public bool BuildLibrary(IProgressMonitor progress)
{
var bestSpectra = new List <SpectrumMzInfo>();
foreach (var nodePep in _doc.Peptides)
{
foreach (var nodeTranGroup in nodePep.TransitionGroups.Where(nodeTranGroup => nodeTranGroup.Results != null))
{
// For each precursor, export the spectrum with the highest TIC within peak boundaries
DbSpectrum bestSpectrum = null;
var bestDistance = double.MaxValue;
foreach (var result in nodeTranGroup.Results)
{
if (result.IsEmpty)
{
continue;
}
foreach (var resultsFile in result.Where(resultsFile => resultsFile.RetentionTime.HasValue))
{
foreach (var spectrum in _library.GetSpectraByPrecursor(null, nodeTranGroup.PrecursorMz))
{
var currentDistance = Math.Abs(spectrum.RetentionTime - resultsFile.RetentionTime.Value);
if (currentDistance < bestDistance)
{
bestSpectrum = spectrum;
bestDistance = currentDistance;
}
}
}
}
if (bestSpectrum != null)
{
bestSpectra.Add(new SpectrumMzInfo {
SourceFile = bestSpectrum.ResultsFile.FilePath,
PrecursorMz = bestSpectrum.PrecursorMz,
SpectrumPeaks = _library.LoadSpectrum(bestSpectrum),
Key = nodeTranGroup.GetLibKey(_doc.Settings, nodePep),
RetentionTimes = new[] { new SpectrumMzInfo.IonMobilityAndRT(bestSpectrum.ResultsFile.FilePath, IonMobilityAndCCS.EMPTY, bestSpectrum.RetentionTime, true) }.ToList()
});
}
}
}
using (var blibDb = BlibDb.CreateBlibDb(_libSpec.FilePath))
{
return(blibDb.CreateLibraryFromSpectra(new BiblioSpecLiteSpec(BLIB_NAME_INTERNAL, _libSpec.FilePath), bestSpectra, BLIB_NAME_INTERNAL, progress) != null);
}
}
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);
}
}
private void ShareMinimal(ZipFileShare zip)
{
TemporaryDirectory tempDir = null;
try
{
var docOriginal = Document;
if (Document.Settings.HasBackgroundProteome)
{
// Remove any background proteome reference
Document = Document.ChangeSettings(Document.Settings.ChangePeptideSettings(
set => set.ChangeBackgroundProteome(BackgroundProteome.NONE)));
}
if (Document.Settings.HasRTCalcPersisted)
{
// Minimize any persistable retention time calculator
tempDir = new TemporaryDirectory();
string tempDbPath = Document.Settings.PeptideSettings.Prediction.RetentionTime
.Calculator.PersistMinimized(tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath);
}
}
if (Document.Settings.HasOptimizationLibraryPersisted)
{
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
string tempDbPath = Document.Settings.TransitionSettings.Prediction.OptimizedLibrary.PersistMinimized(
tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath);
}
}
if (Document.Settings.HasIonMobilityLibraryPersisted)
{
// Minimize any persistable ion mobility predictor
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
string tempDbPath = Document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary
.PersistMinimized(tempDir.DirPath, Document, null, out _);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath);
}
}
if (Document.Settings.HasLibraries)
{
// Minimize all libraries in a temporary directory, and add them
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
Document = BlibDb.MinimizeLibraries(Document, tempDir.DirPath,
Path.GetFileNameWithoutExtension(DocumentPath),
null,
ProgressMonitor);
if (ProgressMonitor != null && ProgressMonitor.IsCanceled)
{
return;
}
foreach (var librarySpec in Document.Settings.PeptideSettings.Libraries.LibrarySpecs)
{
var tempLibPath = Path.Combine(tempDir.DirPath, Path.GetFileName(librarySpec.FilePath) ?? string.Empty);
zip.AddFile(tempLibPath);
// If there is a .redundant.blib file that corresponds to a .blib file
// in the temp temporary directory, add that as well
IncludeRedundantBlib(librarySpec, zip, tempLibPath);
}
}
var auditLogDocPath = DocumentPath;
tempDir = ShareDataAndView(zip, tempDir);
if (ReferenceEquals(docOriginal, Document) && null == ShareType.SkylineVersion)
{
zip.AddFile(DocumentPath);
}
else
{
tempDir = ShareDocument(zip, tempDir, out auditLogDocPath);
}
SafeAuditLog(zip, auditLogDocPath);
Save(zip);
}
finally
{
DeleteTempDir(tempDir);
