/// <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 void TestLibIonMobilityInfo()
{
const double HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC = -.01;
var dbIon1 = new DbIonMobilityPeptide("JKLMN", 1.2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC) { Id = 12345 };
var dbIon2 = new DbIonMobilityPeptide(dbIon1);
DbIonMobilityPeptide dbIon3 = null;
Assert.AreEqual(dbIon1.GetHashCode(), dbIon2.GetHashCode());
Assert.IsFalse(dbIon1.Equals(null));
Assert.IsTrue(dbIon1.Equals(dbIon2 as object));
// ReSharper disable once ExpressionIsAlwaysNull
Assert.IsFalse(dbIon1.Equals(dbIon3 as object));
Assert.IsTrue(dbIon1.Equals(dbIon1));
Assert.IsTrue(dbIon1.Equals(dbIon1 as object));
Assert.IsTrue(dbIon1.Equals(dbIon2));
dbIon1.CollisionalCrossSection = 1.3;
dbIon1.PeptideModSeq = "foo";
Assert.AreNotEqual(dbIon1.CollisionalCrossSection, dbIon2.CollisionalCrossSection);
Assert.AreNotEqual(dbIon1.Sequence, dbIon2.Sequence);
Assert.AreNotEqual(dbIon1.PeptideModSeq, dbIon2.PeptideModSeq);
var dictCCS1 = new Dictionary<LibKey, IonMobilityInfo[]>();
var ccs1 = new List<IonMobilityInfo> { new IonMobilityInfo(1, true, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), new IonMobilityInfo(2, true, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC) }; // Collisional cross sections
var ccs2 = new List<IonMobilityInfo> { new IonMobilityInfo(3, true, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), new IonMobilityInfo(4, true, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC) }; // Collisional cross sections
const string seq1 = "JKLM";
const string seq2 = "KLMN";
dictCCS1.Add(new LibKey(seq1,1),ccs1.ToArray());
dictCCS1.Add(new LibKey(seq2,1),ccs2.ToArray());
var lib = new List<LibraryIonMobilityInfo> { new LibraryIonMobilityInfo("test", dictCCS1) };
var peptideTimes = CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib, 1, null);
var validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPeptide[] ?? peptideTimes.ToArray();
Assert.AreEqual(2, validatingIonMobilityPeptides.Count());
Assert.AreEqual(1.5, validatingIonMobilityPeptides[0].CollisionalCrossSection);
Assert.AreEqual(3.5, validatingIonMobilityPeptides[1].CollisionalCrossSection);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyDriftTimeOffsetMsec);
var dictCCS2 = new Dictionary<LibKey, IonMobilityInfo[]>();
var ccs3 = new List<IonMobilityInfo> { new IonMobilityInfo(4, false, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), new IonMobilityInfo(5, false, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC) }; // Drift times
const string seq3 = "KLMNJ";
dictCCS2.Add(new LibKey(seq3, 1), ccs3.ToArray());
lib.Add(new LibraryIonMobilityInfo("test2", dictCCS2));
List<LibraryIonMobilityInfo> lib1 = lib;
AssertEx.ThrowsException<Exception>(() => CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib1, 2, null),
String.Format(
Resources.CollisionalCrossSectionGridViewDriver_ProcessIonMobilityValues_Cannot_import_measured_drift_time_for_sequence__0___no_collisional_cross_section_conversion_parameters_were_provided_for_charge_state__1__,
seq3, 1));
var regressions = new Dictionary<int, RegressionLine> {{1, new RegressionLine(2, 1)}};
lib = new List<LibraryIonMobilityInfo> { new LibraryIonMobilityInfo("test", dictCCS2) };
peptideTimes = CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib, 1, regressions);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPeptide[] ?? peptideTimes.ToArray();
Assert.AreEqual(1, validatingIonMobilityPeptides.Count());
Assert.AreEqual(1.75, validatingIonMobilityPeptides[0].CollisionalCrossSection);
}
public IonMobilityDb UpdatePeptides(IList <ValidatingIonMobilityPeptide> newPeptides, IList <ValidatingIonMobilityPeptide> oldPeptides)
{
var dictOld = new Dictionary <String, ValidatingIonMobilityPeptide>();
foreach (var ionMobilityPeptide in oldPeptides) // Not using ToDict in case of duplicate entries
{
ValidatingIonMobilityPeptide pep;
if (!dictOld.TryGetValue(ionMobilityPeptide.Sequence, out pep))
{
dictOld[ionMobilityPeptide.Sequence] = ionMobilityPeptide;
}
}
var dictNew = new Dictionary <String, ValidatingIonMobilityPeptide>();
foreach (var ionMobilityPeptide in newPeptides) // Not using ToDict in case of duplicate entries
{
ValidatingIonMobilityPeptide pep;
if (!dictNew.TryGetValue(ionMobilityPeptide.Sequence, out pep))
{
dictNew[ionMobilityPeptide.Sequence] = ionMobilityPeptide;
}
}
using (var session = OpenWriteSession())
using (var transaction = session.BeginTransaction())
