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
});
}
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);
}
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 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));
}
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 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()
{
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);
}
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);
}
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);
}
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);
}
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));
// 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(),
"redundant 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", 6);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 7);
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", 8);
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", 9);
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", 12);
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);
var allChromGraph = WaitForOpenForm <AllChromatogramsGraph>();
RunUI(() =>
{
allChromGraph.Left = SkylineWindow.Right + 20;
allChromGraph.Activate();
});
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 13);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <AddModificationsDlg>("Add mods alert", 14);
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", 15);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
});
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();
});
const int skylineWindowWidth = 1160;
const int skylineWindowHeight = 792;
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = skylineWindowHeight;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 16);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
RunUI(() =>
{
SkylineWindow.Width = 500;
var peakAreas = SkylineWindow.GraphPeakArea;
var peakAreasFloating = peakAreas.Parent.Parent;
peakAreasFloating.Left = SkylineWindow.Right + 20;
peakAreasFloating.Top = SkylineWindow.Top;
peakAreasFloating.Size = new Size(504, 643);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 18);
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 19);
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", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
const int skylineWindowNarrowWidth = 788;
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
alignmentForm.Width = 660;
alignmentForm.Height = 561;
alignmentForm.Left = SkylineWindow.Right + 20;
alignmentForm.Splitter.SplitterDistance = 75;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 22);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 23);
const string TIP_NAME = "5b_MCF7_TiTip3";
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen();
ClickChromatogram(TIP_NAME, 34.5, 366);
TreeNode selectedNode = null;
RunUI(() => selectedNode = SkylineWindow.SequenceTree.SelectedNode);
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0]);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = selectedNode);
TakeCoverShot();
return;
}
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 31.8, 42.2, 280); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 24);
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
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 25);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 26, "Transition pick list unfiltered", 26); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 42.2, 520); // set the view for screenshot
RunUI(() =>
{
SkylineWindow.Height = 550;
SkylineWindow.ArrangeGraphsTabbed();
});
ActivateReplicate(TIP_NAME);
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
ActivateReplicate(TIP_NAME);
ClickChromatogram(TIP_NAME, 37.3, 142);
PauseForScreenShot("MS1 spectrum graph 37.32 minutes", 28);
ClickChromatogram(TIP_NAME, 33.2, 328.1);
PauseForScreenShot("MS1 spectrum graph 33.19 minutes", 29);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
SkylineWindow.ArrangeGraphs(DisplayGraphsType.Column);
});
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 30);
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, 300); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 31);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 31);
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", 32);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 33);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
if (IsPauseForScreenShots)
{
RestoreViewOnScreen(34);
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 34);
}
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", 34);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
// page 36 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);
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = 720;
});
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 35);
ClickChromatogram(TIP_NAME, 37.5, 1107.3);
