private SrmDocument RemoveTransitions(SrmDocument document, params int[] indexes)
{
foreach (var i in indexes)
{
var pathToTran = document.GetPathTo((int)SrmDocument.Level.Transitions, i - 1); // Numbers are from the 1-based status bar
document = (SrmDocument)document.RemoveChild(pathToTran.Parent, document.FindNode(pathToTran));
}
return(document);
}
private void PerformTestMeasuredDriftValues(bool asSmallMolecules)
{
if (asSmallMolecules)
{
if (!RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
TestSmallMolecules = false; // No need to add the magic small molecule test node
}
var testFilesDir = new TestFilesDir(TestContext, @"Test\Results\BlibDriftTimeTest.zip"); // Re-used from BlibDriftTimeTest
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
// This was a malformed document, which caused problems after a fix to not recalculate
// document library settings on open. To avoid rewriting this test for the document
// which now contains 2 precursors, the first precursor is removed immediately.
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var pathFirstPeptide = docOriginal.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodeFirstPeptide = (DocNodeParent)docOriginal.FindNode(pathFirstPeptide);
docOriginal = (SrmDocument)docOriginal.RemoveChild(pathFirstPeptide, nodeFirstPeptide.Children[0]);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOriginal = refine.ConvertToSmallMolecules(docOriginal, testFilesDir.FullPath);
}
using (var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath))
{
var doc = docContainer.Document;
// Import an mz5 file that contains drift info
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714" + ExtensionTestContext.ExtMz5)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
document = document.ChangeSettings(document.Settings.ChangePeptidePrediction(prediction => new PeptidePrediction(null, IonMobilityPredictor.EMPTY)));
// Verify ability to extract predictions from raw data
var newPred = document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.ChangeMeasuredIonMobilityValuesFromResults(
document, docContainer.DocumentFilePath);
var result = newPred.MeasuredMobilityIons;
Assert.AreEqual(TestSmallMolecules ? 2 : 1, result.Count);
const double expectedDT = 4.0019;
var expectedOffset = .4829;
Assert.AreEqual(expectedDT, result.Values.First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result.Values.First().HighEnergyIonMobilityValueOffset, .001);
// Check ability to update, and to preserve unchanged
var revised = new Dictionary <LibKey, IonMobilityAndCCS>();
var libKey = result.Keys.First();
revised.Add(libKey, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(4, eIonMobilityUnits.drift_time_msec), null, 0.234)); // N.B. CCS handling would require actual raw data in this test, it's covered in a perf test
var libKey2 = new LibKey("DEADEELS", asSmallMolecules ? Adduct.NonProteomicProtonatedFromCharge(2) : Adduct.DOUBLY_PROTONATED);
revised.Add(libKey2, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, 0.123));
document =
document.ChangeSettings(
document.Settings.ChangePeptidePrediction(prediction => new PeptidePrediction(null, new IonMobilityPredictor("test", revised, null, null, IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType.resolving_power, 40, 0, 0))));
newPred = document.Settings.PeptideSettings.Prediction.ChangeDriftTimePredictor(
document.Settings.PeptideSettings.Prediction.IonMobilityPredictor.ChangeMeasuredIonMobilityValuesFromResults(
document, docContainer.DocumentFilePath)).IonMobilityPredictor;
result = newPred.MeasuredMobilityIons;
Assert.AreEqual(TestSmallMolecules ? 3 : 2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].HighEnergyIonMobilityValueOffset, .001);
Assert.AreEqual(5, result[libKey2].IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].HighEnergyIonMobilityValueOffset, .001);
}
}
public void LibraryMultipleTest()
{
var streamManager = new MemoryStreamManager();
var loader = new LibraryLoadTest.TestLibraryLoader {
StreamManager = streamManager
};
// Create library files
const string hunterText = LibraryLoadTest.TEXT_LIB_YEAST_NIST1 + "\n" + LibraryLoadTest.TEXT_LIB_YEAST_NIST2;
LibraryLoadTest.CreateHunterFile(streamManager, loader, hunterText);
const string biblioText = LibraryLoadTest.TEXT_LIB_YEAST_NIST2 + "\n" + LibraryLoadTest.TEXT_LIB_YEAST_NIST3;
LibraryLoadTest.CreateBiblioFile(streamManager, loader, biblioText);
const string nistText = LibraryLoadTest.TEXT_LIB_YEAST_NIST3 + "\n" + LibraryLoadTest.TEXT_LIB_YEAST_NIST4;
