public void MultiLabelTypeListTest()
{
TestSmallMolecules = false; // we don't expect to roundtrip export/import of transition lists for non-proteomic molecules
int startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangeTransitionInstrument(inst => inst.ChangeMaxMz(1800)));
// Add some FASTA
IdentityPath path, pathRoot = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(ExampleText.TEXT_FASTA_YEAST_LIB), false, pathRoot, out path);
const int initProt = 2, initPep = 26, initTran = 89;
AssertEx.IsDocumentState(docFasta, ++startRev, initProt, initPep, initTran);
// Add multiple heavy types
var settings = docFasta.Settings.ChangePeptideModifications(mods => new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(LABEL_TYPE13_C, HEAVY_MODS_13_C),
new TypedModifications(LABEL_TYPE15_N, HEAVY_MODS_15_N)
}));
var docMulti = docFasta.ChangeSettings(settings);
// CONSIDER: make explicit S-Lens, cone voltage, CE etc roundtrip?
// docMulti.MoleculeTransitionGroups.FirstOrDefault().ChangeExplicitValues(ExplicitTransitionGroupValues.TEST)
// Make sure transition lists export to various formats and roundtrip
VerifyExportRoundTrip(new ThermoMassListExporter(docMulti), docFasta);
// Add Oxidation (M) as a static modification to challenge new mass list importing flexibility
VerifyExportRoundTrip(new AbiMassListExporter(AddOxidationM(docMulti)), AddOxidationM(docFasta));
VerifyExportRoundTrip(new AgilentMassListExporter(docMulti), docFasta);
VerifyExportRoundTrip(new WatersMassListExporter(docMulti), docFasta);
}
protected override void DoTest()
{
var document = new SrmDocument(SrmSettingsList.GetDefault());
var staticMods = document.Settings.PeptideSettings.Modifications.StaticModifications.ToList();
staticMods.Add(UniMod.GetModification("Phospho (ST)", true).ChangeVariable(true));
var heavyMods = new List <StaticMod> {
UniMod.GetModification("Label:13C(6)15N(4) (C-term R)", false)
};
document = document.ChangeSettings(document.Settings
.ChangePeptideModifications(mods => mods.ChangeStaticModifications(staticMods)
.ChangeModifications(IsotopeLabelType.heavy, heavyMods))
.ChangeTransitionFilter(filt => filt.ChangePeptidePrecursorCharges(Adduct.ProtonatedFromCharges(2, 3, 4, 5))));
Assert.IsTrue(SkylineWindow.SetDocument(document, SkylineWindow.Document));
RunUI(() => SkylineWindow.Paste(TextUtil.LineSeparate(PEPTIDE_MODIFIED, PEPTIDE_UNMODIFIED)));
document = WaitForDocumentChangeLoaded(document);
RunUI(() => SkylineWindow.Paste(PEPTIDE_EXTRA));
var docPaste1 = WaitForDocumentChangeLoaded(document);
AssertEx.IsDocumentState(docPaste1, null, 2, 6, 44, 129);
TestErrorMessages();
TestUse();
}
public CommandLineUI(string[] args, CommandStatusWriter consoleOut)
{
_commandArgs = new CommandArgs(consoleOut, false);
if (!_commandArgs.ParseArgs(args))
{
consoleOut.WriteLine(Resources.CommandLine_Run_Exiting___);
return;
}
Program.UnitTest = Program.FunctionalTest = true;
Program.TestExceptions = new List <Exception>();
Program.NoSaveSettings = true;
Program.DisableJoining = _commandArgs.ImportDisableJoining;
Program.NoAllChromatogramsGraph = _commandArgs.NoAllChromatogramsGraph;
Settings.Default.AutoShowAllChromatogramsGraph = !_commandArgs.HideAllChromatogramsGraph;
LocalizationHelper.InitThread();
// Run test in new thread (Skyline on main thread).
