private SrmDocument ConnectLibrarySpecs(SrmDocument document, string documentPath)
{
string docLibFile = null;
if (!string.IsNullOrEmpty(documentPath) && document.Settings.PeptideSettings.Libraries.HasDocumentLibrary)
{
docLibFile = BiblioSpecLiteSpec.GetLibraryFileName(documentPath);
if (!File.Exists(docLibFile))
{
Assert.Fail(Resources.CommandLine_ConnectLibrarySpecs_Error__Could_not_find_the_spectral_library__0__for_this_document_, docLibFile);
}
}
var settings = document.Settings.ConnectLibrarySpecs((library, librarySpec) =>
{
string name = library != null ? library.Name : librarySpec.Name;
LibrarySpec spec;
if (Settings.Default.SpectralLibraryList.TryGetValue(name, out spec))
{
if (File.Exists(spec.FilePath))
{
return(spec);
}
}
string fileName = library != null ? library.FileNameHint : Path.GetFileName(librarySpec.FilePath);
if (fileName != null)
{
// First look for the file name in the document directory
string pathLibrary = PathEx.FindExistingRelativeFile(documentPath, fileName);
if (pathLibrary != null)
{
return(CreateLibrarySpec(library, librarySpec, pathLibrary, true));
}
// In the user's default library directory
pathLibrary = Path.Combine(Settings.Default.LibraryDirectory, fileName);
if (File.Exists(pathLibrary))
{
return(CreateLibrarySpec(library, librarySpec, pathLibrary, false));
}
}
Assert.Fail(Resources.CommandLine_ConnectLibrarySpecs_Warning__Could_not_find_the_spectral_library__0_, name);
return(CreateLibrarySpec(library, librarySpec, null, false));
}, docLibFile);
if (ReferenceEquals(settings, document.Settings))
{
return(document);
}
// If the libraries were moved to disconnected state, then avoid updating
// the document tree for this change, or it will strip all the library
// information off the document nodes.
if (settings.PeptideSettings.Libraries.DisconnectedLibraries != null)
{
return(document.ChangeSettingsNoDiff(settings));
}
return(document.ChangeSettings(settings));
}
private SrmDocument ConnectLibrarySpecs(SrmDocument document, string documentPath)
{
string docLibFile = null;
if (!string.IsNullOrEmpty(documentPath) && document.Settings.PeptideSettings.Libraries.HasDocumentLibrary)
{
docLibFile = BiblioSpecLiteSpec.GetLibraryFileName(documentPath);
if (!File.Exists(docLibFile))
{
_out.WriteLine(Resources.CommandLine_ConnectLibrarySpecs_Error__Could_not_find_the_spectral_library__0__for_this_document_, docLibFile);
return null;
}
}
var settings = document.Settings.ConnectLibrarySpecs(library =>
{
LibrarySpec spec;
if (Settings.Default.SpectralLibraryList.TryGetValue(library.Name, out spec))
{
if (File.Exists(spec.FilePath))
return spec;
}
string fileName = library.FileNameHint;
if (fileName != null)
{
// First look for the file name in the document directory
string pathLibrary = Path.Combine(Path.GetDirectoryName(documentPath) ?? string.Empty, fileName);
if (File.Exists(pathLibrary))
return library.CreateSpec(pathLibrary).ChangeDocumentLocal(true);
// In the user's default library directory
pathLibrary = Path.Combine(Settings.Default.LibraryDirectory, fileName);
if (File.Exists(pathLibrary))
return library.CreateSpec(pathLibrary);
}
_out.WriteLine(Resources.CommandLine_ConnectLibrarySpecs_Warning__Could_not_find_the_spectral_library__0_, library.Name);
return library.CreateSpec(null);
}, docLibFile);
if (ReferenceEquals(settings, document.Settings))
return document;
// If the libraries were moved to disconnected state, then avoid updating
// the document tree for this change, or it will strip all the library
// information off the document nodes.
if (settings.PeptideSettings.Libraries.DisconnectedLibraries != null)
return document.ChangeSettingsNoDiff(settings);
return document.ChangeSettings(settings);
}
/// <summary>
/// Minimizes all libraries in a document to produce a new document with
/// just the library information necessary for the spectra referenced by
/// the nodes in the document.
