public void LibraryTransitionTest()
{
LibraryManager libraryManager;
TestDocumentContainer docContainer;
int startRev;
SrmDocument docLoaded = CreateNISTLibraryDocument(out libraryManager, out docContainer, out startRev);
// Test tolerance range
SrmSettings settings = docLoaded.Settings.ChangeTransitionLibraries(l =>
l.ChangeIonMatchTolerance(TransitionLibraries.MIN_MATCH_TOLERANCE));
SrmDocument docLowTol = docLoaded.ChangeSettings(settings);
// Use the original low tolerance for transition testing, since
// the new low tolerance is for high accuracy data.
docLowTol = docLowTol.ChangeSettings(settings.ChangeTransitionLibraries(l =>
l.ChangeIonMatchTolerance(0.1)));
settings = docLowTol.Settings.ChangeTransitionLibraries(l =>
l.ChangeIonMatchTolerance(TransitionLibraries.MAX_MATCH_TOLERANCE));
SrmDocument docHighTol = docLoaded.ChangeSettings(settings);
Assert.AreEqual(docLowTol.PeptideTransitionCount, docHighTol.PeptideTransitionCount);
var transLow = docLowTol.PeptideTransitions.ToArray();
var transHigh = docHighTol.PeptideTransitions.ToArray();
int diffCount = 0;
for (int i = 0; i < transLow.Length; i++)
{
if (!Equals(transLow[i], transHigh[i]))
{
diffCount++;
}
}
Assert.AreEqual(2, diffCount);
Assert.IsTrue(ArrayUtil.ReferencesEqual(docLoaded.PeptideTransitionGroups.ToArray(), docHighTol.PeptideTransitionGroups.ToArray()));
Assert.IsTrue(HasMaxTransitionRank(docHighTol, 3));
SrmSettings setThrow = settings;
AssertEx.ThrowsException <InvalidDataException>(() =>
setThrow.ChangeTransitionLibraries(l => l.ChangeIonMatchTolerance(TransitionLibraries.MAX_MATCH_TOLERANCE * 2)));
AssertEx.ThrowsException <InvalidDataException>(() =>
setThrow.ChangeTransitionLibraries(l => l.ChangeIonMatchTolerance(TransitionLibraries.MIN_MATCH_TOLERANCE / 2)));
// Picked transition count
settings = docLoaded.Settings.ChangeTransitionLibraries(l => l.ChangeIonCount(5));
SrmDocument docHighIons = docLoaded.ChangeSettings(settings);
AssertEx.IsDocumentState(docHighIons, ++startRev, 2, 4, 20);
Assert.IsTrue(HasMaxTransitionRank(docHighIons, 5));
Assert.IsFalse(HasMinTransitionOrdinal(docHighIons, 4));
settings = settings.ChangeTransitionLibraries(l => l.ChangePick(TransitionLibraryPick.none));
SrmDocument docFilteredIons = docHighIons.ChangeSettings(settings);
AssertEx.IsDocumentState(docFilteredIons, ++startRev, 2, 4, 15); // Proline ions
Assert.IsFalse(HasMaxTransitionRank(docFilteredIons, 5));
settings = settings.ChangeTransitionFilter(f => f.ChangeFragmentRangeFirstName("ion 4")
.ChangeFragmentRangeLastName("last ion").ChangeMeasuredIons(new MeasuredIon[0]));
settings = settings.ChangeTransitionLibraries(l => l.ChangePick(TransitionLibraryPick.filter));
SrmDocument docRankedFiltered = docFilteredIons.ChangeSettings(settings);
AssertEx.IsDocumentState(docRankedFiltered, ++startRev, 2, 4, 20);
Assert.IsTrue(HasMaxTransitionRank(docRankedFiltered, 5));
Assert.IsTrue(HasMinTransitionOrdinal(docRankedFiltered, 4));
AssertEx.Serializable(docRankedFiltered, (doc1, doc2) => ValidateLibraryDocs(doc1, doc2, libraryManager));
}