Program.Init();
Settings.Default.SrmSettingsList[0] = SrmSettingsList.GetDefault();
// Reset defaults with names from resources for testing different languages
Settings.Default.BackgroundProteomeList[0] = BackgroundProteomeList.GetDefault();
Settings.Default.DeclusterPotentialList[0] = DeclusterPotentialList.GetDefault();
Settings.Default.RetentionTimeList[0] = RetentionTimeList.GetDefault();
Settings.Default.ShowStartupForm = false;
var threadTest = new Thread(Run);
LocalizationHelper.InitThread(threadTest);
threadTest.Start();
Program.Main();
threadTest.Join();
}
public void TestAllColumnToolTipsAreLocalized()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
SkylineDataSchema skylineDataSchema = new SkylineDataSchema(documentContainer, SkylineDataSchema.GetLocalizedSchemaLocalizer());
var missingCaptions = new HashSet <ColumnCaption>();
foreach (var columnDescriptor in
EnumerateAllColumnDescriptors(skylineDataSchema, STARTING_TYPES))
{
var invariantDescription = skylineDataSchema.GetColumnDescription(columnDescriptor);
if (string.IsNullOrEmpty(invariantDescription))
{
var invariantCaption = skylineDataSchema.GetColumnCaption(columnDescriptor) as ColumnCaption;
if (invariantCaption != null)
{
missingCaptions.Add(invariantCaption);
}
}
}
if (missingCaptions.Count == 0)
{
return;
}
StringWriter message = new StringWriter();
WriteResXFile(message, missingCaptions);
Assert.Fail("Missing localized tooltips for column captions: {0}", message.ToString().Replace("<data", "\r\n<data"));
}
public void TestGenerateResxFile()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
GenerateResXFile(new StringWriter() /* Console.Out */, new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT), STARTING_TYPES);
}
public void TestPermuteComplexIons()
{
var mainPeptide = new Peptide("MERCURY");
var srmSettings = SrmSettingsList.GetDefault();
var transitionFilter = srmSettings.TransitionSettings.Filter;
transitionFilter = transitionFilter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b });
srmSettings = srmSettings.ChangeTransitionSettings(
srmSettings.TransitionSettings.ChangeFilter(transitionFilter));
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("disulfide", "C", null, "-H2");
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 6, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
Assert.AreNotEqual(0, complexFragmentIons.Length);
}
public void TestAuditLogSerialization()
{
const int entryCount = 20000;
var document = new SrmDocument(SrmSettingsList.GetDefault());
var simpleEntry = AuditLogEntry.CreateSimpleEntry(document, MessageType.test_only, string.Empty);
var entries = Enumerable.Range(0, entryCount).Select(index => simpleEntry).ToArray();
Array.Reverse(entries);
AuditLogEntry headEntry = null;
foreach (var entry in entries)
{
if (headEntry == null)
{
headEntry = entry;
}
else
{
headEntry = entry.ChangeParent(headEntry);
}
}
Assert.IsNotNull(headEntry);
Assert.AreEqual(entryCount, headEntry.Count);
Assert.AreEqual(headEntry.Count, headEntry.Enumerate().Count());
var auditLogList = new AuditLogList(headEntry);
var serializedAuditLog = new StringWriter();
var serializer = new XmlSerializer(typeof(AuditLogList));
serializer.Serialize(serializedAuditLog, auditLogList);
var roundTrip = (AuditLogList)serializer.Deserialize(new StringReader(serializedAuditLog.ToString()));
Assert.IsNotNull(roundTrip);
Assert.AreEqual(auditLogList.AuditLogEntries.Count, roundTrip.AuditLogEntries.Count);
}
//[TestMethod]
public void TestDdaSmall()
{
ChorusAccount TEST_ACCOUNT = new ChorusAccount("https://chorusproject.org", "*****@*****.**", "pwd");
var stream = typeof(ChromTaskListTest).Assembly.GetManifestResourceStream(typeof(ChromTaskListTest),
"DdaSmall.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequest = (ChromatogramRequestDocument) new XmlSerializer(typeof(ChromatogramRequestDocument)).Deserialize(stream);
var chromTaskList = new ChromTaskList(() => { }, new SrmDocument(SrmSettingsList.GetDefault()), TEST_ACCOUNT,
TEST_ACCOUNT.GetChorusUrl().SetFileId(28836), ChromTaskList.ChunkChromatogramRequest(chromatogramRequest, 100));
chromTaskList.SetMinimumSimultaneousTasks(10);
var failedTasks = new HashSet <ChromatogramGeneratorTask>();
foreach (var chromKey in chromTaskList.ChromKeys)
{
TimeIntensities timeIntensities;
chromTaskList.GetChromatogram(chromKey, out timeIntensities);
if (null == timeIntensities)
{
var task = chromTaskList.GetGeneratorTask(chromKey);
if (failedTasks.Add(task))
{
var memoryStream = new MemoryStream();