PauseForScreenShot("MS1 spectrum graph 37.50 minutes", 36);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(true);
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
});
RestoreViewOnScreen(36); // float the Library Match window
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)", 37);
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)", 37);
RestoreViewOnScreen(37); // back to normal view
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 38);
// 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)", 39); // 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);
}
private void LowResTest()
{
string documentFile = GetTestPath(@"Low Res\BSA_Protea_label_free_meth3.sky");
WaitForCondition(() => File.Exists(documentFile));
RunUI(() => SkylineWindow.OpenFile(documentFile));
bool AsSmallMolecules = AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none;
const int expectedMoleculeCount = 9;
int expectedTransitionGroupCount = 10;
int expectedTransitionCount = 78;
var document = SkylineWindow.Document;
if (AsSmallMolecules)
{
ConvertDocumentToSmallMolecules(AsSmallMoleculesTestMode);
document = SkylineWindow.Document;
Assert.AreEqual(document.PeptideTransitionGroupCount, 0);
Assert.AreEqual(document.MoleculeTransitionGroupCount, expectedTransitionGroupCount);
Assert.AreEqual(document.PeptideTransitionCount, 0);
Assert.AreEqual(document.MoleculeTransitionCount, expectedTransitionCount);
}
AssertEx.IsDocumentState(document, null, 3, expectedMoleculeCount, expectedTransitionGroupCount, expectedTransitionCount);
// p. 3 Select first peptide
RunUI(() => SkylineWindow.SelectedPath = document.GetPathTo((int)SrmDocument.Level.Molecules, 0));
PauseForScreenShot("Main window", 3);
// p. 4 Configure Document for Thermo raw files
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab blank", 5);
RunUI(() =>
{
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.qit;
transitionSettingsUI.AcquisitionMethod = FullScanAcquisitionMethod.Targeted;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab low res", 6);
RunUI(() =>
{
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 2);
// p.6 - library ion match tolerance same as extraction window
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonMatchTolerance = 0.7;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab match tolerance same as MS/MS resolution", 8);
RunUI(() =>
{
// p.6
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.FragmentTypes += ", p";
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
var docFullScan = WaitForDocumentChange(document);
var tranSettingsFullScan = docFullScan.Settings.TransitionSettings;
Assert.AreEqual(FullScanPrecursorIsotopes.Count, tranSettingsFullScan.FullScan.PrecursorIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.qit, tranSettingsFullScan.FullScan.PrecursorMassAnalyzer);
Assert.AreEqual(FullScanAcquisitionMethod.Targeted, tranSettingsFullScan.FullScan.AcquisitionMethod);
Assert.IsTrue(ArrayUtil.EqualsDeep(new[] { IonType.y, IonType.b, IonType.precursor },
tranSettingsFullScan.Filter.IonTypes));
}
RunUI(() => SkylineWindow.ExpandPrecursors());
// Check all the precursors on picklists
bool pausedForScreenShot = false;
foreach (PeptideGroupTreeNode node in SkylineWindow.SequenceTree.GetSequenceNodes())
{
foreach (TreeNode child in node.Nodes)
{
foreach (SrmTreeNodeParent grandChild in child.Nodes)
{
// Because of RunUI must copy to local variable first.
SrmTreeNodeParent child1 = grandChild;
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = child1);
var picklist = ShowDialog <PopupPickList>(() => SkylineWindow.SequenceTree.ShowPickList(false));
RunUI(() =>
{
picklist.SetItemChecked(0, true);
Assert.IsTrue(picklist.GetItemLabel(0).Contains(IonType.precursor.GetLocalizedString()));
Assert.IsTrue(picklist.GetItemChecked(0));
});
if (!pausedForScreenShot)
{
PauseForScreenShot <PopupPickList>("Transitions popup pick-list", 10);
pausedForScreenShot = true;
}
OkDialog(picklist, picklist.OnOk);
}
}
}
WaitForDocumentLoaded();
if (!AsSmallMolecules) // No libraries for small molecules, yet
{
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.IsFalse(nodeGroup.HasLibInfo && nodeGroup.Transitions.All(nodeTran => !nodeTran.HasLibInfo));
}
}
// All transition groups should now have a precursor transition
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.AreEqual(IonType.precursor, nodeGroup.Transitions.First().Transition.IonType);
}
// p.8
ExportMethodDlg exportMethodDlg =
ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.SetInstrument("Thermo LTQ");
Assert.AreEqual("Thermo LTQ", exportMethodDlg.InstrumentType);
exportMethodDlg.SetMethodType(ExportMethodType.Standard);
exportMethodDlg.SetTemplateFile(GetTestPath(@"Low Res\TargetedMSMS_template.meth"));
});
PauseForScreenShot <ExportMethodDlg.MethodView>("Export Method form", 11);
// p. 10 Ok the error box.
