellationToken.None);
regr = aligned.Regression;
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, _nce)).ToArray(),
CancellationToken.None);
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctPeps = _peptides.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p).Distinct(
new SystemLinqExtensionMethods.FuncEqualityComparer <PrositRetentionTimeModel.PeptideDocNodeWrapper>(
(p1, p2) => p1.Node.ModifiedSequence == p2.Node.ModifiedSequence)).ToArray();
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, _document.Settings,
distinctPeps, CancellationToken.None);
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = regr?.Conversion?.GetY(iRT) ?? iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
public bool BuildPeptideSearchLibrary(CancelEventArgs e)
{
// Nothing to build, if now search files were specified
if (!SearchFilenames.Any())
{
var libraries = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
if (!libraries.HasLibraries)
{
return(false);
}
var libSpec = libraries.LibrarySpecs.FirstOrDefault(s => s.IsDocumentLibrary);
return(libSpec != null && LoadPeptideSearchLibrary(libSpec));
}
double cutOffScore;
MessageBoxHelper helper = new MessageBoxHelper(WizardForm);
if (!helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
e.Cancel = true;
return(false);
}
ImportPeptideSearch.CutoffScore = cutOffScore;
BiblioSpecLiteBuilder builder;
try
{
builder = ImportPeptideSearch.GetLibBuilder(SkylineWindow.Document, SkylineWindow.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
}
catch (FileEx.DeleteException de)
{
MessageDlg.ShowException(this, de);
return(false);
}
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_Peptide_Search_Library,
Message = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_document_library_for_peptide_search_,
})
{
// Disable the wizard, because the LongWaitDlg does not
try
{
ImportPeptideSearch.ClosePeptideSearchLibraryStreams(SkylineWindow.DocumentUI);
var status = longWaitDlg.PerformWork(WizardForm, 800,
monitor => LibraryManager.BuildLibraryBackground(SkylineWindow, builder, monitor, new LibraryManager.BuildState(null, null)));
if (status.IsError)
{
MessageDlg.ShowException(WizardForm, status.ErrorException);
return(false);
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Failed_to_build_the_library__0__,
Path.GetFileName(BiblioSpecLiteSpec.GetLibraryFileName(SkylineWindow.DocumentFilePath))), x.Message), x);
return(false);
}
}
var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);
Settings.Default.SpectralLibraryList.Insert(0, docLibSpec);
// Go ahead and load the library - we'll need it for
// the modifications and chromatograms page.
if (!LoadPeptideSearchLibrary(docLibSpec))
{
return(false);
}
var selectedIrtStandard = comboStandards.SelectedItem as IrtStandard;
var addedIrts = false;
if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.NULL)
{
addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
}
var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(SkylineWindow.Document, docLibSpec);
if (docNew == null)
{
return(false);
}
if (addedIrts)
{
docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
}
SkylineWindow.ModifyDocument(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Add_document_spectral_library, doc => docNew);
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
{
MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
}
return(true);
}
private bool ImportTransitionList(CommandArgs commandArgs)
{
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Importing_transiton_list__0____, Path.GetFileName(commandArgs.TransitionListPath));
IdentityPath selectPath;
List<MeasuredRetentionTime> irtPeptides;
List<SpectrumMzInfo> librarySpectra;
List<TransitionImportErrorInfo> errorList;
List<PeptideGroupDocNode> peptideGroups;
var retentionTimeRegression = _doc.Settings.PeptideSettings.Prediction.RetentionTime;
RCalcIrt calcIrt = retentionTimeRegression != null ? (retentionTimeRegression.Calculator as RCalcIrt) : null;
var progressMonitor = new CommandProgressMonitor(_out, new ProgressStatus(string.Empty));
var inputs = new MassListInputs(commandArgs.TransitionListPath);
var docNew = _doc.ImportMassList(inputs, progressMonitor, null,
out selectPath, out irtPeptides, out librarySpectra, out errorList, out peptideGroups);
// If nothing was imported (e.g. operation was canceled or zero error-free transitions) and also no errors, just return
if (ReferenceEquals(docNew, _doc) && !errorList.Any())
return true;
// Show the errors or as warnings, if error transitions are ignore
if (errorList.Any())
{
string messageFormat = !commandArgs.IsIgnoreTransitionErrors
? Resources.CommandLine_ImportTransitionList_Error___line__0___column__1____2_
: Resources.CommandLine_ImportTransitionList_Warning___line__0___column__1____2_;
foreach (var errorMessage in errorList)
{
_out.WriteLine(messageFormat, errorMessage.Row, errorMessage.Column, errorMessage.ErrorMessage);
}
if (!commandArgs.IsIgnoreTransitionErrors)
return false;
}
if (!commandArgs.IsTransitionListAssayLibrary)
{
_doc = docNew;
return true;
}
if (irtPeptides.Count == 0 || librarySpectra.Count == 0)
{
if (irtPeptides.Any())
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Error__Imported_assay_library__0__lacks_ion_abundance_values_);
else if (librarySpectra.Any())
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Error__Imported_assay_library__0__lacks_iRT_values_);
else
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Error__Imported_assay_library__0__lacks_iRT_and_ion_abundance_values_);
return false;
}
string destinationPath = commandArgs.SaveFile ?? commandArgs.SkylineFile;
string documentLibrary = BiblioSpecLiteSpec.GetLibraryFileName(destinationPath);
// ReSharper disable once AssignNullToNotNullAttribute
string outputLibraryPath = Path.Combine(Path.GetDirectoryName(documentLibrary),
Path.GetFileNameWithoutExtension(documentLibrary) + BiblioSpecLiteSpec.ASSAY_NAME +
BiblioSpecLiteSpec.EXT);
bool libraryExists = File.Exists(outputLibraryPath);
string libraryName = Path.GetFileNameWithoutExtension(destinationPath) + BiblioSpecLiteSpec.ASSAY_NAME;
int indexOldLibrary = docNew.Settings.PeptideSettings.Libraries.LibrarySpecs.IndexOf(
spec => spec != null && spec.FilePath == outputLibraryPath);
bool libraryLinkedToDoc = indexOldLibrary != -1;
if (libraryExists && !libraryLinkedToDoc)
{
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Error__There_is_an_existing_library_with_the_same_name__0__as_the_document_library_to_be_created_,
libraryName);
return false;
}
var dbIrtPeptides = irtPeptides.Select(rt => new DbIrtPeptide(rt.PeptideSequence, rt.RetentionTime, false, TimeSource.scan)).ToList();
var dbIrtPeptidesFilter = ImportAssayLibraryHelper.GetUnscoredIrtPeptides(dbIrtPeptides, calcIrt);
// If there are no iRT peptides with different values than the database, don't import any iRT's
bool checkPeptides = false;
if (dbIrtPeptidesFilter.Any())
{
if (calcIrt == null)
{
string irtDatabasePath = commandArgs.IrtDatabasePath;
if (string.IsNullOrEmpty(irtDatabasePath))
irtDatabasePath = Path.ChangeExtension(destinationPath, IrtDb.EXT);
if (!string.IsNullOrEmpty(commandArgs.IrtStandardsPath))
{
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Importing_iRT_transition_list__0_, commandArgs.IrtStandardsPath);
var irtInputs = new MassListInputs(commandArgs.IrtStandardsPath);
try
{
List<SpectrumMzInfo> irtLibrarySpectra;
docNew = docNew.ImportMassList(irtInputs, null, out selectPath, out irtPeptides, out irtLibrarySpectra, out errorList);
if (errorList.Any())
{
throw new InvalidDataException(errorList[0].ErrorMessage);
}
librarySpectra.AddRange(irtLibrarySpectra);
dbIrtPeptidesFilter.AddRange(irtPeptides.Select(rt => new DbIrtPeptide(rt.PeptideSequence, rt.RetentionTime, true, TimeSource.scan)));
}
catch (Exception x)
{
_out.WriteLine(Resources.CommandLine_Run_Error__Failed_importing_the_file__0____1_, commandArgs.IrtStandardsPath, x.Message);
return false;
}
if (!CreateIrtDatabase(irtDatabasePath, commandArgs))
return false;
}
else if (!string.IsNullOrEmpty(commandArgs.IrtGroupName))
{
var nodeGroupIrt = docNew.PeptideGroups.FirstOrDefault(nodeGroup => nodeGroup.Name == commandArgs.IrtGroupName);
if (nodeGroupIrt == null)
{
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Error__The_name__0__specified_with__1__was_not_found_in_the_imported_assay_library_,
commandArgs.IrtGroupName, CommandArgs.ArgText(CommandArgs.ARG_IRT_STANDARDS_GROUP_NAME));
return false;
}
var irtPeptideSequences = new HashSet<string>(nodeGroupIrt.Peptides.Select(pep => pep.ModifiedSequence));
dbIrtPeptidesFilter.ForEach(pep => pep.Standard = irtPeptideSequences.Contains(pep.PeptideModSeq));
if (!CreateIrtDatabase(irtDatabasePath, commandArgs))
return false;
}
else if (!File.Exists(irtDatabasePath))
{
_out.Write(Resources.CommandLine_ImportTransitionList_Error__To_create_the_iRT_database___0___for_this_assay_library__you_must_specify_the_iRT_standards_using_either_of_the_arguments__1__or__2_,
irtDatabasePath, CommandArgs.ArgText(CommandArgs.ARG_IRT_STANDARDS_GROUP_NAME), CommandArgs.ArgText(CommandArgs.ARG_IRT_STANDARDS_FILE));
return false;
}
else
{
checkPeptides = true;
}
string irtCalcName = commandArgs.IrtCalcName ?? Path.GetFileNameWithoutExtension(destinationPath);
calcIrt = new RCalcIrt(irtCalcName, irtDatabasePath);
retentionTimeRegression = new RetentionTimeRegression(calcIrt.Name, calcIrt, null, null, 10, new List<MeasuredRetentionTime>());
docNew = docNew.ChangeSettings(docNew.Settings.ChangePeptidePrediction(prediction =>
prediction.ChangeRetentionTime(retentionTimeRegression)));
}
string dbPath = calcIrt.DatabasePath;
IrtDb db = IrtDb.GetIrtDb(dbPath, null);
if (checkPeptides)
{
var standards = docNew.Molecules.Where(m => db.IsStandard(m.RawTextId)).ToArray();
if (standards.Length != db.StandardPeptideCount)
{
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Warning__The_document_is_missing_iRT_standards);
foreach (var rawTextId in db.StandardPeptides.Where(s => !standards.Contains(nodePep => s == nodePep.RawTextId)))
{
_out.WriteLine(" " + rawTextId); // Not L10N
}
}
}
var oldPeptides = db.GetPeptides().ToList();
IList<DbIrtPeptide.Conflict> conflicts;
dbIrtPeptidesFilter = DbIrtPeptide.MakeUnique(dbIrtPeptidesFilter);
DbIrtPeptide.FindNonConflicts(oldPeptides, dbIrtPeptidesFilter, null, out conflicts);
// Warn about peptides that are present in the import and already in the database
foreach (var conflict in conflicts)
{
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Warning__The_iRT_calculator_already_contains__0__with_the_value__1___Ignoring__2_,
conflict.ExistingPeptide.PeptideModSeq, conflict.ExistingPeptide.Irt, conflict.NewPeptide.Irt);
}
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Importing__0__iRT_values_into_the_iRT_calculator__1_, dbIrtPeptidesFilter.Count, calcIrt.Name);
docNew = docNew.AddIrtPeptides(dbIrtPeptidesFilter, false, progressMonitor);
if (docNew == null)
return false;
}
librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(librarySpectra);
if (libraryLinkedToDoc)
{
string oldName = docNew.Settings.PeptideSettings.Libraries.LibrarySpecs[indexOldLibrary].Name;
var libraryOld = docNew.Settings.PeptideSettings.Libraries.GetLibrary(oldName);
var additionalSpectra = SpectrumMzInfo.GetInfoFromLibrary(libraryOld);
additionalSpectra = SpectrumMzInfo.RemoveDuplicateSpectra(additionalSpectra);
librarySpectra = SpectrumMzInfo.MergeWithOverwrite(librarySpectra, additionalSpectra);
foreach (var stream in libraryOld.ReadStreams)
stream.CloseStream();
}
if (librarySpectra.Any())
{
// Delete the existing library; either it's not tied to the document or we've already extracted the spectra
_out.WriteLine(Resources.CommandLine_ImportTransitionList_Adding__0__spectra_to_the_library__1_, librarySpectra.Count, libraryName);
if (libraryExists)
{
FileEx.SafeDelete(outputLibraryPath);
FileEx.SafeDelete(Path.ChangeExtension(outputLibraryPath, BiblioSpecLiteSpec.EXT_REDUNDANT));
}
using (var blibDb = BlibDb.CreateBlibDb(outputLibraryPath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(libraryName, outputLibraryPath);
var docLibrary = blibDb.CreateLibraryFromSpectra(docLibrarySpec, librarySpectra, libraryName,
progressMonitor);
if (docLibrary == null)
return false;
var newSettings = docNew.Settings.ChangePeptideLibraries(
libs => libs.ChangeLibrary(docLibrary, docLibrarySpec, indexOldLibrary));
docNew = docNew.ChangeSettings(newSettings, new SrmSettingsChangeMonitor(progressMonitor,
Resources.SkylineWindow_ImportMassList_Finishing_up_import));
}
}
_doc = docNew;
return true;
}
public SrmSettings ConnectLibrarySpecs(Func<Library, LibrarySpec> findLibrarySpec, string docLibPath = null)
{
var libraries = PeptideSettings.Libraries;
bool hasDocLib = libraries.HasDocumentLibrary && null != docLibPath;
if (!libraries.HasLibraries && !hasDocLib)
return this;
int len = libraries.Libraries.Count;
int docLibShift = hasDocLib ? 1 : 0;
LibrarySpec[] librarySpecs = new LibrarySpec[len + docLibShift];
for (int i = 0; i < len; i++)
{
int iSpec = i + docLibShift;
var library = libraries.Libraries[i];
if (library == null)
{
librarySpecs[iSpec] = libraries.LibrarySpecs[i];
if (librarySpecs[iSpec] == null)
throw new InvalidDataException(Resources.SrmSettings_ConnectLibrarySpecs_Settings_missing_library_spec);
continue;
}
librarySpecs[iSpec] = findLibrarySpec(library);
if (librarySpecs[iSpec] == null)
return null; // Canceled
if (librarySpecs[iSpec].FilePath == null)
{
// Disconnect the libraries, if not canceled, but no path
// specified.