var xmlWriter = XmlWriter.Create(memoryStream, new XmlWriterSettings {
Encoding = Encoding.UTF8
});
new XmlSerializer(typeof(ChromatogramRequestDocument)).Serialize(xmlWriter, task.ChromatogramRequestDocument);
Console.Out.WriteLine("Failed to get data for {0}", Encoding.UTF8.GetString(memoryStream.ToArray()));
}
}
}
Assert.AreEqual(0, failedTasks.Count);
}
public void TestAllColumnCaptionsAreLocalized()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
SkylineDataSchema skylineDataSchema = new SkylineDataSchema(documentContainer, SkylineDataSchema.GetLocalizedSchemaLocalizer());
var missingCaptions = new HashSet <ColumnCaption>();
foreach (var columnDescriptor in
EnumerateAllColumnDescriptors(skylineDataSchema, STARTING_TYPES))
{
var invariantCaption = skylineDataSchema.GetColumnCaption(columnDescriptor) as ColumnCaption;
if (invariantCaption != null && !skylineDataSchema.DataSchemaLocalizer.HasEntry(invariantCaption))
{
missingCaptions.Add(invariantCaption);
}
}
if (missingCaptions.Count == 0)
{
return;
}
StringWriter message = new StringWriter();
WriteResXFile(message, missingCaptions);
Assert.Fail("Missing localized column captions {0}", message);
}
public void TestCheckForUnusedColumnTooltips()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
SkylineDataSchema dataSchema = new SkylineDataSchema(documentContainer, DataSchemaLocalizer.INVARIANT);
var columnCaptions = new HashSet <string>();
var resourceManager = ColumnToolTips.ResourceManager;
var resourceSet = resourceManager.GetResourceSet(CultureInfo.InvariantCulture, true, true);
var enumerator = resourceSet.GetEnumerator();
while (enumerator.MoveNext())
{
string key = enumerator.Key as string;
if (null != key)
{
columnCaptions.Add(key);
}
}
foreach (var columnDescriptor in EnumerateAllColumnDescriptors(dataSchema, STARTING_TYPES))
{
var invariantCaption = dataSchema.GetColumnCaption(columnDescriptor);
columnCaptions.Remove(invariantCaption.GetCaption(DataSchemaLocalizer.INVARIANT));
}
var unusedCaptions = columnCaptions.ToArray();
Assert.AreEqual(0, unusedCaptions.Length, "Unused entries found in ColumnToolTips.resx: {0}", string.Join(",", unusedCaptions));
}
private void PrepareDocument(string documentFile)
{
RunUI(SkylineWindow.NewDocument);
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(documentFile)));
}
public void TestThermoDIAChunked()
{
if (!RunPerfTests)
{
return; // PerfTests only run when the global "allow perf tests" flag is set
}
var xmlSerializer = new XmlSerializer(typeof(ChromatogramRequestDocument));
var stream = typeof(PerfChorusGenerateChromatograms).Assembly.GetManifestResourceStream(
typeof(PerfChorusGenerateChromatograms), "ThermoDIA.ChorusRequest.xml");
Assert.IsNotNull(stream);
var chromatogramRequestDocument = (ChromatogramRequestDocument)xmlSerializer.Deserialize(stream);
var chorusUrl = TEST_ACCOUNT.GetChorusUrl().SetFileId(28836);
var srmDocument = new SrmDocument(SrmSettingsList.GetDefault());
foreach (int chunkChromatogramCount in new[] { 50, 100, 150, 200, 300 })
{
ChromTaskList chromTaskList = new ChromTaskList(() => { }, srmDocument, TEST_ACCOUNT, chorusUrl, ChromTaskList.ChunkChromatogramRequest(chromatogramRequestDocument, chunkChromatogramCount));
chromTaskList.SetMinimumSimultaneousTasks(30);
DateTime startTime = DateTime.Now;
while (chromTaskList.PercentComplete < 100)
{
Thread.Sleep(100);
}
DateTime endTime = DateTime.Now;
Assert.AreEqual(0, chromTaskList.ListExceptions().Count);
Console.Out.WriteLine("*******************************************");
Console.Out.WriteLine("Chromatograms per chunk: {0}", chunkChromatogramCount);
Console.Out.WriteLine("Number of chunks: {0}", chromTaskList.TaskCount);
Console.Out.WriteLine("Elapsed time {0}", endTime.Subtract(startTime));
Console.Out.WriteLine("*******************************************");
}
}
public void TestAuditLogRef()
{
const string TEST_PREFIX = "test";
const int TEST_ENTRY_COUNT = 3;
var document = new SrmDocument(SrmSettingsList.GetDefault());
Assert.IsTrue(document.AuditLog.AuditLogEntries.IsRoot);
Assert.AreEqual(0, AuditLogEntryRef.PROTOTYPE.ListChildrenOfParent(document).Count());
AuditLogEntry headEntry = document.AuditLog.AuditLogEntries;
for (int i = 0; i < TEST_ENTRY_COUNT; i++)
{
var auditLogEntry = AuditLogEntry.CreateTestOnlyEntry(DateTime.UtcNow, SrmDocument.DOCUMENT_TYPE.mixed, TEST_PREFIX + i);
headEntry = auditLogEntry.ChangeParent(headEntry);
}
Assert.IsNotNull(headEntry);
Assert.AreEqual(TEST_ENTRY_COUNT, headEntry.Count);
document = document.ChangeAuditLog(headEntry);
