public PepV01(FastaSeqV01 fastaSequence, int begin, int end, int missedCleavages,
double mh, double?rt)
: this(fastaSequence, begin, end, missedCleavages)
{
MassH = new TypedMass(mh, MassType.MonoisotopicMassH);
PredictedRetentionTime = rt;
}
private static CellDesc CreateIon(IonType type, int ordinal, TypedMass massH, Adduct charge,
IEnumerable <DocNode> choices, ICollection <DocNode> chosen, Transition tranSelected,
RenderTools rt)
{
double mz = SequenceMassCalc.GetMZ(massH, charge);
CellDesc cell = CreateData(string.Format(@"{0:F02}", mz), rt);
foreach (TransitionDocNode nodeTran in choices)
{
Transition tran = nodeTran.Transition;
if (tran.IonType == type &&
tran.Ordinal == ordinal &&
tran.Adduct == charge)
{
cell.Font = rt.FontBold;
if (Equals(tran, tranSelected))
{
cell.Brush = rt.BrushSelected; // Stop after selected
break;
}
if (!chosen.Contains(nodeTran))
{
cell.Brush = rt.BrushChoice; // Keep looking
}
else
{
cell.Brush = rt.BrushChosen; // Stop after chosen
break;
}
}
}
return(cell);
}
public void TestGetFragmentFormula()
{
var pepseq = "PEPTIDE";
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var precursor = FragmentedMolecule.EMPTY.ChangeModifiedSequence(
new ModifiedSequence(pepseq, new ModifiedSequence.Modification[0], MassType.Monoisotopic));
var peptide = new Peptide(precursor.UnmodifiedSequence);
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var settings = SrmSettingsList.GetDefault();
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings,
ExplicitMods.EMPTY, null, null, null, new TransitionDocNode[0], false);
foreach (var ionType in new[] { IonType.a, IonType.b, IonType.c, IonType.x, IonType.y, IonType.z })
{
for (int ordinal = 1; ordinal < pepseq.Length; ordinal++)
{
var transition = new Transition(transitionGroup, ionType, Transition.OrdinalToOffset(ionType, ordinal, pepseq.Length), 0, Adduct.SINGLY_PROTONATED);
var fragment = precursor.ChangeFragmentIon(ionType, ordinal);
var actualMassDistribution = FragmentedMolecule.Settings.DEFAULT.GetMassDistribution(
fragment.FragmentFormula, 0, 0);
var expectedMz = sequenceMassCalc.GetFragmentMass(transition, transitionGroupDocNode.IsotopeDist);
if (expectedMz.IsMassH())
{
expectedMz = new TypedMass(expectedMz.Value - BioMassCalc.MassProton, expectedMz.MassType & ~MassType.bMassH);
}
var actualMz = actualMassDistribution.MostAbundanceMass;
if (Math.Abs(expectedMz - actualMz) > .001)
{
Assert.AreEqual(expectedMz, actualMz, .001, "Ion type {0} Ordinal {1}", ionType, ordinal);
}
}
}
}
public TransitionDocNode(Transition id,
TransitionLosses losses,
TypedMass massH,
TransitionQuantInfo quantInfo)
: this(id, Annotations.EMPTY, losses, massH, quantInfo, null)
{
}
public TransitionDocNode(Transition id,
TransitionLosses losses,
TypedMass massH,
TransitionQuantInfo quantInfo,
ExplicitTransitionValues explicitTransitionValues)
: this(id, Annotations.EMPTY, losses, massH, quantInfo, explicitTransitionValues, null)
{
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
return(new TransitionDocNode(transition, losses, precursorMassH, quantInfo));
}
public CustomMolecule(string formula, TypedMass monoisotopicMass, TypedMass averageMass, string name, MoleculeAccessionNumbers moleculeAccessionNumbers)
