/// <summary>
/// Given two keys that match each other (i.e. the modification masses are within the other's margin of error)
/// return a key which has the lower precision of the two.
/// For instance, if one key is C[+57.021464]PEPTIDER[+10] and the is C[+57.02]PEPTIDEK[10.0083],
/// the result be C[+57.02]PEPTIDER[+10].
/// </summary>
private PeptideLibraryKey MostGeneralPeptideKey(PeptideLibraryKey key1, PeptideLibraryKey key2)
{
Assume.AreEqual(key1.UnmodifiedSequence, key2.UnmodifiedSequence);
var mods1 = key1.GetModifications();
var mods2 = key2.GetModifications();
Assume.AreEqual(mods1.Count, mods2.Count);
var newMods = new List <KeyValuePair <int, string> >(mods1.Count);
for (int i = 0; i < mods1.Count; i++)
{
var mod1 = mods1[i];
var mod2 = mods2[i];
Assume.AreEqual(mod1.Key, mod2.Key);
if (mod1.Value == mod2.Value)
{
newMods.Add(mod1);
continue;
}
MassModification massMod1 = MassModification.Parse(mod1.Value);
MassModification massMod2 = MassModification.Parse(mod2.Value);
if (massMod1.Precision <= massMod2.Precision)
{
newMods.Add(mod1);
}
else
{
newMods.Add(mod2);
}
}
return(new PeptideLibraryKey(MakeModifiedSequence(key1.UnmodifiedSequence, newMods), key1.Charge));
}
// Unit test of annotations handler class
private static void TestSpectrumPeakAnnotations()
{
var noNote = SpectrumPeakAnnotation.Create(new CustomIon(null, Adduct.FromChargeNoMass(-2), 100, 101, "noNote"), null);
var noName = SpectrumPeakAnnotation.Create(new CustomIon(null, Adduct.FromChargeNoMass(-2), 100, 101, null), "noted");
var fullIon = new CustomIon("C12H5O3", Adduct.FromStringAssumeChargeOnly("M-H2O+"), null, null, "full");
var full = SpectrumPeakAnnotation.Create(fullIon, "noted");
var fullToo = SpectrumPeakAnnotation.Create(fullIon, "noted");
var nameOnlyTab = SpectrumPeakAnnotation.Create(new CustomIon(null, Adduct.FromChargeNoMass(-2), 100, 101, "test\ttabs"), "noted"); // Check tab escape
var fullIonTabs = new CustomIon("C12H5", Adduct.FromChargeNoMass(-2), null, null, "full\ttabs");
var tabbedFull = SpectrumPeakAnnotation.Create(fullIonTabs, "noted\ttabs"); // Check tab escape
Assume.AreEqual(full, fullToo);
Assume.AreNotEqual(full, tabbedFull);
var tests = new List <List <SpectrumPeakAnnotation> >
{
new List <SpectrumPeakAnnotation> {
noNote, noName, full
},
new List <SpectrumPeakAnnotation> {
fullToo, nameOnlyTab, tabbedFull
}
};
var cached = SpectrumPeakAnnotation.ToCacheFormat(tests);
var roundtrip = SpectrumPeakAnnotation.FromCacheFormat(cached);
int i = 0;
foreach (var annotsPerPeak in tests)
{
Assume.IsTrue(CollectionUtil.EqualsDeep(annotsPerPeak, roundtrip[i++]));
}
}
/// <summary>
/// Modify the XML that CreateXmlReader will parse for next caller. Finds each
/// occuraece of elementName and changes or adds attribute name from attributesList.
/// Expects as many occurences of elementName as there are members in attributesList
/// </summary>
public void ModifyAttributesInElement(string elementName, string attributeName, IList <string> attributesList)
{
var elementOpenA = string.Format("<{0} ", elementName); // Not L10N
var elementOpenB = string.Format("<{0}>", elementName); // Not L10N
var elementsA = XmlText.Split(new[] { elementOpenA }, StringSplitOptions.None);
var elementsB = XmlText.Split(new[] { elementOpenB }, StringSplitOptions.None);
var elements = elementsA.Length > elementsB.Length ? elementsA : elementsB;
var elementOpen = elementsA.Length > elementsB.Length ? elementOpenA : elementOpenB;
var attr = string.Format(" {0}=", attributeName); // Not L10N
Assume.AreEqual(elements.Length, attributesList.Count + 1, "Trouble in XML lookahead"); // Not L10N
for (var e = 1; e < elements.Length; e++)
{
var element = elements[e];
var attrStart = element.IndexOf(attr, StringComparison.InvariantCulture);
var tagEnd = element.IndexOf(">", StringComparison.InvariantCulture); // Not L10N
if (attrStart > tagEnd)
{
attrStart = -1; // That attr belonged to a child element
}
var newAttr = string.Format(" {0}\"{1}\" ", attr, attributesList[e - 1]); // Not L10N
if (attrStart == -1)
{
elements[e] = newAttr + elements[e];
}
else
{
var attrEnd = element.IndexOf("\"", attrStart + attr.Length + 1, StringComparison.InvariantCulture); // Not L10N
elements[e] = elements[e].Substring(0, attrStart) + newAttr + elements[e].Substring(attrEnd + 1);
}
}
XmlText = string.Join(elementOpen, elements);
}
private string FormatLinkedPeptides(Func <IEnumerable <Modification>, string> modFormatter)
{
List <Tuple <int, Modification> > linkedModifications = new List <Tuple <int, Modification> >();
StringBuilder peptideSequences = new StringBuilder();
StringBuilder crosslinks = new StringBuilder();
int totalPeptides = 1;
foreach (var mod in GetModifications().Where(mod => null != mod.ExplicitMod.LinkedPeptide))
{
totalPeptides += mod.ExplicitMod.LinkedPeptide.CountDescendents();
if (mod.LinkedPeptideSequence == null)
{
crosslinks.Append(FormatCrosslinkMod(modFormatter, totalPeptides, mod, 0, 0));
}
else
{
linkedModifications.Add(Tuple.Create(0, mod));
}
}
int peptideIndex = 0;
while (linkedModifications.Any())
{
peptideIndex++;
var linkedModTuple = linkedModifications[0];
linkedModifications.RemoveAt(0);
var linkedModification = linkedModTuple.Item2;
if (linkedModTuple.Item2.LinkedPeptideSequence != null)
{
foreach (var mod in linkedModTuple.Item2.LinkedPeptideSequence.GetModifications()
.Where(mod => null != mod.ExplicitMod.LinkedPeptide))
{
if (mod.LinkedPeptideSequence == null)
{
crosslinks.Append(FormatCrosslinkMod(modFormatter, totalPeptides, mod, peptideIndex,
peptideIndex));
}
else
{
linkedModifications.Add(Tuple.Create(peptideIndex, mod));
}
}
}
peptideSequences.Append(@"-");
peptideSequences.Append(linkedModification.LinkedPeptideSequence.FormatSelf(modFormatter));
crosslinks.Append(FormatCrosslinkMod(modFormatter, totalPeptides, linkedModification,
linkedModTuple.Item1, peptideIndex));
}
if (crosslinks.Length == 0)
{
Assume.AreEqual(0, peptideSequences.Length);
return(string.Empty);
}
return(peptideSequences + @"-" + crosslinks);
}
private void CheckRefSpectra(IList <DbRefSpectra> spectra, string name, string formula, string precursorAdduct,
double precursorMz, ushort numPeaks, string[] fragmentNames = null,
double?ionMobility = null, double?ionMobilityHighEnergyOffset = null)
{
if (_convertedFromPeptides)
{
name = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + name;
}
for (var i = 0; i < spectra.Count; i++)
{
var spectrum = spectra[i];
if (spectrum.MoleculeName.Equals(name) &&
spectrum.ChemicalFormula.Equals(formula) &&
spectrum.PrecursorCharge.Equals(Adduct.FromStringAssumeProtonated(precursorAdduct).AdductCharge) &&
spectrum.PrecursorAdduct.Equals(precursorAdduct) &&
Math.Abs(spectrum.PrecursorMZ - precursorMz) < 0.001 &&
spectrum.NumPeaks.Equals(numPeaks))
{
// Found the item - check its fragment info if provided
// This demonstrates fix for "Issue 689: File > Export > Spectral Library losing information from small molecule documents",
// point 3 "Ion annotations do not preserve the ion names from the document but instead always use 'ion[mass]' for the annotations
// when the document gave them names."