var auditLogRefs = AuditLogEntryRef.PROTOTYPE.ListChildrenOfParent(document).Cast <AuditLogEntryRef>().ToList();
Assert.AreEqual(TEST_ENTRY_COUNT, auditLogRefs.Count);
var extraLogEntry = AuditLogEntry
.CreateTestOnlyEntry(DateTime.UtcNow, SrmDocument.DOCUMENT_TYPE.mixed, "extra entry")
.ChangeParent(document.AuditLog.AuditLogEntries);
var document2 = document.ChangeAuditLog(extraLogEntry);
Assert.AreEqual(TEST_ENTRY_COUNT + 1, AuditLogEntryRef.PROTOTYPE.ListChildrenOfParent(document2).Count());
foreach (var auditLogRef in auditLogRefs)
{
var entry1 = auditLogRef.FindAuditLogEntry(document);
var entry2 = auditLogRef.FindAuditLogEntry(document2);
Assert.AreEqual(entry1, entry2);
}
}
public void LibraryNoIonsTest()
{
var streamManager = new MemoryStreamManager();
var loader = new LibraryLoadTest.TestLibraryLoader {
StreamManager = streamManager
};
// Create X! Hunter library with 20 lowest intensity peaks in NIST library
LibraryLoadTest.CreateHunterFile(streamManager, loader, LibraryLoadTest.TEXT_LIB_YEAST_NIST, true);
var hunterSpec = new XHunterLibSpec("Yeast (X!)", LibraryLoadTest.PATH_HUNTER_LIB);
// For serialization, add the library spec to the settings
TestLibraryList = new SpectralLibraryList {
hunterSpec
};
var libraryManager = new LibraryManager {
StreamManager = streamManager
};
var docContainer = new TestDocumentContainer();
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(new LibrarySpec[] { hunterSpec }));
int startRev;
SrmDocument docLoaded = CreateLibraryDocument(settings, ExampleText.TEXT_FASTA_YEAST_LIB, false,
docContainer, libraryManager, out startRev);
// Peptides should have been chosen, but no transitions, since the spectra are garbage
AssertEx.IsDocumentState(docLoaded, startRev, 2, 4, 0);
}
public void TestCrosslinkGetNeutralFormula()
{
var mainPeptide = new Peptide("MERCURY");
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(srmSettings.PeptideSettings.Modifications
.ChangeStaticModifications(new StaticMod[0])));
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
null, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var unlinkedFormula = mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C37H61N13O11S2Se", unlinkedFormula.ToString());
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 2, null);
var linkedPeptideFormula = linkedPeptide.GetNeutralFormula(srmSettings, IsotopeLabelType.light);
Assert.AreEqual("C30H53N11O12S", linkedPeptideFormula.ToString());
var crosslinkMod = new StaticMod("disulfide", null, null, "-H2");
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(3, crosslinkMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
var crosslinkedFormula =
mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, explicitModsWithCrosslink);
Assert.AreEqual("C67H112N24O23S3Se", crosslinkedFormula.Molecule.ToString());
}
public void TestSingleAminoAcidLinkedPeptide()
{
var srmSettings = SrmSettingsList.GetDefault();
var mainPeptide = new Peptide("A");
var staticMod = new StaticMod("crosslinker", null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("D"), 0, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null,
ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
var modsWithoutLinkedPeptide = new ExplicitMods(mainPeptide, new[] { new ExplicitMod(0, staticMod), }, new TypedExplicitModifications[0]);
Assert.AreEqual("C3H7NO2", AminoAcidFormulas.Default.GetFormula("A").ToString());
Assert.AreEqual("C3H7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null).Molecule.ToString());
Assert.AreEqual("CH7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithoutLinkedPeptide).Molecule.ToString());
Assert.AreEqual("C4H7NO4", AminoAcidFormulas.Default.GetFormula("D").ToString());
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual("C5H14N2O6", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithLinkedPeptide).Molecule.ToString());
var mainComplexFragmentIon = new ComplexFragmentIon(new Transition(mainTransitionGroup, IonType.precursor, mainPeptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, modsWithLinkedPeptide.Crosslinks);
var linkedComplexFragmentIon = new ComplexFragmentIon(
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
var complexFragmentIon =
mainComplexFragmentIon.AddChild(new ModificationSite(0, staticMod.Name), linkedComplexFragmentIon);
var transition = complexFragmentIon.MakeTransitionDocNode(srmSettings, modsWithLinkedPeptide, null);
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var expectedMz = sequenceMassCalc.GetPrecursorMass("A") + sequenceMassCalc.GetPrecursorMass("D") - 24 - BioMassCalc.MassProton;
