public static BiblioSpecLibrary Load(BiblioSpecLibSpec spec, ILoadMonitor loader)
{
var library = new BiblioSpecLibrary(spec)
{
FilePath = spec.FilePath
};
if (library.Load(loader))
{
return(library);
}
return(null);
}
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));
}
public void BiblioSpecLoadLibrary()
{
var streamManager = new MemoryStreamManager();
var loader = new TestLibraryLoader { StreamManager = streamManager };
Library libNist = CreateBiblioFile(streamManager, loader, TEXT_LIB_YEAST_NIST);
Assert.AreEqual(1, streamManager.BinaryFiles.Count);
var librarySpecBiblio = new BiblioSpecLibSpec("Yeast (BS)", PATH_BIBLIOSPEC_LIB);
Library libBiblioSpec = librarySpecBiblio.LoadLibrary(loader);
CheckLibrary(libBiblioSpec, 100);
Assert.IsFalse(libNist.IsSameLibrary(libBiblioSpec));
}
public static BiblioSpecLibrary Load(BiblioSpecLibSpec spec, ILoadMonitor loader)
{
var library = new BiblioSpecLibrary(spec) { FilePath = spec.FilePath };
if (library.Load(loader))
return library;
return null;
}