{
Formula = formula;
MonoisotopicMass = monoisotopicMass;
AverageMass = averageMass;
Name = name ?? string.Empty;
AccessionNumbers = moleculeAccessionNumbers ?? MoleculeAccessionNumbers.EMPTY;
Validate();
}
private static Adduct CalcProductCharge(TypedMass productMassH, int?productZ, double productMz, double tolerance, bool isCustomIon,
Adduct maxCharge, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
return(CalcCharge(productMassH, productMz, tolerance, isCustomIon,
productZ ?? Transition.MIN_PRODUCT_CHARGE,
productZ ?? Math.Min(maxCharge.AdductCharge, Transition.MAX_PRODUCT_CHARGE),
Transition.MassShifts,
massShiftType,
out massShift,
out nearestCharge));
}
private TransitionDocNode CreateTransitionNode(int massIndex, TypedMass precursorMassH, TransitionIsotopeDistInfo isotopeDistInfo,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, Adduct productAdduct, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, massIndex, productAdduct, customMolecule);
var quantInfo = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses,
Transition.CalcMass(precursorMassH, losses), transitionRanks).ChangeIsotopeDistInfo(isotopeDistInfo);
var transitionDocNode = new TransitionDocNode(transition, losses, precursorMassH, quantInfo, ExplicitTransitionValues.EMPTY);
if (massIndex < 0)
{
transitionDocNode = transitionDocNode.ChangeQuantitative(false);
}
return(transitionDocNode);
}
/// <summary>
/// Calculates the matching charge within a tolerance for a mass, assuming (de)protonation.
/// </summary>
/// <param name="mass">The mass to calculate charge for (actually massH if !IsCustomIon)</param>
/// <param name="mz">The desired m/z value the charge should produce</param>
/// <param name="tolerance">How far off the actual m/z is allowed to be</param>
/// <param name="isCustomIon">Is this a custom ion formula?</param>
/// <param name="minCharge">Minimum charge to consider</param>
/// <param name="maxCharge">Maximum charge to consider</param>
/// <param name="massShifts">Possible mass shifts that may have been applied to decoys</param>
/// <param name="massShiftType"></param>
/// <param name="massShift">Mass shift required to to achieve this charge state or zero</param>
/// <param name="nearestCharge">closest matching charge, useful when return value is null</param>
/// <returns>A matching charge or null, in which case the closest non-matching charge can be found in the nearestCharge value.</returns>
public static Adduct CalcCharge(TypedMass mass, double mz, double tolerance, bool isCustomIon, int minCharge, int maxCharge,
ICollection <int> massShifts, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
Assume.IsTrue(minCharge <= maxCharge);
massShift = 0;
nearestCharge = 0;
double nearestDelta = double.MaxValue;
for (int i = minCharge; i <= maxCharge; i++)
{
if (i != 0) // Avoid z=0 if we're entertaining negative charge states
{
double calculatedMz = isCustomIon
? Adduct.FromChargeProtonated(i).MzFromNeutralMass(mass)
: SequenceMassCalc.GetMZ(mass, i);
double delta = mz - calculatedMz;
double deltaAbs = Math.Abs(delta);