return ChangePeptideSettings(PeptideSettings.ChangeLibraries(libraries.Disconnect()));
}
}
if (hasDocLib)
{
string docLibName = Path.GetFileNameWithoutExtension(docLibPath);
librarySpecs[0] = new BiblioSpecLiteSpec(docLibName, docLibPath).ChangeDocumentLibrary(true);
}
if (ArrayUtil.EqualsDeep(librarySpecs, libraries.LibrarySpecs))
return this;
libraries = libraries.ChangeLibrarySpecs(librarySpecs);
return ChangePeptideSettings(PeptideSettings.ChangeLibraries(libraries));
}
private void ImportMassList(MassListInputs inputs, string description)
{
SrmTreeNode nodePaste = SequenceTree.SelectedNode as SrmTreeNode;
IdentityPath insertPath = nodePaste != null ? nodePaste.Path : null;
IdentityPath selectPath = null;
List<MeasuredRetentionTime> irtPeptides = null;
List<SpectrumMzInfo> librarySpectra = null;
List<TransitionImportErrorInfo> errorList = null;
List<PeptideGroupDocNode> peptideGroups = null;
RetentionTimeRegression retentionTimeRegressionStore = null;
var docCurrent = DocumentUI;
SrmDocument docNew = null;
var retentionTimeRegression = docCurrent.Settings.PeptideSettings.Prediction.RetentionTime;
RCalcIrt calcIrt = retentionTimeRegression != null ? (retentionTimeRegression.Calculator as RCalcIrt) : null;
using (var longWaitDlg = new LongWaitDlg(this) {Text = description})
{
longWaitDlg.PerformWork(this, 1000, longWaitBroker =>
{
docNew = docCurrent.ImportMassList(inputs, longWaitBroker,
insertPath, out selectPath, out irtPeptides, out librarySpectra, out errorList, out peptideGroups);
});
}
bool isDocumentSame = ReferenceEquals(docNew, docCurrent);
// If nothing was imported (e.g. operation was canceled or zero error-free transitions) and also no errors, just return
if (isDocumentSame && !errorList.Any())
return;
// Show the errors, giving the option to accept the transitions without errors,
// if there are any
if (errorList.Any())
{
using (var errorDlg = new ImportTransitionListErrorDlg(errorList, isDocumentSame))
{
if (errorDlg.ShowDialog(this) == DialogResult.Cancel || isDocumentSame)
{
return;
}
}
}
var dbIrtPeptides = irtPeptides.Select(rt => new DbIrtPeptide(rt.PeptideSequence, rt.RetentionTime, false, TimeSource.scan)).ToList();
var dbIrtPeptidesFilter = ImportAssayLibraryHelper.GetUnscoredIrtPeptides(dbIrtPeptides, calcIrt);
bool overwriteExisting = false;
MassListInputs irtInputs = null;
// If there are no iRT peptides or none with different values than the database, don't import any iRT's
if (dbIrtPeptidesFilter.Any())
{
// Ask whether or not to include iRT peptides in the paste
string useIrtMessage = calcIrt == null
? Resources.SkylineWindow_ImportMassList_The_transition_list_appears_to_contain_iRT_values__but_the_document_does_not_have_an_iRT_calculator___Create_a_new_calculator_and_add_these_iRT_values_
: Resources.SkylineWindow_ImportMassList_The_transition_list_appears_to_contain_iRT_library_values___Add_these_iRT_values_to_the_iRT_calculator_;
string yesButton = calcIrt == null
? Resources.SkylineWindow_ImportMassList__Create___
: Resources.SkylineWindow_ImportMassList_Add;
var useIrtResult = MultiButtonMsgDlg.Show(this, useIrtMessage,
yesButton, Resources.SkylineWindow_ImportMassList__Skip, true);
if (useIrtResult == DialogResult.Cancel)
{
return;
}
if (useIrtResult == DialogResult.Yes)
{
if (calcIrt == null)
{
// If there is no iRT calculator, ask the user to create one
using (var dlg = new CreateIrtCalculatorDlg(docNew, DocumentFilePath, Settings.Default.RTScoreCalculatorList, peptideGroups))
{
if (dlg.ShowDialog(this) != DialogResult.OK)
{
return;
}
docNew = dlg.Document;
calcIrt = (RCalcIrt)docNew.Settings.PeptideSettings.Prediction.RetentionTime.Calculator;
dlg.UpdateLists(librarySpectra, dbIrtPeptidesFilter);
if (!string.IsNullOrEmpty(dlg.IrtFile))
irtInputs = new MassListInputs(dlg.IrtFile);
}
}
string dbPath = calcIrt.DatabasePath;
IrtDb db = File.Exists(dbPath) ? IrtDb.GetIrtDb(dbPath, null) : IrtDb.CreateIrtDb(dbPath);
var oldPeptides = db.GetPeptides().ToList();
IList<DbIrtPeptide.Conflict> conflicts;
dbIrtPeptidesFilter = DbIrtPeptide.MakeUnique(dbIrtPeptidesFilter);
DbIrtPeptide.FindNonConflicts(oldPeptides, dbIrtPeptidesFilter, null, out conflicts);
// Ask whether to keep or overwrite peptides that are present in the import and already in the database
if (conflicts.Any())
{
string messageOverwrite = string.Format(Resources.SkylineWindow_ImportMassList_The_iRT_calculator_already_contains__0__of_the_imported_peptides_,
conflicts.Count);
var overwriteResult = MultiButtonMsgDlg.Show(this,
TextUtil.LineSeparate(messageOverwrite, conflicts.Count == 1
? Resources.SkylineWindow_ImportMassList_Keep_the_existing_iRT_value_or_overwrite_with_the_imported_value_
: Resources.SkylineWindow_ImportMassList_Keep_the_existing_iRT_values_or_overwrite_with_imported_values_),
Resources.SkylineWindow_ImportMassList__Keep, Resources.SkylineWindow_ImportMassList__Overwrite, true);
if (overwriteResult == DialogResult.Cancel)
{
return;
}
overwriteExisting = overwriteResult == DialogResult.No;
}
using (var longWaitDlg = new LongWaitDlg(this) { Text = Resources.SkylineWindow_ImportMassList_Adding_iRT_values_})
{
longWaitDlg.PerformWork(this, 100, progressMonitor =>
docNew = docNew.AddIrtPeptides(dbIrtPeptidesFilter, overwriteExisting, progressMonitor));
}
if (docNew == null)
return;
retentionTimeRegressionStore = docNew.Settings.PeptideSettings.Prediction.RetentionTime;
}
}
BiblioSpecLiteSpec docLibrarySpec = null;
BiblioSpecLiteLibrary docLibrary = null;
int indexOldLibrary = -1;
if (librarySpectra.Any())
{
string addLibraryMessage = Resources.SkylineWindow_ImportMassList_The_transition_list_appears_to_contain_spectral_library_intensities___Create_a_document_library_from_these_intensities_;
var addLibraryResult = MultiButtonMsgDlg.Show(this, addLibraryMessage,
Resources.SkylineWindow_ImportMassList__Create___, Resources.SkylineWindow_ImportMassList__Skip,
true);
if (addLibraryResult == DialogResult.Cancel)
{
return;
}
if (addLibraryResult == DialogResult.Yes)
{
// Can't name a library after the document if the document is unsaved
// In this case, prompt to save
if (DocumentFilePath == null)
{
string saveDocumentMessage = Resources.SkylineWindow_ImportMassList_You_must_save_the_Skyline_document_in_order_to_create_a_spectral_library_from_a_transition_list_;
var saveDocumentResult = MultiButtonMsgDlg.Show(this, saveDocumentMessage, MultiButtonMsgDlg.BUTTON_OK);
if (saveDocumentResult == DialogResult.Cancel)
{
return;
}
else if (!SaveDocumentAs())
{
return;
}
}
librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(librarySpectra);
string documentLibrary = BiblioSpecLiteSpec.GetLibraryFileName(DocumentFilePath);
// ReSharper disable once AssignNullToNotNullAttribute
string outputPath = Path.Combine(Path.GetDirectoryName(documentLibrary),
Path.GetFileNameWithoutExtension(documentLibrary) + BiblioSpecLiteSpec.ASSAY_NAME + BiblioSpecLiteSpec.EXT);
bool libraryExists = File.Exists(outputPath);
string name = Path.GetFileNameWithoutExtension(DocumentFilePath) + BiblioSpecLiteSpec.ASSAY_NAME;
indexOldLibrary = docNew.Settings.PeptideSettings.Libraries.LibrarySpecs.IndexOf(spec => spec != null && spec.FilePath == outputPath);
bool libraryLinkedToDoc = indexOldLibrary != -1;
if (libraryLinkedToDoc)
{
string oldName = docNew.Settings.PeptideSettings.Libraries.LibrarySpecs[indexOldLibrary].Name;
var libraryOld = docNew.Settings.PeptideSettings.Libraries.GetLibrary(oldName);
var additionalSpectra = SpectrumMzInfo.GetInfoFromLibrary(libraryOld);
additionalSpectra = SpectrumMzInfo.RemoveDuplicateSpectra(additionalSpectra);
librarySpectra = SpectrumMzInfo.MergeWithOverwrite(librarySpectra, additionalSpectra);
foreach (var stream in libraryOld.ReadStreams)
stream.CloseStream();
}
if (libraryExists && !libraryLinkedToDoc)
{
string replaceLibraryMessage = string.Format(Resources.SkylineWindow_ImportMassList_There_is_an_existing_library_with_the_same_name__0__as_the_document_library_to_be_created___Overwrite_this_library_or_skip_import_of_library_intensities_,
name);
// If the document does not have an assay library linked to it, then ask if user wants to delete the one that we have found
var replaceLibraryResult = MultiButtonMsgDlg.Show(this, replaceLibraryMessage,
Resources.SkylineWindow_ImportMassList__Overwrite, Resources.SkylineWindow_ImportMassList__Skip, true);
if (replaceLibraryResult == DialogResult.Cancel)
return;
if (replaceLibraryResult == DialogResult.No)
librarySpectra.Clear();
}
if (librarySpectra.Any())
{
// Delete the existing library; either it's not tied to the document or we've already extracted the spectra
if (libraryExists)
{
FileEx.SafeDelete(outputPath);
FileEx.SafeDelete(Path.ChangeExtension(outputPath, BiblioSpecLiteSpec.EXT_REDUNDANT));
}
using (var blibDb = BlibDb.CreateBlibDb(outputPath))
{
docLibrarySpec = new BiblioSpecLiteSpec(name, outputPath);
using (var longWaitDlg = new LongWaitDlg(this) { Text = Resources.SkylineWindow_ImportMassList_Creating_Spectral_Library })
{
longWaitDlg.PerformWork(this, 1000, progressMonitor =>
{
docLibrary = blibDb.CreateLibraryFromSpectra(docLibrarySpec, librarySpectra, name, progressMonitor);
if (docLibrary == null)
return;
var newSettings = docNew.Settings.ChangePeptideLibraries(libs => libs.ChangeLibrary(docLibrary, docLibrarySpec, indexOldLibrary));
var status = new ProgressStatus(Resources.SkylineWindow_ImportMassList_Finishing_up_import);
progressMonitor.UpdateProgress(status);
progressMonitor.UpdateProgress(status.ChangePercentComplete(100));
docNew = docNew.ChangeSettings(newSettings);
});
if (docLibrary == null)
return;
}
}
}
}
}
ModifyDocument(description, doc =>
{
if (ReferenceEquals(doc, docCurrent))
return docNew;
try
{
// If the document was changed during the operation, try all the changes again
// using the information given by the user.
docCurrent = DocumentUI;
doc = doc.ImportMassList(inputs, insertPath, out selectPath);
if (irtInputs != null)
{
doc = doc.ImportMassList(irtInputs, null, out selectPath);
}
var newSettings = doc.Settings;
if (retentionTimeRegressionStore != null)
{
newSettings = newSettings.ChangePeptidePrediction(prediction =>
prediction.ChangeRetentionTime(retentionTimeRegressionStore));
}
if (docLibrarySpec != null)
{
newSettings = newSettings.ChangePeptideLibraries(libs =>
libs.ChangeLibrary(docLibrary, docLibrarySpec, indexOldLibrary));
}
if (!ReferenceEquals(doc.Settings, newSettings))
doc = doc.ChangeSettings(newSettings);
}
catch (Exception x)
{
throw new InvalidDataException(string.Format(Resources.SkylineWindow_ImportMassList_Unexpected_document_change_during_operation___0_, x.Message, x));
}
return doc;
});
if (selectPath != null)
SequenceTree.SelectedPath = selectPath;
if (retentionTimeRegressionStore != null)
{
Settings.Default.RetentionTimeList.Add(retentionTimeRegressionStore);
Settings.Default.RTScoreCalculatorList.Add(retentionTimeRegressionStore.Calculator);
}
if (docLibrarySpec != null)
{
Settings.Default.SpectralLibraryList.Insert(0, docLibrarySpec);
}
}
/// <summary>
/// Make a BiblioSpec SQLite library from a list of spectra and their intensities.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="listSpectra">List of existing spectra, by LibKey</param>
/// <param name="libraryName">Name of the library to be created</param>
/// <param name="progressMonitor">Progress monitor to display progress in creating library</param>
/// <returns>A library of type <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary CreateLibraryFromSpectra(BiblioSpecLiteSpec librarySpec,
List<SpectrumMzInfo> listSpectra,
string libraryName,
IProgressMonitor progressMonitor)
{
const string libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
const int majorVer = 1;
const int minorVer = 0;
string libId = libraryName;
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), majorVer, minorVer);
var dictLibrary = new Dictionary<LibKey, BiblioLiteSpectrumInfo>();
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
int progressPercent = 0;
int i = 0;
var status = new ProgressStatus(Resources.BlibDb_CreateLibraryFromSpectra_Creating_spectral_library_for_imported_transition_list);
foreach (var spectrum in listSpectra)
{
++i;
var dbRefSpectrum = RefSpectrumFromPeaks(spectrum);
session.Save(dbRefSpectrum);
dictLibrary.Add(spectrum.Key,
new BiblioLiteSpectrumInfo(spectrum.Key, dbRefSpectrum.Copies,
dbRefSpectrum.NumPeaks,
(int)(dbRefSpectrum.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return null;
int progressNew = (i * 100 / listSpectra.Count);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
}
session.Flush();
session.Clear();
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = majorVer,
MinorVersion = minorVer
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
}
var libraryEntries = dictLibrary.Values.ToArray();
return new BiblioSpecLiteLibrary(librarySpec, libLsid, majorVer, minorVer,
libraryEntries, FileStreamManager.Default);
}
protected override void DoTest()
{
TestSmallMolecules = false; // The presence of the extra test node without any results is incompatible with what's being tested here.
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// show the empty Transition Setting dialog
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsDlg.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab nothing set", 2);
OkDialog(transitionSettingsDlg, transitionSettingsDlg.OkDialog);
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
var ambiguousDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 5);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 6);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 7);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 10);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 11);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <MultiButtonMsgDlg>("Add mods alert", 12);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 13);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = 1160;
SkylineWindow.Height = 792;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 14);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 16);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 17);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 19);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() =>
{
alignmentForm.Width = 711;
alignmentForm.Height = 561;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 20);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 21);
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 32.6, 41.4); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 22);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 23);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 24, "Transition pick list unfiltered", 24); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 39.6); // set the view for screenshot
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 25);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chhromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 26);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 27);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 28);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 29);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 30);
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
// page 32 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = SkylineWindow.GraphChromatograms.ToArray()[TIP3].GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 32);
RestoreViewOnScreen(33); // float the Library Match window TODO this causes a crash at next call to ChangePeakBounds, in pwiz.Skyline.Controls.Graphs.GraphChromatogram.ChromGroupInfos.get() Line 492 , why?
