public void NistLoadLibrary()
{
var streamManager = new MemoryStreamManager();
streamManager.TextFiles.Add(PATH_NIST_LIB, TEXT_LIB_YEAST_NIST);
var loader = new TestLibraryLoader {
StreamManager = streamManager
};
var librarySpec = new NistLibSpec("Yeast (NIST)", PATH_NIST_LIB);
Library lib1 = librarySpec.LoadLibrary(loader);
CheckLibrary(lib1, 100);
Assert.AreEqual(streamManager.BinaryFiles.Count, 1);
Assert.IsTrue(streamManager.IsCached(PATH_NIST_LIB, PATH_NIST_LIB_CACHE));
// Corrupt the cache, and make sure it still possible to get
// a valid library.
byte[] cacheBytes = streamManager.BinaryFiles[PATH_NIST_LIB_CACHE];
int len = cacheBytes.Length;
byte[] corruptedBytes = new byte[len / 2];
Array.Copy(cacheBytes, corruptedBytes, corruptedBytes.Length);
streamManager.BinaryFiles[PATH_NIST_LIB_CACHE] = corruptedBytes;
Library lib2 = librarySpec.LoadLibrary(loader);
CheckLibrary(lib2, 100);
Assert.AreEqual(len, streamManager.BinaryFiles[PATH_NIST_LIB_CACHE].Length);
Assert.IsTrue(lib1.IsSameLibrary(lib2));
Assert.AreEqual(0, lib1.CompareRevisions(lib2));
}
public void NistLoadLibrary()
{
var streamManager = new MemoryStreamManager();
streamManager.TextFiles.Add(PATH_NIST_LIB, TEXT_LIB_YEAST_NIST + TEXT_LIB_BICINE_NIST);
var loader = new TestLibraryLoader {
StreamManager = streamManager
};
var expectedFragmentAnnotations = new Dictionary <int, List <SpectrumPeakAnnotation> >
{
{ 3, MakeTestPeakAnnotation(Adduct.M_PLUS, 41.027f, "testfrag3", "85/86") },
{ 44, MakeTestPeakAnnotation(Adduct.M_PLUS, 128.070f, "testfrag_next_to_last", "83/86") },
{ 45, MakeTestPeakAnnotation(Adduct.M_PLUS, 146.081f, "testfrag_last", "85/86 note") },
};
var librarySpec = new NistLibSpec("Yeast (NIST)", PATH_NIST_LIB);
Library lib1 = librarySpec.LoadLibrary(loader);
CheckLibrary(lib1, 100);
CheckLibrary(lib1, 46, KEYS_LIB_BICENE_NIST);
Assert.AreEqual(streamManager.BinaryFiles.Count, 1);
Assert.IsTrue(streamManager.IsCached(PATH_NIST_LIB, PATH_NIST_LIB_CACHE));
// Corrupt the cache, and make sure it still possible to get
// a valid library.
byte[] cacheBytes = streamManager.BinaryFiles[PATH_NIST_LIB_CACHE];
int len = cacheBytes.Length;
byte[] corruptedBytes = new byte[len / 2];
Array.Copy(cacheBytes, corruptedBytes, corruptedBytes.Length);
streamManager.BinaryFiles[PATH_NIST_LIB_CACHE] = corruptedBytes;
// Check small molecule library with spectrum attributes
TestSpectrumPeakAnnotations(); // First, a quick low-level unit test of annotations handler class
Library lib2 = librarySpec.LoadLibrary(loader);
CheckLibrary(lib2, 100);
CheckLibrary(lib2, 46, KEYS_LIB_BICENE_NIST, expectedFragmentAnnotations);
Assert.AreEqual(len, streamManager.BinaryFiles[PATH_NIST_LIB_CACHE].Length);
Assert.IsTrue(lib1.IsSameLibrary(lib2));
Assert.AreEqual(0, lib1.CompareRevisions(lib2));
}
private static Library CreateLibraryFile(MemoryStreamManager streamManager, ILoadMonitor loader,
string nistText, Action <IStreamManager, Library> write)
{
streamManager.TextFiles[PATH_NIST_LIB] = nistText;
var librarySpec = new NistLibSpec("Temporary (NIST)", PATH_NIST_LIB);
Library libNist = librarySpec.LoadLibrary(loader);
Assert.IsNotNull(libNist);
write(streamManager, libNist);
streamManager.TextFiles.Remove(PATH_NIST_LIB);
streamManager.Delete(PATH_NIST_LIB_CACHE);
return(libNist);
}
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 bool SetLibrary(string name, string path, bool append = true)
{
if (string.IsNullOrWhiteSpace(path))