if (fragmentNames != null)
{
Assume.AreEqual(fragmentNames.Length, spectrum.PeakAnnotations.Count);
foreach (var annotation in spectrum.PeakAnnotations)
{
Assume.IsTrue(fragmentNames.Contains(annotation.Name));
}
}
if (ionMobility.HasValue)
{
AssertEx.AreEqualNullable(spectrum.IonMobility, ionMobility, .00001);
if (ionMobilityHighEnergyOffset.HasValue)
{
AssertEx.AreEqualNullable(spectrum.IonMobilityHighEnergyOffset, ionMobilityHighEnergyOffset, .00001);
}
}
// Item is OK, remove from further searches
spectra.RemoveAt(i);
return;
}
}
Assume.Fail(string.Format("{0}, {1}, precursor charge {2}, precursor m/z {3}, with {4} peaks not found", name, formula, precursorAdduct, precursorMz, numPeaks));
}
/// <summary>
/// Helper function for creating input tensors.
/// type should match T.
/// </summary>
public static TensorProto Create2dTensor <T>(DataType type, Func <TensorProto, RepeatedField <T> > getVal,
ICollection <T> inputs, params long[] dimensions)
{
// Construct Tensor
var tp = new TensorProto {
Dtype = type
};
// Populate with data
getVal(tp).AddRange(inputs);
tp.TensorShape = new TensorShapeProto();
Assume.AreEqual(dimensions.Aggregate(1L, (a, b) => a * b), (long)inputs.Count);
tp.TensorShape.Dim.AddRange(dimensions.Select(d => new TensorShapeProto.Types.Dim {
Size = d
}));
return(tp);
}
private void CompareDocumentTransitions(SrmDocument docA, SrmDocument docB)
{
// Note that we can't just run the lists in parallel - one of these is likely a small molecule conversion of the other,
// and will have its transitions sorted differently
Assume.AreEqual(docA.MoleculeTransitionGroupCount, docB.MoleculeTransitionGroupCount);
foreach (var transGroupDocB in docB.MoleculeTransitionGroups)
{
var transGroupDocA = docA.MoleculeTransitionGroups.FirstOrDefault(a =>
Math.Abs(a.PrecursorMz - transGroupDocB.PrecursorMz) <= 1.5E-6 &&
Equals(a.TransitionCount, transGroupDocB.TransitionCount) &&
Equals(a.TransitionGroup.PrecursorAdduct.AdductCharge, transGroupDocB.TransitionGroup.PrecursorAdduct.AdductCharge) &&
Equals(a.TransitionGroup.LabelType, transGroupDocB.TransitionGroup.LabelType));
Assume.IsNotNull(transGroupDocA, "failed to find matching transition group");
var docBTransitions = transGroupDocB.Transitions.ToArray();
var docBTransitionsMatched = new List <TransitionDocNode>();
// ReSharper disable once PossibleNullReferenceException
foreach (var transDocA in transGroupDocA.Transitions)
{
var a = transDocA;
var transDocB = docBTransitions.FirstOrDefault(b =>
a.Transition.IsPrecursor() == b.Transition.IsPrecursor() &&
Math.Abs(a.Mz - b.Mz) <= 1.0E-5 &&
((a.Results == null)
? (b.Results == null)
: (a.Results.Count == b.Results.Count)));
Assume.IsNotNull(transDocB, "failed to find matching transition");
Assume.IsFalse(docBTransitionsMatched.Contains(transDocB), "transition matched twice");
docBTransitionsMatched.Add(transDocB);
// ReSharper disable PossibleNullReferenceException
using (var docBChromInfos = transDocB.ChromInfos.GetEnumerator())
{
foreach (var infoDocA in transDocA.ChromInfos)
{
Assume.IsTrue(docBChromInfos.MoveNext());
var infoDocB = docBChromInfos.Current;
Assume.IsTrue(infoDocA.Equals(infoDocB));
}
}
// ReSharper restore PossibleNullReferenceException
}
}
}
public MoleculeAccessionNumbers(string keysTSV, string inChiKey = null)
{
var keys = new Dictionary <string, string>(StringComparer.OrdinalIgnoreCase); // Treat "cas" and "CAS" as identical lookups
if (!string.IsNullOrEmpty(keysTSV) || !string.IsNullOrEmpty(inChiKey))
{
if (!string.IsNullOrEmpty(keysTSV))
{
// Pick apart a string like "CAS:58-08-2\tinchi:1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3\tmykey:a:b:c:d"
foreach (var kvp in keysTSV.Split(TextUtil.SEPARATOR_TSV))
{
var pair = kvp.Split(':');
if (pair.Length > 1)
{
var key = pair[0].Trim();
var value = string.Join(":", pair.Skip(1)).Trim(); // In case value contains semicolons // Not L10N
if (!string.IsNullOrEmpty(value))
{
keys.Add(key, value);
}
}
}
}
if (!string.IsNullOrEmpty(inChiKey))
{
if (keys.ContainsKey(TagInChiKey))
{
Assume.AreEqual(inChiKey, keys[TagInChiKey]);
}
else
{
keys.Add(TagInChiKey, inChiKey);
}
}
}
AccessionNumbers = ImmutableSortedList <string, string> .FromValues(keys, ACCESSION_TYPE_SORTER);
}
protected override void DoTest()
{
string skyFile = TestFilesDir.GetTestPath("tims_test.sky");
Program.ExtraRawFileSearchFolder = TestFilesDir.PersistentFilesDir;
var testPath = TestFilesDir.GetTestPath("local.sky");
// Make sure that commandline loading employs 3-array IMS (should be quick if it does)
TestCommandlineImport(skyFile, testPath);
RunUI(() => Settings.Default.ImportResultsSimultaneousFiles = (int)MultiFileLoader.ImportResultsSimultaneousFileOptions.many); // use maximum threads for multiple file import
RunUI(() => SkylineWindow.OpenFile(skyFile));
ImportResults(BSA_50fmol_TIMS_InfusionESI_10precd);
var document = WaitForDocumentLoaded(240000); // mz5 part of this this can take awhile
AssertEx.IsDocumentState(document, null, 1, 34, 89, 1007);
RunUI(() =>
{
// Show that we can reopen a document with 3-array data in it
SkylineWindow.SaveDocument(testPath);
SkylineWindow.NewDocument();
VerifySerialization(testPath, false);
SkylineWindow.LoadFile(testPath);
});
document = WaitForDocumentLoaded(240000);
var transitions = document.MoleculeTransitions.ToArray();
// Verify ability to extract ion mobility peaks from raw data
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate user picking Add from the ion mobility Predictor combo control
var driftTimePredictorDlg = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg.AddDriftTimePredictor);
RunUI(() =>
{
driftTimePredictorDlg.SetOffsetHighEnergySpectraCheckbox(true);
driftTimePredictorDlg.SetPredictorName("test_tims");
driftTimePredictorDlg.SetResolvingPower(40);
driftTimePredictorDlg.GetDriftTimesFromResults();
});
// PauseTest(); // Uncomment this to inspect ion mobility finder results
RunUI(() =>
{
driftTimePredictorDlg.OkDialog(true); // Force overwrite if a named predictor already exists
});
WaitForClosedForm(driftTimePredictorDlg);
RunUI(() =>
{
peptideSettingsDlg.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg);
var docChangedDriftTimePredictor = WaitForDocumentChange(document);
// Reimport data - should shift precursors
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docChangedDriftTimePredictor.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
document = WaitForDocumentChangeLoaded(docChangedDriftTimePredictor);
var transitionsNew = document.MoleculeTransitions.ToArray();
var nChanges = 0;
var nNonEmpty = 0;
for (var i = 0; i < transitions.Length; i++)