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 33);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 33);
RestoreViewOnScreen(34); // back to normal view
pepIndex = JumpToPeptide("GVVDSEDLPLNISR"); // Not L10N
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
PauseForScreenShot("upper - Chromatogram graph metafiles for peptide GVVDSEDLPLNISR", 34);
ZoomBoth(35.05, 36.9, 480);
PauseForScreenShot("lower - Chromatogram graph metafile - effect of zoom ", 34);
ChangePeakBounds(TIP3, pepIndex, 35.7, 36.5); // adjust integration per tutorial
CheckAnnotations(TIP3, pepIndex, atest++); // check the new idotp values
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 35);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 36); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // Not L10N
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio;
dlg.OkDialog();
});
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
/// <summary>
/// Minimizes all libraries in a document to produce a new document with
/// just the library information necessary for the spectra referenced by
/// the nodes in the document.
/// </summary>
/// <param name="document">Document for which to minimize library information</param>
/// <param name="pathDirectory">Directory into which new minimized libraries are built</param>
/// <param name="nameModifier">A name modifier to append to existing names for
/// full libraries to create new library names</param>
/// <param name="progressMonitor">Broker to communicate status and progress</param>
/// <returns>A new document instance with minimized libraries</returns>
public static SrmDocument MinimizeLibraries(SrmDocument document,
string pathDirectory, string nameModifier, IProgressMonitor progressMonitor)
{
var settings = document.Settings;
var pepLibraries = settings.PeptideSettings.Libraries;
if (!pepLibraries.HasLibraries)
{
return(document);
}
if (!pepLibraries.IsLoaded)
{
throw new InvalidOperationException(Resources.BlibDb_MinimizeLibraries_Libraries_must_be_fully_loaded_before_they_can_be_minimzed);
}
// Separate group nodes by the libraries to which they refer
var setUsedLibrarySpecs = new HashSet <LibrarySpec>();
foreach (var librarySpec in pepLibraries.LibrarySpecs)
{
string libraryName = librarySpec.Name;
if (document.MoleculeTransitionGroups.Contains(nodeGroup =>
nodeGroup.HasLibInfo && Equals(nodeGroup.LibInfo.LibraryName, libraryName)))
{
setUsedLibrarySpecs.Add(librarySpec);
}
}
var listLibraries = new List <Library>();
var listLibrarySpecs = new List <LibrarySpec>();
var dictOldNameToNew = new Dictionary <string, string>();
if (setUsedLibrarySpecs.Count > 0)
{
Directory.CreateDirectory(pathDirectory);
var usedNames = new HashSet <string>();
for (int i = 0; i < pepLibraries.LibrarySpecs.Count; i++)
{
var librarySpec = pepLibraries.LibrarySpecs[i];
if (!setUsedLibrarySpecs.Contains(librarySpec))
{
continue;
}
string baseName = Path.GetFileNameWithoutExtension(librarySpec.FilePath);
string fileName = GetUniqueName(baseName, usedNames) + BiblioSpecLiteSpec.EXT;
using (var blibDb = CreateBlibDb(Path.Combine(pathDirectory, fileName)))
{
blibDb.ProgressMonitor = progressMonitor;
var librarySpecMin = librarySpec as BiblioSpecLiteSpec;
if (librarySpecMin == null || !librarySpecMin.IsDocumentLibrary)
{
string nameMin = librarySpec.Name;
// Avoid adding the modifier a second time, if it has
// already been done once.
if (!nameMin.EndsWith(nameModifier + ")")) // Not L10N
{
nameMin = string.Format("{0} ({1})", librarySpec.Name, nameModifier); // Not L10N
}
librarySpecMin = new BiblioSpecLiteSpec(nameMin, blibDb.FilePath);
}
listLibraries.Add(blibDb.MinimizeLibrary(librarySpecMin,
pepLibraries.Libraries[i], document));
// Terminate if user canceled
if (progressMonitor != null && progressMonitor.IsCanceled)
{
return(document);
}
listLibrarySpecs.Add(librarySpecMin);
dictOldNameToNew.Add(librarySpec.Name, librarySpecMin.Name);
}
}
document = (SrmDocument)document.ChangeAll(node =>
{
var nodeGroup = node as TransitionGroupDocNode;
if (nodeGroup == null || !nodeGroup.HasLibInfo)
{
return(node);
}
string libName = nodeGroup.LibInfo.LibraryName;
string libNameNew = dictOldNameToNew[libName];
if (Equals(libName, libNameNew))
{
return(node);
}
var libInfo = nodeGroup.LibInfo.ChangeLibraryName(libNameNew);
return(nodeGroup.ChangeLibInfo(libInfo));
},
(int)SrmDocument.Level.TransitionGroups);
}
return(document.ChangeSettingsNoDiff(settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(listLibrarySpecs, listLibraries))));
}
/// <summary>
/// Minimize any library type to a fully functional BiblioSpec SQLite library.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="library">Existing library to minimize</param>
/// <param name="document">Document for which only used spectra are included in the new library</param>
/// <returns>A new minimized <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary MinimizeLibrary(BiblioSpecLiteSpec librarySpec,
Library library, SrmDocument document)
{
if (!UpdateProgressMessage(string.Format(Resources.BlibDb_MinimizeLibrary_Minimizing_library__0__, library.Name)))
{
return(null);
}
string libAuthority = "unknown.org"; // Not L10N
string libId = library.Name;
// CONSIDER: Use version numbers of the original library?
int libraryRevision = DbLibInfo.INITIAL_LIBRARY_REVISION;
int schemaVersion = 0;
bool saveRetentionTimes = false;
bool saveRedundantLib = false;
var blibLib = library as BiblioSpecLiteLibrary;
if (blibLib != null)
{
string libraryLsid = blibLib.Lsid;
Match matchLsid = REGEX_LSID.Match(libraryLsid);
if (matchLsid.Success)
{
libAuthority = matchLsid.Groups[1].Value;
libId = matchLsid.Groups[2].Value;
}
else
{
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
}
// We will have a RetentionTimes table if schemaVersion if 1 or greater.
saveRetentionTimes = blibLib.SchemaVersion >= 1;
libraryRevision = blibLib.Revision;
schemaVersion = Math.Min(blibLib.SchemaVersion, DbLibInfo.SCHEMA_VERSION_CURRENT);
// If the document has MS1 filtering enabled we will save a minimized version
// of the redundant library, if available.
if (document.Settings.TransitionSettings.FullScan.IsEnabledMs)
{
String redundantLibPath = blibLib.FilePathRedundant;
if (File.Exists(redundantLibPath))
{
string path = BiblioSpecLiteSpec.GetRedundantName(FilePath);
CreateSessionFactory_Redundant(path);
saveRedundantLib = true;
}
}
}
else if (library is BiblioSpecLibrary)
{
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
}
else if (library is XHunterLibrary)
{
libAuthority = XHunterLibrary.DEFAULT_AUTHORITY;
}
else
{
var nistLibrary = library as NistLibrary;
if (nistLibrary != null)
{
libAuthority = NistLibrary.DEFAULT_AUTHORITY;
libId = nistLibrary.Id ?? libId;
}
}
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), libraryRevision, schemaVersion);
var dictLibrary = new Dictionary <LibKey, BiblioLiteSpectrumInfo>();
// Hash table to store the database IDs of any source files in the library
// Source file information is available only in Bibliospec libraries, schema version >= 1
var dictFiles = new Dictionary <string, long>();
var dictFilesRedundant = new Dictionary <string, long>();
ISession redundantSession = null;
ITransaction redundantTransaction = null;
int redundantSpectraCount = 0;
try
{
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
var settings = document.Settings;
int peptideCount = document.PeptideCount;
int savedCount = 0;
foreach (var nodePep in document.Peptides)
{
var mods = nodePep.ExplicitMods;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
// Only get library info from precursors that use the desired library
if (!nodeGroup.HasLibInfo || !Equals(nodeGroup.LibInfo.LibraryName, library.Name))
{
continue;
}
TransitionGroup group = nodeGroup.TransitionGroup;
string peptideSeq = group.Peptide.Sequence;
int precursorCharge = group.PrecursorCharge;
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
var calcPre = settings.GetPrecursorCalc(labelType, mods);
var peptideModSeq = calcPre.GetModifiedSequence(peptideSeq, false);
var libKey = new LibKey(peptideModSeq, precursorCharge);
if (dictLibrary.ContainsKey(libKey))
{
continue;
}
// saveRetentionTimes will be false unless this is a BiblioSpec(schemaVersion >=1) library.
if (!saveRetentionTimes)
{
// get the best spectra
foreach (var spectrumInfo in library.GetSpectra(libKey, labelType, LibraryRedundancy.best))
{
DbRefSpectra refSpectra = MakeRefSpectrum(spectrumInfo,
peptideSeq,
peptideModSeq,
nodeGroup.PrecursorMz,
precursorCharge);
session.Save(refSpectra);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey, refSpectra.Copies,
refSpectra.NumPeaks,
(int)(refSpectra.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
}
session.Flush();
session.Clear();
}
// This is a BiblioSpec(schemaVersion >=1) library.
else
{
// get all the spectra, including the redundant ones if this library has any
var spectra = library.GetSpectra(libKey, labelType, LibraryRedundancy.all_redundant).ToArray();
// Avoid saving to the RefSpectra table for isotope label types that have no spectra
if (spectra.Length == 0)
{
continue;
}
DbRefSpectra refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = nodeGroup.PrecursorMz,
PrecursorCharge = precursorCharge,
PeptideModSeq = peptideModSeq
};
// Get all the information for this reference spectrum.
// For BiblioSpec (schema ver >= 1), this can include retention time information
// for this spectrum as well as any redundant spectra for the peptide.
// Ids of spectra in the redundant library, where available, are also returned.
var redundantSpectraKeys = new List <SpectrumKeyTime>();
BuildRefSpectra(document, session, refSpectra, spectra, dictFiles, redundantSpectraKeys);
session.Save(refSpectra);
session.Flush();
session.Clear();
// TODO(nicksh): preserve retention time information.
var retentionTimesByFileId = default(IndexedRetentionTimes);
var driftTimesByFileId = default(IndexedIonMobilities);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey,
refSpectra.Copies,
refSpectra.NumPeaks,
(int)(refSpectra.Id ?? 0),
retentionTimesByFileId,
driftTimesByFileId));
// Save entries in the redundant library.
if (saveRedundantLib && redundantSpectraKeys.Count > 0)
{
if (redundantSession == null)
{
redundantSession = OpenWriteSession_Redundant();
redundantTransaction = redundantSession.BeginTransaction();
}
SaveRedundantSpectra(redundantSession, redundantSpectraKeys, dictFilesRedundant, refSpectra, library);
redundantSpectraCount += redundantSpectraKeys.Count;
}
}
}
savedCount++;
if (!UpdateProgress(peptideCount, savedCount))
{
return(null);
}
}
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
if (redundantTransaction != null)
{
var scoreType = new DbScoreTypes {
Id = 0, ScoreType = "UNKNOWN"
}; // Not L10N
redundantSession.Save(scoreType);
libInfo = new DbLibInfo
{
LibLSID = libLsid.Replace(":nr:", ":redundant:"), // Not L10N
CreateTime = createTime,
NumSpecs = redundantSpectraCount,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
redundantSession.Save(libInfo);
redundantSession.Flush();
redundantSession.Clear();
redundantTransaction.Commit();
}
}
}
finally
{
if (redundantTransaction != null)
{
redundantTransaction.Dispose();
}
if (redundantSession != null)
{
redundantSession.Dispose();
}
}
var libraryEntries = dictLibrary.Values.ToArray();
return(new BiblioSpecLiteLibrary(librarySpec, libLsid, libraryRevision, schemaVersion,
libraryEntries, FileStreamManager.Default));
}
/// <summary>
/// Make a BiblioSpec SQLite library from a list of spectra and their intensities.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="listSpectra">List of existing spectra, by LibKey</param>
/// <param name="libraryName">Name of the library to be created</param>
/// <param name="progressMonitor">Progress monitor to display progress in creating library</param>
/// <returns>A library of type <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary CreateLibraryFromSpectra(BiblioSpecLiteSpec librarySpec,
List <SpectrumMzInfo> listSpectra,
string libraryName,
IProgressMonitor progressMonitor)
{
const string libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
const int majorVer = 1;
const int minorVer = 0;
string libId = libraryName;
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), majorVer, minorVer);
var dictLibrary = new Dictionary <LibKey, BiblioLiteSpectrumInfo>();
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
int progressPercent = 0;
int i = 0;
var status = new ProgressStatus(Resources.BlibDb_CreateLibraryFromSpectra_Creating_spectral_library_for_imported_transition_list);
foreach (var spectrum in listSpectra)
{
++i;
var dbRefSpectrum = RefSpectrumFromPeaks(spectrum);
session.Save(dbRefSpectrum);
dictLibrary.Add(spectrum.Key,
new BiblioLiteSpectrumInfo(spectrum.Key, dbRefSpectrum.Copies,
dbRefSpectrum.NumPeaks,
(int)(dbRefSpectrum.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
return(null);
}
int progressNew = (i * 100 / listSpectra.Count);
if (progressPercent != progressNew)
{
progressMonitor.UpdateProgress(status = status.ChangePercentComplete(progressNew));
progressPercent = progressNew;
}
}
}
session.Flush();
session.Clear();
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = majorVer,
MinorVersion = minorVer
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
}
var libraryEntries = dictLibrary.Values.ToArray();
return(new BiblioSpecLiteLibrary(librarySpec, libLsid, majorVer, minorVer,
libraryEntries, FileStreamManager.Default));
}
protected override void DoTest()
{
string skyfile = TestFilesDir.GetTestPath("test_pasef_mascot.sky");
RunUI(() =>
{
SkylineWindow.NewDocument(true);
SkylineWindow.SaveDocument(skyfile);
});
Stopwatch loadStopwatch = new Stopwatch();
loadStopwatch.Start();
// Enable use of drift times in spectral library
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
peptideSettingsUI.IsUseSpectralLibraryDriftTimes = true;
peptideSettingsUI.SpectralLibraryDriftTimeResolvingPower = 50;
});
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
var nextFile = "FZGC A 100 ng_Slot1-46_01_440.d";
var searchResults = GetTestPath("F264099.dat");
var doc = SkylineWindow.Document;
var searchResultsList = new[] { searchResults };
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchResultsList);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.95;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = false;
});
var ambiguousDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck); // Expect the ambiguous matches dialog
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
doc = WaitForDocumentChange(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(skyfile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the files should be found, and we should
// just be able to move to the next page.
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page));
RunUI(() =>
{
var importResultsControl = (ImportResultsControl)importPeptideSearchDlg.ImportResultsControl;
importResultsControl.ExcludeSpectrumSourceFiles = false;
importResultsControl.UpdateResultsFiles(new [] { TestFilesDirs[0].PersistentFilesDir }, true); // Go look in the persistent files dir
});
if (searchResultsList.Length > 1)
{
// Deal with the common name start dialog
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
importResultsNameDlg.NoDialog();
});
WaitForClosedForm(importResultsNameDlg);
}
else
{
RunUI(() => importPeptideSearchDlg.ClickNextButtonNoCheck());
}
// Modifications are already set up, so that page should get skipped.