int potentialShift = (int)Math.Round(deltaAbs);
double fractionalDelta = deltaAbs - potentialShift;
if (MatchMz(fractionalDelta, tolerance) && MatchMassShift(potentialShift, massShifts, massShiftType))
{
massShift = potentialShift;
if (delta < 0)
{
massShift = -massShift;
}
var result = i;
nearestCharge = i;
return(Adduct.FromCharge(result, isCustomIon ? Adduct.ADDUCT_TYPE.non_proteomic : Adduct.ADDUCT_TYPE.proteomic));
}
if (deltaAbs < nearestDelta)
{
nearestDelta = deltaAbs;
nearestCharge = i;
}
// If the charge is positive and the calculated m/z is smaller than the desired m/z
// increasing the charge further cannot possibly produce a match
if (massShiftType == MassShiftType.none && minCharge > 0 && delta > 0)
{
break;
}
}
}
Debug.Assert(nearestCharge != 0); // Could only happen if min > max
return(Adduct.EMPTY);
}
public static Adduct CalcPrecursorCharge(TypedMass precursorMassH,
double precursorMz,
double tolerance,
bool isCustomIon,
bool isDecoy,
out int massShift,
out int nearestCharge)
{
return(CalcCharge(precursorMassH, precursorMz, tolerance, isCustomIon,
TransitionGroup.MIN_PRECURSOR_CHARGE,
TransitionGroup.MAX_PRECURSOR_CHARGE,
TransitionGroup.MassShifts,
isDecoy ? MassShiftType.shift_only : MassShiftType.none,
out massShift, out nearestCharge));
}
private static void CheckLabel(string label)
{
string unlabel = label.Substring(0, label.Length - 1);
var adductLabel = Adduct.DICT_ADDUCT_ISOTOPE_NICKNAMES.FirstOrDefault(x => x.Value == label).Key;
var labeled = Adduct.FromStringAssumeProtonated("[2M3C13-Na]");
var unlabeled = Adduct.FromStringAssumeProtonated("[2M-Na]");
var relabeled = Adduct.FromStringAssumeProtonated("[2M3Cl374H2-Na]".Replace("Cl37", adductLabel));
var massNeutral = 5.6;
Assert.AreEqual(
2 * (massNeutral + 3 * (BioMassCalc.MONOISOTOPIC.GetMass("C'") - BioMassCalc.MONOISOTOPIC.GetMass("C"))) -
BioMassCalc.MONOISOTOPIC.GetMass("Na"),
labeled.ApplyToMass(new TypedMass(massNeutral, MassType.Monoisotopic)));
Assert.AreEqual(unlabeled, labeled.ChangeIsotopeLabels(null));
var labels = new Dictionary <string, int> {
{ label, 3 }, { "H2", 4 }
};
Assert.AreEqual(relabeled, labeled.ChangeIsotopeLabels(labels));
var labelsToo = new Dictionary <string, int> {
{ label, 3 }, { "H'", 4 }
};
Assert.AreEqual(relabeled, unlabeled.ChangeIsotopeLabels(labelsToo));
var labelsAlso = new Dictionary <string, int> {
{ adductLabel, 3 }, { "H'", 4 }
}; // Mixed
Assert.AreEqual(relabeled, unlabeled.ChangeIsotopeLabels(labelsAlso));
Assert.AreNotEqual(labeled, unlabeled.ChangeIsotopeLabels(labelsAlso));
// Check Deuterium and Tritium handling
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.GetMass("Cl2Cl'3H5H'4N12"), BioMassCalc.MONOISOTOPIC.GetMass("Cl2Cl'3H5D4N12"));
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.GetMass("Cl2Cl'3H5H\"4N12"), BioMassCalc.MONOISOTOPIC.GetMass("Cl2Cl'3H5T4N12"));
Assert.AreEqual(Molecule.Parse("Cl2Cl'3H5H'4N12".Replace("Cl'", label).Replace("Cl", unlabel)),
Molecule.Parse(relabeled.ApplyIsotopeLabelsToFormula("Cl5H9N12".Replace("Cl", unlabel)))); // Replaces three of five Cl and four of nine H
var m100 = new TypedMass(100, MassType.Monoisotopic);
