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 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 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));
}
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));
}
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);
}
