public static SrmDocument CreateNISTLibraryDocument(string textFasta, bool peptideList, string textLib,
out LibraryManager libraryManager, out TestDocumentContainer docContainer, out int startRev)
{
var streamManager = new MemoryStreamManager();
streamManager.TextFiles.Add(LibraryLoadTest.PATH_NIST_LIB, textLib);
var librarySpec = new NistLibSpec("Yeast (NIST)", LibraryLoadTest.PATH_NIST_LIB);
// For serialization, add the library spec to the settings
TestLibraryList = new SpectralLibraryList { librarySpec };
libraryManager = new LibraryManager { StreamManager = streamManager };
docContainer = new TestDocumentContainer();
SrmSettings settings = SrmSettingsList.GetDefault0_6();
settings = settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(new[] { librarySpec }));
return CreateLibraryDocument(settings, textFasta, peptideList, docContainer, libraryManager, out startRev);
}
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 static void ValidateLibraryDocs(SrmDocument docTarget, SrmDocument docActual, LibraryManager libraryManager)
{
var docContainer = new TestDocumentContainer();
libraryManager.Register(docContainer);
try
{
AssertEx.IsDocumentState(docActual, 0, docTarget.PeptideGroupCount, docTarget.PeptideCount,
docTarget.PeptideTransitionGroupCount, docTarget.PeptideTransitionCount);
docActual = docActual.ChangeSettings(docActual.Settings.ConnectLibrarySpecs(FindLibrarySpec));
Assert.IsTrue(docContainer.SetDocument(docActual, null, true));
SrmDocument docLoaded = docContainer.Document;
AssertEx.DocumentCloned(docTarget, docLoaded);
// Assert.IsTrue(ArrayUtil.ReferencesEqual(docActual.Transitions.ToArray(), docLoaded.Transitions.ToArray()));
// Assert.IsTrue(ArrayUtil.ReferencesEqual(docActual.TransitionGroups.ToArray(), docLoaded.TransitionGroups.ToArray()));
// Assert.IsTrue(ArrayUtil.ReferencesEqual(docActual.Peptides.ToArray(), docLoaded.Peptides.ToArray()));
Assert.IsTrue(ArrayUtil.ReferencesEqual(docActual.Children, docLoaded.Children));
}
finally
{
libraryManager.Unregister(docContainer);
}
}
private static SrmDocument CreateNISTLibraryDocument(out LibraryManager libraryManager,
out TestDocumentContainer docContainer, out int startRev)
{
SrmDocument docLoaded = CreateNISTLibraryDocument(ExampleText.TEXT_FASTA_YEAST_LIB,
false,
LibraryLoadTest.TEXT_LIB_YEAST_NIST,
out libraryManager,
out docContainer,
out startRev);
AssertEx.IsDocumentState(docLoaded, startRev, 2, 4, 12);
return docLoaded;
}
private static SrmDocument CreateLibraryDocument(SrmSettings settings, string textFasta, bool peptideList,
TestDocumentContainer docContainer, BackgroundLoader libraryManager, out int startRev)
{
startRev = 0;
SrmDocument document = new SrmDocument(SrmSettingsList.GetDefault0_6());
Assert.IsTrue(docContainer.SetDocument(document, null));
// Register after first set document
libraryManager.Register(docContainer);
// Add libraries
SrmDocument docLibraries = document.ChangeSettings(settings);
++startRev;
// Add some FASTA
IdentityPath path = IdentityPath.ROOT;
SrmDocument docFasta = docLibraries.ImportFasta(new StringReader(textFasta), peptideList, path, out path);
++startRev;
// Until libraries are loaded, only the sequences should appear
if (!peptideList)
AssertEx.IsDocumentState(docFasta, startRev, textFasta.Count(c => c == '>'), 0, 0);
// Run the library load
Assert.IsTrue(docContainer.SetDocument(docFasta, document, true));
++startRev;
// After library load completes peptides and transitions should have expected library info
SrmDocument docLoaded = docContainer.Document;
// Check expected library inforamation
foreach (var nodePeptide in docLoaded.Peptides)
Assert.IsNull(nodePeptide.Rank);
foreach (var nodeTran in docLoaded.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasLibInfo);
Assert.IsTrue(nodeTran.LibInfo.Rank <= 3);
}
return docLoaded;
}
public void LibraryNoIonsTest()
{
var streamManager = new MemoryStreamManager();
var loader = new LibraryLoadTest.TestLibraryLoader { StreamManager = streamManager };
// Create X! Hunter library with 20 lowest intensity peaks in NIST library
LibraryLoadTest.CreateHunterFile(streamManager, loader, LibraryLoadTest.TEXT_LIB_YEAST_NIST, true);
var hunterSpec = new XHunterLibSpec("Yeast (X!)", LibraryLoadTest.PATH_HUNTER_LIB);
// For serialization, add the library spec to the settings
TestLibraryList = new SpectralLibraryList { hunterSpec };
var libraryManager = new LibraryManager { StreamManager = streamManager };
var docContainer = new TestDocumentContainer();
SrmSettings settings = SrmSettingsList.GetDefault();
settings = settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(new LibrarySpec[] { hunterSpec }));
int startRev;
SrmDocument docLoaded = CreateLibraryDocument(settings, ExampleText.TEXT_FASTA_YEAST_LIB, false,
docContainer, libraryManager, out startRev);
// Peptides should have been chosen, but no transitions, since the spectra are garbage
AssertEx.IsDocumentState(docLoaded, startRev, 2, 4, 0);
}