var mdiff = 2 * (3 * (BioMassCalc.MONOISOTOPIC.GetMass(label) -
BioMassCalc.MONOISOTOPIC.GetMass(unlabel)) +
4 * (BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H2) -
BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.H)));
Assert.AreEqual(m100 + mdiff, relabeled.ApplyIsotopeLabelsToMass(m100),
.005); // Expect increase of 2*(3(Cl37-Cl)+4(H2-H))
var isotopeAsMass = Adduct.FromStringAssumeProtonated("[2M1.23-Na]");
Assert.AreEqual(102.46, isotopeAsMass.ApplyIsotopeLabelsToMass(m100), .005); // Expect increase of 2*1.23
}
public CustomIon(string formula, Adduct adduct, TypedMass monoisotopicMass, TypedMass averageMass, string name)
: base(formula, monoisotopicMass, averageMass, name)
{
if (adduct.IsEmpty)
{
var ionInfo = new IonInfo(NeutralFormula, adduct); // Analyzes the formula to see if it's something like "CH12[M+Na]"
if (!Equals(NeutralFormula, ionInfo.NeutralFormula))
{
Formula = ionInfo.NeutralFormula;
}
Adduct = Adduct.FromStringAssumeProtonated(ionInfo.AdductText);
}
else
{
Adduct = adduct;
}
}
public static CustomMolecule FromTSV(string val)
{
var vals = val.FromEscapedTSV();
var name = vals.Length > 0 ? vals[0] : null;
var formula = vals.Length > 1 ? vals[1] : null;
// ReSharper disable PossibleNullReferenceException
var keysTSV = vals.Length > 2 ? val.Substring(name.Length + formula.Length + 2) : null;
// ReSharper restore PossibleNullReferenceException
if (formula == null && name != null && name.StartsWith(INVARIANT_NAME_DETAIL))
{
// Looks like a mass-only description
Regex r = new Regex(massFormatRegex, RegexOptions.IgnoreCase | RegexOptions.Singleline | RegexOptions.CultureInvariant);
Match m = r.Match(val);
if (m.Success)
{
try
{
var massMono = new TypedMass(double.Parse(m.Groups[1].Value, CultureInfo.InvariantCulture), MassType.Monoisotopic);
var massAvg = new TypedMass(double.Parse(m.Groups[2].Value, CultureInfo.InvariantCulture), MassType.Average);
return(new CustomMolecule(massMono, massAvg));
}
catch
{
Assume.Fail("unable to read custom molecule information"); // Not L10N
}
}
}
else if (formula != null && formula.Contains("/")) // Not L10N
{
// "formula" is actually mono and average masses
try
{
var values = formula.Split('/');
var massMono = new TypedMass(double.Parse(values[0], CultureInfo.InvariantCulture), MassType.Monoisotopic);
var massAvg = new TypedMass(double.Parse(values[1], CultureInfo.InvariantCulture), MassType.Average);
return(new CustomMolecule(massMono, massAvg, name, new MoleculeAccessionNumbers(keysTSV)));
}
catch
{
Assume.Fail("unable to read custom molecule information"); // Not L10N
}
}
return(new CustomMolecule(formula, null, null, name, new MoleculeAccessionNumbers(keysTSV)));
}
public FragmentIon(PepV01 peptide, IonType type, int offset, double mh)
{
_peptide = peptide;
IType = type;
CleavageOffset = offset;
MassH = new TypedMass(mh, MassType.MonoisotopicMassH);
// Derived values
if (IsNTerminal())
{
Ordinal = offset + 1;
AA = peptide.Target.Sequence[offset];
}
else
{
Ordinal = _peptide.Length - offset - 1;
AA = peptide.Target.Sequence[offset + 1];
}
}
/// <summary>
/// Calculates the matching charge within a tolerance for a mass, assuming (de)protonation.