}
}
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);
}
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);
}
private void ShareMinimal(ZipFile zip)
{
TemporaryDirectory tempDir = null;
try
{
var docOriginal = Document;
if (Document.Settings.HasBackgroundProteome)
{
// Remove any background proteome reference
Document = Document.ChangeSettings(Document.Settings.ChangePeptideSettings(
set => set.ChangeBackgroundProteome(BackgroundProteome.NONE)));
}
if (Document.Settings.HasRTCalcPersisted)
{
// Minimize any persistable retention time calculator
tempDir = new TemporaryDirectory();
string tempDbPath = Document.Settings.PeptideSettings.Prediction.RetentionTime
.Calculator.PersistMinimized(tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath, string.Empty);
}
}
if (Document.Settings.HasOptimizationLibraryPersisted)
{
tempDir = new TemporaryDirectory();
string tempDbPath = Document.Settings.TransitionSettings.Prediction.OptimizedLibrary.PersistMinimized(
tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath, string.Empty);
}
}
if (Document.Settings.HasIonMobilityLibraryPersisted)
{
// Minimize any persistable drift time predictor
tempDir = new TemporaryDirectory();
string tempDbPath = Document.Settings.PeptideSettings.Prediction.DriftTimePredictor
.IonMobilityLibrary.PersistMinimized(tempDir.DirPath, Document);
if (tempDbPath != null)
{
zip.AddFile(tempDbPath, string.Empty);
}
}
if (Document.Settings.HasLibraries)
{
// Minimize all libraries in a temporary directory, and add them
if (tempDir == null)
{
tempDir = new TemporaryDirectory();
}
Document = BlibDb.MinimizeLibraries(Document, tempDir.DirPath,
Path.GetFileNameWithoutExtension(DocumentPath),
ProgressMonitor);
if (ProgressMonitor != null && ProgressMonitor.IsCanceled)
{
return;
}
foreach (var librarySpec in Document.Settings.PeptideSettings.Libraries.LibrarySpecs)
{
var tempLibPath = Path.Combine(tempDir.DirPath, Path.GetFileName(librarySpec.FilePath) ?? string.Empty);
zip.AddFile(tempLibPath, string.Empty);
// If there is a .redundant.blib file that corresponds to a .blib file
// in the temp temporary directory, add that as well
IncludeRedundantBlib(librarySpec, zip, tempLibPath);
}
}
ShareDataAndView(zip);
if (ReferenceEquals(docOriginal, Document))
{
zip.AddFile(DocumentPath, string.Empty);
}
else
{
// If minimizing changed the document, then serialize and archive the new document
var stringWriter = new XmlStringWriter();
using (var writer = new XmlTextWriter(stringWriter)
{
Formatting = Formatting.Indented
})
{
XmlSerializer ser = new XmlSerializer(typeof(SrmDocument));
ser.Serialize(writer, Document);
zip.AddEntry(Path.GetFileName(DocumentPath), stringWriter.ToString(), Encoding.UTF8);
}
}
Save(zip);
}
finally
{
if (tempDir != null)
{
try
{
tempDir.Dispose();
}
catch (IOException x)
{
var message = TextUtil.LineSeparate(string.Format(Resources.SrmDocumentSharing_ShareMinimal_Failure_removing_temporary_directory__0__,
tempDir.DirPath),
x.Message);
throw new IOException(message);
}
}
}
}
protected override void DoTest()
{
// 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
};
foreach (var searchFile in searchFiles)
{
Assert.IsTrue(File.Exists(searchFile), string.Format("File {0} does not exist.", searchFile));
}
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);
// Sanity check here, because of failure getting both files for results import below
var searchNames = importPeptideSearchDlg.BuildPepSearchLibControl.SearchFilenames;
Assert.AreEqual(searchFiles.Length, searchNames.Length,
PathsMessage("Unexpected search files found.", searchNames));
var builder = importPeptideSearchDlg.BuildPepSearchLibControl.ImportPeptideSearch.GetLibBuilder(
SkylineWindow.DocumentUI, SkylineWindow.DocumentFilePath, false);
Assert.IsTrue(ArrayUtil.EqualsDeep(searchFiles, builder.InputFiles),
PathsMessage("Unexpected BlibBuild input files.", builder.InputFiles));
importPeptideSearchDlg.BuildPepSearchLibControl.DebugMode = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