{
Assert.AreEqual(transitions[i].Mz, transitionsNew[i].Mz);
if (transitions[i].AveragePeakArea.HasValue)
{
nNonEmpty++;
if (transitions[i].AveragePeakArea != transitionsNew[i].AveragePeakArea) // Using filter should alter peak area
{
nChanges++;
}
}
else
{
Assert.AreEqual(transitions[i].AveragePeakArea, transitionsNew[i].AveragePeakArea);
}
}
Assert.IsTrue(nChanges >= nNonEmpty * .9); // We expect nearly all peaks to change in area with IMS filter in use
// And read some mz5 converted from Bruker in 2-array IMS format, then compare replicates - should be identical
var mz5 = TestFilesDir.GetTestPath(bsaFmolTimsInfusionesiPrecMz5Mz5);
ImportResultsFile(mz5);
document = WaitForDocumentChange(document);
var sb = new StringBuilder();
int trials = 0;
int diffs = 0;
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
Assert.AreEqual(2, nodeGroup.Results.Count);
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
Assume.AreEqual(2, nodeTran.Results.Count);
if (nodeTran.Results[0].Any() || nodeTran.Results[1].Any())
{
trials++;
}
if (Equals(nodeTran.Results[0], nodeTran.Results[1]))
{
continue;
}
var diff = Math.Abs(nodeTran.Results[0].First().Area - nodeTran.Results[1].First().Area) /
Math.Min(nodeTran.Results[0].First().Area, nodeTran.Results[1].First().Area);
diffs++;
if (diff > 0)
{
sb.AppendLine(string.Format("Difference {0} in {1} - {2}",
diff, nodeGroup, nodeTran.Transition));
}
else
{
sb.AppendLine(string.Format("No area difference in {0} - {1}",
nodeGroup, nodeTran.Transition));
}
}
}
if (sb.Length > 0)
{
Assert.Fail(TextUtil.LineSeparate(string.Format("{0} of {1} differences found in peak areas between 2- and 3- array spectra", diffs, trials), sb.ToString()));
}
// Verify that the data was loaded in 3-array IMS format for .d and 2-array for .mz5 (which was converted that way on purpose) by looking at serialization
RunUI(() =>
{
SkylineWindow.SaveDocument(testPath);
});
VerifySerialization(testPath, true);
}
/// <summary>
/// Returns true if Skyline can handle the structure of the crosslinks in this CrosslinkLibraryKey.
/// </summary>
public bool IsSupportedBySkyline()
{
var queue = new List <int>();
var remainingCrosslinks = new List <ImmutableList <int> >();
var consumedPeptides = new HashSet <int>();
foreach (var crosslink in Crosslinks)
{
var peptideIndexesWithLinks = ImmutableList.ValueOf(crosslink.PeptideIndexesWithLinks);
if (peptideIndexesWithLinks.Count == 1)
{
if (crosslink.AaIndexes[peptideIndexesWithLinks[0]].Count() != 2)
{
return(false);
}
}
else if (peptideIndexesWithLinks.Count == 2)
{
if (peptideIndexesWithLinks.Any(index => crosslink.AaIndexes[index].Count() != 1))
{
return(false);
}
if (peptideIndexesWithLinks.Contains(0))
{
Assume.AreEqual(peptideIndexesWithLinks[0], 0);
queue.Add(peptideIndexesWithLinks[1]);
}
else
{
remainingCrosslinks.Add(peptideIndexesWithLinks);
}
}
else
{
return(false);
}
}
consumedPeptides.Add(0);
while (queue.Count != 0)
{
int currentPeptideIndex = queue[0];
queue.RemoveAt(0);
if (!consumedPeptides.Add(currentPeptideIndex))
{
return(false);
}
for (int iCrosslink = remainingCrosslinks.Count - 1; iCrosslink >= 0; iCrosslink--)
{
var crosslinkIndexes = remainingCrosslinks[iCrosslink];
if (!crosslinkIndexes.Contains(currentPeptideIndex))
{
continue;
}
int otherPeptideIndex = crosslinkIndexes.Except(new[] { currentPeptideIndex }).First();
queue.Add(otherPeptideIndex);
remainingCrosslinks.RemoveAt(iCrosslink);
}
}
if (consumedPeptides.Count != PeptideLibraryKeys.Count)
{
return(false);
}
return(true);
}
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckpoints, bool centroided = false)
{
docCheckpoints = new List <SrmDocument>();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
var expectedPepCount = 7;
var expectedTransGroupCount = 7;
var expectedTransCount = 49;
var doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
if (centroided && ExtensionTestContext.CanImportThermoRaw)
{
const double ppm20 = 20.0;
doc = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm20, 0)));
}
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("ah_20101011y_BSA_MS-MS_only_5-2" +
ExtensionTestContext.ExtThermoRaw);
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { new MsDataFilePath(rawPath) }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
docCheckpoints.Add(docResults);
// Refilter allowing multiple precursors per spectrum
SrmDocument docMulti = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(
fs => fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, new IsolationScheme("Test", 2))));
AssertEx.Serializable(docMulti, AssertEx.DocumentCloned);
// Release data cache file
Assume.IsTrue(docContainer.SetDocument(docMulti, docResults));
// And remove it
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 6, 6, 38));
// Import full scan Orbi-Velos data
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_long_acc_template.sky");
expectedPepCount = 3;
expectedTransGroupCount = 3;
expectedTransCount = 21;
doc = InitFullScanDocument(ref docPath, 1, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
docCheckpoints.Add(doc);
Assume.AreEqual(FullScanMassAnalyzerType.orbitrap, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
// Make sure saving this type of document works
AssertEx.Serializable(doc, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(doc, docContainer.Document));
rawPath = testFilesDir.GetTestPath("ah_20101029r_BSA_CID_FT_centroid_3uscan_3" +
ExtensionTestContext.ExtThermoRaw);
measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Accurate", new[] { rawPath }) });
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21));
// Import LTQ data with MS1 and MS/MS
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_test4.sky");
expectedPepCount = 3;
expectedTransGroupCount = 4;
expectedTransCount = 32;
doc = InitFullScanDocument(ref docPath, 3, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
docCheckpoints.Add(doc);
var docBoth = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.Targeted, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, TransitionFullScan.DEFAULT_RES_QIT, null)));
docCheckpoints.Add(docBoth);
AssertEx.Serializable(docBoth, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docBoth, docContainer.Document));
string dataPath = testFilesDir.GetTestPath("klc_20100329v_Protea_Peptide_Curve_200fmol_uL_tech1.mzML");
var listResults = new List <ChromatogramSet>
{
new ChromatogramSet("MS1 and MS/MS", new[] { dataPath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount, expectedTransGroupCount, expectedTransCount - 6));
// The mzML was filtered for the m/z range 410 to 910.