/// </summary>
/// <param name="document">Document for which to minimize library information</param>
/// <param name="pathDirectory">Directory into which new minimized libraries are built</param>
/// <param name="nameModifier">A name modifier to append to existing names for
/// full libraries to create new library names</param>
/// <param name="progressMonitor">Broker to communicate status and progress</param>
/// <returns>A new document instance with minimized libraries</returns>
public static SrmDocument MinimizeLibraries(SrmDocument document,
string pathDirectory, string nameModifier, IProgressMonitor progressMonitor)
{
var settings = document.Settings;
var pepLibraries = settings.PeptideSettings.Libraries;
if (!pepLibraries.HasLibraries)
return document;
if (!pepLibraries.IsLoaded)
throw new InvalidOperationException(Resources.BlibDb_MinimizeLibraries_Libraries_must_be_fully_loaded_before_they_can_be_minimzed);
// Separate group nodes by the libraries to which they refer
var setUsedLibrarySpecs = new HashSet<LibrarySpec>();
foreach (var librarySpec in pepLibraries.LibrarySpecs)
{
string libraryName = librarySpec.Name;
if (document.MoleculeTransitionGroups.Contains(nodeGroup =>
nodeGroup.HasLibInfo && Equals(nodeGroup.LibInfo.LibraryName, libraryName)))
{
setUsedLibrarySpecs.Add(librarySpec);
}
}
var listLibraries = new List<Library>();
var listLibrarySpecs = new List<LibrarySpec>();
var dictOldNameToNew = new Dictionary<string, string>();
if (setUsedLibrarySpecs.Count > 0)
{
Directory.CreateDirectory(pathDirectory);
var usedNames = new HashSet<string>();
for (int i = 0; i < pepLibraries.LibrarySpecs.Count; i++)
{
var librarySpec = pepLibraries.LibrarySpecs[i];
if (!setUsedLibrarySpecs.Contains(librarySpec))
continue;
string baseName = Path.GetFileNameWithoutExtension(librarySpec.FilePath);
string fileName = GetUniqueName(baseName, usedNames) + BiblioSpecLiteSpec.EXT;
using (var blibDb = CreateBlibDb(Path.Combine(pathDirectory, fileName)))
{
blibDb.ProgressMonitor = progressMonitor;
var librarySpecMin = librarySpec as BiblioSpecLiteSpec;
if (librarySpecMin == null || !librarySpecMin.IsDocumentLibrary)
{
string nameMin = librarySpec.Name;
// Avoid adding the modifier a second time, if it has
// already been done once.
if (!nameMin.EndsWith(nameModifier + ")")) // Not L10N
nameMin = string.Format("{0} ({1})", librarySpec.Name, nameModifier); // Not L10N
librarySpecMin = new BiblioSpecLiteSpec(nameMin, blibDb.FilePath);
}
listLibraries.Add(blibDb.MinimizeLibrary(librarySpecMin,
pepLibraries.Libraries[i], document));
// Terminate if user canceled
if (progressMonitor != null && progressMonitor.IsCanceled)
return document;
listLibrarySpecs.Add(librarySpecMin);
dictOldNameToNew.Add(librarySpec.Name, librarySpecMin.Name);
}
}
document = (SrmDocument) document.ChangeAll(node =>
{
var nodeGroup = node as TransitionGroupDocNode;
if (nodeGroup == null || !nodeGroup.HasLibInfo)
return node;
string libName = nodeGroup.LibInfo.LibraryName;
string libNameNew = dictOldNameToNew[libName];
if (Equals(libName, libNameNew))
return node;
var libInfo = nodeGroup.LibInfo.ChangeLibraryName(libNameNew);
return nodeGroup.ChangeLibInfo(libInfo);
},
(int) SrmDocument.Level.TransitionGroups);
}
return document.ChangeSettingsNoDiff(settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(listLibrarySpecs, listLibraries)));
}
/// <summary>
/// Minimizes all libraries in a document to produce a new document with
/// just the library information necessary for the spectra referenced by
/// the nodes in the document.
/// </summary>
/// <param name="document">Document for which to minimize library information</param>
/// <param name="pathDirectory">Directory into which new minimized libraries are built</param>
/// <param name="nameModifier">A name modifier to append to existing names for
/// full libraries to create new library names</param>
/// <param name="progressMonitor">Broker to communicate status and progress</param>
/// <returns>A new document instance with minimized libraries</returns>
public static SrmDocument MinimizeLibraries(SrmDocument document,
string pathDirectory, string nameModifier, IProgressMonitor progressMonitor)
{
var settings = document.Settings;
var pepLibraries = settings.PeptideSettings.Libraries;
if (!pepLibraries.HasLibraries)
{
return(document);
}
if (!pepLibraries.IsLoaded)
{
throw new InvalidOperationException(Resources.BlibDb_MinimizeLibraries_Libraries_must_be_fully_loaded_before_they_can_be_minimzed);
}
// Separate group nodes by the libraries to which they refer
var setUsedLibrarySpecs = new HashSet <LibrarySpec>();
foreach (var librarySpec in pepLibraries.LibrarySpecs)
{
string libraryName = librarySpec.Name;
if (document.MoleculeTransitionGroups.Contains(nodeGroup =>
nodeGroup.HasLibInfo && Equals(nodeGroup.LibInfo.LibraryName, libraryName)))
{
setUsedLibrarySpecs.Add(librarySpec);
}
}
var listLibraries = new List <Library>();
var listLibrarySpecs = new List <LibrarySpec>();
var dictOldNameToNew = new Dictionary <string, string>();
if (setUsedLibrarySpecs.Count > 0)
{
Directory.CreateDirectory(pathDirectory);
var usedNames = new HashSet <string>();
for (int i = 0; i < pepLibraries.LibrarySpecs.Count; i++)
{
var librarySpec = pepLibraries.LibrarySpecs[i];
if (!setUsedLibrarySpecs.Contains(librarySpec))
{
continue;
}
string baseName = Path.GetFileNameWithoutExtension(librarySpec.FilePath);
string fileName = GetUniqueName(baseName, usedNames) + BiblioSpecLiteSpec.EXT;
using (var blibDb = CreateBlibDb(Path.Combine(pathDirectory, fileName)))
{
blibDb.ProgressMonitor = progressMonitor;
var librarySpecMin = librarySpec as BiblioSpecLiteSpec;
if (librarySpecMin == null || !librarySpecMin.IsDocumentLibrary)
{
string nameMin = librarySpec.Name;
// Avoid adding the modifier a second time, if it has
// already been done once.
