/// <summary>
/// Saves the database to a new directory with only the standards and peptides used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which peptides are to be kept</param>
/// <returns>The full path to the file saved</returns>
public override string PersistMinimized(string pathDestDir, SrmDocument document)
{
RequireUsable();
string persistPath = Path.Combine(pathDestDir, Path.GetFileName(PersistencePath) ?? string.Empty); // ReSharper
using (var fs = new FileSaver(persistPath))
{
var irtDbMinimal = IrtDb.CreateIrtDb(fs.SafeName);
// Calculate the minimal set of peptides needed for this document
var dbPeptides = _database.GetPeptides().ToList();
var persistPeptides = dbPeptides.Where(pep => pep.Standard).Select(NewPeptide).ToList();
var dictPeptides = dbPeptides.Where(pep => !pep.Standard).ToDictionary(pep => pep.ModifiedTarget);
foreach (var nodePep in document.Molecules)
{
var modifiedSeq = document.Settings.GetSourceTarget(nodePep);
DbIrtPeptide dbPeptide;
if (dictPeptides.TryGetValue(modifiedSeq, out dbPeptide))
{
persistPeptides.Add(NewPeptide(dbPeptide));
// Only add once
dictPeptides.Remove(modifiedSeq);
}
}
irtDbMinimal.AddPeptides(null, persistPeptides);
fs.Commit();
}
return(persistPath);
}
public bool Equals(IrtDb other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(Equals(other._path, _path) &&
other._modifiedTime.Equals(_modifiedTime));
}
public override RetentionScoreCalculatorSpec Initialize(IProgressMonitor loadMonitor)
{
if (_database != null)
{
return(this);
}
var database = IrtDb.GetIrtDb(DatabasePath, loadMonitor);
// Check for the case where an exception was handled by the progress monitor
if (database == null)
{
return(null);
}
return(ChangeDatabase(database));
}
public RCalcIrt ChangeDatabase(IrtDb database)
{
return(ChangeProp(ImClone(this), im => im._database = database));
}
public bool Equals(IrtDb other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other._path, _path) &&
other._modifiedTime.Equals(_modifiedTime);
}
public RCalcIrt ChangeDatabase(IrtDb database)
{
return ChangeProp(ImClone(this), im => im._database = database);
}