Assert.AreEqual(expectedMz, transition.Mz, .00001);
}
public void SpecialFragmentTest()
{
var docOriginal = new SrmDocument(SrmSettingsList.GetDefault());
IdentityPath path;
var docPeptide = docOriginal.ImportFasta(new StringReader(">peptide1\nPEPMCIDEPR"),
true, IdentityPath.ROOT, out path);
// One of the prolines should have caused an extra transition
Assert.AreEqual(4, docPeptide.PeptideTransitionCount);
Assert.IsTrue(docPeptide.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 8)); // y8
// Switch to the legacy version of the proline fragment where min length is 1
var docLegacyProline = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { MeasuredIonList.NTERM_PROLINE_LEGACY })));
Assert.AreEqual(5, docLegacyProline.PeptideTransitionCount);
// Allow b-ions
var docLegacyProlineB = docLegacyProline.ChangeSettings(docLegacyProline.Settings.ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.b, IonType.y })));
Assert.AreEqual(9, docLegacyProlineB.PeptideTransitionCount);
// Add C-terminal Glu and Asp to the original peptide document
var docGluAsp = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new List <MeasuredIon>(filter.MeasuredIons)
{
MeasuredIonList.CTERM_GLU_ASP
})));
Assert.AreEqual(5, docGluAsp.PeptideTransitionCount);
Assert.IsTrue(docGluAsp.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 3)); // y3
// Use the legacy version instead
var docGluAspLegacy = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new List <MeasuredIon>(filter.MeasuredIons)
{
MeasuredIonList.CTERM_GLU_ASP_LEGACY
})));
Assert.AreEqual(6, docGluAspLegacy.PeptideTransitionCount);
Assert.IsTrue(docGluAspLegacy.PeptideTransitions.Contains(nodeTran => nodeTran.Transition.Ordinal == 2)); // y2
// Add Proline to the C-terminal modification
var docGluAspPro = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { new MeasuredIon("C-term GAP", "EDP", null, SequenceTerminus.C, 1) })));
Assert.AreEqual(8, docGluAspPro.PeptideTransitionCount);
Assert.IsTrue(docGluAspPro.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal == 2 || // y2
nodeTran.Transition.Ordinal == 8)); // y8
// Restrict
var docGluAspProRestrict = docPeptide.ChangeSettings(docPeptide.Settings.ChangeTransitionFilter(filter =>
filter.ChangeMeasuredIons(new[] { new MeasuredIon("C-term GAP", "EDP", "P", SequenceTerminus.C, 1) })));
Assert.AreEqual(6, docGluAspProRestrict.PeptideTransitionCount);
Assert.IsFalse(docGluAspProRestrict.PeptideTransitions.Contains(nodeTran =>
nodeTran.Transition.Ordinal == 2 || // not y2
nodeTran.Transition.Ordinal == 8)); // not y8
}
public void TestLooplinkCrosslinkLibraryKey()
{
var crosslinkLibraryKey = new CrosslinkLibraryKey(new [] { new PeptideLibraryKey("AKIQDKEGIPPDQQR", 0) }, new[] { new CrosslinkLibraryKey.Crosslink("+138.0681", new[] { new [] { 2, 6 } }) }, 3);
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(srmSettings.PeptideSettings.Modifications
.ChangeStaticModifications(
srmSettings.PeptideSettings.Modifications.StaticModifications
.Append(new StaticMod("DSS", "K", null, "C8H10O2").ChangeCrosslinkerSettings(
CrosslinkerSettings.EMPTY)).ToList()
)));
var libKeyModificationMatcher = new LibKeyModificationMatcher();
libKeyModificationMatcher.CreateMatches(srmSettings, new[] { new LibKey(crosslinkLibraryKey) },
new MappedList <string, StaticMod>(), new MappedList <string, StaticMod>());
var peptideDocNode = libKeyModificationMatcher.CreateDocNodeFromSettings(new LibKey(crosslinkLibraryKey),
new Peptide("AKIQDKEGIPPDQQR"), SrmSettingsDiff.ALL, out _);
Assert.IsNotNull(peptideDocNode);
Assert.IsNotNull(peptideDocNode.ExplicitMods);
Assert.AreEqual(1, peptideDocNode.ExplicitMods.Crosslinks.Count);
Assert.AreEqual(null, peptideDocNode.ExplicitMods.Crosslinks[0].Value.Peptide);
}
public void TestComplexIonMz()
{
var srmSettings = SrmSettingsList.GetDefault();
var peptide = new Peptide("DLGEEHFKGLVLIAFSQYLQQCPFDEHVK");
var linkedPeptide = new LinkedPeptide(new Peptide("LVNELTEFAKTCVADESHAGCEK"), 9, null);
var transitionGroup = new TransitionGroup(peptide, Adduct.QUADRUPLY_PROTONATED, IsotopeLabelType.light);
var crosslinkMod = new StaticMod("linker", "K", null, "C8H10O2");
var explicitMod = new ExplicitMod(7, crosslinkMod).ChangeLinkedPeptide(linkedPeptide);
var explicitMods = new ExplicitMods(peptide, new[] { explicitMod }, new List <TypedExplicitModifications>());
var linkedTransition =
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED);
var expectedMzs = new[]
{
Tuple.Create(IonType.b, 2, 1, 229.1183),
Tuple.Create(IonType.b, 10, 3, 1291.2766)
};
