public PrecursorIonMobilities(PrecursorIonMobilities other)
: this(other.Precursor, other.IonMobilities)
{
}
/// <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);
}