/// </summary>
/// <param name="mass">The mass to calculate charge for (actually massH if !IsCustomIon)</param>
/// <param name="mz">The desired m/z value the charge should produce</param>
/// <param name="tolerance">How far off the actual m/z is allowed to be</param>
/// <param name="isCustomIon">Is this a custom ion formula?</param>
/// <param name="minCharge">Minimum charge to consider</param>
/// <param name="maxCharge">Maximum charge to consider</param>
/// <param name="massShifts">Possible mass shifts that may have been applied to decoys</param>
/// <param name="massShiftType"></param>
/// <param name="massShift">Mass shift required to to achieve this charge state or zero</param>
/// <param name="nearestCharge">closest matching charge, useful when return value is null</param>
/// <returns>A matching charge or null, in which case the closest non-matching charge can be found in the nearestCharge value.</returns>
public static Adduct CalcCharge(TypedMass mass, double mz, double tolerance, bool isCustomIon, int minCharge, int maxCharge,
ICollection <int> massShifts, MassShiftType massShiftType, out int massShift, out int nearestCharge)
{
Assume.IsTrue(minCharge <= maxCharge);
massShift = 0;
nearestCharge = 0;
double nearestDelta = double.MaxValue;
for (int i = minCharge; i <= maxCharge; i++)
{
if (i != 0) // Avoid z=0 if we're entertaining negative charge states
{
double delta = mz - (isCustomIon ? Adduct.FromChargeProtonated(i).MzFromNeutralMass(mass) : SequenceMassCalc.GetMZ(mass, i));
double deltaAbs = Math.Abs(delta);
int potentialShift = (int)Math.Round(deltaAbs);
double fractionalDelta = deltaAbs - potentialShift;
if (MatchMz(fractionalDelta, tolerance) && MatchMassShift(potentialShift, massShifts, massShiftType))
{
massShift = potentialShift;
if (delta < 0)
{
massShift = -massShift;
}
var result = i;
nearestCharge = i;
return(Adduct.FromChargeProtonated(result));
}
if (deltaAbs < nearestDelta)
{
nearestDelta = deltaAbs;
nearestCharge = i;
}
}
}
Debug.Assert(nearestCharge != 0); // Could only happen if min > max
return(Adduct.EMPTY);
}
private List <SpectrumPeaksInfo.MI> CalcMIs(TypedMass mass, float[] intensities, int offset)
{
var result = new List <SpectrumPeaksInfo.MI>(PrositConstants.IONS_PER_RESIDUE / 2);
for (var c = 0; c < PrositConstants.IONS_PER_RESIDUE / 2; ++c)
{
// Not a possible charge
if (PeptidePrecursorNCE.NodeGroup.PrecursorCharge <= c)
{
break;
}
result.Add(new SpectrumPeaksInfo.MI
{
Mz = SequenceMassCalc.GetMZ(mass, c + 1),
Intensity = intensities[c + offset]
});
}
return(result);
}
public TransitionDocNode(Transition id,
Annotations annotations,
TransitionLosses losses,
TypedMass mass,
TransitionQuantInfo transitionQuantInfo,
Results <TransitionChromInfo> results)
: base(id, annotations)
{
Losses = losses;
if (losses != null)
{
mass -= losses.Mass;
}
Mz = id.IsCustom() ?
new SignedMz(id.Adduct.MzFromNeutralMass(mass), id.IsNegative()) :
new SignedMz(SequenceMassCalc.GetMZ(mass, id.Adduct) + SequenceMassCalc.GetPeptideInterval(id.DecoyMassShift), id.IsNegative());
MzMassType = mass.MassType;
IsotopeDistInfo = transitionQuantInfo.IsotopeDistInfo;
LibInfo = transitionQuantInfo.LibInfo;
Results = results;
Quantitative = transitionQuantInfo.Quantititative;
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
int?productZ,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double?minDelta = null;
double?minFragmentMass = null, maxFragmentMass = null, maxLoss = null;
if (massShiftType == MassShiftType.none)
{
if (!productZ.HasValue)
{
minFragmentMass = productMz - tolerance;
}
else
{
minFragmentMass = SequenceMassCalc.GetMH(productMz - tolerance, productZ.Value);
maxFragmentMass = SequenceMassCalc.GetMH(productMz + tolerance, productZ.Value);
}
}
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