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__Cannot_set_library_name_without_path_);
return false;
}
else if (!File.Exists(path))
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_file__0__does_not_exist_, path);
return false;
}
else if (path.EndsWith(BiblioSpecLiteSpec.EXT_REDUNDANT))
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_file__0__appears_to_be_a_redundant_library_);
return false;
}
if (string.IsNullOrWhiteSpace(name))
name = Path.GetFileNameWithoutExtension(path);
LibrarySpec librarySpec;
string ext = Path.GetExtension(path);
if (Equals(ext, BiblioSpecLiteSpec.EXT))
librarySpec = new BiblioSpecLiteSpec(name, path);
else if (Equals(ext, BiblioSpecLibSpec.EXT))
librarySpec = new BiblioSpecLibSpec(name, path);
else if (Equals(ext, XHunterLibSpec.EXT))
librarySpec = new XHunterLibSpec(name, path);
else if (Equals(ext, NistLibSpec.EXT))
librarySpec = new NistLibSpec(name, path);
else if (Equals(ext, SpectrastSpec.EXT))
librarySpec = new SpectrastSpec(name, path);
else
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_file__0__is_not_a_supported_spectral_library_file_format_, path);
return false;
}
// Check for conflicting names
foreach (var docLibrarySpec in _doc.Settings.PeptideSettings.Libraries.LibrarySpecs)
{
if (docLibrarySpec.Name == librarySpec.Name || docLibrarySpec.FilePath == librarySpec.FilePath)
{
_out.WriteLine(Resources.CommandLine_SetLibrary_Error__The_library_you_are_trying_to_add_conflicts_with_a_library_already_in_the_file_);
return false;
}
}
var librarySpecs = append ?
new List<LibrarySpec>(_doc.Settings.PeptideSettings.Libraries.LibrarySpecs) { librarySpec } :
new List<LibrarySpec>{ librarySpec };
SrmSettings newSettings = _doc.Settings.ChangePeptideLibraries(l => l.ChangeLibrarySpecs(librarySpecs));
_doc = _doc.ChangeSettings(newSettings);
return true;
}
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 Library CreateLibraryFile(MemoryStreamManager streamManager, ILoadMonitor loader,
string nistText, Action<IStreamManager, Library> write)
{
streamManager.TextFiles[PATH_NIST_LIB] = nistText;
var librarySpec = new NistLibSpec("Temporary (NIST)", PATH_NIST_LIB);
Library libNist = librarySpec.LoadLibrary(loader);
Assert.IsNotNull(libNist);
write(streamManager, libNist);
streamManager.TextFiles.Remove(PATH_NIST_LIB);
streamManager.Delete(PATH_NIST_LIB_CACHE);
return libNist;
}
public void NistLoadLibrary()
{
var streamManager = new MemoryStreamManager();
streamManager.TextFiles.Add(PATH_NIST_LIB, TEXT_LIB_YEAST_NIST);
var loader = new TestLibraryLoader {StreamManager = streamManager};
var librarySpec = new NistLibSpec("Yeast (NIST)", PATH_NIST_LIB);
Library lib1 = librarySpec.LoadLibrary(loader);
CheckLibrary(lib1, 100);
Assert.AreEqual(streamManager.BinaryFiles.Count, 1);
Assert.IsTrue(streamManager.IsCached(PATH_NIST_LIB, PATH_NIST_LIB_CACHE));
// Corrupt the cache, and make sure it still possible to get
// a valid library.
byte[] cacheBytes = streamManager.BinaryFiles[PATH_NIST_LIB_CACHE];
int len = cacheBytes.Length;
byte[] corruptedBytes = new byte[len/2];
Array.Copy(cacheBytes, corruptedBytes, corruptedBytes.Length);
streamManager.BinaryFiles[PATH_NIST_LIB_CACHE] = corruptedBytes;
Library lib2 = librarySpec.LoadLibrary(loader);
CheckLibrary(lib2, 100);
Assert.AreEqual(len, streamManager.BinaryFiles[PATH_NIST_LIB_CACHE].Length);
Assert.IsTrue(lib1.IsSameLibrary(lib2));
Assert.AreEqual(0, lib1.CompareRevisions(lib2));
}
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));
}