foreach (var tuple in expectedMzs)
{
int offset = Transition.OrdinalToOffset(tuple.Item1, tuple.Item2, peptide.Sequence.Length);
var transition = new Transition(transitionGroup, tuple.Item1, offset, 0, Adduct.FromChargeProtonated(tuple.Item3));
var complexFragmentIon = new ComplexFragmentIon(transition, null, explicitMods.Crosslinks);
if (complexFragmentIon.IncludesAaIndex(explicitMod.IndexAA))
{
complexFragmentIon = complexFragmentIon.AddChild(explicitMod.ModificationSite,
new ComplexFragmentIon(linkedTransition, null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE));
}
var complexTransitionDocNode = complexFragmentIon.MakeTransitionDocNode(srmSettings, explicitMods, null);
Assert.AreEqual(tuple.Item4, complexTransitionDocNode.Mz, .0001, "{0}{1}{2}", tuple.Item1, tuple.Item2,
Transition.GetChargeIndicator(Adduct.FromChargeProtonated(tuple.Item3)));
}
}
public void TestCrosslinkModSerialization()
{
var settings = SrmSettingsList.GetDefault();
var crosslinkerDef = new StaticMod("disulfide", null, null, "-H2")
.ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
settings = settings.ChangePeptideSettings(settings.PeptideSettings.ChangeModifications(
settings.PeptideSettings.Modifications.ChangeStaticModifications(new[] { crosslinkerDef })));
settings = settings.ChangeTransitionSettings(settings.TransitionSettings.ChangeFilter(
settings.TransitionSettings.Filter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b })
)); var mainPeptide = new Peptide("MERCURY");
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 2, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, true);
var peptideDocNode = new PeptideDocNode(mainPeptide, settings, explicitModsWithCrosslink, null, ExplicitRetentionTimeInfo.EMPTY, new [] { transitionGroupDocNode }, false);
peptideDocNode = peptideDocNode.ChangeSettings(settings, SrmSettingsDiff.ALL);
Assert.AreNotEqual(0, peptideDocNode.TransitionCount);
var peptideGroupDocNode = new PeptideGroupDocNode(new PeptideGroup(), Annotations.EMPTY, "Peptides", null, new [] { peptideDocNode });
var srmDocument = (SrmDocument) new SrmDocument(settings).ChangeChildren(new[] { peptideGroupDocNode });
AssertEx.Serializable(srmDocument);
string docXML = null;
AssertEx.RoundTrip(srmDocument, ref docXML);
Assert.IsNotNull(docXML);
}
public void Initialize(ImportPeptideSearchDlg.Workflow workflow)
{
if (workflow != ImportPeptideSearchDlg.Workflow.dia)
{
int offset = lblTolerance.Top - cbExclusionUseDIAWindow.Top;
Array.ForEach(new Control[] { lblTolerance, txtTolerance, lblToleranceUnits, lblIonCount, txtIonCount, lblIonCountUnits }, c => c.Top -= offset);
cbExclusionUseDIAWindow.Hide();
}
// If these are just the document defaults, use something more appropriate for DIA
else
{
var settingsCurrent = _documentContainer.Document.Settings.TransitionSettings;
var settings = settingsCurrent;
var defSettings = SrmSettingsList.GetDefault().TransitionSettings;
if (Equals(settings.Filter, defSettings.Filter))
{
settings = settings.ChangeFilter(settings.Filter
.ChangePeptidePrecursorCharges(new[] { Adduct.DOUBLY_PROTONATED, Adduct.TRIPLY_PROTONATED })
.ChangePeptideProductCharges(new[] { Adduct.SINGLY_PROTONATED, Adduct.DOUBLY_PROTONATED })
.ChangePeptideIonTypes(new[] { IonType.y, IonType.b, IonType.precursor }));
}
if (Equals(settings.Libraries, defSettings.Libraries))
{
settings = settings.ChangeLibraries(settings.Libraries.ChangeIonMatchTolerance(0.05)
.ChangeIonCount(6)
.ChangeMinIonCount(6));
}
if (!ReferenceEquals(settings, settingsCurrent))
{
SetFields(settings);
}
}
}
public void TestComplexIonGetNeutralFormula()
{
var srmSettings = SrmSettingsList.GetDefault();
var fullTransitionGroup = new TransitionGroupDocNode(
new TransitionGroup(new Peptide("ELVIS"), Adduct.SINGLY_PROTONATED, IsotopeLabelType.light),
Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY,
null, null, false);
var fullFormula = fullTransitionGroup.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C25H45N5O9", fullFormula.Molecule.ToString());
var hydrolysisDef = new StaticMod("hydrolysis", null, ModTerminus.C, "-H2O")
.ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
var crossLinkMod = new ExplicitMod(1, hydrolysisDef)
.ChangeLinkedPeptide(new LinkedPeptide(new Peptide("VIS"), 0, null));
var mainPeptide = new Peptide("EL");
var explicitMods = new ExplicitMods(mainPeptide, new[] { crossLinkMod }, new TypedExplicitModifications[0]);
var mainTransitionGroup = new TransitionGroupDocNode(
new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light),
Annotations.EMPTY, srmSettings,