maxLoss = Math.Max(maxLoss ?? 0, lossesTrial.Mass);
}
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
if (maxLoss.HasValue)
{
maxFragmentMass += maxLoss.Value;
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
// The peptide length is 1 longer than the mass array
for (int ord = len; ord > 0; ord--)
{
int offset = Transition.OrdinalToOffset(type, ord, len + 1);
var productMassBase = productMasses[type, offset];
// Until below the maximum fragment mass no possible matches
if (maxFragmentMass.HasValue && productMassBase > maxFragmentMass.Value)
{
continue;
}
// Once below the minimum fragment mass no more possible matches, so stop
if (minFragmentMass.HasValue && productMassBase < minFragmentMass.Value)
{
break;
}
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMassBase;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
bestOrdinal = ord;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
public CustomMolecule(TypedMass monoisotopicMass, TypedMass averageMass, string name = null, MoleculeAccessionNumbers moleculeAccessionNumbers = null)
: this(null, monoisotopicMass, averageMass, name, moleculeAccessionNumbers)
{
}
public IsotopeDistInfo(MassDistribution massDistribution,
TypedMass monoisotopicMass,
Adduct adduct,
Func <double, double> calcFilterWindow,
double massResolution,
double minimumAbundance)
{
_monoisotopicMass = monoisotopicMass;
_adduct = adduct.Unlabeled; // Don't reapply explicit isotope labels
// Get peak center of mass values for the given resolution
var q1FilterValues = MassDistribution.NewInstance(massDistribution, massResolution, 0).Keys.ToList();
// Find the monoisotopic m/z and make sure it is exactly the expected number
double monoMz = _adduct.MzFromNeutralMass(_monoisotopicMass);
double monoMzDist = monoMz;
int monoMassIndex = 0;
for (int i = 0; i < q1FilterValues.Count; i++)
{
double peakCenterMz = q1FilterValues[i];
double filterWindow = calcFilterWindow(peakCenterMz);
double startMz = peakCenterMz - filterWindow / 2;
double endMz = startMz + filterWindow;
if (startMz < monoMz && monoMz < endMz)
{
monoMzDist = q1FilterValues[i];
q1FilterValues[i] = monoMz;
monoMassIndex = i;
break;
}
}
// Insert a M-1 peak, even if it is not expected in the isotope mass distribution
if (monoMassIndex == 0 && q1FilterValues.Count > 1)
{
// Use the delta from the original distribution monoMz to the next peak
q1FilterValues.Insert(0, monoMz + monoMzDist - q1FilterValues[1]);
monoMassIndex++;
}
if (!q1FilterValues.Any())
{
// This should never happen, but just in case it does happen, we safely exit the constructor
ExpectedPeaks = ImmutableList.Singleton(new MzRankProportion(monoMz, 0, 1.0f));
MonoMassIndex = BaseMassIndex = 0;
return;
}
var signedQ1FilterValues = q1FilterValues.Select(q => new SignedMz(q, adduct.AdductCharge < 0)).ToList();
// Use the filtering algorithm that will be used on real data to determine the
// expected proportions of the mass distribution that will end up filtered into
// peaks
// CONSIDER: Mass accuracy information is not calculated here
var key = new PrecursorTextId(signedQ1FilterValues[monoMassIndex], null, null, ChromExtractor.summed);
var filter = new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, 0, null, null, false, false);
filter.AddQ1FilterValues(signedQ1FilterValues, calcFilterWindow);
var expectedSpectrum = filter.FilterQ1SpectrumList(new[] { new MsDataSpectrum
{
Mzs = massDistribution.Keys.ToArray(), Intensities = massDistribution.Values.ToArray(), NegativeCharge = (adduct.AdductCharge < 0)
} });
int startIndex = expectedSpectrum.Intensities.IndexOf(inten => inten >= minimumAbundance);
if (startIndex == -1)
{
// This can happen if the amino acid modifications are messed up,
// and the peptide mass is negative or something.