{
var messageDlg = ShowDialog <MessageDlg>(() => exportMethodDlg.OkDialog(GetTestPath(@"Low Res\TargetedMSMS_BSA_Protea.meth")));
PauseForScreenShot <MessageDlg>("Error message (expected)", 12);
OkDialog(messageDlg, messageDlg.OkDialog);
}
// Making a report by hand p.11
ExportLiveReportDlg exportReportDlg = ShowDialog <ExportLiveReportDlg>(() => SkylineWindow.ShowExportReportDialog());
var editReportListDlg = ShowDialog <ManageViewsForm>(exportReportDlg.EditList);
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(PropertyPath.Parse("Proteins!*.Name")));
viewEditor.ChooseColumnsTab.AddSelectedColumn();
Assert.AreEqual(1, viewEditor.ChooseColumnsTab.ColumnCount);
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.ModifiedSequence"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Charge"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Mz"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(4, viewEditor.ChooseColumnsTab.ColumnCount);
});
PauseForScreenShot <ViewEditor>("Edit Report form", 13);
{
var previewReportDlg = ShowDialog <DocumentGridForm>(viewEditor.ShowPreview);
var expectedRows = 10 + (TestSmallMolecules ? 1 : 0);
WaitForConditionUI(() => previewReportDlg.IsComplete && previewReportDlg.RowCount == expectedRows);
RunUI(() =>
{
Assert.AreEqual(4, previewReportDlg.ColumnCount);
var precursors =
SkylineWindow.Document.MoleculeTransitionGroups.ToArray();
const int precursorIndex = 3;
for (int i = 0; i < expectedRows; i++)
{
Assert.AreEqual(precursors[i].PrecursorMz, double.Parse(previewReportDlg.DataGridView.Rows[i].Cells[precursorIndex].Value.ToString()), 0.000001);
}
var precursorMzCol = previewReportDlg.DataGridView.Columns[precursorIndex];
Assert.IsNotNull(precursorMzCol);
previewReportDlg.DataGridView.Sort(precursorMzCol, ListSortDirection.Ascending);
});
PauseForScreenShot <DocumentGridForm>("Preview New Report window", 14);
OkDialog(previewReportDlg, previewReportDlg.Close);
}
// Press the Esc key until all forms have been dismissed.
RunUI(() =>
{
viewEditor.Close();
editReportListDlg.Close();
exportReportDlg.CancelClick();
});
WaitForClosedForm(viewEditor);
WaitForClosedForm(editReportListDlg);
WaitForClosedForm(exportReportDlg);
//p. 12 Import Full-Scan Data
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
RunUI(() => importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.prm);
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library blank page", 15);
const int prefixLen = 35;
const string lowResDir = "Low Res";
const string searchDir = "search";
const string lowRes20Base = "klc_20100329v_Protea_Peptide_Curve_20fmol_uL_tech1";
string lowRes20File = GetTestPath(Path.Combine(lowResDir, lowRes20Base + ExtThermoRaw));
string lowRes20FileRaw = Path.ChangeExtension(lowRes20File, ExtThermoRaw);
string lowRes20Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes20Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes20FileName = (Path.GetFileNameWithoutExtension(lowRes20File) ?? "").Substring(prefixLen);
const string lowRes80Base = "klc_20100329v_Protea_Peptide_Curve_80fmol_uL_tech1";
string lowRes80File = GetTestPath(Path.Combine(lowResDir, lowRes80Base + ExtThermoRaw));
string lowRes80Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes80Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes80FileName = (Path.GetFileNameWithoutExtension(lowRes80File) ?? "").Substring(prefixLen);
string[] searchFiles = { lowRes20Search, lowRes80Search };
var doc = SkylineWindow.Document;
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.99;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library with files page", 16);
RunDlg <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck, dlg => dlg.OkDialog());
doc = WaitForDocumentChangeLoaded(doc);
// 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);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search Extract Chromatograms page", 17);
// 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.
TryWaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
var correctPage = false;
ImportPeptideSearchDlg.Pages currentPage = 0;
RunUI(() => correctPage = ImportPeptideSearchDlg.Pages.chromatograms_page == (currentPage = importPeptideSearchDlg.CurrentPage));
if (!correctPage)
{
WaitForConditionUI(1, // Immediate timeout - just want the richer error message that WaitForConditionUI provides
() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page,
string.Format("Expected to be on chromatograms_page, on {0} instead", currentPage));
}
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Modifications are already set up, so that page should get skipped.
// We're on the "Configure Transition Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// We're on the "Configure Full-Scan Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
doc = WaitForDocumentChange(doc);
// Add FASTA also skipped because filter for document peptides was chosen.
WaitForClosedForm(importPeptideSearchDlg);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 18);
WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
WaitForClosedAllChromatogramsGraph();
expectedTransitionGroupCount = 10; // Expect this many with results
expectedTransitionCount = 87; // Expect this many with results
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes20FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes80FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.CollapsePrecursors();
SkylineWindow.Width = 1070;
});
// Select the first precursor.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "LVNELTEFAK" : "K.LVNELTEFAK.T [65, 74]");
}
else
{
FindNode(document.MoleculeTransitionGroups.First().CustomIon.DisplayName);
}
// Ensure Graphs look like p17. (checked)
WaitForGraphs();
RestoreViewOnScreen(18);
PauseForScreenShot("Main window with data imported", 19);
const double minDotp = 0.9;
foreach (var nodeGroup in SkylineWindow.Document.PeptideTransitionGroups)
{
double dotp = nodeGroup.Results[0][0].LibraryDotProduct ?? 0;
Assert.IsTrue(Math.Round(dotp, 2) >= minDotp, string.Format("Library dot-product {0} found below {1}", dotp, minDotp));
}
RunUI(() => SkylineWindow.AutoZoomBestPeak());
// Ensure Graphs look like p18. (checked)
WaitForGraphs();
PauseForScreenShot("Chromatogram graphs clipped from main window with zoomed peaks", 20);
RestoreViewOnScreen(21);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(lowRes20FileRaw, 77.7722)));
PauseForScreenShot <GraphSpectrum>("Library Match view clipped from main window with noisy spectrum", 21);
RunUI(() =>
{
SkylineWindow.ShowGraphSpectrum(false);
Assert.IsFalse(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ShowPeptideIDTimes(false);
});
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(46.8, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(46.8, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowProductTransitions();
});
WaitForCondition(() => !SkylineWindow.GraphPeakArea.IsHidden);
if (!AsSmallMolecules) // No libraries (yet?)
{
WaitForDotProducts();
}
RunUI(() =>
{
// Graph p.15
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 22);
if (!AsSmallMolecules) // No libraries (yet?)
{
VerifyDotProducts(0.99, 0.98);
}
// Check graph p15. (checked)
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
// p. 16 screenshot of full 5-point dilution curve
// Select precursor
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "DRVYIHPF" : "R.DRVYIHPF.- [34, 41]"); // May be localized " (missed 1)"
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1047");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile with split graphs", 24);
RunUI(() =>
{
SkylineWindow.Size = new Size(990, 620);
SkylineWindow.ShowGraphPeakArea(false);
});
PauseForScreenShot("Chromatogram graphs clipped from main window with split graphs", 25);
// PeakAreaGraph Normalize to total p.20.
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowProductTransitions();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
// Ensure graph looks like p20.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]");
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]"); // Phosphorylated
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1333");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("figure 1a - Area Replicate graph metafile for IKNLQSLDPSH", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(9, SkylineWindow.GraphPeakArea.CurveCount);
});
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "HLVDEPQNLIK" : "K.HLVDEPQNLIK.Q [401, 411]");
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1306");
}
WaitForGraphs();
PauseForScreenShot("figure 1b - Area replicate graph metafile for HLVDEPQNLIK", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(7, SkylineWindow.GraphPeakArea.CurveCount);
});
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
WaitForCondition(() => SkylineWindow.GraphPeakArea.IsHidden);
RunUI(() => SkylineWindow.SaveDocument());
}