private string FindSpectralLibrary(string libraryName, string fileName)
{
string result = null;
RunUIAction(() =>
{
using (var dlg = new MissingFileDlg
{
ItemName = libraryName,
FileHint = fileName,
ItemType = Resources.SkylineWindow_ConnectLibrarySpecs_Spectral_Library,
Title = Resources.SkylineWindow_ConnectLibrarySpecs_Find_Spectral_Library
})
{
if (dlg.ShowDialog(this) == DialogResult.OK)
result = dlg.FilePath;
}
});
return result;
}
private OptimizationLibrary FindOptimizationDatabase(IWin32Window parent, string documentPath, OptimizationLibrary optLib)
{
if (optLib.IsNone)
return optLib;
OptimizationLibrary lib;
if (Settings.Default.OptimizationLibraryList.TryGetValue(optLib.Name, out lib))
{
if (lib != null && File.Exists(lib.DatabasePath))
return lib;
}
if (documentPath == null)
return null;
// First look for the file name in the document directory
string fileName = Path.GetFileName(optLib.DatabasePath);
string filePath = Path.Combine(Path.GetDirectoryName(documentPath) ?? string.Empty, fileName ?? string.Empty);
if (File.Exists(filePath))
{
try
{
return optLib.ChangeDatabasePath(filePath);
}
// ReSharper disable once EmptyGeneralCatchClause
catch (Exception)
{
//Todo: should this fail silenty or raise another dialog box?
}
}
do
{
using (var dlg = new MissingFileDlg
{
ItemName = optLib.Name,
ItemType = Resources.SkylineWindow_FindOptimizationDatabase_Optimization_Library,
Filter = TextUtil.FileDialogFilterAll(Resources.SkylineWindow_FindOptimizationDatabase_Optimization_Library_Files, OptimizationDb.EXT),
FileHint = Path.GetFileName(optLib.DatabasePath),
FileDlgInitialPath = Path.GetDirectoryName(documentPath),
Title = Resources.SkylineWindow_FindOptimizationDatabase_Find_Optimization_Library
})
{
if (dlg.ShowDialog(parent) == DialogResult.OK)
{
if (dlg.FilePath == null)
return OptimizationLibrary.NONE;
try
{
return optLib.ChangeDatabasePath(dlg.FilePath);
}
catch (OptimizationsOpeningException e)
{
var message = TextUtil.SpaceSeparate(
Resources.SkylineWindow_FindOptimizationDatabase_The_database_file_specified_could_not_be_opened_,
e.Message); // Not L10N
MessageBox.Show(message);
}
}
else
{
return null;
}
}
}
while (true);
}
private RCalcIrt FindIrtDatabase(IWin32Window parent, string documentPath, RCalcIrt irtCalc)
{
RetentionScoreCalculatorSpec result;
if (Settings.Default.RTScoreCalculatorList.TryGetValue(irtCalc.Name, out result))
{
var calc = result as RCalcIrt;
if (calc != null && File.Exists(calc.DatabasePath))
return calc;
}
if (documentPath == null)
return null;
// First look for the file name in the document directory
string fileName = Path.GetFileName(irtCalc.DatabasePath);
string filePath = Path.Combine(Path.GetDirectoryName(documentPath) ?? string.Empty, fileName ?? string.Empty);
if (File.Exists(filePath))
{
try
{
return irtCalc.ChangeDatabasePath(filePath);
}
catch (CalculatorException)
{
//Todo: should this fail silenty or raise another dialog box?
}
}
do
{
using (var dlg = new MissingFileDlg
{
ItemName = irtCalc.Name,
ItemType = Resources.SkylineWindow_FindIrtDatabase_iRT_Calculator,
Filter = TextUtil.FileDialogFilterAll(Resources.SkylineWindow_FindIrtDatabase_iRT_Database_Files, IrtDb.EXT),
FileHint = Path.GetFileName(irtCalc.DatabasePath),
FileDlgInitialPath = Path.GetDirectoryName(documentPath),
Title = Resources.SkylineWindow_FindIrtDatabase_Find_iRT_Calculator
})
{
if (dlg.ShowDialog(parent) == DialogResult.OK)
{
if (dlg.FilePath == null)
return RCalcIrt.NONE;
try
{
return irtCalc.ChangeDatabasePath(dlg.FilePath);
}
catch (DatabaseOpeningException e)
{
var message = TextUtil.SpaceSeparate(
Resources.SkylineWindow_FindIrtDatabase_The_database_file_specified_could_not_be_opened,
e.Message); // Not L10N
MessageBox.Show(message);
}
}
else
{
return null;
}
}
}
while (true);
}
private IonMobilityLibrarySpec FindIonMobilityLibrary(IWin32Window parent, string documentPath, IonMobilityLibrarySpec ionMobilityLibrarySpec)
{
IonMobilityLibrarySpec result;
if (Settings.Default.IonMobilityLibraryList.TryGetValue(ionMobilityLibrarySpec.Name, out result))
{
if (result != null && File.Exists(result.PersistencePath))
return result;
}
if (documentPath == null)
return null;
// First look for the file name in the document directory
string fileName = Path.GetFileName(ionMobilityLibrarySpec.PersistencePath);
string filePath = Path.Combine(Path.GetDirectoryName(documentPath) ?? string.Empty, fileName ?? string.Empty);
if (File.Exists(filePath))
{
try
{
var ionMobilityLib = ionMobilityLibrarySpec as IonMobilityLibrary;
if (ionMobilityLib != null)
return ionMobilityLib.ChangeDatabasePath(filePath);
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
//Todo: should this fail silenty or raise another dialog box?