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assume.IsTrue(nodeTran.HasResults);
Assume.IsNotNull(nodeTran.Results[0]);
if (410 > nodeTran.Mz || nodeTran.Mz > 910)
{
Assume.IsTrue(nodeTran.Results[0][0].IsForcedIntegration);
}
else
{
Assume.IsFalse(nodeTran.Results[0][0].IsForcedIntegration);
}
}
// Import LTQ data with MS1 and MS/MS using multiple files for a single replicate
listResults.Add(new ChromatogramSet("Multi-file", new[]
{
testFilesDir.GetTestPath("both_DRV.mzML"),
testFilesDir.GetTestPath("both_KVP.mzML"),
}));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount - 1, expectedTransGroupCount - 1, expectedTransCount - 6));
if (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
return; // Can't work with isotope distributions when we don't have ion formulas
}
int indexResults = listResults.Count - 1;
var matchIdentifierDRV = "DRV";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
matchIdentifierDRV = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierDRV;
}
int index = 0;
foreach (var nodeTran in docContainer.Document.MoleculeTransitions)
{
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(listResults.Count, nodeTran.Results.Count);
var peptide = nodeTran.Transition.Group.Peptide;
if (peptide.IsCustomMolecule && index == 24)
{
// Conversion to small molecule loses some of the nuance of "Sequence" vs "FastaSequence", comparisons are inexact
Assume.AreEqual("pep_DRVY[+80.0]IHPF", nodeTran.PrimaryCustomIonEquivalenceKey);
break;
}
// DRV without FASTA sequence should not have data for non-precursor transitions
if (!peptide.TextId.StartsWith(matchIdentifierDRV) ||
(!peptide.IsCustomMolecule && !peptide.Begin.HasValue))
{
Assume.IsNotNull(nodeTran.Results[indexResults]);
Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
}
else if (nodeTran.Transition.IonType != IonType.precursor)
{
Assert.IsTrue(nodeTran.Results[indexResults].IsEmpty);
}
else
{
// Random, bogus peaks chosen in both files
Assume.IsNotNull(nodeTran.Results[indexResults]);
Assume.AreEqual(2, nodeTran.Results[indexResults].Count);
Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
Assume.IsFalse(nodeTran.Results[indexResults][1].IsEmpty);
}
index++;
}
// Verify handling of bad request for vendor centroided data - out-of-range PPM
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docBad = doc;
AssertEx.ThrowsException <InvalidDataException>(() =>
docBad.ChangeSettings(docBad.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, 50 * 1000, 400))),
string.Format(Resources.TransitionFullScan_ValidateRes_Mass_accuracy_must_be_between__0__and__1__for_centroided_data_,
TransitionFullScan.MIN_CENTROID_PPM, TransitionFullScan.MAX_CENTROID_PPM));
// Verify relationship between PPM and resolving power
const double ppm = 20.0; // Should yield same filter width as resolving power 50,000 in TOF
var docNoCentroid = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm, 0)));
AssertEx.Serializable(docNoCentroid, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docNoCentroid, docContainer.Document));
const double mzTest = 400.0;
var filterWidth = docNoCentroid.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assume.AreEqual(mzTest * 2.0 * ppm * 1E-6, filterWidth);
// Verify relationship between normal and high-selectivity extraction
var docTofNormal = docNoCentroid.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
AssertEx.Serializable(docTofNormal, AssertEx.DocumentCloned);
var docTofSelective = docTofNormal.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 25 * 1000, null)
.ChangeUseSelectiveExtraction(true)));
AssertEx.Serializable(docTofSelective, AssertEx.DocumentCloned);
var filterWidthTof = docTofNormal.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
var filterWidthSelective = docTofSelective.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assume.AreEqual(filterWidth, filterWidthTof);
Assume.AreEqual(filterWidth, filterWidthSelective);
// Verify handling of bad request for vendor centroided data - ask for centroiding in mzML
const string fileName = "S_2_LVN.mzML";
var filePath = testFilesDir.GetTestPath(fileName);
AssertEx.ThrowsException <AssertFailedException>(() =>
{
listResults = new List <ChromatogramSet> {
new ChromatogramSet("rep1", new[] { new MsDataFilePath(filePath) }),
};
docContainer.ChangeMeasuredResults(new MeasuredResults(listResults.ToArray()), 1, 1, 1);
},
string.Format(Resources.NoCentroidedDataException_NoCentroidedDataException_No_centroided_data_available_for_file___0_____Adjust_your_Full_Scan_settings_, filePath));
// Import FT data with only MS1
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
Assume.AreEqual(filterWidth, docMs1.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest));
docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 50 * 1000, mzTest)));
AssertEx.Serializable(docMs1, AssertEx.DocumentCloned);
Assume.IsTrue(docContainer.SetDocument(docMs1, docContainer.Document));
const string rep1 = "rep1";
listResults = new List <ChromatogramSet>
{
new ChromatogramSet(rep1, new[] { filePath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
var matchIdentifierLVN = "LVN";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
matchIdentifierLVN = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierLVN;
}
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(1, nodeTran.Results.Count);
if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN))
{
Assume.IsFalse(nodeTran.Results[0][0].IsEmpty);
}
else
{
Assume.IsTrue(nodeTran.Results[0][0].IsEmpty);
}
}
}
const string rep2 = "rep2";
listResults.Add(new ChromatogramSet(rep2, new[] { testFilesDir.GetTestPath("S_2_NVN.mzML") }));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assume.IsTrue(nodeTran.HasResults);
Assume.AreEqual(2, nodeTran.Results.Count);
if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN))
{
Assume.IsTrue(nodeTran.Results[1][0].IsEmpty);
}
else
{
Assume.IsFalse(nodeTran.Results[1][0].IsEmpty);
}
}
}
// Chromatograms should be present in the cache for a number of isotopes.
