/// <summary>
/// Saves the database to a new directory with only the charged peptides used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which charged peptides are to be kept</param>
/// <param name="smallMoleculeConversionMap">Used for changing charge,modifedSeq to adduct,molecule in small molecule conversion</param>
/// <returns>The full path to the file saved</returns>
public override string PersistMinimized(string pathDestDir,
SrmDocument document, IDictionary <LibKey, LibKey> smallMoleculeConversionMap)
{
RequireUsable();
var fname = Path.GetFileName(PersistencePath);
if (smallMoleculeConversionMap != null && fname != null &&
!fname.Contains(BiblioSpecLiteSpec.DotConvertedToSmallMolecules))
{
fname = fname.Replace(IonMobilityDb.EXT, BiblioSpecLiteSpec.DotConvertedToSmallMolecules + IonMobilityDb.EXT);
}
string persistPath = Path.Combine(pathDestDir, fname ?? String.Empty);
using (var fs = new FileSaver(persistPath))
{
var ionMobilityDbMinimal = IonMobilityDb.CreateIonMobilityDb(fs.SafeName);
// Calculate the minimal set of peptides needed for this document
var dbPeptides = _database.GetPeptides().ToList();
var persistPeptides = new List <ValidatingIonMobilityPeptide>();
var dictPeptides = dbPeptides.ToDictionary(pep => pep.GetLibKey());
foreach (var pair in document.MoleculePrecursorPairs)
{
var test =
new ValidatingIonMobilityPeptide(pair.NodePep.ModifiedTarget, pair.NodeGroup.PrecursorAdduct, 0, 0);
var key = test.GetLibKey();
DbIonMobilityPeptide dbPeptide;
if (dictPeptides.TryGetValue(key, out dbPeptide))
{
if (smallMoleculeConversionMap != null)
{
// We are in the midst of converting a document to small molecules for test purposes
LibKey smallMolInfo;
if (smallMoleculeConversionMap.TryGetValue(new LibKey(pair.NodePep.ModifiedSequence, pair.NodeGroup.PrecursorCharge), out smallMolInfo))
{
var precursorAdduct = smallMolInfo.Adduct;
var smallMoleculeAttributes = smallMolInfo.SmallMoleculeLibraryAttributes;
dbPeptide = new DbIonMobilityPeptide(smallMoleculeAttributes, precursorAdduct, dbPeptide.CollisionalCrossSection, dbPeptide.HighEnergyDriftTimeOffsetMsec);
}
else
{
// Not being converted
Assume.IsTrue(pair.NodeGroup.Peptide.IsDecoy);
continue;
}
}
persistPeptides.Add(new ValidatingIonMobilityPeptide(dbPeptide));
// Only add once
dictPeptides.Remove(key);
}
}
ionMobilityDbMinimal.UpdatePeptides(persistPeptides, new ValidatingIonMobilityPeptide[0]);
fs.Commit();
}
return(persistPath);
}
/// <summary>
/// Saves the database to a new directory with only the charged peptides used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which charged 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);
using (var fs = new FileSaver(persistPath))
{
var ionMobilityDbMinimal = IonMobilityDb.CreateIonMobilityDb(fs.SafeName);
// Calculate the minimal set of peptides needed for this document
var dbPeptides = _database.GetPeptides().ToList();
var persistPeptides = new List <ValidatingIonMobilityPeptide>();
var dictPeptides = dbPeptides.ToDictionary(pep => pep.PeptideModSeq);
foreach (var peptide in document.Molecules)
{
string modifiedSeq = document.Settings.GetSourceTextId(peptide);
DbIonMobilityPeptide dbPeptide;
if (dictPeptides.TryGetValue(modifiedSeq, out dbPeptide))
{
persistPeptides.Add(new ValidatingIonMobilityPeptide(dbPeptide.Sequence, dbPeptide.CollisionalCrossSection, dbPeptide.HighEnergyDriftTimeOffsetMsec));
// Only add once
dictPeptides.Remove(modifiedSeq);
}
}
ionMobilityDbMinimal.UpdatePeptides(persistPeptides, new ValidatingIonMobilityPeptide[0]);
fs.Commit();
}
return(persistPath);
}
