/// <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);
}
/// <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);
}
public static IonMobilityLibrary CreateFromResults(SrmDocument document, string documentFilePath, bool useHighEnergyOffset,
string libraryName, string dbPath, IProgressMonitor progressMonitor = null)
{
// Overwrite any existing measurements with newly derived ones
var measured = CreateFromResults(document, documentFilePath, useHighEnergyOffset, progressMonitor);
var ionMobilityDb = IonMobilityDb.CreateIonMobilityDb(dbPath, libraryName, false).
UpdateIonMobilities(measured.Select(m => new PrecursorIonMobilities(
m.Key, m.Value)).ToList());
return(new IonMobilityLibrary(libraryName, dbPath, ionMobilityDb));
}
public bool Equals(IonMobilityDb other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(Equals(other._path, _path) &&
other._modifiedTime.Equals(_modifiedTime));
}
public override IonMobilityLibrarySpec Initialize(IProgressMonitor loadMonitor)
{
if (_database != null)
{
return(this);
}
var database = IonMobilityDb.GetIonMobilityDb(DatabasePath, loadMonitor);
// Check for the case where an exception was handled by the progress monitor
if (database == null)
{
return(null);
}
return(ChangeDatabase(database));
}
public static IonMobilityLibrary CreateFromDictionary(string libraryName, string dbDir, IDictionary <LibKey, List <IonMobilityAndCCS> > dict)
{
var fname = Path.GetFullPath(dbDir.Contains(IonMobilityDb.EXT) ? dbDir : Path.Combine(dbDir, libraryName + IonMobilityDb.EXT));
IonMobilityDb ionMobilityDb;
using (var fs = new FileSaver(fname))
{
ionMobilityDb = IonMobilityDb.CreateIonMobilityDb(fs.SafeName, libraryName, false);
if (dict != null)
{
var list = dict.Select(kvp => new PrecursorIonMobilities(kvp.Key, kvp.Value));
ionMobilityDb = ionMobilityDb.UpdateIonMobilities(list);
}
fs.Commit();
}
return(new IonMobilityLibrary(libraryName, fname, ionMobilityDb));
}
public bool Equals(IonMobilityDb other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return Equals(other._path, _path) &&
other._modifiedTime.Equals(_modifiedTime);
}
public IonMobilityLibrary ChangeDatabase(IonMobilityDb database)
{
return(ChangeProp(ImClone(this), im => im._database = database));
}
public IonMobilityLibrary ChangeDatabase(IonMobilityDb database)
{
return ChangeProp(ImClone(this), im => im._database = database);
}
/// <summary>
/// Saves the database to a new directory with only the ions used
/// in a given document.
/// </summary>
/// <param name="pathDestDir">The directory to save to</param>
/// <param name="document">The document for which ions are to be kept</param>
/// <param name="smallMoleculeConversionMap">Used for changing charge,modifedSeq to adduct,molecule in small molecule conversion</param>
/// <param name="loadedDatabase">Returns in-memory representation of the revised ion mobility table</param>
/// <returns>The full path to the file saved</returns>
public string PersistMinimized(string pathDestDir,
SrmDocument document, IDictionary <LibKey, LibKey> smallMoleculeConversionMap, out IonMobilityDb loadedDatabase)
{
RequireUsable();
var fname = Path.GetFileName(FilePath);
if (smallMoleculeConversionMap != null && fname != null &&
!fname.Contains(BiblioSpecLiteSpec.DotConvertedToSmallMolecules))
{
fname = fname.Replace(IonMobilityDb.EXT, BiblioSpecLiteSpec.DotConvertedToSmallMolecules + IonMobilityDb.EXT);
}
fname = fname ?? string.Empty; // Keeps ReSharper from complaining about possible null
string persistPath = Path.Combine(pathDestDir, fname);
using (var fs = new FileSaver(persistPath))
{
var libraryName = fname.Replace(IonMobilityDb.EXT, String.Empty);
var ionMobilityDbMinimal = IonMobilityDb.CreateIonMobilityDb(fs.SafeName, libraryName, true);
// Calculate the minimal set of peptides needed for this document
var dbPrecursors = _database.DictLibrary.LibKeys;
var persistIonMobilities = new List <PrecursorIonMobilities>();
var dictPrecursors = dbPrecursors.ToDictionary(p => p.LibraryKey);
foreach (var pair in document.MoleculePrecursorPairs)
{
var test =
new PrecursorIonMobilities(pair.NodePep.ModifiedTarget, pair.NodeGroup.PrecursorAdduct, 0, 0, 0, eIonMobilityUnits.none);
var key = test.Precursor;
if (dictPrecursors.TryGetValue(key, out var dbPrecursor))
{
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;
dbPrecursor = new LibKey(smallMoleculeAttributes, precursorAdduct);
}
else
{
// Not being converted
Assume.IsTrue(pair.NodeGroup.Peptide.IsDecoy);
continue;
}
}
persistIonMobilities.Add(new PrecursorIonMobilities(dbPrecursor, test.IonMobilities));
// Only add once
dictPrecursors.Remove(key);
}
}
loadedDatabase = ionMobilityDbMinimal.UpdateIonMobilities(persistIonMobilities);
fs.Commit();
}
return(persistPath);
}
public IonMobilityLibrary(string name, string filePath, IonMobilityDb loadedDatabase) : base(name, filePath)
{
_database = loadedDatabase;
}