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new [] { 2, 3, 4, 5 });
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof);
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.UseSpectralLibraryIonMobilityValuesControl.SetUseSpectralLibraryDriftTimes(true));
// Verify error handling in ion mobility control
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.UseSpectralLibraryIonMobilityValuesControl.SetResolvingPowerText("fish"));
var errDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() => errDlg.OkDialog());
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.UseSpectralLibraryIonMobilityValuesControl.SetResolvingPower(40));
RunUI(() => importPeptideSearchDlg.ClickNextButton()); // Accept the full scan settings
// We're on the "Import FASTA" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("human_and_yeast.fasta"));
});
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
WaitForConditionUI(() => peptidesPerProteinDlg.DocumentFinalCalculated);
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
WaitForClosedForm(importPeptideSearchDlg);
var doc1 = WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
AssertEx.IsDocumentState(doc1, null, 7906, 28510, 28510, 85530);
loadStopwatch.Stop();
DebugLog.Info("load time = {0}", loadStopwatch.ElapsedMilliseconds);
var errmsg = "";
LibraryIonMobilityInfo libraryIonMobilityInfo;
doc1.Settings.PeptideSettings.Libraries.Libraries.First().TryGetIonMobilityInfos(0, out libraryIonMobilityInfo);
var driftInfoExplicitDT = libraryIonMobilityInfo;
var instrumentInfo = new DataFileInstrumentInfo(new MsDataFileImpl(GetTestPath(nextFile)));
var dictExplicitDT = driftInfoExplicitDT.GetIonMobilityDict();
foreach (var pep in doc1.Peptides)
{
foreach (var nodeGroup in pep.TransitionGroups)
{
double windowDT;
var calculatedDriftTime = doc1.Settings.GetIonMobility(
pep, nodeGroup, libraryIonMobilityInfo, instrumentInfo, 0, out windowDT);
var libKey = new LibKey(pep.ModifiedSequence, nodeGroup.PrecursorAdduct);
IonMobilityAndCCS[] infoValueExplicitDT;
if (!dictExplicitDT.TryGetValue(libKey, out infoValueExplicitDT))
{
errmsg += "No ionMobility value found for " + libKey + "\n";
}
else
{
var ionMobilityInfo = infoValueExplicitDT[0];
var delta = Math.Abs(ionMobilityInfo.IonMobility.Mobility.Value - calculatedDriftTime.IonMobility.Mobility.Value);
var acceptableDelta = 1;
if (delta > acceptableDelta)
{
errmsg += String.Format("calculated DT ({0}) and explicit DT ({1}, CCS={4}) do not agree (abs delta = {2}) for {3}\n",
calculatedDriftTime.IonMobility, ionMobilityInfo.IonMobility,
delta, libKey,
ionMobilityInfo.CollisionalCrossSectionSqA ?? 0);
}
}
}
}
float tolerance = (float)doc1.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = doc1.Settings.MeasuredResults;
foreach (var pair in doc1.PeptidePrecursorPairs)
{
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out var chromGroupInfo));
foreach (var chromGroup in chromGroupInfo)
{
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
}
Assert.IsTrue(errmsg.Length == 0, errmsg);
Assert.AreEqual(1093425, maxHeight, 1);
// Does CCS show up in reports?
TestReports(doc1);
}
public void UpdateLists(string documentFilePath)
{
Settings defSet = Settings.Default;
// Make sure all settings are contained in the appropriate lists.
// CONSIDER: Simple List.Contains() checks mean that values with the same name
// but differing values will be overwritten.
if (!defSet.EnzymeList.Contains(PeptideSettings.Enzyme))
defSet.EnzymeList.Add(PeptideSettings.Enzyme);
// Extra null checks to avoid ReSharper warnings.
if (PeptideSettings.Prediction != null)
{
if (PeptideSettings.Prediction.RetentionTime != null)
{
if (!defSet.RetentionTimeList.Contains(PeptideSettings.Prediction.RetentionTime))
defSet.RetentionTimeList.Add(PeptideSettings.Prediction.RetentionTime);
if (!defSet.RTScoreCalculatorList.Contains(PeptideSettings.Prediction.RetentionTime.Calculator))
defSet.RTScoreCalculatorList.Add(PeptideSettings.Prediction.RetentionTime.Calculator);
}
if (PeptideSettings.Prediction.DriftTimePredictor != null)
{
if (!defSet.DriftTimePredictorList.Contains(PeptideSettings.Prediction.DriftTimePredictor))
defSet.DriftTimePredictorList.Add(PeptideSettings.Prediction.DriftTimePredictor);
if (PeptideSettings.Prediction.DriftTimePredictor.IonMobilityLibrary != null &&
!defSet.IonMobilityLibraryList.Contains(PeptideSettings.Prediction.DriftTimePredictor.IonMobilityLibrary))
{
defSet.IonMobilityLibraryList.Add(PeptideSettings.Prediction.DriftTimePredictor.IonMobilityLibrary);
}
}
}
if (PeptideSettings.Filter != null)
{
foreach (PeptideExcludeRegex exclude in PeptideSettings.Filter.Exclusions)
{
if (!defSet.PeptideExcludeList.Contains(exclude))
defSet.PeptideExcludeList.Add(exclude);
}
}
// First remove all old document local specs.
defSet.SpectralLibraryList.RemoveDocumentLocalLibraries();
// Then add any specs belonging to this document.
if (PeptideSettings.Libraries.HasLibraries)
{
foreach (LibrarySpec librarySpec in PeptideSettings.Libraries.LibrarySpecs)
{
if (librarySpec != null && !defSet.SpectralLibraryList.Contains(librarySpec))
defSet.SpectralLibraryList.Add(librarySpec);
}
}
// If this document has a document library, add it to the specs list
if (PeptideSettings.Libraries.HasDocumentLibrary)
{
string outputPath = Path.ChangeExtension(documentFilePath, BiblioSpecLiteSpec.EXT);
if (File.Exists(outputPath))
{
string docFileName = Path.GetFileNameWithoutExtension(documentFilePath);
var documentLibSpec = new BiblioSpecLiteSpec(docFileName, outputPath);
if (!defSet.SpectralLibraryList.Contains(documentLibSpec))
{
defSet.SpectralLibraryList.Add(documentLibSpec.ChangeDocumentLibrary(true));
}
}
}
if (PeptideSettings.Integration.PeakScoringModel != null &&
!Equals(PeptideSettings.Integration.PeakScoringModel.Name, LegacyScoringModel.DEFAULT_NAME))
{
defSet.PeakScoringModelList.Add(PeptideSettings.Integration.PeakScoringModel);
}
UpdateDefaultModifications(true, true);
if (TransitionSettings.Prediction != null)
{
TransitionPrediction prediction = TransitionSettings.Prediction;
if (!defSet.CollisionEnergyList.Contains(prediction.CollisionEnergy))
defSet.CollisionEnergyList.Add(prediction.CollisionEnergy);
if (prediction.DeclusteringPotential != null &&
!defSet.DeclusterPotentialList.Contains(prediction.DeclusteringPotential))
defSet.DeclusterPotentialList.Add(prediction.DeclusteringPotential);
if (prediction.CompensationVoltage != null &&
!defSet.CompensationVoltageList.Contains(prediction.CompensationVoltage))
defSet.CompensationVoltageList.Add(prediction.CompensationVoltage);
if (!Equals(prediction.OptimizedLibrary, OptimizationLibrary.NONE) &&
Equals(defSet.GetOptimizationLibraryByName(prediction.OptimizedLibrary.Name), OptimizationLibrary.NONE))
defSet.OptimizationLibraryList.Add(prediction.OptimizedLibrary);
}
if (TransitionSettings.Filter != null)
{
foreach (var measuredIon in TransitionSettings.Filter.MeasuredIons)
{
if (!defSet.MeasuredIonList.Contains(measuredIon))
defSet.MeasuredIonList.Add(measuredIon);
}
}
if (TransitionSettings.FullScan.IsotopeEnrichments != null)
{
if (!defSet.IsotopeEnrichmentsList.ContainsKey(TransitionSettings.FullScan.IsotopeEnrichments.Name))
{
defSet.IsotopeEnrichmentsList.Add(TransitionSettings.FullScan.IsotopeEnrichments);
}
}
if (TransitionSettings.FullScan.IsolationScheme != null)
{
if (!defSet.IsolationSchemeList.ContainsKey(TransitionSettings.FullScan.IsolationScheme.Name))
{
defSet.IsolationSchemeList.Add(TransitionSettings.FullScan.IsolationScheme);
}
}
foreach (var annotationDef in DataSettings.AnnotationDefs)
{
if (!defSet.AnnotationDefList.Contains(annotationDef))
{
defSet.AnnotationDefList.Add(annotationDef);
}
}
foreach (var groupComparisonDef in DataSettings.GroupComparisonDefs)
{
if (!defSet.GroupComparisonDefList.Contains(groupComparisonDef))
{
defSet.GroupComparisonDefList.Add(groupComparisonDef);
}
}
var mainViewSpecList = defSet.PersistedViews.GetViewSpecList(PersistedViews.MainGroup.Id);
foreach (var viewSpec in DataSettings.ViewSpecList.ViewSpecs)
{
mainViewSpecList = mainViewSpecList.ReplaceView(viewSpec.Name, viewSpec);
}
defSet.PersistedViews.SetViewSpecList(PersistedViews.MainGroup.Id, mainViewSpecList);
if (!PeptideSettings.BackgroundProteome.IsNone)
{
if (!defSet.BackgroundProteomeList.ContainsKey(PeptideSettings.BackgroundProteome.Name))
{
defSet.BackgroundProteomeList.Add(PeptideSettings.BackgroundProteome);
}
}
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
IProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
{
return(false);
}
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
PreferEmbeddedSpectra = PreferEmbeddedSpectra,
DebugMode = DebugMode,
};
bool retry = true;
do
{
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status,
out _buildCommandArgs, out _buildOutput, out _ambiguousMatches))
{
return(false);
}
retry = false;
}
catch (IOException x)
{
if (IsLibraryMissingExternalSpectraError(x, out string spectrumFilename, out string resultsFilepath))
{
// replace the relative path to the results file (e.g. msms.txt) with the absolute path
string fullResultsFilepath = InputFiles.SingleOrDefault(o => o.EndsWith(resultsFilepath)) ??
throw new InvalidDataException(@"no results filepath from BiblioSpec error message", x);
// TODO: this will break if BiblioSpec output is translated to other languages
string messageWithFullFilepath =
x.Message.Replace(@"search results file '" + resultsFilepath,
@"search results file '" + fullResultsFilepath);
var response =
progress.UpdateProgress(
status.ChangeErrorException(new IOException(messageWithFullFilepath, x)));
if (response == UpdateProgressResponse.cancel)
{
return(false);
}
else if (response == UpdateProgressResponse.normal)
{
blibBuilder.PreferEmbeddedSpectra = true;
}
continue;
}
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return(false);
}
} while (retry);
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return(false);
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return(false);
}
finally
{
if (!KeepRedundant)
{
FileEx.SafeDelete(redundantLibrary, true);
}
}
return(true);
}
public bool SetLibrary(string name, string path, bool append = true)
{
if (string.IsNullOrWhiteSpace(path))
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__Cannot_set_library_name_without_path_);
return false;
}
else if (!File.Exists(path))
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_file__0__does_not_exist_, path);
return false;
}
else if (path.EndsWith(BiblioSpecLiteSpec.EXT_REDUNDANT))
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_file__0__appears_to_be_a_redundant_library_);
return false;
}
if (string.IsNullOrWhiteSpace(name))
name = Path.GetFileNameWithoutExtension(path);
LibrarySpec librarySpec;
string ext = Path.GetExtension(path);
if (Equals(ext, BiblioSpecLiteSpec.EXT))
librarySpec = new BiblioSpecLiteSpec(name, path);
else if (Equals(ext, BiblioSpecLibSpec.EXT))
librarySpec = new BiblioSpecLibSpec(name, path);
else if (Equals(ext, XHunterLibSpec.EXT))
librarySpec = new XHunterLibSpec(name, path);
else if (Equals(ext, NistLibSpec.EXT))
librarySpec = new NistLibSpec(name, path);
else if (Equals(ext, SpectrastSpec.EXT))
librarySpec = new SpectrastSpec(name, path);
else
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_file__0__is_not_a_supported_spectral_library_file_format_, path);
return false;
}
// Check for conflicting names
foreach (var docLibrarySpec in _doc.Settings.PeptideSettings.Libraries.LibrarySpecs)
{
if (docLibrarySpec.Name == librarySpec.Name || docLibrarySpec.FilePath == librarySpec.FilePath)
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_library_you_are_trying_to_add_conflicts_with_a_library_already_in_the_file_);
return false;
}
}
var librarySpecs = append ?
