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);
}
public void TestLibraryRankedSpectrumInfoSpeed()
{
var testFilesDir = new TestFilesDir(TestContext, @"Test\LibraryRankedSpectrumInfoSpeedTest.zip");
SrmDocument srmDocument;
using (var stream = File.OpenRead(testFilesDir.GetTestPath("LibraryRankedSpectrumInfoSpeedTest.sky")))
{
srmDocument = (SrmDocument) new XmlSerializer(typeof(SrmDocument)).Deserialize(stream);
}
var unloadedLibrary = srmDocument.Settings.PeptideSettings.Libraries.Libraries.FirstOrDefault();
Assert.IsNotNull(unloadedLibrary);
var streamManager = new MemoryStreamManager();
var loader = new LibraryLoadTest.TestLibraryLoader {
StreamManager = streamManager
};
var librarySpec = unloadedLibrary.CreateSpec(testFilesDir.GetTestPath("LibraryRankedSpectrumInfoSpeedTest.blib"));
var library = librarySpec.LoadLibrary(loader);
Assert.IsTrue(library.IsLoaded);
var peptideLibraries = srmDocument.Settings.PeptideSettings.Libraries.ChangeLibraries(new[] { library });
var settingsWithLibraries =
srmDocument.Settings.ChangePeptideSettings(
srmDocument.Settings.PeptideSettings.ChangeLibraries(peptideLibraries));
// List of peptides to test with: <peptide sequence, description, expected # of matched ions, expected ranked ions>
Tuple <string, string, int, double[]>[] testPeptides = new[]
{
// ReSharper disable StringLiteralTypo
Tuple.Create("MEIVK", "Short Peptide",
20, new[] { 131.1, 147.1, 187.1 }),
Tuple.Create("EIYYTPDPSELAAKEEPAKEEAPAPTPAASAPAPAAAAPAPVAAAAPAAAAAEIADEPVK", "Long Peptide",
55, new[] { 587.4, 771.4, 900.5 }),
Tuple.Create("LVGFT[+80]FR", "Short Peptide with 1 Neutral Loss",
24, new[] { 305.1334, 322.0948, 325.2004 }),
Tuple.Create("DLKEILSGFHNAGPVAGAGAASGAAAAGGDAAAEEEKEEEAAEES[+80]DDDMGFGLFD",
"Long peptide with 1 Neutral Loss",
43, new[] { 790.1161, 825.5901, 889.6103 }),
Tuple.Create("MLPTS[+80]VS[+80]R", "Short peptide with 2 neutral losses",
36, new[] { 305.6439, 340.5001, 343.2071 }),
Tuple.Create("RNPDFEDDDFLGGDFDEDEIDEESS[+80]EEEEEEKT[+80]QKK", "Long peptide with 2 neutral losses",
65, new[] { 483.2214, 552.9168, 626.2743 })
// ReSharper restore StringLiteralTypo
};
Console.Out.WriteLine();
foreach (var tuple in testPeptides)
{
var peptideDocNode = srmDocument.Molecules.FirstOrDefault(pep => pep.ModifiedSequenceDisplay == tuple.Item1);
Assert.IsNotNull(peptideDocNode, "Could not find peptide {0}", tuple.Item1);
var transitionGroup = peptideDocNode.TransitionGroups.FirstOrDefault();
Assert.IsNotNull(transitionGroup);
var spectrum = library
.GetSpectra(new LibKey(peptideDocNode.ModifiedTarget, transitionGroup.PrecursorAdduct),
transitionGroup.LabelType, LibraryRedundancy.all).FirstOrDefault();
Assert.IsNotNull(spectrum);
var startTime = DateTime.UtcNow;
LibraryRankedSpectrumInfo libraryRankedSpectrum = null;
int repeatCount = 50;
for (int i = 0; i < repeatCount; i++)
{
libraryRankedSpectrum = LibraryRankedSpectrumInfo.NewLibraryRankedSpectrumInfo(spectrum.SpectrumPeaksInfo,
transitionGroup.LabelType, transitionGroup, settingsWithLibraries, peptideDocNode.ExplicitMods,
false, TransitionGroup.MAX_MATCHED_MSMS_PEAKS);
Assert.IsNotNull(libraryRankedSpectrum);
}
var endTime = DateTime.UtcNow;
Console.Out.WriteLine("Time to get LibraryRankedSpectrumInfo for {0} {1} times: {2}", tuple.Item2, repeatCount, endTime.Subtract(startTime));
Assert.IsNotNull(libraryRankedSpectrum);
var rankedMzs = libraryRankedSpectrum.PeaksRanked.Select(peak => Math.Round(peak.ObservedMz, 4)).Take(3).ToArray();
Console.Out.WriteLine("{0} matched peaks. First {1}/{2} ranked peaks: {{ {3} }}",
libraryRankedSpectrum.PeaksMatched.Count(), rankedMzs.Length,
libraryRankedSpectrum.PeaksRanked.Count(), string.Join(",", rankedMzs));
if (!IsRecording)
{
CollectionAssert.AreEqual(tuple.Item4, rankedMzs);
Assert.AreEqual(tuple.Item3, libraryRankedSpectrum.PeaksMatched.Count());
}
}
}
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));
}