streamManager.TextFiles.Add(LibraryLoadTest.PATH_NIST_LIB, nistText);
var hunterSpec = new XHunterLibSpec("Yeast (X!)", LibraryLoadTest.PATH_HUNTER_LIB);
var bilbioSpec = new BiblioSpecLibSpec("Yeast (BS)", LibraryLoadTest.PATH_BIBLIOSPEC_LIB);
var nistSpec = new NistLibSpec("Yeast (NIST)", LibraryLoadTest.PATH_NIST_LIB);
// For serialization, add the library spec to the settings
TestLibraryList = new SpectralLibraryList {
hunterSpec, bilbioSpec, nistSpec
};
var libraryManager = new LibraryManager {
StreamManager = streamManager
};
var docContainer = new TestDocumentContainer();
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(new LibrarySpec[] { hunterSpec, bilbioSpec, nistSpec }));
int startRev;
SrmDocument docLoaded = CreateLibraryDocument(settings, ExampleText.TEXT_FASTA_YEAST_LIB, false,
docContainer, libraryManager, out startRev);
AssertEx.IsDocumentState(docLoaded, startRev, 2, 4, 12);
Assert.IsTrue(HasLibraryInfo(docLoaded, typeof(XHunterSpectrumHeaderInfo)));
Assert.IsTrue(HasLibraryInfo(docLoaded, typeof(BiblioSpecSpectrumHeaderInfo)));
Assert.IsTrue(HasLibraryInfo(docLoaded, typeof(NistSpectrumHeaderInfo)));
// Remove the rank 1 transition from each transition group
TransitionDocNode[] transitionNodes = docLoaded.PeptideTransitions.ToArray();
for (int i = 0; i < transitionNodes.Length; i++)
{
var nodeTran = transitionNodes[i];
if (nodeTran.LibInfo.Rank != 1)
{
continue;
}
var path = docLoaded.GetPathTo((int)SrmDocument.Level.TransitionGroups, i / 3);
docLoaded = (SrmDocument)docLoaded.RemoveChild(path, nodeTran);
++startRev;
}
AssertEx.IsDocumentState(docLoaded, startRev, 2, 4, 8);
// Make sure this can be serialized and deserialized without causing
// a recalculation of the nodes in the tree.
AssertEx.Serializable(docLoaded, (doc1, doc2) => ValidateLibraryDocs(doc1, doc2, libraryManager));
}
private void PerformTestMeasuredDriftValues(bool asSmallMolecules)
{
if (asSmallMolecules)
{
if (!RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
}
var testFilesDir = new TestFilesDir(TestContext, @"TestData\Results\BlibDriftTimeTest.zip"); // Re-used from BlibDriftTimeTest
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
// This was a malformed document, which caused problems after a fix to not recalculate
// document library settings on open. To avoid rewriting this test for the document
// which now contains 2 precursors, the first precursor is removed immediately.
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var pathFirstPeptide = docOriginal.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodeFirstPeptide = (DocNodeParent)docOriginal.FindNode(pathFirstPeptide);
docOriginal = (SrmDocument)docOriginal.RemoveChild(pathFirstPeptide, nodeFirstPeptide.Children[0]);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOriginal = refine.ConvertToSmallMolecules(docOriginal, testFilesDir.FullPath);
}
using (var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath))
{
var doc = docContainer.Document;
// Import an mz5 file that contains drift info
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714" + ExtensionTestContext.ExtMz5)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
// Clear out any current settings
document = document.ChangeSettings(document.Settings.ChangeTransitionIonMobilityFiltering(s => TransitionIonMobilityFiltering.EMPTY));
// Verify ability to extract predictions from raw data
var libraryName0 = "test0";
var dbPath0 = testFilesDir.GetTestPath(libraryName0 + IonMobilityDb.EXT);
var newIMFiltering = document.Settings.TransitionSettings.IonMobilityFiltering.ChangeLibrary(
IonMobilityLibrary.CreateFromResults(
document, docContainer.DocumentFilePath, true,
libraryName0, dbPath0));
var result = newIMFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(1, result.Count);
var expectedDT = 4.0019;
var expectedOffset = .4829;
Assert.AreEqual(expectedDT, result.Values.First().First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result.Values.First().First().HighEnergyIonMobilityValueOffset ?? 0, .001);
// Check ability to update, and to preserve unchanged
var revised = new List <PrecursorIonMobilities>();
var libKey = result.Keys.First();
revised.Add(new PrecursorIonMobilities(libKey, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(expectedDT = 4, eIonMobilityUnits.drift_time_msec), null, expectedOffset = 0.234))); // N.B. CCS handling would require actual raw data in this test, it's covered in a perf test
var pepSequence = "DEADEELS";
var libKey2 = asSmallMolecules ?
