/// <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); }