public void SettingsChangeTranGroups()
{
SrmDocument docFasta = CreateMixedDoc();
SrmSettings settings = docFasta.Settings;
// Add heavy mod
SrmDocument docFasta2 = docFasta.ChangeSettings(settings.ChangePeptideModifications(
m => m.ChangeModifications(IsotopeLabelType.heavy, new[] { new StaticMod("N-Terminal K", "K", ModTerminus.C, "H7", LabelAtoms.None, null, null) })));
CheckNTerminalKGroups(docFasta2);
Assert.AreEqual(docFasta.PeptideCount, docFasta2.PeptideCount);
// Add multiple charges with heavy mod
var newCharges = Adduct.ProtonatedFromCharges(2, 3, 4);
settings = docFasta2.Settings;
SrmDocument docFasta3 = docFasta2.ChangeSettings(settings.ChangeTransitionFilter(
f => f.ChangePeptidePrecursorCharges(newCharges)));
CheckNTerminalKGroups(docFasta3);
Assert.AreEqual(docFasta.PeptideCount, docFasta3.PeptideCount);
// Use charge that will cause filtering on instrument maximum m/z
docFasta2 = docFasta.ChangeSettings(settings.ChangeTransitionFilter(
f => f.ChangePeptidePrecursorCharges(Adduct.ProtonatedFromCharges(1))));
Assert.IsTrue(docFasta.PeptideTransitionGroupCount < docFasta2.PeptideTransitionGroupCount);
Assert.AreEqual(docFasta.PeptideCount, docFasta2.PeptideCount);
}
public void SettingsChangeTrans()
{
SrmDocument docFasta = CreateMixedDoc();
SrmSettings settings = docFasta.Settings;
SrmDocument docFastaNoP = docFasta.ChangeSettings(settings.ChangeTransitionFilter(
f => f.ChangeMeasuredIons(new MeasuredIon[0])));
// Fixed start and end positions
SrmDocument docFasta2 = CheckTranstions(docFastaNoP, "ion 1", "last ion", 1);
CheckTranstions(docFasta2, "ion 2", "last ion - 1", 3);
docFasta2 = CheckTranstions(docFastaNoP, "ion 3", "last ion - 2", 5);
CheckTranstions(docFasta2, "ion 4", "last ion - 3", 7);
// Check ion types including precursor
var docPrec = docFasta2.ChangeSettings(docFasta2.Settings.ChangeTransitionFilter(f =>
f.ChangePeptideIonTypes(new[] { IonType.y, IonType.precursor })));
Assert.AreEqual(docFasta2.PeptideTransitionCount + docFasta2.PeptideTransitionGroupCount, docPrec.PeptideTransitionCount);
docPrec = docFasta2.ChangeSettings(docFasta2.Settings.ChangeTransitionFilter(f =>
f.ChangePeptideIonTypes(new[] { IonType.precursor })));
Assert.AreEqual(docFasta2.PeptideTransitionGroupCount, docPrec.PeptideTransitionCount);
AssertEx.Serializable(docPrec, AssertEx.DocumentCloned);
// TODO: Finish this test
}
private static SrmDocument CheckTranstions(SrmDocument document, string startName, string endName, int ionDiff)
{
SrmSettings settings = document.Settings;
SrmDocument docNew = document.ChangeSettings(settings.ChangeTransitionFilter(
f => f.ChangeFragmentRangeFirstName(startName).ChangeFragmentRangeLastName(endName)).
ChangeTransitionInstrument(i => i.ChangeMaxMz(5000)));
// length-n ions
foreach (PeptideDocNode nodePeptide in docNew.Peptides)
{
Assert.AreEqual(Math.Max(0, nodePeptide.Peptide.Sequence.Length - ionDiff),
nodePeptide.TransitionCount);
}
return(docNew);
}
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));
}