new List<LibrarySpec>(_doc.Settings.PeptideSettings.Libraries.LibrarySpecs) { librarySpec } :
new List<LibrarySpec>{ librarySpec };
SrmSettings newSettings = _doc.Settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(librarySpecs));
_doc = _doc.ChangeSettings(newSettings);
return true;
}
protected override void DoTest()
{
// Create the modification and library spec used in this test
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T", null, true, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var multipleLossMod = new StaticMod("Multiple Loss-only", "D", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[]
{
new FragmentLoss("NH3"),
new FragmentLoss("H2O"),
new FragmentLoss(null, 20, 25)
});
var heavyKMod = new StaticMod("Heavy K", "K", ModTerminus.C, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var librarySpec = new BiblioSpecLiteSpec("Phospho Library",
TestFilesDir.GetTestPath("phospho_30882_v2.blib"));
// Prepare settings for this test
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
Settings.Default.StaticModList.Add(phosphoLossMod);
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.Add(heavyKMod);
Settings.Default.SpectralLibraryList.Clear();
Settings.Default.SpectralLibraryList.Add(librarySpec);
// Prepare document settings for this test
const int countIons = 6;
var settings = SrmSettingsList.GetDefault()
.ChangePeptideModifications(mods => mods.ChangeStaticModifications(new List<StaticMod>(mods.StaticModifications) { phosphoLossMod }))
.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec }))
.ChangeTransitionLibraries(tlib => tlib.ChangeIonCount(countIons));
RunUI(() => SkylineWindow.ModifyDocument("Set test settings",
doc => doc.ChangeSettings(settings)));
WaitForDocumentLoaded();
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_SPROT));
var docLibLoss = SkylineWindow.Document;
AssertEx.IsDocumentState(docLibLoss, null, 3, 4, 24);
Assert.AreEqual(7, GetLossCount(docLibLoss, 1));
string lossLabel = "-" + Math.Round(phosphoLossMod.Losses[0].MonoisotopicMass, 1);
for (int i = 0; i < docLibLoss.PeptideTransitionGroupCount; i++)
{
var pathTranGroup = docLibLoss.GetPathTo((int) SrmDocument.Level.TransitionGroups, i);
var nodeGroup = (TransitionGroupDocNode) docLibLoss.FindNode(pathTranGroup);
if (!nodeGroup.Children.Contains(child => ((TransitionDocNode) child).HasLoss))
continue;
// Select the transition groups that contain loss ions
SelectNode(SrmDocument.Level.TransitionGroups, i);
WaitForGraphs();
// Make sure the spectrum graph contains some -98 ions
RunUI(() => Assert.IsTrue(SkylineWindow.GraphSpectrum.IonLabels.Contains(label => label.Contains(lossLabel)),
string.Format("Missing loss labels in spectrum graph for {0}", nodeGroup.TransitionGroup.Peptide.Sequence)));
// Make sure the transition tree nodes contain -98 ions
RunUI(() => Assert.IsTrue(GetChildLabels(SkylineWindow.SelectedNode).Contains(label => label.Contains(lossLabel)),
string.Format("Missing loss labels in transition tree nodes for {0}", nodeGroup.TransitionGroup.Peptide.Sequence)));
}
// Make the settings significantly more complex
// - 2 neutral losses
// - a second modification with 3 potential neutral losses
// - a heavy labeling modification
// - only ions between precursor m/z and last ion
// - allow both y- and b- ions
// - no proline peaks
// - only use filtered ions to match library
RunUI(() => SkylineWindow.ModifyDocument("Set test settings", doc =>
doc.ChangeSettings(doc.Settings.ChangePeptideModifications(mod =>
mod.ChangeMaxNeutralLosses(2)
.ChangeStaticModifications(new List<StaticMod>(mod.StaticModifications) {multipleLossMod})
.ChangeHeavyModifications(new[] { heavyKMod }))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName("m/z > precursor")
.ChangeFragmentRangeLastName("last ion")
.ChangeIonTypes(new[] { IonType.y, IonType.b })
.ChangeMeasuredIons(new MeasuredIon[0]))
.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.filter)))));
var docComplex = WaitForDocumentChange(docLibLoss);
// The document has 2 variable mod peptides at the protein terminus
Assert.AreEqual(docLibLoss.PeptideTransitionGroupCount*2 - 2, docComplex.PeptideTransitionGroupCount);
Assert.AreEqual(4, GetLossCount(docComplex, 2));
Assert.AreEqual(16, GetLossCount(docComplex, 1));
foreach (var nodePep in docComplex.Peptides)
{
if (nodePep.Children.Count != 2)
continue;
var nodeGroup1 = (TransitionGroupDocNode)nodePep.Children[0];
var nodeGroup2 = (TransitionGroupDocNode)nodePep.Children[1];
Assert.IsTrue(nodeGroup1.EquivalentChildren(nodeGroup2));
}
// CONSIDER: Can't check cloned because of libraries. Maybe add a new method for this
// AssertEx.Serializable(docComplex, AssertEx.DocumentCloned);
SelectNode(SrmDocument.Level.Molecules, 1);
WaitForGraphs();
// Verify that the ion labels in the graph match those in the tree view
RunUI(() =>
{
var nodePepSelected = (PeptideDocNode) docComplex.FindNode(SkylineWindow.SelectedPath);
string[] ionLabels = SkylineWindow.GraphSpectrum.IonLabels.ToArray();
foreach (TransitionGroupDocNode nodeGroup in nodePepSelected.Children)
{
var setSeenRanks = new HashSet<int>();
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
Assert.IsTrue(nodeTran.HasLibInfo);
// Make sure the rank has not been seen
int rankTran = nodeTran.LibInfo.Rank;
Assert.IsFalse(setSeenRanks.Contains(rankTran));
setSeenRanks.Add(rankTran);
// And it is within the expected range
Assert.IsTrue(1 <= rankTran && rankTran <= countIons);
// Make sure there is a matching label in the spectrum graph
var regexRank = nodeTran.HasLoss ?
new Regex(string.Format(@"(\w)(\d+) -([^ +]+).* \({0}\)", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rankTran))) :
new Regex(string.Format(@"(\w)(\d+).* \({0}\)", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rankTran)));
int iLabel = ionLabels.IndexOf(regexRank.IsMatch);
Assert.IsTrue(iLabel != -1);
var match = regexRank.Match(ionLabels[iLabel]);
Assert.AreEqual(nodeTran.Transition.IonType.ToString(), match.Groups[1].Value);
Assert.AreEqual(nodeTran.Transition.Ordinal, int.Parse(match.Groups[2].Value));
if (nodeTran.HasLoss)
Assert.AreEqual(nodeTran.Losses.Mass, double.Parse(match.Groups[3].Value), 0.1);
}
}
});
// Make sure setting losses as included Never works
{
var docBeforeNever = SkylineWindow.Document;
var peptideSettingsUINever = ShowDialog<PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlgNever = ShowEditStaticModsDlg(peptideSettingsUINever);
RunUI(() => editModsDlgNever.SelectItem(phosphoLossMod.Name));
var editModDlgNever = ShowDialog<EditStaticModDlg>(editModsDlgNever.EditItem);
RunUI(() => editModDlgNever.LossSelectedIndex = 0);
RunDlg<EditFragmentLossDlg>(editModDlgNever.EditLoss, dlg =>
{
dlg.Inclusion = LossInclusion.Never;
dlg.OkDialog();
});
RunDlg<MultiButtonMsgDlg>(editModDlgNever.OkDialog, dlg => dlg.Btn1Click());
OkDialog(editModsDlgNever, editModsDlgNever.OkDialog);
OkDialog(peptideSettingsUINever, peptideSettingsUINever.OkDialog);
var docAfterNever = WaitForDocumentChange(docBeforeNever);
Assert.AreEqual(0, GetLossCount(docAfterNever, 1));
}
}
private bool BuildPeptideSearchLibrary(CancelEventArgs e)
{
// Nothing to build, if now search files were specified
if (!SearchFilenames.Any())
{
var libraries = DocumentContainer.Document.Settings.PeptideSettings.Libraries;
if (!libraries.HasLibraries)
{
return(false);
}
var libSpec = libraries.LibrarySpecs.FirstOrDefault(s => s.IsDocumentLibrary);
return(libSpec != null && LoadPeptideSearchLibrary(libSpec));
}
double cutOffScore;
MessageBoxHelper helper = new MessageBoxHelper(WizardForm);
if (!helper.ValidateDecimalTextBox(textCutoff, 0, 1.0, out cutOffScore))
{
e.Cancel = true;
return(false);
}
ImportPeptideSearch.CutoffScore = cutOffScore;
BiblioSpecLiteBuilder builder;
try
{
builder = ImportPeptideSearch.GetLibBuilder(DocumentContainer.Document, DocumentContainer.DocumentFilePath, cbIncludeAmbiguousMatches.Checked);
builder.PreferEmbeddedSpectra = PreferEmbeddedSpectra;
}
catch (FileEx.DeleteException de)
{
MessageDlg.ShowException(this, de);
return(false);
}
bool retry = false;
do
{
using (var longWaitDlg = new LongWaitDlg
{
Text = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_Peptide_Search_Library,
Message = Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Building_document_library_for_peptide_search_,
})
{
// Disable the wizard, because the LongWaitDlg does not
try
{
ImportPeptideSearch.ClosePeptideSearchLibraryStreams(DocumentContainer.Document);
var status = longWaitDlg.PerformWork(WizardForm, 800,
monitor => LibraryManager.BuildLibraryBackground(DocumentContainer, builder, monitor, new LibraryManager.BuildState(null, null)));
if (status.IsError)
{
// E.g. could not find external raw data for MaxQuant msms.txt; ask user if they want to retry with "prefer embedded spectra" option
if (BiblioSpecLiteBuilder.IsLibraryMissingExternalSpectraError(status.ErrorException))
{
var response = ShowLibraryMissingExternalSpectraError(WizardForm, status.ErrorException);
if (response == UpdateProgressResponse.cancel)
{
return(false);
}
else if (response == UpdateProgressResponse.normal)
{
builder.PreferEmbeddedSpectra = true;
}
retry = true;
}
else
{
MessageDlg.ShowException(WizardForm, status.ErrorException);
return(false);
}
}
}
catch (Exception x)
{
MessageDlg.ShowWithException(WizardForm, TextUtil.LineSeparate(string.Format(Resources.BuildPeptideSearchLibraryControl_BuildPeptideSearchLibrary_Failed_to_build_the_library__0__,
Path.GetFileName(BiblioSpecLiteSpec.GetLibraryFileName(DocumentContainer.DocumentFilePath))), x.Message), x);
return(false);
}
}
} while (retry);
var docLibSpec = builder.LibrarySpec.ChangeDocumentLibrary(true);
Settings.Default.SpectralLibraryList.Insert(0, docLibSpec);
// Go ahead and load the library - we'll need it for
// the modifications and chromatograms page.
if (!LoadPeptideSearchLibrary(docLibSpec))
{
return(false);
}
var selectedIrtStandard = comboStandards.SelectedItem as IrtStandard;
var addedIrts = false;
if (selectedIrtStandard != null && selectedIrtStandard != IrtStandard.EMPTY)
{
addedIrts = AddIrtLibraryTable(docLibSpec.FilePath, selectedIrtStandard);
}
var docNew = ImportPeptideSearch.AddDocumentSpectralLibrary(DocumentContainer.Document, docLibSpec);
if (docNew == null)
{
return(false);
}
if (addedIrts)
{
docNew = ImportPeptideSearch.AddRetentionTimePredictor(docNew, docLibSpec);
}
DocumentContainer.ModifyDocumentNoUndo(doc => docNew);
if (!string.IsNullOrEmpty(builder.AmbiguousMatchesMessage))
{
MessageDlg.Show(WizardForm, builder.AmbiguousMatchesMessage);
}
return(true);
}
protected override void DoTest()
{
// Create the modification and library spec used in this test
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T", null, true, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
var multipleLossMod = new StaticMod("Multiple Loss-only", "D", null, false, null,
LabelAtoms.None, RelativeRT.Matching, null, null, new[]
{
new FragmentLoss("NH3"),
new FragmentLoss("H2O"),
new FragmentLoss(null, 20, 25)
});
var heavyKMod = new StaticMod("Heavy K", "K", ModTerminus.C, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var librarySpec = new BiblioSpecLiteSpec("Phospho Library",
TestFilesDir.GetTestPath("phospho_30882_v2.blib"));
// Prepare settings for this test
Settings.Default.StaticModList.Clear();
Settings.Default.StaticModList.AddRange(StaticModList.GetDefaultsOn());
Settings.Default.StaticModList.Add(phosphoLossMod);
Settings.Default.HeavyModList.Clear();
Settings.Default.HeavyModList.Add(heavyKMod);
Settings.Default.SpectralLibraryList.Clear();
Settings.Default.SpectralLibraryList.Add(librarySpec);
// Prepare document settings for this test
const int countIons = 6;
var settings = SrmSettingsList.GetDefault()
.ChangePeptideModifications(mods => mods.ChangeStaticModifications(new List <StaticMod>(mods.StaticModifications)
{
phosphoLossMod
}))
.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec }))
.ChangeTransitionLibraries(tlib => tlib.ChangeIonCount(countIons));
RunUI(() => SkylineWindow.ModifyDocument("Set test settings",
doc => doc.ChangeSettings(settings)));
WaitForDocumentLoaded();
// Add FASTA sequence
RunUI(() => SkylineWindow.Paste(TEXT_FASTA_SPROT));
var docLibLoss = SkylineWindow.Document;
AssertEx.IsDocumentState(docLibLoss, null, 3, 4, 24);
Assert.AreEqual(7, GetLossCount(docLibLoss, 1));
string lossLabel = "-" + Math.Round(phosphoLossMod.Losses[0].MonoisotopicMass, 1);
for (int i = 0; i < docLibLoss.PeptideTransitionGroupCount; i++)
{
var pathTranGroup = docLibLoss.GetPathTo((int)SrmDocument.Level.TransitionGroups, i);
var nodeGroup = (TransitionGroupDocNode)docLibLoss.FindNode(pathTranGroup);
if (!nodeGroup.Children.Contains(child => ((TransitionDocNode)child).HasLoss))
{
continue;
}
// Select the transition groups that contain loss ions
SelectNode(SrmDocument.Level.TransitionGroups, i);
WaitForGraphs();
// Make sure the spectrum graph contains some -98 ions
RunUI(() => Assert.IsTrue(SkylineWindow.GraphSpectrum.IonLabels.Contains(label => label.Contains(lossLabel)),
string.Format("Missing loss labels in spectrum graph for {0}", nodeGroup.TransitionGroup.Peptide.Target)));
// Make sure the transition tree nodes contain -98 ions
RunUI(() => Assert.IsTrue(GetChildLabels(SkylineWindow.SelectedNode).Contains(label => label.Contains(lossLabel)),
string.Format("Missing loss labels in transition tree nodes for {0}", nodeGroup.TransitionGroup.Peptide.Target)));
}
// Make the settings significantly more complex
// - 2 neutral losses
// - a second modification with 3 potential neutral losses
// - a heavy labeling modification
// - only ions between precursor m/z and last ion
// - allow both y- and b- ions
// - no proline peaks
// - only use filtered ions to match library
RunUI(() => SkylineWindow.ModifyDocument("Set test settings", doc =>
doc.ChangeSettings(doc.Settings.ChangePeptideModifications(mod =>
mod.ChangeMaxNeutralLosses(2)
.ChangeStaticModifications(new List <StaticMod>(mod.StaticModifications)
{
multipleLossMod
})
.ChangeModifications(IsotopeLabelType.heavy, new[] { heavyKMod }))
.ChangeTransitionFilter(filter =>
filter.ChangeFragmentRangeFirstName("m/z > precursor")
.ChangeFragmentRangeLastName("last ion")
.ChangePeptideIonTypes(new[] { IonType.y, IonType.b })
.ChangeMeasuredIons(new MeasuredIon[0]))
.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.filter)))));
var docComplex = WaitForDocumentChange(docLibLoss);
// The document has 2 variable mod peptides at the protein terminus
Assert.AreEqual(docLibLoss.PeptideTransitionGroupCount * 2 - 2, docComplex.PeptideTransitionGroupCount);
Assert.AreEqual(4, GetLossCount(docComplex, 2));
Assert.AreEqual(16, GetLossCount(docComplex, 1));
foreach (var nodePep in docComplex.Peptides)
{
if (nodePep.Children.Count != 2)
{
continue;
}
var nodeGroup1 = (TransitionGroupDocNode)nodePep.Children[0];
var nodeGroup2 = (TransitionGroupDocNode)nodePep.Children[1];
Assert.IsTrue(nodeGroup1.EquivalentChildren(nodeGroup2));
}
// CONSIDER: Can't check cloned because of libraries. Maybe add a new method for this
// AssertEx.Serializable(docComplex, AssertEx.DocumentCloned);
SelectNode(SrmDocument.Level.Molecules, 1);
WaitForGraphs();
// Verify that the ion labels in the graph match those in the tree view
RunUI(() =>
{
var nodePepSelected = (PeptideDocNode)docComplex.FindNode(SkylineWindow.SelectedPath);
string[] ionLabels = SkylineWindow.GraphSpectrum.IonLabels.ToArray();
foreach (TransitionGroupDocNode nodeGroup in nodePepSelected.Children)
{
var setSeenRanks = new HashSet <int>();
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
Assert.IsTrue(nodeTran.HasLibInfo);
// Make sure the rank has not been seen
int rankTran = nodeTran.LibInfo.Rank;
Assert.IsFalse(setSeenRanks.Contains(rankTran));
setSeenRanks.Add(rankTran);
// And it is within the expected range
Assert.IsTrue(1 <= rankTran && rankTran <= countIons);
// Make sure there is a matching label in the spectrum graph
var regexRank = nodeTran.HasLoss ?
