public int CompareTo(object obj)
{
if (obj == null)
{
return(1);
}
var other = obj as OptimizationKey;
if (other == null)
{
throw new ArgumentException(Resources.OptimizationKey_CompareTo_Cannot_compare_OptimizationKey_to_an_object_of_a_different_type);
}
else if (!Equals(OptType, other.OptType))
{
return(OptType.CompareTo(other.OptType));
}
else if (!Equals(PeptideModSeq, other.PeptideModSeq))
{
return(PeptideModSeq.CompareTo(other.PeptideModSeq));
}
else if (!PrecursorAdduct.Equals(other.PrecursorAdduct))
{
return(PrecursorAdduct.CompareTo(other.PrecursorAdduct));
}
else if (FragmentIon != other.FragmentIon)
{
return(String.Compare(FragmentIon, other.FragmentIon, StringComparison.InvariantCulture));
}
else
{
return(ProductAdduct.CompareTo(other.ProductAdduct));
}
}
public override int GetHashCode()
{
unchecked
{
int result = _peptide.GetHashCode();
result = (result * 397) ^ PrecursorAdduct.GetHashCode();
result = (result * 397) ^ LabelType.GetHashCode();
result = (result * 397) ^ (DecoyMassShift ?? 0);
return(result);
}
}
public override int GetHashCode()
{
unchecked
{
int result = (PeptideModSeq != null ? PeptideModSeq.GetHashCode() : 0);
result = (result * 397) ^ OptType.GetHashCode();
result = (result * 397) ^ PrecursorAdduct.GetHashCode();
if (FragmentIon != null)
{
result = (result * 397) ^ FragmentIon.GetHashCode();
}
result = (result * 397) ^ ProductAdduct.GetHashCode();
return(result);
}
}
public IEnumerable <TransitionDocNode> GetPrecursorTransitions(SrmSettings settings,
ExplicitMods mods,
IPrecursorMassCalc calcPredictPre,
IFragmentMassCalc calcPredict,
double precursorMz,
IsotopeDistInfo isotopeDist,
IList <IList <ExplicitLoss> > potentialLosses,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool libraryFilter,
bool useFilter)
{
var tranSettings = settings.TransitionSettings;
var fullScan = tranSettings.FullScan;
int minMz = tranSettings.Instrument.GetMinMz(precursorMz);
int maxMz = tranSettings.Instrument.MaxMz;
bool precursorMS1 = fullScan.IsEnabledMs;
MassType massType = tranSettings.Prediction.FragmentMassType;
MassType massTypeIon = precursorMS1 ? tranSettings.Prediction.PrecursorMassType : massType;
var sequence = Peptide.Target;
var ionTypes = IsProteomic ? tranSettings.Filter.PeptideIonTypes : tranSettings.Filter.SmallMoleculeIonTypes;
bool precursorNoProducts = precursorMS1 && !fullScan.IsEnabledMsMs &&
ionTypes.Count == 1 && ionTypes[0] == IonType.precursor;
var precursorMassPredict = precursorMS1
? calcPredictPre.GetPrecursorMass(sequence)
: calcPredict.GetPrecursorFragmentMass(sequence);
foreach (var losses in CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double ionMz = IsProteomic ?
SequenceMassCalc.GetMZ(Transition.CalcMass(precursorMassPredict, losses), PrecursorAdduct) :
PrecursorAdduct.MzFromNeutralMass(CustomMolecule.GetMass(massTypeIon), massTypeIon);
if (losses == null)
{
if (precursorMS1 && isotopeDist != null)
{
foreach (int i in fullScan.SelectMassIndices(isotopeDist, useFilter))
{
var precursorMS1Mass = isotopeDist.GetMassI(i, DecoyMassShift);
ionMz = SequenceMassCalc.GetMZ(precursorMS1Mass, PrecursorAdduct);
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
var isotopeDistInfo = new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(i), isotopeDist.GetProportionI(i));
yield return(CreateTransitionNode(i, precursorMS1Mass, isotopeDistInfo, null, transitionRanks));
}
continue;
}
}
// If there was loss, it is possible (though not likely) that the ion m/z value
// will now fall below the minimum measurable value for the instrument
else if (minMz > ionMz)
{
continue;
}
// If filtering precursors from MS1 scans, then ranking in MS/MS does not apply
bool precursorIsProduct = !precursorMS1 || losses != null;
// Skip product ion precursors, if the should not be included
if (useFilter && precursorIsProduct && precursorNoProducts)
{
continue;
}
if (!useFilter || !precursorIsProduct ||
!libraryFilter || IsMatched(transitionRanks, ionMz, IonType.precursor,
PrecursorAdduct, losses))
{
yield return(CreateTransitionNode(0, precursorMassPredict, null, losses,
precursorIsProduct ? transitionRanks : null));
}
}
}
