public BackgroundProteome(BackgroundProteomeSpec backgroundProteomeSpec, bool queryDigestions)
: base(backgroundProteomeSpec.Name, backgroundProteomeSpec.DatabasePath)
{
DigestionNames = new HashSet <string>();
if (!IsNone)
{
try
{
using (var proteomeDb = OpenProteomeDb())
{
if (queryDigestions)
{
DigestionNames.UnionWith(proteomeDb.ListDigestions().Select(digestion => digestion.Name));
}
}
}
catch (Exception)
{
DatabaseInvalid = true;
}
}
if (queryDigestions)
{
DatabaseValidated = true;
}
}
public override bool Equals(object obj)
{
if (this == obj)
{
return(true);
}
BackgroundProteomeSpec that = obj as BackgroundProteomeSpec;
if (that == null)
{
return(false);
}
return(Name == that.Name && DatabasePath == that.DatabasePath);
}
public BackgroundProteome(BackgroundProteomeSpec backgroundProteomeSpec)
: base(backgroundProteomeSpec.Name, backgroundProteomeSpec.DatabasePath)
{
_cache = new BackgroundProteomeMetadataCache(this);
if (!IsNone)
{
try
{
OpenProteomeDb();
}
catch (Exception)
{
DatabaseInvalid = true;
}
}
DatabaseValidated = true;
}
public BackgroundProteome(BackgroundProteomeSpec backgroundProteomeSpec, bool queryDigestions)
: base(backgroundProteomeSpec.Name, backgroundProteomeSpec.DatabasePath)
{
DigestionNames = new HashSet<string>();
if (!IsNone)
{
try
{
using (var proteomeDb = OpenProteomeDb())
{
if (queryDigestions)
DigestionNames.UnionWith(proteomeDb.ListDigestions().Select(digestion => digestion.Name));
}
}
catch (Exception)
{
DatabaseInvalid = true;
}
}
if (queryDigestions)
DatabaseValidated = true;
}
private BackgroundProteomeSpec FindBackgroundProteome(string documentPath, BackgroundProteomeSpec backgroundProteomeSpec)
{
var result = Settings.Default.BackgroundProteomeList.GetBackgroundProteomeSpec(backgroundProteomeSpec.Name);
if (result != null)
{
if (result.IsNone || File.Exists(result.DatabasePath))
return result;
}
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, fileName ?? string.Empty);
if (File.Exists(pathBackgroundProteome))
return new BackgroundProteomeSpec(backgroundProteomeSpec.Name, pathBackgroundProteome);
_out.WriteLine(Resources.CommandLine_FindBackgroundProteome_Warning__Could_not_find_the_background_proteome_file__0__, Path.GetFileName(fileName));
return BackgroundProteomeList.GetDefault();
}
public bool EqualsSpec(BackgroundProteomeSpec other)
{
return(Name == other.Name && DatabasePath == other.DatabasePath);
}
public void OkDialog()
{
if (!_messageBoxHelper.ValidateNameTextBox(textName, out _name))
{
return;
}
if (_backgroundProteomeSpec == null || _name != _backgroundProteomeSpec.Name)
{
foreach (BackgroundProteomeSpec backgroundProteomeSpec in _existing)
{
if (_name == backgroundProteomeSpec.Name)
{
_messageBoxHelper.ShowTextBoxError(textName, Resources.BuildBackgroundProteomeDlg_OkDialog_The_background_proteome__0__already_exists, _name);
return;
}
}
}
if (string.IsNullOrEmpty(textPath.Text))
{
_messageBoxHelper.ShowTextBoxError(textPath, Resources.BuildBackgroundProteomeDlg_OkDialog_You_must_specify_a_proteome_file);
return;
}
try
{
if (textPath.Text != Path.GetFullPath(textPath.Text))
{
_messageBoxHelper.ShowTextBoxError(textPath, Resources.BuildBackgroundProteomeDlg_OkDialog_Please_specify_a_full_path_to_the_proteome_file);
return;
}
else if (!File.Exists(textPath.Text))
{
_messageBoxHelper.ShowTextBoxError(textPath,
string.Format(Resources.BuildBackgroundProteomeDlg_OkDialog_The_proteome_file__0__does_not_exist, textPath.Text));
return;
}
ProteomeDb.OpenProteomeDb(textPath.Text);
}
catch (Exception x)
{
// In case exception is thrown opening protdb
string message = TextUtil.LineSeparate(Resources.BuildBackgroundProteomeDlg_OkDialog_The_proteome_file_is_not_valid,
Resources.BuildBackgroundProteomeDlg_OkDialog_Choose_a_valid_proteome_file__or_click_the__Create__button_to_create_a_new_one_from_FASTA_files);
MessageDlg.ShowWithException(this, message, x);
return;
}
_databasePath = textPath.Text;
_name = textName.Text;
_backgroundProteomeSpec = new BackgroundProteomeSpec(_name, _databasePath);
DialogResult = DialogResult.OK;
Close();
}
public BackgroundProteome(BackgroundProteomeSpec backgroundProteomeSpec) : this(backgroundProteomeSpec, false)
{
// We intentionally do not copy the _needsProteinMetadataSearch member
}
private bool? _needsProteinMetadataSearch; // Nullable for lazy evaluation, for quicker ctor
#endregion Fields
#region Constructors
public BackgroundProteome(BackgroundProteomeSpec backgroundProteomeSpec)
: this(backgroundProteomeSpec, false)
{
// We intentionally do not copy the _needsProteinMetadataSearch member
}
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;
}
public BackgroundProteome(BackgroundProteomeSpec backgroundProteomeSpec) : this(backgroundProteomeSpec, false)
{
// We intentionally do not copy cache information
}