var ambiguousDlg = ShowDialog <MessageDlg>(() => importPeptideSearchDlg.ClickNextButton());
RunUI(() => AssertEx.Contains(ambiguousDlg.Message,
Resources.BiblioSpecLiteBuilder_AmbiguousMatches_The_library_built_successfully__Spectra_matching_the_following_peptides_had_multiple_ambiguous_peptide_matches_and_were_excluded_));
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);
// Verify input paths sent to BlibBuild
string buildArgs = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildCommandArgs;
string buildOutput = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildOutput;
var argLines = buildArgs.Split(new[] { Environment.NewLine }, StringSplitOptions.None);
var dirCommon = PathEx.GetCommonRoot(searchFiles);
var searchLines = searchFiles.Select(f => PathEx.RemovePrefix(f, dirCommon)).ToArray();
Assert.IsTrue(ArrayUtil.EqualsDeep(searchLines, argLines.Skip(1).ToArray()), buildArgs);
// Verify resulting .blib file contains the expected files
var docLib = librarySettings.Libraries[0];
int expectedFileCount = searchFiles.Length;
int expectedRedundantSpectra = 813; // 446 with TiTip only
int expectedSpectra = 552; // 428 with TiTip3 only
if (expectedFileCount != docLib.FileCount)
{
var searchFileNames = searchFiles.Select(Path.GetFileName).ToArray();
using (var blibDbRedundant = BlibDb.OpenBlibDb(redundantDocLibPath))
{
VerifyLib(searchFileNames, expectedRedundantSpectra, blibDbRedundant.GetIdFilePaths(), blibDbRedundant.GetSpectraCount(),
"redunant library", buildArgs, buildOutput);
}
using (var blibDb = BlibDb.OpenBlibDb(docLibPath))
{
VerifyLib(searchFileNames, expectedSpectra, blibDb.GetIdFilePaths(), blibDb.GetSpectraCount(),
"SQLite library", buildArgs, buildOutput);
}
VerifyLib(searchFileNames, expectedSpectra, docLib.LibraryDetails.DataFiles.Select(d => d.IdFilePath).ToArray(), docLib.SpectrumCount,
"in memory", buildArgs, buildOutput);
}
// 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 &&
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count > 0 &&
importPeptideSearchDlg.IsNextButtonEnabled);
// Wait for extra for both source files in the list
TryWaitForConditionUI(10 * 1000, () => importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count == searchFiles.Length);
RunUI(() =>
{
// Check for missing files
var missingFiles = importPeptideSearchDlg.ImportResultsControl.MissingResultsFiles.ToArray();
Assert.AreEqual(0, missingFiles.Length,
PathsMessage("Unexpected missing file found.", missingFiles));
// Check for expected results files
var resultsNames = importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Select(f => f.Name).ToArray();
Assert.AreEqual(searchFiles.Length, importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count,
PathsMessage("Unexpected results files found.", resultsNames));
// Check for expected common prefix
var commonPrefix = ImportResultsDlg.GetCommonPrefix(resultsNames);
Assert.IsFalse(string.IsNullOrEmpty(commonPrefix),
PathsMessage("File names do not have a common prefix.", resultsNames));
Assert.AreEqual("100803_000", commonPrefix);
});
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 = GetGraphChromatogram(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();
});
doc = WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
// CONSIDER: This refinement seems to be a no-op. Not sure why it is here.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // This would get rid of proteins with no peptides (none exist)
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio; // This would get rid of undetected transitions (none exist)
dlg.OkDialog(); // Will not change the document or add an Undo entry
});
// Nothing should have changed on the UI thread
RunUI(() => Assert.AreSame(doc, SkylineWindow.DocumentUI));
// 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);
// Because this was showing up in the nightly test failures
WaitForConditionUI(() => exportMethodDlg.IsDisposed);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