new Regex(string.Format(@"(\w)(\d+) -([^ +]+).* \({0}\)", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rankTran))) :
new Regex(string.Format(@"(\w)(\d+).* \({0}\)", string.Format(Resources.AbstractSpectrumGraphItem_GetLabel_rank__0__, rankTran)));
int iLabel = ionLabels.IndexOf(regexRank.IsMatch);
Assert.IsTrue(iLabel != -1);
var match = regexRank.Match(ionLabels[iLabel]);
Assert.AreEqual(nodeTran.Transition.IonType.ToString(), match.Groups[1].Value);
Assert.AreEqual(nodeTran.Transition.Ordinal, int.Parse(match.Groups[2].Value));
if (nodeTran.HasLoss)
{
Assert.AreEqual(nodeTran.Losses.Mass, double.Parse(match.Groups[3].Value), 0.1);
}
}
}
});
// Make sure setting losses as included Never works
{
var docBeforeNever = SkylineWindow.Document;
var peptideSettingsUINever = ShowDialog <PeptideSettingsUI>(() =>
SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Modifications));
var editModsDlgNever = ShowEditStaticModsDlg(peptideSettingsUINever);
RunUI(() => editModsDlgNever.SelectItem(phosphoLossMod.Name));
var editModDlgNever = ShowDialog <EditStaticModDlg>(editModsDlgNever.EditItem);
RunUI(() => editModDlgNever.LossSelectedIndex = 0);
RunDlg <EditFragmentLossDlg>(editModDlgNever.EditLoss, dlg =>
{
dlg.Inclusion = LossInclusion.Never;
dlg.OkDialog();
});
RunDlg <MultiButtonMsgDlg>(editModDlgNever.OkDialog, dlg => dlg.Btn1Click());
OkDialog(editModsDlgNever, editModsDlgNever.OkDialog);
OkDialog(peptideSettingsUINever, peptideSettingsUINever.OkDialog);
var docAfterNever = WaitForDocumentChange(docBeforeNever);
Assert.AreEqual(0, GetLossCount(docAfterNever, 1));
}
}
private bool BuildLibraryOrThrow(IProgressMonitor progress, ref IProgressStatus progressStatus)
{
progressStatus = progressStatus.ChangeSegments(0, 5);
var standardSpectra = new List <SpectrumMzInfo>();
// First get predictions for iRT standards specified by the user which may or may not be in the document
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY) && !ReferenceEquals(IrtStandard, IrtStandard.AUTO))
{
var standardPeptidesToAdd = ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
progressStatus = progressStatus.NextSegment();
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, IsotopeLabelType.light, _nce)).ToArray(),
CancellationToken.None);
progressStatus = progressStatus.NextSegment();
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctModifiedSequences = new HashSet <string>();
var distinctPeps = new List <PrositRetentionTimeModel.PeptideDocNodeWrapper>();
foreach (var p in _peptides)
{
if (distinctModifiedSequences.Add(p.ModifiedSequence))
{
distinctPeps.Add(new PrositRetentionTimeModel.PeptideDocNodeWrapper(p));
}
}
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, ref progressStatus, _document.Settings,
distinctPeps, CancellationToken.None);
progressStatus = progressStatus.NextSegment();
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
progressStatus = progressStatus.NextSegment().ChangeMessage(Resources.SkylineWindow_SaveDocument_Saving___);
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress, ref progressStatus);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
/* TODO bspratt drift time libs for small molecules
[TestMethod]
public void WatersImsMsePredictedDriftTimesChromatogramTestAsSmallMolecules()
{
WatersImsMseChromatogramTest(DriftFilterType.predictor, true);
}
[TestMethod]
public void WatersImsMseLibraryDriftTimesChromatogramTestAsSmallMolecules()
{
WatersImsMseChromatogramTest(DriftFilterType.library, true);
}
*/
private void WatersImsMseChromatogramTest(DriftFilterType mode,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
TestSmallMolecules = false; // Don't need that extra magic node
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky", asSmallMolecules, out docPath);
AssertEx.IsDocumentState(document, (withDriftTimePredictor || (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)) ? 1 : 0, 1, 1, 1, 8); // Drift time lib load bumps the doc version
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var docOriginal = doc;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("mse-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(100)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
testModeStr = "with drift times from spectral library";
}
var listChromatograms = new List<ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
const string path = @"waters-mobility.mz5";
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, new MsDataFilePath(path)) ??
new ChromatogramSet(Path.GetFileName(path).Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(1, document.MoleculePrecursorPairs.Count());
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, testModeStr);
var chromGroup = chromGroupInfo[0];
var expectedPeaks = ((asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 6 : 5);
Assert.AreEqual(withDriftTimeFilter ? 3 : expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assert.AreEqual(withDriftTimeFilter? 5226 : 20075 , maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// 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(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assert.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath = testFilesDir.GetTestPath(complete==1?"share_complete.zip":"share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath, complete==1);
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest -- sharing document",
})
{
longWaitDlg.PerformWork(null, 1000, share.Share);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
var files = share.ListEntries().ToArray();
Assert.IsTrue(files.Contains(withDriftTimePredictor ? "scaled.imdb" : "mse-mobility.filtered-scaled.blib"));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest",
})
{
longWaitDlg.PerformWork(null, 1000, share.Extract);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
using (TextReader reader = new StreamReader(share.DocumentPath))
{
XmlSerializer documentSerializer = new XmlSerializer(typeof(SrmDocument));
var document2 = (SrmDocument) documentSerializer.Deserialize(reader);
Assert.IsNotNull(document2);
var im = document.Settings.GetIonMobilities(new MsDataFilePath(path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
pep, nodeGroup, im, out windowDT);
Assert.AreEqual(3.86124, centerDriftTime.DriftTimeMsec(false) ?? 0, .0001, testModeStr);
Assert.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
}
protected override void DoTest()
{
string skyfile = TestFilesDir.GetTestPath("test.sky");
RunUI(() => SkylineWindow.SaveDocument(skyfile));
Stopwatch loadStopwatch = new Stopwatch();
loadStopwatch.Start();
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
string lo = GetTestPath("40minG_WBP_wide_z2-3_low_BSA_5pmol_02.pep.xml");
string mid = GetTestPath("40minG_WBP_wide_z2-3_mid_BSA_5pmol_01.pep.xml");
string up = GetTestPath("40minG_WBP_wide_z2-3_up_BSA_5pmol_02.pep.xml");
string[] searchFiles = { lo, mid, up };
var doc = SkylineWindow.Document;
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.95;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = false;
});
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(skyfile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the files should be found, and we should
// just be able to move to the next page.
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page));
RunUI(() =>
{
var importResultsControl = (ImportResultsControl)importPeptideSearchDlg.ImportResultsControl;
importResultsControl.ExcludeSpectrumSourceFiles = true;
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
importResultsNameDlg.NoDialog();
});
WaitForClosedForm(importResultsNameDlg);
// Modifications are already set up, so that page should get skipped.
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new [] { 2, 3, 4, 5 });
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof);
// Enable use of drift times in spectral library
Assume.IsTrue(importPeptideSearchDlg.FullScanSettingsControl.IonMobilityFiltering.Visible);
Assume.IsTrue(importPeptideSearchDlg.FullScanSettingsControl.IonMobilityFiltering.Enabled);
var useDriftTimes = true; // For debugging convenience, if you want to see how this works without IM filtering
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.IonMobilityFiltering.IsUseSpectralLibraryIonMobilities = useDriftTimes);
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.IonMobilityFiltering.IonMobilityFilterResolvingPower = 50);
RunUI(() => importPeptideSearchDlg.ClickNextButton()); // Accept the full scan settings
// We're on the "Import FASTA" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("SwissProt.bsa-mature"));
});
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
WaitForClosedForm(importPeptideSearchDlg);
WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
var doc1 = WaitForDocumentLoaded(400000);
AssertEx.IsDocumentState(doc1, null, 1, 40, 54, 162);
loadStopwatch.Stop();
DebugLog.Info("load time = {0}", loadStopwatch.ElapsedMilliseconds);
float tolerance = (float)doc1.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = doc1.Settings.MeasuredResults;
foreach (var pair in doc1.PeptidePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
foreach (var chromGroup in chromGroupInfo)
{
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
}
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
Assert.AreEqual(useDriftTimes ? 972186 : 1643104, maxHeight, 1);
}
public bool BuildLibrary(IProgressMonitor progress)
{
_ambiguousMatches = null;
IProgressStatus status = new ProgressStatus(Resources.BiblioSpecLiteBuilder_BuildLibrary_Preparing_to_build_library);
progress.UpdateProgress(status);
if (InputFiles.Any(f => f.EndsWith(EXT_PILOT)))
{
try
{
InputFiles = VendorIssueHelper.ConvertPilotFiles(InputFiles, progress, status);
if (progress.IsCanceled)
{
return(false);
}
}
catch (Exception x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
}
string message = string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Building__0__library,
Path.GetFileName(OutputPath));
progress.UpdateProgress(status = status.ChangeMessage(message));
string redundantLibrary = BiblioSpecLiteSpec.GetRedundantName(OutputPath);
var blibBuilder = new BlibBuild(redundantLibrary, InputFiles, TargetSequences)
{
IncludeAmbiguousMatches = IncludeAmbiguousMatches,
CutOffScore = CutOffScore,
Id = Id,
};
try
{
if (!blibBuilder.BuildLibrary(Action, progress, ref status, out _ambiguousMatches))
{
return(false);
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch (Exception x)
{
Console.WriteLine(x.Message);
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_redundant_library__0__,
redundantLibrary))));
return(false);
}
var blibFilter = new BlibFilter();
status = new ProgressStatus(message);
progress.UpdateProgress(status);
// Write the non-redundant library to a temporary file first
try
{
using (var saver = new FileSaver(OutputPath))
{
if (!blibFilter.Filter(redundantLibrary, saver.SafeName, progress, ref status))
{
return(false);
}
saver.Commit();
}
}
catch (IOException x)
{
progress.UpdateProgress(status.ChangeErrorException(x));
return(false);
}
catch
{
progress.UpdateProgress(status.ChangeErrorException(
new Exception(string.Format(Resources.BiblioSpecLiteBuilder_BuildLibrary_Failed_trying_to_build_the_library__0__,
OutputPath))));
return(false);
}
finally
{
if (!KeepRedundant)
{
FileEx.SafeDelete(redundantLibrary, true);
}
}
return(true);
}
private void Testit(
bool useDriftTimes, // If false, don't use any drift information in chromatogram extraction
ref LibraryIonMobilityInfo driftInfoExplicitDT
)
{
bool CCSonly = driftInfoExplicitDT != null; // If true, force conversion from CCS to DT
var ext = useDriftTimes ? (CCSonly ? "CCS" : "DT") : "train";
string skyfile = TestFilesDir.GetTestPath("test_" + ext + ".sky");
RunUI(() =>
{
SkylineWindow.NewDocument(true);
SkylineWindow.SaveDocument(skyfile);
});
Stopwatch loadStopwatch = new Stopwatch();
loadStopwatch.Start();
// Enable use of drift times in spectral library
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
peptideSettingsUI.IsUseSpectralLibraryDriftTimes = useDriftTimes;
peptideSettingsUI.SpectralLibraryDriftTimeResolvingPower = 50;
});
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
var basename = _testCase == 1 ? "40minG_WBP_wide_z2-3_mid_BSA_5pmol_01" : "09_BSAtrypticdigest_5uL_IMQTOF_AltFramesdtramp_dAJS009";
var nextFile = _testCase == 1 ? null : "10_BSAtrypticdigest_5uL_IMQTOF_AltFramesdtramp_dAJS010.d";
var searchResults = GetTestPath(basename + ".pep.xml");
var doc = SkylineWindow.Document;
if (CCSonly || !useDriftTimes)
{
// Hide the drift time info provided by SpectrumMill, so we have to convert from CCS
var mzxmlFile = searchResults.Replace("pep.xml", "mzXML");
var fileContents = File.ReadAllText(mzxmlFile);
fileContents = fileContents.Replace(" DT=", " xx=");
if (!useDriftTimes)
{
fileContents = fileContents.Replace(" CCS=", " xxx=");
}
File.WriteAllText(mzxmlFile, fileContents);
}
var searchResultsList = new[] { searchResults };
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchResultsList);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.95;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = false;
});
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(skyfile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the files should be found, and we should
// just be able to move to the next page.
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page));
RunUI(() =>
{
var importResultsControl = (ImportResultsControl)importPeptideSearchDlg.ImportResultsControl;
importResultsControl.ExcludeSpectrumSourceFiles = true;
importResultsControl.UpdateResultsFiles(new [] { TestFilesDirs[0].PersistentFilesDir }, true); // Go look in the persistent files dir
});
if (searchResultsList.Length > 1)
{
// Deal with the common name start dialog
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
importResultsNameDlg.NoDialog();
});
WaitForClosedForm(importResultsNameDlg);
}
else
{
RunUI(() => importPeptideSearchDlg.ClickNextButtonNoCheck());
}
// Modifications are already set up, so that page should get skipped.