{
// Remove peptides that are no longer in the list
foreach (var peptideOld in oldPeptides)
{
ValidatingIonMobilityPeptide pep;
if (!dictNew.TryGetValue(peptideOld.Sequence, out pep))
{
session.Delete(peptideOld);
}
}
// Add or update peptides that have changed from the old list
foreach (var peptideNew in newPeptides)
{
ValidatingIonMobilityPeptide pep;
if (!dictOld.TryGetValue(peptideNew.Sequence, out pep))
{
// Create a new instance, because not doing this causes a BindingSource leak
var peptideNewDisconnected = new DbIonMobilityPeptide(peptideNew);
session.SaveOrUpdate(peptideNewDisconnected);
}
}
transaction.Commit();
}
return(ChangeProp(ImClone(this), im => im.LoadPeptides(newPeptides)));
}
public virtual bool Equals(DbIonMobilityPeptide other)
{
if (ReferenceEquals(null, other))
{
return(false);
}
if (ReferenceEquals(this, other))
{
return(true);
}
return(base.Equals(other) &&
Equals(other.PeptideModSeq, PeptideModSeq) &&
other.HighEnergyDriftTimeOffsetMsec.Equals(other.HighEnergyDriftTimeOffsetMsec) &&
other.CollisionalCrossSection.Equals(CollisionalCrossSection));
}
private void LoadPeptides(IEnumerable <DbIonMobilityPeptide> peptides)
{
var dictLibrary = new Dictionary <LibKey, DbIonMobilityPeptide>();
foreach (var pep in peptides)
{
var dict = dictLibrary;
try
{
DbIonMobilityPeptide ignored;
var adduct = pep.GetPrecursorAdduct();
if (adduct.IsEmpty)
{
// Older formats didn't consider charge to be a factor is CCS, so just fake up M+H, M+2H and M+3H
for (int z = 1; z <= 3; z++)
{
var newPep = new DbIonMobilityPeptide(pep.GetNormalizedModifiedSequence(),
Adduct.FromChargeProtonated(z), pep.CollisionalCrossSection, pep.HighEnergyDriftTimeOffsetMsec);
var key = newPep.GetLibKey();
if (!dict.TryGetValue(key, out ignored))
{
dict.Add(key, newPep);
}
}
}
else
{
var key = pep.GetLibKey();
if (!dict.TryGetValue(key, out ignored))
{
dict.Add(key, pep);
}
}
}
catch (ArgumentException)
{
}
}
DictLibrary = dictLibrary;
}
public IonMobilityDb UpdatePeptides(IList<ValidatingIonMobilityPeptide> newPeptides, IList<ValidatingIonMobilityPeptide> oldPeptides)
{
var dictOld = new Dictionary<String, ValidatingIonMobilityPeptide>();
foreach (var ionMobilityPeptide in oldPeptides) // Not using ToDict in case of duplicate entries
{
ValidatingIonMobilityPeptide pep;
if (!dictOld.TryGetValue(ionMobilityPeptide.Sequence, out pep))
dictOld[ionMobilityPeptide.Sequence] = ionMobilityPeptide;
}
var dictNew = new Dictionary<String, ValidatingIonMobilityPeptide>();
foreach (var ionMobilityPeptide in newPeptides) // Not using ToDict in case of duplicate entries
{
ValidatingIonMobilityPeptide pep;
if (!dictNew.TryGetValue(ionMobilityPeptide.Sequence, out pep))
dictNew[ionMobilityPeptide.Sequence] = ionMobilityPeptide;
}
using (var session = OpenWriteSession())
using (var transaction = session.BeginTransaction())
{
// Remove peptides that are no longer in the list
foreach (var peptideOld in oldPeptides)
{
ValidatingIonMobilityPeptide pep;
if (!dictNew.TryGetValue(peptideOld.Sequence, out pep))
session.Delete(peptideOld);
}
// Add or update peptides that have changed from the old list
foreach (var peptideNew in newPeptides)
{
ValidatingIonMobilityPeptide pep;
if (!dictOld.TryGetValue(peptideNew.Sequence, out pep))
{
// Create a new instance, because not doing this causes a BindingSource leak
var peptideNewDisconnected = new DbIonMobilityPeptide(peptideNew);
session.SaveOrUpdate(peptideNewDisconnected);
}
}
transaction.Commit();
}
return ChangeProp(ImClone(this), im => im.LoadPeptides(newPeptides));
}
public DbIonMobilityPeptide(DbIonMobilityPeptide other)
: this(other.ModifiedTarget, other.CollisionalCrossSection, other.HighEnergyDriftTimeOffsetMsec,
other._adduct)
{
Id = other.Id;
}
public virtual bool Equals(DbIonMobilityPeptide other)
{
if (ReferenceEquals(null, other)) return false;
if (ReferenceEquals(this, other)) return true;
return base.Equals(other) &&
Equals(other.PeptideModSeq, PeptideModSeq) &&
other.HighEnergyDriftTimeOffsetMsec.Equals(other.HighEnergyDriftTimeOffsetMsec) &&
other.CollisionalCrossSection.Equals(CollisionalCrossSection);
}
public DbIonMobilityPeptide(DbIonMobilityPeptide other)
: this(other.PeptideModSeq, other.CollisionalCrossSection, other.HighEnergyDriftTimeOffsetMsec)
{
Id = other.Id;
}
public DbIonMobilityPeptide(DbIonMobilityPeptide other)
: this(other.PeptideModSeq, other.CollisionalCrossSection, other.HighEnergyDriftTimeOffsetMsec)
{
Id = other.Id;
}