}
}
do
{
using (var dlg = new MissingFileDlg
{
ItemName = ionMobilityLibrarySpec.Name,
ItemType = Resources.SkylineWindow_FindIonMobilityLibrary_Ion_Mobility_Library,
Filter = TextUtil.FileDialogFilterAll(Resources.SkylineWindow_FindIonMobilityDatabase_ion_mobility_library_files, IonMobilityDb.EXT),
FileHint = Path.GetFileName(ionMobilityLibrarySpec.PersistencePath),
FileDlgInitialPath = Path.GetDirectoryName(documentPath),
Title = Resources.SkylineWindow_FindIonMobilityLibrary_Find_Ion_Mobility_Library
})
{
if (dlg.ShowDialog(parent) == DialogResult.OK)
{
if (dlg.FilePath == null)
return IonMobilityLibrary.NONE;
try
{
var ionMobilityLib = ionMobilityLibrarySpec as IonMobilityLibrary;
if (ionMobilityLib != null)
return ionMobilityLib.ChangeDatabasePath(dlg.FilePath);
}
catch (DatabaseOpeningException e)
{
var message = TextUtil.SpaceSeparate(
Resources.SkylineWindow_FindIonMobilityDatabase_The_ion_mobility_library_specified_could_not_be_opened_,
e.Message);
MessageBox.Show(message);
}
}
else
{
return null;
}
}
}
while (true);
}
private BackgroundProteomeSpec FindBackgroundProteome(IWin32Window parent, string documentPath, BackgroundProteomeSpec backgroundProteomeSpec)
{
var result = Settings.Default.BackgroundProteomeList.GetBackgroundProteomeSpec(backgroundProteomeSpec.Name);
if (result != null)
{
if (File.Exists(result.DatabasePath))
return result;
}
if (documentPath == null)
return null;
// Is the saved path correct? Then just use that.
if (File.Exists(backgroundProteomeSpec.DatabasePath))
return new BackgroundProteomeSpec(backgroundProteomeSpec.Name, backgroundProteomeSpec.DatabasePath);
string fileName = Path.GetFileName(backgroundProteomeSpec.DatabasePath);
// First look for the file name in the document directory
string pathBackgroundProteome = Path.Combine(Path.GetDirectoryName(documentPath) ?? string.Empty, fileName ?? string.Empty);
if (File.Exists(pathBackgroundProteome))
return new BackgroundProteomeSpec(backgroundProteomeSpec.Name, pathBackgroundProteome);
// In the user's default library directory
pathBackgroundProteome = Path.Combine(Settings.Default.ProteomeDbDirectory ?? string.Empty, fileName ?? string.Empty);
if (File.Exists(pathBackgroundProteome))
return new BackgroundProteomeSpec(backgroundProteomeSpec.Name, pathBackgroundProteome);
using (var dlg = new MissingFileDlg
{
FileHint = fileName,
ItemName = backgroundProteomeSpec.Name,
ItemType = Resources.SkylineWindow_FindBackgroundProteome_Background_Proteome,
Filter = TextUtil.FileDialogFilterAll(Resources.SkylineWindow_FindBackgroundProteome_Proteome_File, ProteomeDb.EXT_PROTDB),
FileDlgInitialPath = Settings.Default.ProteomeDbDirectory,
Title = Resources.SkylineWindow_FindBackgroundProteome_Find_Background_Proteome
})
{
if (dlg.ShowDialog(parent) == DialogResult.OK)
{
if (dlg.FilePath == null)
{
return BackgroundProteomeList.GetDefault();
}
Settings.Default.ProteomeDbDirectory = Path.GetDirectoryName(dlg.FilePath);
return new BackgroundProteomeSpec(backgroundProteomeSpec.Name, dlg.FilePath);
}
}
return null;
}
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);
}