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new [] { 2, 3, 4, 5 });
RunUI(() => importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof);
RunUI(() => importPeptideSearchDlg.ClickNextButton()); // Accept the full scan settings
// We're on the "Import FASTA" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("SwissProt.bsa-mature"));
});
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
WaitForClosedForm(importPeptideSearchDlg);
var doc1 = WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
if (_testCase == 1)
{
AssertEx.IsDocumentState(doc1, null, 1, 34, 45, 135);
}
else
{
AssertEx.IsDocumentState(doc1, null, 1, 36, 43, 129);
}
loadStopwatch.Stop();
DebugLog.Info("load time = {0}", loadStopwatch.ElapsedMilliseconds);
var errmsg = "";
if (!useDriftTimes)
{
// Inspect the loaded data directly to derive DT and CCS
// Verify ability to extract predictions from raw data
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate user picking Edit Current from the Drift Time Predictor combo control
var driftTimePredictorDlg = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg.AddDriftTimePredictor);
RunUI(() =>
{
driftTimePredictorDlg.SetPredictorName("test");
driftTimePredictorDlg.SetResolvingPower(50);
driftTimePredictorDlg.GetDriftTimesFromResults();
driftTimePredictorDlg.OkDialog();
});
WaitForClosedForm(driftTimePredictorDlg);
RunUI(() =>
{
peptideSettingsDlg.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg);
var document = SkylineWindow.Document;
var measuredDTs = document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.MeasuredMobilityIons;
Assert.IsNotNull(driftInfoExplicitDT, "driftInfoExplicitDT != null");
var explicitDTs = driftInfoExplicitDT.GetIonMobilityDict();
string errMsgAll = string.Empty;
// A handful of peptides that really should have been trained on a clean sample
// CONSIDER: or are they multiple conformers? They have multiple hits with distinct IM in the pepXML
var expectedDiffs = LibKeyMap <double> .FromDictionary(new Dictionary <LibKey, double>
{
{ new PeptideLibraryKey("LC[+57.0]VLHEK", 2), 18.09 },
{ new PeptideLibraryKey("EC[+57.0]C[+57.0]DKPLLEK", 3), 7.0 },
{ new PeptideLibraryKey("SHC[+57.0]IAEVEK", 3), 6.0 },
{ new PeptideLibraryKey("DDPHAC[+57.0]YSTVFDK", 2), 24.0 }
}).AsDictionary();
foreach (var pair in doc1.PeptidePrecursorPairs)
{
string errMsg = string.Empty;
var key = new LibKey(pair.NodePep.ModifiedSequence, pair.NodeGroup.PrecursorAdduct);
double tolerCCS = 5;
if (expectedDiffs.ContainsKey(key))
{
tolerCCS = expectedDiffs[key] + .1;
}
if (!explicitDTs.ContainsKey(key))
{
errMsg += "Could not locate explicit IMS info for " + key + "\n";
}
var given = explicitDTs[key][0];
var measured = measuredDTs[key];
var msg = CheckDeltaPct(given.CollisionalCrossSectionSqA ?? 0, measured.CollisionalCrossSectionSqA ?? 0, tolerCCS, "measured CCS", key.ToString());
if (!string.IsNullOrEmpty(msg))
{
errMsg += msg + CheckDeltaPct(given.IonMobility.Mobility.Value, measured.IonMobility.Mobility.Value, -1, "measured drift time", key.ToString());
}
else
{
errMsg += CheckDelta(given.IonMobility.Mobility.Value, measured.IonMobility.Mobility.Value, 10.0, "measured drift time", key.ToString());
}
errMsg += CheckDelta(given.HighEnergyIonMobilityValueOffset, measured.HighEnergyIonMobilityValueOffset, 2.0, "measured drift time high energy offset", key.ToString());
if (!string.IsNullOrEmpty(errMsg))
{
errMsgAll += "\n" + errMsg;
}
}
if (!string.IsNullOrEmpty(errMsgAll))
{
Assert.Fail(errMsgAll);
}
return;
}
LibraryIonMobilityInfo libraryIonMobilityInfo;
doc1.Settings.PeptideSettings.Libraries.Libraries.First().TryGetIonMobilityInfos(doc1.MoleculeLibKeys.ToArray(), 0, out libraryIonMobilityInfo);
if (driftInfoExplicitDT == null)
{
driftInfoExplicitDT = libraryIonMobilityInfo;
}
else
{
var instrumentInfo = new DataFileInstrumentInfo(new MsDataFileImpl(GetTestPath(basename + ".d")));
var dictExplicitDT = driftInfoExplicitDT.GetIonMobilityDict();
foreach (var pep in doc1.Peptides)
{
foreach (var nodeGroup in pep.TransitionGroups)
{
double windowDT;
var calculatedDriftTime = doc1.Settings.GetIonMobility(
pep, nodeGroup, null, libraryIonMobilityInfo, instrumentInfo, 0, out windowDT);
var libKey = new LibKey(pep.ModifiedSequence, nodeGroup.PrecursorAdduct);
IonMobilityAndCCS[] infoValueExplicitDT;
if (!dictExplicitDT.TryGetValue(libKey, out infoValueExplicitDT))
{
errmsg += "No driftinfo value found for " + libKey + "\n";
}
else
{
var ionMobilityInfo = infoValueExplicitDT[0];
var delta = Math.Abs(ionMobilityInfo.IonMobility.Mobility.Value - calculatedDriftTime.IonMobility.Mobility.Value);
var acceptableDelta = (libKey.Sequence.StartsWith("DDPHAC") || libKey.Sequence.EndsWith("VLHEK")) ? 3: 1; // These were ambiguous matches
if (delta > acceptableDelta)
{
errmsg += String.Format("calculated DT ({0}) and explicit DT ({1}, CCS={4}) do not agree (abs delta = {2}) for {3}\n",
calculatedDriftTime.IonMobility, ionMobilityInfo.IonMobility,
delta, libKey,
ionMobilityInfo.CollisionalCrossSectionSqA ?? 0);
}
}
}
}
}
float tolerance = (float)doc1.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = doc1.Settings.MeasuredResults;
var numPeaks = _testCase == 1 ?
new[] { 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 10, 7, 10, 10, 10, 10, 8, 10, 10, 10, 10, 10, 10, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 10, 10, 8, 10, 10, 10, 10, 10 } :
new[] { 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 };
int npIndex = 0;
foreach (var pair in doc1.PeptidePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
foreach (var chromGroup in chromGroupInfo)
{
if (numPeaks[npIndex] != chromGroup.NumPeaks)
{
errmsg += String.Format("unexpected peak count {0} instead of {1} in chromatogram {2}\r\n", chromGroup.NumPeaks, numPeaks[npIndex], npIndex);
}
npIndex++;
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
}
Assert.IsTrue(errmsg.Length == 0, errmsg);
Assert.AreEqual(_testCase == 1 ? 2265204 : 1326442, maxHeight, 1);
// Does CCS show up in reports?
var expectedDtWindow = _testCase == 1 ? 0.74 : 0.94;
TestReports(doc1, 0, expectedDtWindow);
if (nextFile != null)
{
// Verify that we can use library generated for one file as the default for another without its own library
ImportResults(nextFile);
TestReports(SkylineWindow.Document, 1, expectedDtWindow);
}
// And verify roundtrip of ion mobility
AssertEx.RoundTrip(SkylineWindow.Document);
RunUI(() =>
{
SkylineWindow.SaveDocument(skyfile);
SkylineWindow.NewDocument(true);
SkylineWindow.OpenFile(skyfile);
});
TestReports(SkylineWindow.Document, 1, expectedDtWindow);
// Watch for problem with reimport after changed DT window
var docResolvingPower = SkylineWindow.Document;
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once ConditionIsAlwaysTrueOrFalse
peptideSettingsUI2.IsUseSpectralLibraryDriftTimes = useDriftTimes;
peptideSettingsUI2.SpectralLibraryDriftTimeResolvingPower = 40;
});
OkDialog(peptideSettingsUI2, peptideSettingsUI2.OkDialog);
var docReimport = WaitForDocumentChangeLoaded(docResolvingPower);
// Reimport data for a replicate
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docReimport.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(docReimport);
var expectedDtWindow0 = _testCase == 2 ? 1.175 : 0.92;
var expectedDtWindow1 = _testCase == 2 ? 0.94 : 0.92;
TestReports(SkylineWindow.Document, 0, expectedDtWindow0, string.Format(" row {0} case {1} ccsOnly {2}", 0, _testCase, CCSonly));
TestReports(SkylineWindow.Document, 1, expectedDtWindow1, string.Format(" row {0} case {1} ccsOnly {2}", 1, _testCase, CCSonly));
}
/// <summary>
/// Minimize any library type to a fully functional BiblioSpec SQLite library.
/// </summary>
/// <param name="librarySpec">Library spec for which the new library is created</param>
/// <param name="library">Existing library to minimize</param>
/// <param name="document">Document for which only used spectra are included in the new library</param>
/// <returns>A new minimized <see cref="BiblioSpecLiteLibrary"/></returns>
public BiblioSpecLiteLibrary MinimizeLibrary(BiblioSpecLiteSpec librarySpec,
Library library, SrmDocument document)
{
if (!UpdateProgressMessage(string.Format(Resources.BlibDb_MinimizeLibrary_Minimizing_library__0__, library.Name)))
return null;
string libAuthority = "unknown.org"; // Not L10N
string libId = library.Name;
// CONSIDER: Use version numbers of the original library?
int libraryRevision = DbLibInfo.INITIAL_LIBRARY_REVISION;
int schemaVersion = 0;
bool saveRetentionTimes = false;
bool saveRedundantLib = false;
var blibLib = library as BiblioSpecLiteLibrary;
if (blibLib != null)
{
string libraryLsid = blibLib.Lsid;
Match matchLsid = REGEX_LSID.Match(libraryLsid);
if (matchLsid.Success)
{
libAuthority = matchLsid.Groups[1].Value;
libId = matchLsid.Groups[2].Value;
}
else
{
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
}
// We will have a RetentionTimes table if schemaVersion if 1 or greater.
saveRetentionTimes = blibLib.SchemaVersion >= 1;
libraryRevision = blibLib.Revision;
schemaVersion = Math.Min(blibLib.SchemaVersion, DbLibInfo.SCHEMA_VERSION_CURRENT);
// If the document has MS1 filtering enabled we will save a minimized version
// of the redundant library, if available.
if(document.Settings.TransitionSettings.FullScan.IsEnabledMs)
{
String redundantLibPath = blibLib.FilePathRedundant;
if(File.Exists(redundantLibPath))
{
string path = BiblioSpecLiteSpec.GetRedundantName(FilePath);
CreateSessionFactory_Redundant(path);
saveRedundantLib = true;
}
}
}
else if (library is BiblioSpecLibrary)
libAuthority = BiblioSpecLiteLibrary.DEFAULT_AUTHORITY;
else if (library is XHunterLibrary)
libAuthority = XHunterLibrary.DEFAULT_AUTHORITY;
else
{
var nistLibrary = library as NistLibrary;
if (nistLibrary != null)
{
libAuthority = NistLibrary.DEFAULT_AUTHORITY;
libId = nistLibrary.Id ?? libId;
}
}
// Use a very specific LSID, since it really only matches this document.
string libLsid = string.Format("urn:lsid:{0}:spectral_libary:bibliospec:nr:minimal:{1}:{2}:{3}.{4}", // Not L10N
libAuthority, libId, Guid.NewGuid(), libraryRevision, schemaVersion);
var dictLibrary = new Dictionary<LibKey, BiblioLiteSpectrumInfo>();
// Hash table to store the database IDs of any source files in the library
// Source file information is available only in Bibliospec libraries, schema version >= 1
var dictFiles = new Dictionary<string, long>();
var dictFilesRedundant = new Dictionary<string, long>();
ISession redundantSession = null;
ITransaction redundantTransaction = null;
int redundantSpectraCount = 0;
try
{
using (ISession session = OpenWriteSession())
using (ITransaction transaction = session.BeginTransaction())
{
var settings = document.Settings;
int peptideCount = document.PeptideCount;
int savedCount = 0;
foreach (var nodePep in document.Peptides)
{
var mods = nodePep.ExplicitMods;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
// Only get library info from precursors that use the desired library
if (!nodeGroup.HasLibInfo || !Equals(nodeGroup.LibInfo.LibraryName, library.Name))
continue;
TransitionGroup group = nodeGroup.TransitionGroup;
string peptideSeq = group.Peptide.Sequence;
int precursorCharge = group.PrecursorCharge;
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
var calcPre = settings.GetPrecursorCalc(labelType, mods);
var peptideModSeq = calcPre.GetModifiedSequence(peptideSeq, false);
var libKey = new LibKey(peptideModSeq, precursorCharge);
if (dictLibrary.ContainsKey(libKey))
continue;
// saveRetentionTimes will be false unless this is a BiblioSpec(schemaVersion >=1) library.
if (!saveRetentionTimes)
{
// get the best spectra
foreach (var spectrumInfo in library.GetSpectra(libKey, labelType, LibraryRedundancy.best))
{
DbRefSpectra refSpectra = MakeRefSpectrum(spectrumInfo,
peptideSeq,
peptideModSeq,
nodeGroup.PrecursorMz,
precursorCharge);
session.Save(refSpectra);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey, refSpectra.Copies,
refSpectra.NumPeaks,
(int) (refSpectra.Id ?? 0),
default(IndexedRetentionTimes),
default(IndexedIonMobilities)));
}
session.Flush();
session.Clear();
}
// This is a BiblioSpec(schemaVersion >=1) library.
else
{
// get all the spectra, including the redundant ones if this library has any
var spectra = library.GetSpectra(libKey, labelType, LibraryRedundancy.all_redundant).ToArray();
// Avoid saving to the RefSpectra table for isotope label types that have no spectra
if (spectra.Length == 0)
continue;
DbRefSpectra refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = nodeGroup.PrecursorMz,
PrecursorCharge = precursorCharge,
PeptideModSeq = peptideModSeq
};
// Get all the information for this reference spectrum.
// For BiblioSpec (schema ver >= 1), this can include retention time information
// for this spectrum as well as any redundant spectra for the peptide.
// Ids of spectra in the redundant library, where available, are also returned.
var redundantSpectraKeys = new List<SpectrumKeyTime>();
BuildRefSpectra(document, session, refSpectra, spectra, dictFiles, redundantSpectraKeys);
session.Save(refSpectra);
session.Flush();
session.Clear();
// TODO(nicksh): preserve retention time information.
var retentionTimesByFileId = default(IndexedRetentionTimes);
var driftTimesByFileId = default(IndexedIonMobilities);
dictLibrary.Add(libKey,
new BiblioLiteSpectrumInfo(libKey,
refSpectra.Copies,
refSpectra.NumPeaks,
(int) (refSpectra.Id ?? 0),
retentionTimesByFileId,
driftTimesByFileId));
// Save entries in the redundant library.
if (saveRedundantLib && redundantSpectraKeys.Count > 0)
{
if (redundantSession == null)
{
redundantSession = OpenWriteSession_Redundant();
redundantTransaction = redundantSession.BeginTransaction();
}
SaveRedundantSpectra(redundantSession, redundantSpectraKeys, dictFilesRedundant, refSpectra, library);
redundantSpectraCount += redundantSpectraKeys.Count;
}
}
}
savedCount++;
if (!UpdateProgress(peptideCount, savedCount))
return null;
}
// Simulate ctime(d), which is what BlibBuild uses.
string createTime = string.Format("{0:ddd MMM dd HH:mm:ss yyyy}", DateTime.Now); // Not L10N? different date/time format in different countries
DbLibInfo libInfo = new DbLibInfo
{
LibLSID = libLsid,
CreateTime = createTime,
NumSpecs = dictLibrary.Count,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
session.Save(libInfo);
session.Flush();
session.Clear();
transaction.Commit();
if (redundantTransaction != null)
{
var scoreType = new DbScoreTypes {Id = 0, ScoreType = "UNKNOWN"}; // Not L10N
redundantSession.Save(scoreType);
libInfo = new DbLibInfo
{
LibLSID = libLsid.Replace(":nr:", ":redundant:"), // Not L10N
CreateTime = createTime,
NumSpecs = redundantSpectraCount,
MajorVersion = libraryRevision,
MinorVersion = schemaVersion
};
redundantSession.Save(libInfo);
redundantSession.Flush();
redundantSession.Clear();
redundantTransaction.Commit();
}
}
}
finally
{
if(redundantTransaction != null)
{
redundantTransaction.Dispose();
}
if (redundantSession != null)
{
redundantSession.Dispose();
}
}
var libraryEntries = dictLibrary.Values.ToArray();
return new BiblioSpecLiteLibrary(librarySpec, libLsid, libraryRevision, schemaVersion,
libraryEntries, FileStreamManager.Default);
}
protected override void DoTest()
{
string skyfile = TestFilesDir.GetTestPath("Mix1_SkylineIMS_Test-reimport_RP50.sky");
RunUI(() => SkylineWindow.OpenFile(skyfile));
var doc0 = WaitForDocumentLoaded();
AssertEx.IsDocumentState(doc0, null, 4, 218, 429, 3176);
Stopwatch loadStopwatch = new Stopwatch();
loadStopwatch.Start();
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
const string ID12692Base = "ID12692_01_UCA168_3727_040714";
string ID12692Search = GetTestPath(ID12692Base + "_IA_final_fragment.csv");
string[] searchFiles = { ID12692Search };
var doc = SkylineWindow.Document;
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.95;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = true;
});
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(skyfile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the files should be found, and we should
// just be able to move to the next page.