var docMs1Isotopes = docContainer.Document.ChangeSettings(doc.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count,
3, IsotopeEnrichmentsList.DEFAULT))
.ChangeTransitionFilter(filter => filter.ChangePeptideIonTypes(new[] { IonType.precursor })
.ChangeSmallMoleculeIonTypes(new[] { IonType.precursor })));
docCheckpoints.Add(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 2); // Need to reset auto-manage for transitions
var refineAutoSelect = new RefinementSettings {
AutoPickChildrenAll = PickLevel.transitions
};
docMs1Isotopes = refineAutoSelect.Refine(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 6);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep1, 1, 1, 0, 3, 0);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep2, 1, 1, 0, 3, 0);
docCheckpoints.Add(docMs1Isotopes);
// Add M-1 transitions, and verify that they have chromatogram data also, but
// empty peaks in all cases
var docMs1All = docMs1Isotopes.ChangeSettings(docMs1Isotopes.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent,
0, IsotopeEnrichmentsList.DEFAULT))
.ChangeTransitionIntegration(i => i.ChangeIntegrateAll(false))); // For compatibility with v2.5 and earlier
docCheckpoints.Add(docMs1All);
AssertEx.IsDocumentState(docMs1All, null, 2, 2, 10);
AssertResult.IsDocumentResultsState(docMs1All, rep1, 1, 1, 0, 4, 0);
AssertResult.IsDocumentResultsState(docMs1All, rep2, 1, 1, 0, 4, 0);
var ms1AllTranstions = docMs1All.MoleculeTransitions.ToArray();
var tranM1 = ms1AllTranstions[0];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsForcedIntegration);
tranM1 = ms1AllTranstions[5];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty);
Assert.IsTrue(tranM1.Results[0][0].IsForcedIntegration && tranM1.Results[1][0].IsEmpty);
}
}
public void DoFullScanSettingsTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckPoints)
{
docCheckPoints = new List <SrmDocument>();
var doc0 = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType());
var refine = new RefinementSettings();
var docSM = refine.ConvertToSmallMolecules(doc0, ".", asSmallMolecules);
docCheckPoints.Add(docSM);
Assert.IsFalse(docSM.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist != null));
AssertEx.Serializable(docSM, AssertEx.Cloned);
double c13Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C13) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C);
double n15Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N15) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N);
// Verify isotope distributions calculated when MS1 filtering enabled
var enrichments = IsotopeEnrichmentsList.DEFAULT;
var docIsotopes = docSM.ChangeSettings(docSM.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 3, enrichments)));
docCheckPoints.Add(docIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.tof,
docIsotopes.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
Assert.IsFalse(docIsotopes.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docIsotopes.MoleculeTransitionGroups)
{
Assert.AreEqual(3, nodeGroup.Children.Count);
var isotopePeaks = nodeGroup.IsotopeDist;
Assert.IsNotNull(isotopePeaks);
Assert.IsTrue(nodeGroup.HasIsotopeDist);
// The peaks should always includ at least M-1
Assume.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Within 2.5% of 100% of the entire isotope distribution
Assert.AreEqual(1.0, isotopePeaks.ExpectedProportions.Sum(), 0.025);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip accuracy anyway)
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.IsotopeDist.GetMZI(0), SequenceMassCalc.MassTolerance);
Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.TransitionGroup.IsCustomIon ?
BioMassCalc.CalculateIonMz(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorAdduct.Unlabeled) :
SequenceMassCalc.GetMZ(nodeGroup.IsotopeDist.GetMassI(0),
nodeGroup.TransitionGroup.PrecursorAdduct), SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
// All positive should be close to 13C - C, and 0 should be the same as the next delta
double expectedDelta = (massIndex > 0 ? c13Delta : GetMassDelta(isotopePeaks, massIndex + 1));
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (nodeGroup.TransitionGroup.LabelType.Name.Contains("15N"))
{
// All positive should be close to 13C, and all negative 15N
double expectedDelta = (massIndex > 0 ? c13Delta : n15Delta);
Assert.AreEqual(expectedDelta, massDelta, 0.0015);
}
else if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else
{
Assert.AreEqual(c13Delta, massDelta, 0.001);
}
}
}
AssertEx.Serializable(docIsotopes, AssertEx.Cloned);
// Narrow the resolution, and verify that predicted proportion of the isotope
// distribution captured is reduced for all precursors
var docIsotopesFt = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 500 * 1000, 400)));
docCheckPoints.Add(docIsotopesFt);
var tranGroupsOld = docIsotopes.MoleculeTransitionGroups.ToArray();
var tranGroupsNew = docIsotopesFt.MoleculeTransitionGroups.ToArray();
Assume.AreEqual(tranGroupsOld.Length, tranGroupsNew.Length);
for (int i = 0; i < tranGroupsOld.Length; i++)
{
Assert.AreNotSame(tranGroupsOld[i], tranGroupsNew[i]);
Assert.AreNotSame(tranGroupsOld[i].IsotopeDist, tranGroupsNew[i].IsotopeDist);
Assert.IsTrue(tranGroupsOld[i].IsotopeDist.ExpectedProportions.Sum() >
tranGroupsNew[i].IsotopeDist.ExpectedProportions.Sum());
}
// Use Min % of base peak and verify variation in transitions used
const float minPercent1 = 10;
var docIsotopesP1 = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent1, enrichments)));
docCheckPoints.Add(docIsotopesP1);
tranGroupsNew = docIsotopesP1.MoleculeTransitionGroups.ToArray();
int maxTran = 0;
for (int i = 0; i < tranGroupsOld.Length; i++)
{
// Isotope distributions should not have changed
var isotopePeaks = tranGroupsNew[i].IsotopeDist;
Assert.AreSame(tranGroupsOld[i].IsotopeDist, isotopePeaks);
// Expected transitions should be present
maxTran = Math.Max(maxTran, tranGroupsNew[i].Children.Count);
foreach (TransitionDocNode nodeTran in tranGroupsNew[i].Children)
{
int massIndex = nodeTran.Transition.MassIndex;
Assume.IsTrue(minPercent1 <= isotopePeaks.GetProportionI(massIndex) * 100.0 / isotopePeaks.BaseMassPercent);
}
}
Assume.AreEqual(5, maxTran);
AssertEx.Serializable(docIsotopesP1, AssertEx.Cloned); // Express any failure in terms of XML diffs
// Use 10%, and check that 15N modifications all have M-1
const float minPercent2 = 5;
var docIsotopesP2 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichments)));
docCheckPoints.Add(docIsotopesP2);
foreach (var nodeGroup in docIsotopesP2.MoleculeTransitionGroups)
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.Name.EndsWith("15N"))
{
Assume.AreEqual(-1, firstChild.Transition.MassIndex);
}
else
{
Assume.AreNotEqual(-1, firstChild.Transition.MassIndex);
}
}
AssertEx.Serializable(docIsotopesP2, AssertEx.Cloned);
// Use lower enrichment of 13C, and verify that this add M-1 for 13C labeled precursors