explicitMods, null,
ExplicitTransitionGroupValues.EMPTY,
null, null, false);
var mainFullFormula = mainTransitionGroup.GetNeutralFormula(srmSettings, explicitMods);
Assert.AreEqual(fullFormula, mainFullFormula);
}
public void NeutralLossListTest()
{
TestSmallMolecules = false; // No concept of neutral loss for small molecules
var phosphoLossMod = new StaticMod("Phospho Loss", "S, T, Y", null, false, "HPO3",
LabelAtoms.None, RelativeRT.Matching, null, null, new[] { new FragmentLoss("H3PO4"), });
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault().ChangePeptideModifications(mods =>
mods.ChangeStaticModifications(new List <StaticMod>(mods.StaticModifications)
{
phosphoLossMod
})));
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = document.ImportFasta(new StringReader(TEXT_FASTA_YEAST_7), false, path, out path);
Assert.AreEqual(0, GetLossCount(docFasta, 1));
// Insert losses into the first transition group
var pathPeptide = docFasta.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodePep = (PeptideDocNode)docFasta.FindNode(pathPeptide);
var nodeGroup = (TransitionGroupDocNode)nodePep.Children[0];
var listChildren = new List <DocNode>(nodeGroup.Children);
foreach (var nodeTran in nodeGroup.GetTransitions(docFasta.Settings,
nodePep.ExplicitMods, nodeGroup.PrecursorMz, null, null, null, false))
{
if (!nodeTran.HasLoss)
{
continue;
}
var tran = nodeTran.Transition;
int matchIndex = listChildren.IndexOf(node =>
Equals(tran, ((TransitionDocNode)node).Transition));
if (matchIndex == -1)
{
continue;
}
while (matchIndex < listChildren.Count &&
Equals(tran, ((TransitionDocNode)listChildren[matchIndex]).Transition))
{
matchIndex++;
}
listChildren.Insert(matchIndex, nodeTran);
}
var docLosses = (SrmDocument)docFasta.ReplaceChild(pathPeptide,
nodeGroup.ChangeChildren(listChildren));
int lossCount = GetLossCount(docLosses, 1);
Assert.IsTrue(lossCount > 0);
var docRoundTripped = AssertEx.RoundTripTransitionList(new ThermoMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
docRoundTripped = AssertEx.RoundTripTransitionList(new AgilentMassListExporter(docLosses));
Assert.AreEqual(lossCount, GetLossCount(docRoundTripped, 1));
}
public static BrowsingDataSchema GetBrowsingDataSchema()
{
var memoryDocumentContainer = new MemoryDocumentContainer();
var document = new SrmDocument(SrmSettingsList.GetDefault());
memoryDocumentContainer.SetDocument(document, memoryDocumentContainer.Document);
return(new BrowsingDataSchema(memoryDocumentContainer, GetLocalizedSchemaLocalizer()));
}
public override void Dispose()
{
base.Dispose();
var docEmpty = new SrmDocument(SrmSettingsList.GetDefault());
Assert.IsTrue(SetDocument(docEmpty, Document));
}
private SkylineDataSchema GetDataSchema()
{
var document = new SrmDocument(SrmSettingsList.GetDefault());
var container = new MemoryDocumentContainer();
Assert.IsTrue(container.SetDocument(document, container.Document));
return(new SkylineDataSchema(container, DataSchemaLocalizer.INVARIANT));
}
public void MultiLabelExplicitSerialTest()
{
// Create a simple document and add two peptides
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault());
const string pepSequence1 = "QFVLSCVILR";
const string pepSequence2 = "DIEVYCDGAITTK";
var reader = new StringReader(string.Join("\n", new[] { ">peptides1", pepSequence1, pepSequence2 }));
IdentityPath path;
document = document.ImportFasta(reader, true, IdentityPath.ROOT, out path);
Assert.AreEqual(2, document.PeptideCount);
// Add some modifications in two new label types
var modCarb = new StaticMod("Carbamidomethyl Cysteine", "C", null, "C2H3ON");
var modOther = new StaticMod("Another Cysteine", "C", null, "CO8N2");
var staticMods = new[] { modCarb, modOther };
var mod15N = new StaticMod("All 15N", null, null, null, LabelAtoms.N15, null, null);
var modK13C = new StaticMod("13C K", "K", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modR13C = new StaticMod("13C R", "R", ModTerminus.C, null, LabelAtoms.C13, null, null);
var modV13C = new StaticMod("Heavy V", "V", null, null, LabelAtoms.C13 | LabelAtoms.N15, null, null);
var heavyMods = new[] { mod15N, modK13C, modR13C, modV13C };
var labelTypeAA = new IsotopeLabelType("heavy AA", IsotopeLabelType.FirstHeavy);
var labelTypeAll = new IsotopeLabelType("heavy All", IsotopeLabelType.FirstHeavy + 1);
var settings = document.Settings;
settings = settings.ChangePeptideModifications(mods =>
new PeptideModifications(mods.StaticModifications,
new[]
{
new TypedModifications(labelTypeAA, new[] { modK13C, modR13C }),
