public void FullScanPrecursorTransitionsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestA\FullScanPrecursor.zip");
string docPath = testFilesDir.GetTestPath("FullScanPrecursor.sky");
SrmDocument doc = ResultsUtil.DeserializeDocument(docPath);
AssertEx.IsDocumentState(doc, 0, 1, 4, 5, 52);
var docContainer = new ResultsTestDocumentContainer(doc, docPath);
var mitoLibSpec = new BiblioSpecLiteSpec("mito2", testFilesDir.GetTestPath("mito2.blib"));
doc = docContainer.ChangeLibSpecs(new [] { mitoLibSpec });
Assert.IsTrue(doc.IsLoaded);
// Switch to only precursor ions
var docPrecOnly = doc.ChangeSettings(doc.Settings.ChangeTransitionFilter(filter =>
filter.ChangeIonTypes(new[] { IonType.precursor })));
// All precursors should have 3 precursor transitions (M, M+1 and M+2)
AssertEx.IsDocumentState(docPrecOnly, 3, 1, 4, 5, 15);
Assert.IsFalse(docPrecOnly.PeptideTransitions.Any(nodeTran => nodeTran.Transition.IonType != IonType.precursor));
// Use low resolution MS1 filtering
var docLowMs1 = docPrecOnly.ChangeSettings(docPrecOnly.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, 0.5, null)));
// All precursors should have one precursor transition
AssertEx.IsDocumentState(docLowMs1, 4, 1, 4, 5, 5);
// Add y-ions to low resolution filtering
var docLowMs1Y = docLowMs1.ChangeSettings(docLowMs1.Settings.ChangeTransitionFilter(filter =>
filter.ChangeIonTypes(new[] { IonType.precursor, IonType.y })));
AssertEx.IsDocumentState(docLowMs1Y, 5, 1, 4, 5, 33);
// Turn off MS1 filtering
var docNoMs1 = docPrecOnly.ChangeSettings(docPrecOnly.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.None, null, null)));
// One of the precursors should have no transitions, since its spectrum has no precursor match
AssertEx.IsDocumentState(docNoMs1, 4, 1, 4, 5, 4);
// Turn off MS/MS library matching
var docNoLibMatch = docNoMs1.ChangeSettings(docNoMs1.Settings.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.none)));
// All precursors should have a single precursor transition
AssertEx.IsDocumentState(docNoLibMatch, 5, 1, 4, 5, 5);
// Use library plus filter matching
var docLibPlusMatch = docNoMs1.ChangeSettings(docNoMs1.Settings.ChangeTransitionLibraries(lib =>
lib.ChangePick(TransitionLibraryPick.all_plus)));
// All precursors should have a single precursor transition
AssertEx.IsDocumentState(docLibPlusMatch, 5, 1, 4, 5, 5);
// Release the library stream, and dispose of the directory
docContainer.ChangeLibSpecs(new LibrarySpec[0]);
testFilesDir.Dispose();
}