var enrichmentsLow13C = enrichments.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.C13, 0.9));
var docIsotopesLow13C = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichmentsLow13C)));
tranGroupsNew = docIsotopesLow13C.MoleculeTransitionGroups.ToArray();
for (int i = 0; i < tranGroupsOld.Length; i++)
{
var nodeGroup = tranGroupsNew[i];
if (!Equals(nodeGroup.TransitionGroup.LabelType.Name, "heavy"))
{
Assert.AreSame(tranGroupsOld[i].IsotopeDist, nodeGroup.IsotopeDist);
}
else
{
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
Assert.IsTrue(firstChild.Transition.MassIndex < 0);
}
}
AssertEx.Serializable(docIsotopesLow13C, AssertEx.Cloned); // Express any failure as XML diffs
// Use 0%, and check that everything has M-1 and lower
var enrichmentsLow = enrichmentsLow13C.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.N15, 0.97));
var docIsotopesLowP0 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, 0, enrichmentsLow)));
docCheckPoints.Add(docIsotopesLowP0);
foreach (var nodeGroup in docIsotopesLowP0.MoleculeTransitionGroups)
{
Assume.AreEqual(nodeGroup.IsotopeDist.CountPeaks, nodeGroup.Children.Count);
var firstChild = (TransitionDocNode)nodeGroup.Children[0];
if (nodeGroup.TransitionGroup.LabelType.IsLight)
{
Assert.AreEqual(-1, firstChild.Transition.MassIndex);
}
else
{
Assert.IsTrue(-1 > firstChild.Transition.MassIndex);
}
}
AssertEx.Serializable(docIsotopesLowP0, AssertEx.Cloned);
// Test a document with variable and heavy modifications, which caused problems for
// the original implementation
var docVariable = ResultsUtil.DeserializeDocument("HeavyVariable.sky", GetType());
Assert.IsFalse(docVariable.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null));
foreach (var nodeGroup in docVariable.MoleculeTransitionGroups)
{
var isotopePeaks = nodeGroup.IsotopeDist;
Assert.IsNotNull(isotopePeaks);
// The peaks should always includ at least M-1
Assert.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0);
// Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip tolerance anyway)
var mzI = nodeGroup.IsotopeDist.GetMZI(0);
Assert.AreEqual(nodeGroup.PrecursorMz, mzI, SequenceMassCalc.MassTolerance);
// Check isotope distribution masses
for (int i = 1; i < isotopePeaks.CountPeaks; i++)
{
int massIndex = isotopePeaks.PeakIndexToMassIndex(i);
Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex));
double massDelta = GetMassDelta(isotopePeaks, massIndex);
bool containsSulfur = nodeGroup.TransitionGroup.Peptide.IsCustomMolecule
? (nodeGroup.CustomMolecule.Formula.IndexOfAny("S".ToCharArray()) != -1)
: (nodeGroup.TransitionGroup.Peptide.Sequence.IndexOfAny("CM".ToCharArray()) != -1);
if (massIndex == 0)
{
double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0
? GetMassDelta(isotopePeaks, massIndex + 1)
: 1.0017);
Assert.AreEqual(expectedDelta, massDelta, 0.001);
}
else if (!containsSulfur || massIndex == 1)
{
Assert.AreEqual(c13Delta, massDelta, 0.001);
}
else
{
Assert.AreEqual(1.00075, massDelta, 0.001);
}
}
}
docCheckPoints.Add(docVariable);
}
protected override void DoTest()
{
// Load a document with results loaded without drift filter
string skyFile = TestFilesDir.GetTestPath("tims_test.sky");
Program.ExtraRawFileSearchFolder = TestFilesDir.PersistentFilesDir; // So we don't have to reload the raw files, which have moved relative to skyd file
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentLoaded(240000); // If it decides to remake chromatograms this can take awhile
AssertEx.IsDocumentState(document, null, 1, 34, 89, 1007);
RunUI(() =>
{
SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("local.sky")); // Avoid "document changed since last edit" message
document = SkylineWindow.DocumentUI;
});
var transitions = document.MoleculeTransitions.ToArray();
// Verify ability to extract predictions from raw data
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(
() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction));
// Simulate user picking Add from the ion mobility Predictor combo control
var driftTimePredictorDlg = ShowDialog <EditDriftTimePredictorDlg>(peptideSettingsDlg.AddDriftTimePredictor);
RunUI(() =>
{
driftTimePredictorDlg.SetOffsetHighEnergySpectraCheckbox(true);
driftTimePredictorDlg.SetPredictorName("test_tims");
driftTimePredictorDlg.SetResolvingPower(40);
driftTimePredictorDlg.GetDriftTimesFromResults();
driftTimePredictorDlg.OkDialog(true); // Force overwrite if a named predictor already exists
});
WaitForClosedForm(driftTimePredictorDlg);
RunUI(() =>
{
peptideSettingsDlg.OkDialog();
});
WaitForClosedForm(peptideSettingsDlg);
var docChangedDriftTimePredictor = WaitForDocumentChange(document);
// Reimport data - should shift precursors
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
var chromatograms = docChangedDriftTimePredictor.Settings.MeasuredResults.Chromatograms;
dlg.SelectedChromatograms = new[] { chromatograms[0] };
dlg.ReimportResults();
dlg.OkDialog();
});
document = WaitForDocumentChangeLoaded(docChangedDriftTimePredictor);
var transitionsNew = document.MoleculeTransitions.ToArray();
var nChanges = 0;
var nNonEmpty = 0;
for (var i = 0; i < transitions.Length; i++)
{
Assume.AreEqual(transitions[i].Mz, transitionsNew[i].Mz);
if (transitions[i].AveragePeakArea.HasValue)
{
nNonEmpty++;
if (transitions[i].AveragePeakArea != transitionsNew[i].AveragePeakArea) // Using filter should alter peak area
{
nChanges++;
}
}
else
{
Assume.AreEqual(transitions[i].AveragePeakArea, transitionsNew[i].AveragePeakArea);
}
}
Assume.IsTrue(nChanges >= nNonEmpty * .9); // We expect nearly all peaks to change in area with IMS filter in use
// And read some mz5 converted from Bruker, then compare replicates - should be identical
var mz5 = TestFilesDir.GetTestPath(bsaFmolTimsInfusionesiPrecMz5Mz5);
ImportResultsFile(mz5);
document = WaitForDocumentChange(document);
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
Assume.AreEqual(2, nodeGroup.Results.Count);
foreach (TransitionDocNode nodeTran in nodeGroup.Children)
{
Assume.AreEqual(2, nodeTran.Results.Count);
Assume.AreEqual(nodeTran.Results[0], nodeTran.Results[1]);
}
}
}
private void WatersImsMseChromatogramTest(DriftFilterType mode,
IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType driftPeakWidthCalcType,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
TestSmallMolecules = false; // Don't need that extra magic node
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, driftPeakWidthCalcType, withDriftTimeFilter, withDriftTimePredictor, out docPath);
AssertEx.IsDocumentState(document, null, 1, 1, 1, 8); // Drift time lib load bumps the doc version, so does small mol conversion
var listChromatograms = new List <ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
string mz5Path = "waters-mobility" + ExtensionTestContext.ExtMz5;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
testModeStr = "with drift times from spectral library";
}
listChromatograms.Add(AssertResult.FindChromatogramSet(document, new MsDataFilePath(mz5Path)) ??