new LibKey(SmallMoleculeLibraryAttributes.Create(pepSequence, "C12H5", null, null, null, null), Adduct.M_PLUS_2H) :
new LibKey(pepSequence, Adduct.DOUBLY_PROTONATED);
revised.Add(new PrecursorIonMobilities(libKey2, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, 0.123)));
var libraryName = "test";
var dbPath = testFilesDir.GetTestPath(libraryName + IonMobilityDb.EXT);
var imsdb = IonMobilityDb.CreateIonMobilityDb(dbPath, libraryName, false, revised);
var newLibIM = new IonMobilityLibrary(libraryName, dbPath, imsdb);
var ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power, 40, 0, 0, 0);
var calculator = ionMobilityWindowWidthCalculator;
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(calculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width, 40, 0, 0, 100);
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(ionMobilityWindowWidthCalculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
}
}
public void RunTestFindNode(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
TestDirectoryName = asSmallMolecules.ToString();
}
TestSmallMolecules = false; // Don't need the magic test node, we have an explicit test
SrmDocument doc = CreateStudy7Doc();
doc = (new RefinementSettings()).ConvertToSmallMolecules(doc, asSmallMolecules);
var displaySettings = new DisplaySettings(null, false, 0, 0); //, ProteinDisplayMode.ByName);
// Find every other transition, searching down.
List <TransitionDocNode> listTransitions = doc.MoleculeTransitions.ToList();
var pathFound = doc.GetPathTo(0, 0);
int i;
for (i = 0; i < doc.MoleculeTransitionCount; i += 2)
{
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[i].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, i), pathFound);
}
// Test wrapping in search down.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[0].Mz), displaySettings, false, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, 0), pathFound);
// Find every other peptide searching up while for each finding one of its children searching down.
pathFound = doc.LastNodePath;
List <PeptideDocNode> listPeptides = new List <PeptideDocNode>();
listPeptides.AddRange(doc.Molecules);
List <TransitionGroupDocNode> listTransitionGroups = new List <TransitionGroupDocNode>();
listTransitionGroups.AddRange(doc.MoleculeTransitionGroups);
for (int x = doc.MoleculeCount; x > 0; x -= 2)
{
// Test case insensitivity.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
// Test parents can find children.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[x * 2 - 1].PrecursorMz.Value), displaySettings,
false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, x * 2 - 1), pathFound);
// Test Children can find parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound);
}
// Test wrapping in search up.
pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[listTransitionGroups.Count - 1].PrecursorMz.Value),
displaySettings, false, true);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, listTransitionGroups.Count - 1), pathFound);
// Test children can find other parents.
pathFound = doc.SearchDocumentForString(pathFound, listPeptides[0].ToString().ToLowerInvariant(), displaySettings, true, false);
Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, 0), pathFound);
// Test forward and backward searching in succession
const string heavyText = "heavy";
int countHeavyForward = CountOccurrances(doc, heavyText, displaySettings, false, true);
Assert.IsTrue(countHeavyForward > 0);
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText, displaySettings, true, true));
// More tests of case insensitive searching
Assert.AreEqual(0, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, true));
Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, false));
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
Assert.AreEqual(1, CountOccurrances(doc, "hgflpr", displaySettings, true, false));
}
// Test mismatched transitions finder
var missmatchFinder = new FindOptions().ChangeCustomFinders(new[] { new MismatchedIsotopeTransitionsFinder() });
Assert.AreEqual(4, CountOccurrances(doc, missmatchFinder, displaySettings));
var docRemoved = (SrmDocument)doc.RemoveChild(doc.Children[1]).RemoveChild(doc.Children[2]);
Assert.AreEqual(0, CountOccurrances(docRemoved, missmatchFinder, displaySettings));
var refineRemoveHeavy = new RefinementSettings {
RefineLabelType = IsotopeLabelType.heavy
};
var docLight = refineRemoveHeavy.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docLight, missmatchFinder, displaySettings));
var refineRemoveLight = new RefinementSettings {
RefineLabelType = IsotopeLabelType.light
};
var docHeavy = refineRemoveLight.Refine(doc);
Assert.AreEqual(0, CountOccurrances(docHeavy, missmatchFinder, displaySettings));
var docMulti = ResultsUtil.DeserializeDocument("MultiLabel.sky", typeof(MultiLabelRatioTest));
docMulti = (new RefinementSettings()).ConvertToSmallMolecules(docMulti, asSmallMolecules);
Assert.AreEqual(0, CountOccurrances(docMulti, missmatchFinder, displaySettings));
var pathTranMultiRemove = docMulti.GetPathTo((int)SrmDocument.Level.Transitions, 7);
var tranMultiRemove = docMulti.FindNode(pathTranMultiRemove);
var docMultiRemoved = (SrmDocument)docMulti.RemoveChild(pathTranMultiRemove.Parent, tranMultiRemove);
Assert.AreEqual(2, CountOccurrances(docMultiRemoved, missmatchFinder, displaySettings));
var tranGroupMultiRemove = docMulti.FindNode(pathTranMultiRemove.Parent);
var docMultiGroupRemoved = (SrmDocument)
docMulti.RemoveChild(pathTranMultiRemove.Parent.Parent, tranGroupMultiRemove);
Assert.AreEqual(0, CountOccurrances(docMultiGroupRemoved, missmatchFinder, displaySettings));
}