new TypedModifications(labelTypeAll, new[] { mod15N })
}));
document = document.ChangeSettings(settings);
Assert.AreEqual(6, document.PeptideTransitionGroupCount);
// Add modifications to light and heavy AA in the first peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodePepMod = (PeptideDocNode)document.FindNode(path);
var explicitMod = new ExplicitMods(nodePepMod.Peptide,
new[] { new ExplicitMod(pepSequence1.IndexOf('C'), modOther) },
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAA, new ExplicitMod[0]) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
// Add a modification to heavy All in the second peptide
path = document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
nodePepMod = (PeptideDocNode)document.FindNode(path);
explicitMod = new ExplicitMods(nodePepMod.Peptide, null,
new[] { new TypedExplicitModifications(nodePepMod.Peptide, labelTypeAll,
new[] { new ExplicitMod(pepSequence2.IndexOf('V'), modV13C) }) });
document = document.ChangePeptideMods(path, explicitMod, staticMods, heavyMods);
Assert.AreEqual(5, document.PeptideTransitionGroupCount);
AssertEx.Serializable(document, 3, AssertEx.DocumentCloned);
}
public IEnumerable <SkylineDataSchema> EnumerateDataSchemas()
{
var documentContainer = new MemoryDocumentContainer();
Assert.IsTrue(documentContainer.SetDocument(new SrmDocument(SrmSettingsList.GetDefault()), documentContainer.Document));
var dataSchema = new SkylineDataSchema(documentContainer, SkylineDataSchema.GetLocalizedSchemaLocalizer());
yield return(dataSchema);
}
public void TestTransitionGroupDocNodeGetNeutralFormula()
{
var peptide = new Peptide("PEPTIDE");
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var srmSettings = SrmSettingsList.GetDefault();
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var moleculeOffset = transitionGroupDocNode.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C34H53N7O15", moleculeOffset.Molecule.ToString());
}
public void DynamicMinMzTest()
{
var revisionIndex = 1;
var settings = SrmSettingsList.GetDefault().ChangeTransitionFilter(filter =>
filter.ChangePeptideIonTypes(new[] { IonType.y, IonType.b })
.ChangeFragmentRangeFirstName("ion 1")
.ChangeFragmentRangeLastName("last ion"));
var docOriginal = new SrmDocument(settings);
IdentityPath path;
var docPeptides = docOriginal.ImportFasta(new StringReader(">peptides\nESTIGNSAFELLLEVAK\nTVYHAGTK"),
true, IdentityPath.ROOT, out path);
AssertEx.IsDocumentState(docPeptides, revisionIndex++, 1, 2, 2, 40);
// Both precursors should contain 1 and 2 ions
foreach (var nodeGroup in docPeptides.PeptideTransitionGroups)
{
Assert.IsTrue(nodeGroup.Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 1));
Assert.IsTrue(nodeGroup.Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 2));
}
// Switch to using dynamic minimum for product ions
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeIsDynamicMin(true));
var docDynamicMin = docPeptides.ChangeSettings(settings);
AssertEx.IsDocumentState(docDynamicMin, revisionIndex++, 1, 2, 35);
var arrayNodeGroups = docDynamicMin.PeptideTransitionGroups.ToArray();
// The larger precursor should no longer have 1 or 2 ions
Assert.IsFalse(arrayNodeGroups[0].Children.Contains(node =>
((TransitionDocNode)node).Transition.Ordinal == 1 ||
((TransitionDocNode)node).Transition.Ordinal == 2));
// But the smaller precursor should retain at least one of both
Assert.IsTrue(arrayNodeGroups[1].Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 1));
Assert.IsTrue(arrayNodeGroups[1].Children.Contains(node => ((TransitionDocNode)node).Transition.Ordinal == 2));
// Use a minimum that is high enough to exclude the smaller precursor
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeMinMz(500));
var docHighMinDynamicMz = docDynamicMin.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighMinDynamicMz, revisionIndex++, 1, 2, 1, 22);
// Because of the dynamic minimum for product ions, the remaining precursor should not have changed
var nodeGroupHigh = docHighMinDynamicMz.PeptideTransitionGroups.ToArray()[0];
Assert.AreSame(arrayNodeGroups[0], nodeGroupHigh);
// Remove dynamic minimum, and verify that product ions are removed
settings = settings.ChangeTransitionInstrument(instrument => instrument.ChangeIsDynamicMin(false));
var docHighMinMz = docHighMinDynamicMz.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighMinMz, revisionIndex, 1, 2, 1, 17);
// No library test, because it is hard to test. Many of the library
// spectra are likely gathered with LTQs which apply the same dynamic
// minimum to the ms/ms peaks they measure.
}