new ChromatogramSet(Path.GetFileName(mz5Path).Replace('.', '_'), new[] { mz5Path }));
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
var doc = docContainer.Document;
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assume.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
}
document = ConvertToSmallMolecules(document, ref docPath, new[] { mz5Path }, asSmallMolecules);
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assume.AreEqual(1, document.MoleculePrecursorPairs.Count());
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assume.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assume.AreEqual(1, chromGroupInfo.Length, testModeStr);
var chromGroup = chromGroupInfo[0];
int expectedPeaks;
if (withDriftTimeFilter)
{
expectedPeaks = 3;
}
else if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
expectedPeaks = 5;
}
else
{
expectedPeaks = 6; // No libraries
}
Assume.AreEqual(expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assume.AreEqual(withDriftTimeFilter ? 5226 : 20075, maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => !nodePep.Results[0].IsEmpty))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assume.AreEqual(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assume.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assume.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath =
testFilesDir.GetTestPath(complete == 1 ? "share_complete.zip" : "share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath,
new ShareType(complete == 1, SkylineVersion.CURRENT)); // Explicitly declaring version number forces a save before zip
share.Share(new SilentProgressMonitor());
var files = share.ListEntries().ToArray();
var imdbFile = withDriftTimePredictor ? "scaled.imdb" : "waters-mobility.filtered-scaled.blib";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var ext = "." + imdbFile.Split('.').Last();
imdbFile = imdbFile.Replace(ext, BiblioSpecLiteSpec.DotConvertedToSmallMolecules + ext);
}
Assume.IsTrue(files.Contains(imdbFile));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
share.Extract(new SilentProgressMonitor());
using (var cmdline = new CommandLine())
{
Assume.IsTrue(cmdline.OpenSkyFile(share.DocumentPath)); // Handles any path shifts in database files, like our .imdb file
var document2 = cmdline.Document;
Assume.IsNotNull(document2);
Assume.IsTrue(docContainer.SetDocument(document2, docContainer.Document, true));
docContainer.AssertComplete();
document2 = docContainer.Document;
var im = document2.Settings.GetIonMobilities(new MsDataFilePath(mz5Path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document2.Settings.GetIonMobility(
pep, nodeGroup, null, im, null, driftTimeMax, out windowDT);
Assume.AreEqual(3.86124, centerDriftTime.IonMobility.Mobility.Value, .0001, testModeStr);
Assume.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
}
}
protected override void DoTest()
{
var startPage = _showStartPage ? WaitForOpenForm <StartPage>() : null;
var modeDlg = WaitForOpenForm <NoModeUIDlg>(); // Expect a dialog asking user to select a default UI mode
RunUI(() =>
{
modeDlg.SelectModeUI(SrmDocument.DOCUMENT_TYPE.small_molecules);
modeDlg.ClickOk();
});
WaitForClosedForm(modeDlg);
if (_showStartPage)
{
// ReSharper disable PossibleNullReferenceException
Assert.AreEqual(SrmDocument.DOCUMENT_TYPE.small_molecules, startPage.GetModeUIHelper().GetUIToolBarButtonState());
// Verify that start page UI is updated
Assert.IsFalse(startPage.GetVisibleBoxPanels().Where(c => c is ActionBoxControl).Any(c => ((ActionBoxControl)c).IsProteomicOnly));
RunUI(() => startPage.DoAction(skylineWindow => true)); // Start a new file
// ReSharper restore PossibleNullReferenceException
WaitForOpenForm <SkylineWindow>();
}
// Verify that Skyline UI isn't showing anything proteomic
Assert.AreEqual(SrmDocument.DOCUMENT_TYPE.small_molecules, SkylineWindow.GetModeUIHelper().GetUIToolBarButtonState());
Assert.IsFalse(SkylineWindow.HasProteomicMenuItems);
RunUI(() =>
{
SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("blank.sky"));
});
// Verify handling of start page invoked from Skyline menu with a populated document
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("Proteomic.sky")));
Assert.IsTrue(SkylineWindow.HasProteomicMenuItems);
startPage = ShowDialog <StartPage>(SkylineWindow.OpenStartPage);
RunDlg <AlertDlg>(() => startPage.SetUIMode(SrmDocument.DOCUMENT_TYPE.small_molecules), alertDlg => alertDlg.ClickYes());
Assert.IsTrue(SkylineWindow.Document.MoleculeCount == 0); // Document should be empty
RunUI(() => startPage.DoAction(skylineWindow => true)); // Close the start window
Assert.IsFalse(SkylineWindow.HasProteomicMenuItems);
if (!_showStartPage)
{
return; // No need to do the rest of this this twice
}
foreach (SrmDocument.DOCUMENT_TYPE uimode in Enum.GetValues(typeof(SrmDocument.DOCUMENT_TYPE)))
{
if (uimode == SrmDocument.DOCUMENT_TYPE.none)
{
continue;
}
// Loading a purely proteomic doc should change UI mode to straight up proteomic
TestUIModesFileLoadAction(uimode, // Initial UI mode
"Proteomic.sky", // Doc to be loaded
SrmDocument.DOCUMENT_TYPE.proteomic); // Resulting UI mode
// Loading a purely small mol doc should change UI mode to straight up small mol
TestUIModesFileLoadAction(uimode, // Initial UI mode
"SmallMol.sky", // Doc to be loaded
SrmDocument.DOCUMENT_TYPE.small_molecules); // Resulting UI mode
// Loading a mixed doc should change UI mode to mixed
TestUIModesFileLoadAction(uimode, // Initial UI mode
"Mixed.sky", // Doc to be loaded
SrmDocument.DOCUMENT_TYPE.mixed); // Resulting UI mode
// Loading an empty doc shouldn't have any effect on UI mode
TestUIModesFileLoadAction(uimode, // Initial UI mode
"blank.sky", // Doc to be loaded
uimode); // Resulting UI mode
// Test behavior in an empty document
RunUI(() =>
{
SkylineWindow.NewDocument();
SkylineWindow.SetUIMode(uimode);
Assert.AreEqual(uimode, SkylineWindow.ModeUI);
});
// Test per-ui-mode persistence of "peptide" settings tab choice
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => Assume.AreEqual(peptideSettingsDlg.SelectedTab, (PeptideSettingsUI.TABS)uimode));
OkDialog(peptideSettingsDlg, peptideSettingsDlg.CancelDialog);
}
TestPeptideToMoleculeText(); // Exercise the UI peptide->molecule translation code
// Test interaction of buttons in non-empty documents
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.small_molecules, SrmDocument.DOCUMENT_TYPE.small_molecules, false);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.small_molecules, SrmDocument.DOCUMENT_TYPE.proteomic, true);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.small_molecules, SrmDocument.DOCUMENT_TYPE.mixed, false);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.proteomic, SrmDocument.DOCUMENT_TYPE.proteomic, false);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.proteomic, SrmDocument.DOCUMENT_TYPE.small_molecules, true);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.proteomic, SrmDocument.DOCUMENT_TYPE.mixed, false);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.mixed, SrmDocument.DOCUMENT_TYPE.mixed, false);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.mixed, SrmDocument.DOCUMENT_TYPE.small_molecules, true);
TestUIModesClickAction(SrmDocument.DOCUMENT_TYPE.mixed, SrmDocument.DOCUMENT_TYPE.proteomic, true);
// Verify operation of small-mol-only UI elements
foreach (SrmDocument.DOCUMENT_TYPE uimode2 in Enum.GetValues(typeof(SrmDocument.DOCUMENT_TYPE)))
{
if (uimode2 == SrmDocument.DOCUMENT_TYPE.none)
{
continue;
}
RunUI(() =>
{
SkylineWindow.NewDocument();
SkylineWindow.SetUIMode(uimode2);
});
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
Assert.AreEqual(uimode2 == SrmDocument.DOCUMENT_TYPE.small_molecules, peptideSettingsUI.SmallMoleculeLabelsTabEnabled);
if (uimode2 == SrmDocument.DOCUMENT_TYPE.small_molecules)
{
// Verify operation of internal standard list edit
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Labels;
});
}
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
}
public void TestAuditLogSerialization()
{
var datetime = AuditLogEntry.ParseSerializedTimeStamp("2019-01-01T05:02:03+04", out var tzoffset); // Accept ISO format, which may omit minutes in offset
Assume.AreEqual(DateTimeKind.Utc, datetime.Kind);
Assume.AreEqual(1, datetime.Hour); // Local time was 5AM, 4 hour offset to GMT.