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page));
RunUI(() => importPeptideSearchDlg.ClickNextButton());
// Modifications are already set up, so that page should get skipped.
RunUI(() => importPeptideSearchDlg.ClickNextButton()); // Accept the full scan settings
/* No lockmass correction for IMS data due to Waters DLL limitations as of Nov 2015
* var lockmassDlg = ShowDialog<ImportResultsLockMassDlg>(() => importPeptideSearchDlg.ClickNextButton()); // Accept the full scan settings, lockmass correction dialog should appear
* RunUI(() =>
* {
* var mz = 785.8426; // Glu-Fib ESI 2+, per Will T
* lockmassDlg.LockmassPositive = mz;
* lockmassDlg.LockmassNegative = mz;
* lockmassDlg.LockmassTolerance = 10.0;
* });
* RunUI(lockmassDlg.OkDialog);
* WaitForClosedForm<ImportResultsLockMassDlg>();
*/
// Add FASTA also skipped because filter for document peptides was chosen.
WaitForClosedForm(importPeptideSearchDlg);
WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
var doc1 = WaitForDocumentLoaded(400000);
AssertEx.IsDocumentState(doc1, null, 4, 63, 6, 42); // Was 4, 63, 4, 30 before drift time based charge state detection was added to final_fragments reader
loadStopwatch.Stop();
DebugLog.Info("load time = {0}", loadStopwatch.ElapsedMilliseconds);
float tolerance = (float)doc1.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = doc1.Settings.MeasuredResults;
var numPeaks = new[] { 8, 10, 10, 10, 10, 10, 10 };
int npIndex = 0;
var errmsg = "";
foreach (var pair in doc1.PeptidePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
foreach (var chromGroup in chromGroupInfo)
{
if (numPeaks[npIndex] != chromGroup.NumPeaks)
{
errmsg += String.Format("unexpected peak count {0} instead of {1} in chromatogram {2}\r\n", chromGroup.NumPeaks, numPeaks[npIndex], npIndex);
}
npIndex++;
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
}
Assert.IsTrue(errmsg.Length == 0, errmsg);
Assert.AreEqual(3617.529, maxHeight, 1);
}
public void TestModificationMatcher()
{
InitSeqs();
var carbC = StaticModList.GetDefaultsOn()[0];
// Test exception thrown if unable to match - mass.
UpdateMatcherFail(STR_FAIL_MASS);
UpdateMatcherFail(STR_FAIL_NOT_A_NUMBER);
// Test exception thrown if unable to match - name.
UpdateMatcherFail(STR_FAIL_NAME);
// Can't match empty modifications.
UpdateMatcherFail(STR_FAIL_EMPTY_MOD);
UpdateMatcherFail(STR_FAIL_EMPTY_MOD2);
// Can't match double modifications.
UpdateMatcherFail(STR_FAIL_DOUBLE_MOD);
// Test exception thrown if unimod not specified correctly
UpdateMatcherFail(STR_FAIL_UNIMOD);
UpdateMatcherFail(STR_UNKNOWN_UNIMOD);
// Can't phosphorylate tryptophan
UpdateMatcherFail(STR_FAIL_WRONG_AA_UNIMOD);
// Can't put C-terminal modification in middle of peptide
UpdateMatcherFail(STR_FAIL_UNIMOD_TERMINUS);
// Test mods in UniMod match correctly.
UpdateMatcher(StaticModList.GetDefaultsOn(), HeavyModList.GetDefaultsOn(), null, null);
// A sequence with no modifications should not be explicitly modified.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_NO_MODS).HasExplicitMods);
var nodeCysOxi = MATCHER.GetModifiedNode(STR_CYS_AND_OXI);
Assert.IsTrue(nodeCysOxi.HasExplicitMods);
Assert.IsFalse(nodeCysOxi.ExplicitMods.HasHeavyModifications);
// Modifications should match by name.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification.Name, "Phospho (ST)")));
// Test can find terminal modification
Assert.IsTrue(MATCHER.GetModifiedNode(STR_TERM_ONLY).ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Label:13C(6) (C-term R)", false))));
// Test can find matches on terminus that are not terminal
Assert.IsTrue(MATCHER.GetModifiedNode(STR_MOD_BY_NAME).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.Terminus == null));
// Test matching negative masses
Assert.IsTrue(MATCHER.GetModifiedNode(STR_AMMONIA_LOSS).ExplicitMods.StaticModifications.Contains(mod =>
mod.Modification.EquivalentAll(UniMod.GetModification("Ammonia-loss (N-term C)", true))));
// General and specific
// If all AAs modified, try for most general modification.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15)
.ExplicitMods.HeavyModifications.Contains(mod => mod.Modification.Equivalent(LABEL15_N)));
// Updating the settings.
// Peptide settings should change to include new mods.
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath firstAdded;
IdentityPath nextAdded;
docNew = docNew.AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(), "PepGroup1", "",
new[] { MATCHER.GetModifiedNode(STR_MOD_BY_NAME) }) }, true, null, out firstAdded, out nextAdded);
var pepSetNew = MATCHER.GetDocModifications(docNew);
Assert.IsTrue(pepSetNew.StaticModifications.Contains(UniMod.GetModification("Phospho (ST)", true).ChangeExplicit(true)));
// Update the document to the new settings.
var pepSetNew1 = pepSetNew;
var settingsNew2 = docNew.Settings.ChangePeptideModifications(mods => pepSetNew1);
var lightGlobalMods = new MappedList <string, StaticMod>();
lightGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.StaticModifications);
var heavyGlobalMods = new MappedList <string, StaticMod>();
heavyGlobalMods.AddRange(settingsNew2.PeptideSettings.Modifications.AllHeavyModifications);
// Match again. Test FoundMatches string should now be empty.
MATCHER.CreateMatches(docNew.Settings.ChangePeptideModifications(mods => pepSetNew1),
new List <string> {
STR_MOD_BY_NAME
}, lightGlobalMods, heavyGlobalMods);
Assert.IsTrue(string.IsNullOrEmpty(MATCHER.FoundMatches));
// Adding 15N to the settings.
UpdateMatcher(new[] { carbC }, new[] { LABEL15_N }, null, null);
// Test sequences with only explicit heavy mods should not have explicit light mods
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_ONLY).ExplicitMods.StaticModifications);
// Test sequences with only explicit light mods should not have explicit heavy mods
Assert.IsFalse(MATCHER.GetModifiedNode(STR_LIGHT_ONLY).ExplicitMods.HasHeavyModifications);
// Test global mods take precendence over UniMod
UpdateMatcher(new[] { carbC }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.StaticModifications
.Contains(mod => Equals(mod.Modification, OXIDATION_M_GLOBAL)));
// Test document mods take precendence over UniMod
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, null, new[] { OXIDATION_M_GLOBAL }, new[] { LABEL15_N });
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
// Test exception thrown if match doesn't make sense - wrong AA.
UpdateMatcherFail(STR_FAIL_OX_ON_D);
// Test exception thrown if match doesn't make sense - wrong terminus.
_seqs.Add(STR_FAIL_OX_TERM);
AssertEx.ThrowsException <FormatException>(() => UpdateMatcher(new[] { OXIDATION_M_C_TERM }, null, null, null));
_seqs.Remove(STR_FAIL_OX_TERM);
// Heavy 15N - All AAs.
UpdateMatcher(new[] { carbC, METHIONINE_OXIDATION }, new[] { LABEL15_N }, null, null);
// Node should be created from document settings if possible.
Assert.IsNull(MATCHER.GetModifiedNode(STR_HEAVY_15).ExplicitMods);
// Heavy 15N - specific AA.
// If only a specific AA is modified, there must be an explicit mod.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).HasExplicitMods);
// Test variable mods match correctly.
// Put variable mod in global mod and not on doc - make sure don't get variable mod,
// should get explicit mod in that case.
var variableMetOx = METHIONINE_OXIDATION.ChangeVariable(true);
UpdateMatcher(new[] { carbC }, null, new[] { variableMetOx }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add variable mod to doc
UpdateMatcher(new[] { carbC, variableMetOx }, null, null, null);
// Mod can be created by the settings.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).HasExplicitMods);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).ExplicitMods.IsVariableStaticMods);
// Mod cannot be created by the settings.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS).ExplicitMods.IsVariableStaticMods);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_OXI_PHOS_CAP).ExplicitMods.IsVariableStaticMods);
// Add Met Ox to global. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { MET_OX_ROUNDED }, null);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Test: +15.99 finds UniMod.
Assert.IsFalse(MATCHER.GetModifiedNode(STR_HEAVY_15).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
// Add Methionine Oxidation before Met Ox. Test: +16 finds it.
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
Assert.IsFalse(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, MET_OX_ROUNDED)));
Assert.IsTrue(MATCHER.GetModifiedNode(STR_CYS_AND_OXI).
ExplicitMods.StaticModifications.Contains(mod => Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test long masses rounded.
Assert.IsTrue(MATCHER.GetModifiedNode(STR_METOX_LONG_MASS).ExplicitMods.StaticModifications.Contains(mod =>
Equals(mod.Modification, METHIONINE_OXIDATION)));
// Test UniMod label types
var node = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(node);
Assert.IsNull(node.ExplicitMods.StaticModifications);
Assert.IsTrue(node.ExplicitMods.HeavyModifications.Contains(mod =>
Equals(mod.Modification, N_TERM_LABEL)));
UpdateMatcherWithNoSequences(new[] { carbC }, new[] { N_TERM_LABEL }, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
var nodeNew = MATCHER.GetModifiedNode(STR_UNIMOD_LABEL);
Assert.IsNotNull(nodeNew);
Assert.IsTrue(nodeNew.TransitionGroups.Any(group => Equals(group.TransitionGroup.LabelType, IsotopeLabelType.heavy)));
UpdateMatcher(new[] { carbC }, null, new[] { METHIONINE_OXIDATION, MET_OX_ROUNDED }, null);
// Test case where there are lots of unimod labels
var nodeUniAll = MATCHER.GetModifiedNode(STR_UNIMOD_ALL);
Assert.AreEqual(nodeUniAll.ExplicitMods.HeavyModifications.Count, 10);
Assert.IsNull(nodeUniAll.ExplicitMods.StaticModifications);
foreach (var mod in nodeUniAll.ExplicitMods.HeavyModifications)
{
Assert.AreEqual(mod.Modification.ShortName, "+01");
Assert.AreEqual(mod.Modification.UnimodId, 994);
}
// Test unimod terminal label
var nodeUniTerm = MATCHER.GetModifiedNode(STR_UNIMOD_TERMINUS);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications.Count, 1);
Assert.IsNull(nodeUniTerm.ExplicitMods.StaticModifications);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.Terminus, ModTerminus.C);
Assert.AreEqual(nodeUniTerm.ExplicitMods.HeavyModifications[0].Modification.UnimodId, 298);
// Basic multi-label test
var heavyLabelType2 = new IsotopeLabelType("Heavy2", 1);
var typedMod = new TypedModifications(heavyLabelType2, new List <StaticMod> {
LABEL15_N
});
var peptideMods = new PeptideModifications(new List <StaticMod>(), new List <TypedModifications> {
typedMod
});
var settingsMultiLabel = SrmSettingsList.GetDefault().ChangePeptideModifications(mods => peptideMods);
var defSetSetLight = new MappedList <string, StaticMod>();
defSetSetLight.AddRange(StaticModList.GetDefaultsOn());
var defSetHeavy = new MappedList <string, StaticMod>();
defSetHeavy.AddRange(HeavyModList.GetDefaultsOn());
defSetHeavy.Add(LABEL15_N);
MATCHER.CreateMatches(settingsMultiLabel, new List <string> {
STR_HEAVY_15_F
}, defSetSetLight, defSetHeavy);
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F).ExplicitMods.GetHeavyModifications().Contains(mod => Equals(mod.LabelType, heavyLabelType2)));
// Peptide settings should not change.
var docNew0 = new SrmDocument(settingsMultiLabel).AddPeptideGroups(new[] { new PeptideGroupDocNode(new PeptideGroup(),
"PepGroup1", "", new[] { MATCHER.GetModifiedNode(STR_HEAVY_15_F) }) }, true, null, out firstAdded, out nextAdded);
var settingsNew = MATCHER.GetDocModifications(docNew0);
Assert.AreEqual(settingsMultiLabel.PeptideSettings.Modifications.ChangeHasHeavyModifications(false),
settingsNew.ChangeHasHeavyModifications(false));
// Finding specific modifications.
// If only specific AA modified, try for most specific modification.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_F });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_F)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'F')));
// If only some AAs modified, try for most specific modifications.
UpdateMatcher(null, null, null, null, new[] { STR_HEAVY_15_NOT_ALL });
Assert.IsTrue(MATCHER.GetModifiedNode(STR_HEAVY_15_NOT_ALL)
.ExplicitMods.HeavyModifications.Contains(mod =>
mod.Modification.AminoAcids.Contains(c => c == 'I')));
using (var testDir = new TestFilesDir(TestContext, ZIP_FILE))
using (var modMatchDocContainer = InitMatchDocContainer(testDir))
{
var libkeyModMatcher = new LibKeyModificationMatcher();
var anlLibSpec = new BiblioSpecLiteSpec("ANL_Combo", testDir.GetTestPath("ANL_Combined.blib"));
var yeastLibSpec = new BiblioSpecLiteSpec("Yeast", testDir.GetTestPath("Yeast_atlas_small.blib"));
modMatchDocContainer.ChangeLibSpecs(new[] { anlLibSpec, yeastLibSpec });
var docLibraries = modMatchDocContainer.Document.Settings.PeptideSettings.Libraries.Libraries;
int anlLibIndex = docLibraries.IndexOf(library => Equals(library.Name, anlLibSpec.Name));
int yeastLibIndex = docLibraries.IndexOf(library => Equals(library.Name, yeastLibSpec.Name));
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[anlLibIndex].Keys, defSetSetLight, defSetHeavy);
// Test can match 15N
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.HeavyMod != null && match.HeavyMod.Equivalent(LABEL15_N)));
var uniModMetOx = UniMod.GetModification("Oxidation (M)", true);
// Test can match Met Ox
Assert.IsTrue(libkeyModMatcher.Matches.Values.Contains(match =>
match.StructuralMod != null && match.StructuralMod.Equivalent(uniModMetOx)));
// Test can match 15N and Met ox!
Assert.IsTrue(libkeyModMatcher.Matches.Contains(match => match.Key.Mass == 17 &&
match.Value.StructuralMod != null && match.Value.StructuralMod.Equivalent(uniModMetOx) &&
match.Value.HeavyMod != null && match.Value.HeavyMod.Equivalent(LABEL15_N)));
// Test can match Cysteine (Implicit) and Met Ox (variable)
libkeyModMatcher.CreateMatches(modMatchDocContainer.Document.Settings,
docLibraries[yeastLibIndex].Keys, defSetSetLight, defSetHeavy);
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals(UniMod.GetModification(StaticModList.DEFAULT_NAME, true).Formula) && !mod.IsVariable));
Assert.IsTrue(libkeyModMatcher.MatcherPepMods.StaticModifications.Contains(mod =>
mod.Formula.Equals("O") && mod.IsVariable));
}
}