if (!nameMin.EndsWith(nameModifier + ")")) // Not L10N
{
nameMin = string.Format("{0} ({1})", librarySpec.Name, nameModifier); // Not L10N
}
librarySpecMin = new BiblioSpecLiteSpec(nameMin, blibDb.FilePath);
}
listLibraries.Add(blibDb.MinimizeLibrary(librarySpecMin,
pepLibraries.Libraries[i], document));
// Terminate if user canceled
if (progressMonitor != null && progressMonitor.IsCanceled)
{
return(document);
}
listLibrarySpecs.Add(librarySpecMin);
dictOldNameToNew.Add(librarySpec.Name, librarySpecMin.Name);
}
}
document = (SrmDocument)document.ChangeAll(node =>
{
var nodeGroup = node as TransitionGroupDocNode;
if (nodeGroup == null || !nodeGroup.HasLibInfo)
{
return(node);
}
string libName = nodeGroup.LibInfo.LibraryName;
string libNameNew = dictOldNameToNew[libName];
if (Equals(libName, libNameNew))
{
return(node);
}
var libInfo = nodeGroup.LibInfo.ChangeLibraryName(libNameNew);
return(nodeGroup.ChangeLibInfo(libInfo));
},
(int)SrmDocument.Level.TransitionGroups);
}
return(document.ChangeSettingsNoDiff(settings.ChangePeptideLibraries(
lib => lib.ChangeLibraries(listLibrarySpecs, listLibraries))));
}
private SrmDocument ConnectLibrarySpecs(IWin32Window parent, SrmDocument document, string documentPath)
{
string docLibFile = null;
if (!string.IsNullOrEmpty(documentPath) && document.Settings.PeptideSettings.Libraries.HasDocumentLibrary)
{
docLibFile = BiblioSpecLiteSpec.GetLibraryFileName(documentPath);
if (!File.Exists(docLibFile))
{
MessageDlg.Show(this, string.Format(Resources.SkylineWindow_ConnectLibrarySpecs_Could_not_find_the_spectral_library__0__for_this_document__Without_the_library__no_spectrum_ID_information_will_be_available_, docLibFile));
}
}
var settings = document.Settings.ConnectLibrarySpecs(library =>
{
LibrarySpec spec;
if (Settings.Default.SpectralLibraryList.TryGetValue(library.Name, out spec))
{
if (File.Exists(spec.FilePath))
return spec;
}
if (documentPath == null)
return null;
string fileName = library.FileNameHint;
if (fileName != null)
{
// First look for the file name in the document directory
string pathLibrary = Path.Combine(Path.GetDirectoryName(documentPath) ?? string.Empty, fileName);
if (File.Exists(pathLibrary))
return library.CreateSpec(pathLibrary).ChangeDocumentLocal(true);
// In the user's default library directory
pathLibrary = Path.Combine(Settings.Default.LibraryDirectory ?? string.Empty, fileName);
if (File.Exists(pathLibrary))
return library.CreateSpec(pathLibrary);
}
using (var dlg = new MissingFileDlg
{
ItemName = library.Name,
ItemType = Resources.SkylineWindow_ConnectLibrarySpecs_Spectral_Library,
Filter = library.SpecFilter,
FileHint = fileName,
FileDlgInitialPath = Path.GetDirectoryName(documentPath),
Title = Resources.SkylineWindow_ConnectLibrarySpecs_Find_Spectral_Library
})
{
if (dlg.ShowDialog(parent) == DialogResult.OK)
{
Settings.Default.LibraryDirectory = Path.GetDirectoryName(dlg.FilePath);
return library.CreateSpec(dlg.FilePath);
}
}
return null;
}, docLibFile);
if (settings == null)
return null; // User cancelled
if (ReferenceEquals(settings, document.Settings))
return document;
// If the libraries were moved to disconnected state, then avoid updating
// the document tree for this change, or it will strip all the library
// information off the document nodes.
if (settings.PeptideSettings.Libraries.DisconnectedLibraries != null)
return document.ChangeSettingsNoDiff(settings);
return document.ChangeSettings(settings);
}