Assume.AreEqual(new TimeSpan(4, 0, 0), tzoffset);
var xsd = AuditLogEntry.FormatSerializationString(datetime, tzoffset);
Assume.AreEqual("2019-01-01T05:02:03+04:00", xsd);
var zulu = AuditLogEntry.ParseSerializedTimeStamp("2019-01-01T01:02:03Z", out tzoffset);
Assume.AreEqual(tzoffset, TimeSpan.Zero);
Assume.AreEqual(datetime, zulu);
AuditLogEntry.ParseSerializedTimeStamp("2019-01-01T01:02:03-04:30", out tzoffset);
Assume.AreEqual(new TimeSpan(-4, -30, 0), tzoffset);
datetime = AuditLogEntry.ParseSerializedTimeStamp("2018-12-31T23:02:03-04", out tzoffset);
Assume.AreEqual(datetime, AuditLogEntry.ParseSerializedTimeStamp("2019-01-01T03:02:03Z", out tzoffset));
// Test backward compatibility - this file with 4.2 log should load without any problems
Assume.IsTrue(AuditLogList.ReadFromXmlTextReader(new XmlTextReader(new StringReader(Test42FormatSkyl)), out var loggedSkylineDocumentHash, out var old));
Assume.AreEqual("tgnQ8fDiKLMIS236kpdJIXNR+fw=", old.RootHash.ActualHash.HashString);
Assume.AreEqual("AjigWTmQeAO94/jAlwubVMp4FRg=", loggedSkylineDocumentHash); // Note that this is a base64 representation of the 4.2 hex representation "<document_hash>0238A05939907803BDE3F8C0970B9B54CA781518</document_hash>
var then = DateTime.Parse("2019-03-08 00:02:03Z", CultureInfo.InvariantCulture, DateTimeStyles.AssumeUniversal).ToUniversalTime(); // Just before DST
const int entryCount = 20000; // Enough to ensure stack overflow in case of some design error per Nick
var timestep = new TimeSpan(1, 0, 1); // 20000 hours should be sufficient to take us into and out of daylight savings twice
AuditLogEntry headEntry = null;
for (var index = 0; index++ < entryCount;)
{
var documentType = (SrmDocument.DOCUMENT_TYPE)(index % ((int)SrmDocument.DOCUMENT_TYPE.none + 1));
var entry = AuditLogEntry.CreateTestOnlyEntry(then, documentType, string.Empty);
then += timestep;
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 currentCulture = Thread.CurrentThread.CurrentCulture;
Thread.CurrentThread.CurrentCulture = CultureInfo.InvariantCulture; // Logs are meant to be culture invariant
var roundTrip = (AuditLogList)serializer.Deserialize(new StringReader(serializedAuditLog.ToString()));
Assert.IsNotNull(roundTrip);
Assert.AreEqual(auditLogList.AuditLogEntries.Count, roundTrip.AuditLogEntries.Count);
var entries = auditLogList.AuditLogEntries.Enumerate().ToArray();
var roundtripEntries = roundTrip.AuditLogEntries.Enumerate().ToArray();
for (var i = 0; i < auditLogList.AuditLogEntries.Count; i++)
{
Assert.AreEqual(entries[i].TimeStampUTC, roundtripEntries[i].TimeStampUTC);
Assert.AreEqual(entries[i].TimeZoneOffset, roundtripEntries[i].TimeZoneOffset);
Assert.AreEqual(entries[i].SkylineVersion, roundtripEntries[i].SkylineVersion);
Assert.AreEqual(entries[i].User, roundtripEntries[i].User);
Assert.AreEqual(entries[i].DocumentType == SrmDocument.DOCUMENT_TYPE.proteomic ? SrmDocument.DOCUMENT_TYPE.none : entries[i].DocumentType, roundtripEntries[i].DocumentType);
Assert.AreEqual(entries[i].Hash.ActualHash, roundtripEntries[i].Hash.ActualHash);
// No Skyl hash until sserialized, so can't compare here
}
Thread.CurrentThread.CurrentCulture = currentCulture;
// Make sure current system timezone isn't messing with us
Assert.AreEqual(14, roundtripEntries[100].TimeStampUTC.Day);
Assert.AreEqual(8, roundtripEntries[100].TimeStampUTC.Hour);
Assert.AreEqual(27, roundtripEntries[10000].TimeStampUTC.Day);
Assert.AreEqual(17, roundtripEntries[10000].TimeStampUTC.Hour);
}
private void CheckDocumentGridAndColumns(string docName,
string viewName,
int rowCount, int colCount, // Expected row and column count for document grid
SrmDocument.DOCUMENT_TYPE expectedDocumentType,
string expectedProductIonFormula = null,
string expectedFragmentIon = null,
string expectedMolecularFormula = null,
string expectedPrecursorNeutralFormula = null,
string expectedPrecursorIonFormula = null)
{
var oldDoc = SkylineWindow.Document;
OpenDocument(docName);
WaitForDocumentChangeLoaded(oldDoc);
Assume.AreEqual(expectedDocumentType, SkylineWindow.Document.DocumentType);
WaitForClosedForm <DocumentGridForm>();
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(viewName));
WaitForCondition(() => (documentGrid.RowCount == rowCount)); // Let it initialize
int iteration = 0;
WaitForCondition(() =>
{
bool result = documentGrid.ColumnCount == colCount;
if (!result && iteration++ > 9)
{
Assert.AreNotEqual(colCount, documentGrid.ColumnCount); // Put breakpoint on this line, if you have changed columns and need to update the numbers
}
return(result);
}); // Let it initialize
var colProductIonFormula = documentGrid.FindColumn(PropertyPath.Parse("ProductIonFormula"));
var colProductNeutralFormula = documentGrid.FindColumn(PropertyPath.Parse("ProductNeutralFormula"));
var colProductAdduct = documentGrid.FindColumn(PropertyPath.Parse("ProductAdduct"));
var colFragmentIon = documentGrid.FindColumn(PropertyPath.Parse("FragmentIonType"));
var colMoleculeFormula = documentGrid.FindColumn(PropertyPath.Parse("Precursor.Peptide.MoleculeFormula"));
var colPrecursorNeutralFormula = documentGrid.FindColumn(PropertyPath.Parse("Precursor.NeutralFormula"));
var colPrecursorIonFormula = documentGrid.FindColumn(PropertyPath.Parse("Precursor.IonFormula"));
if (expectedProductIonFormula == null)
{
Assert.IsNull(colProductIonFormula);
Assert.IsNull(colProductNeutralFormula);
Assert.IsNull(colProductAdduct);
}
else
{
RunUI(() =>
{
var formula = documentGrid.DataGridView.Rows[0].Cells[colProductIonFormula.Index].Value.ToString();
if (expectedProductIonFormula.Contains("["))
{
var formulaNeutral = documentGrid.DataGridView.Rows[0].Cells[colProductNeutralFormula.Index].Value.ToString();
var adduct = documentGrid.DataGridView.Rows[0].Cells[colProductAdduct.Index].Value.ToString();
Assert.AreEqual(expectedProductIonFormula, formulaNeutral + adduct);
}
else
{
Assert.AreEqual(expectedProductIonFormula, formula);
}
if (!string.IsNullOrEmpty(expectedMolecularFormula))
{
Assert.AreEqual(expectedMolecularFormula, documentGrid.DataGridView.Rows[0].Cells[colMoleculeFormula.Index].Value.ToString());
Assert.AreEqual(expectedPrecursorNeutralFormula, documentGrid.DataGridView.Rows[0].Cells[colPrecursorNeutralFormula.Index].Value.ToString());
Assert.AreEqual(expectedPrecursorIonFormula, documentGrid.DataGridView.Rows[0].Cells[colPrecursorIonFormula.Index].Value.ToString());
}
});
}
if (expectedFragmentIon == null)
{
Assert.IsNull(colFragmentIon);
}
else
{
RunUI(() =>
{
var frag = documentGrid.DataGridView.Rows[0].Cells[colFragmentIon.Index].Value.ToString();
Assert.AreEqual(expectedFragmentIon, frag);
});
}
RunUI(() => documentGrid.Close());
}