ExpectedPeaks = ImmutableList.Singleton(new MzRankProportion(monoMz, 0, 1.0f));
MonoMassIndex = BaseMassIndex = 0;
return;
}
// Always include the M-1 peak, even if it is expected to have zero intensity
if (startIndex > monoMassIndex - 1)
{
startIndex = monoMassIndex - 1;
}
if (startIndex < 0)
{
startIndex = 0;
}
int endIndex = expectedSpectrum.Intensities.LastIndexOf(inten => inten >= minimumAbundance) + 1;
int countPeaks = endIndex - startIndex;
var listProportionIndices = new List <KeyValuePair <float, int> >(countPeaks);
for (int i = 0; i < countPeaks; i++)
{
listProportionIndices.Add(new KeyValuePair <float, int>(
expectedSpectrum.Intensities[i + startIndex], i));
}
// Sort proportions descending.
listProportionIndices.Sort((p1, p2) => Comparer.Default.Compare(p2.Key, p1.Key));
// Set proportions and ranks back in the original locations
var expectedProportionRanks = new KeyValuePair <float, int> [countPeaks];
for (int i = 0; i < countPeaks; i++)
{
expectedProportionRanks[listProportionIndices[i].Value] =
new KeyValuePair <float, int>(listProportionIndices[i].Key, i + 1);
}
MonoMassIndex = monoMassIndex - startIndex;
// Find the base peak and fill in the masses and proportions
var expectedPeaks = new List <MzRankProportion>();
for (int i = 0; i < countPeaks; i++)
{
float expectedProportion = expectedProportionRanks[i].Key;
int rank = expectedProportionRanks[i].Value;
expectedPeaks.Add(new MzRankProportion(q1FilterValues[i + startIndex], rank, expectedProportion));
if (expectedProportion > expectedProportionRanks[BaseMassIndex].Key)
{
BaseMassIndex = i;
}
}
ExpectedPeaks = expectedPeaks;
}
public static TypedMass CalcMass(TypedMass massH, TransitionLosses losses)
{
return(massH - (losses != null ? losses.Mass : 0));
}
public void CalcMass(SequenceMassCalc massCalc)
{
MassH = massCalc.GetPrecursorMass(Target.Sequence);
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var charge = 0;
if (textCharge.Visible &&
!helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge))
{
return;
}
var adduct = Adduct.NonProteomicProtonatedFromCharge(charge);
if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue)
{
helper.ShowTextBoxError(textRetentionTimeWindow,
Resources
.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
return;
}
if (Adduct.IsEmpty || Adduct.AdductCharge != adduct.AdductCharge)
{
Adduct =
adduct; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty
}
if (string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
// Can the text fields be understood as mz?
if (!_formulaBox.ValidateAverageText(helper))
{
return;
}
if (!_formulaBox.ValidateMonoText(helper))
{
return;
}
}
var monoMass = new TypedMass(_formulaBox.MonoMass ?? 0, MassType.Monoisotopic);
var averageMass = new TypedMass(_formulaBox.AverageMass ?? 0, MassType.Average);
if (monoMass < CustomMolecule.MIN_MASS || averageMass < CustomMolecule.MIN_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__,
CustomMolecule.MIN_MASS));
return;
}
if (monoMass > CustomMolecule.MAX_MASS || averageMass > CustomMolecule.MAX_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__,
CustomMolecule.MAX_MASS));
return;
}
if ((_transitionSettings != null) &&
(!_transitionSettings.IsMeasurablePrecursor(
adduct.MzFromNeutralMass(monoMass, MassType.Monoisotopic)) ||
!_transitionSettings.IsMeasurablePrecursor(adduct.MzFromNeutralMass(averageMass, MassType.Average))))
{
_formulaBox.ShowTextBoxErrorFormula(helper,
Resources
.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_);
return;
}
if (_usageMode == UsageMode.precursor)
{
// Only the adduct should be changing
SetResult(_resultCustomMolecule, Adduct);
}
else if (!string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
try
{
var name = textName.Text;
if (string.IsNullOrEmpty(name))
{
name = _formulaBox.NeutralFormula; // Clip off any adduct description
}
SetResult(new CustomMolecule(_formulaBox.NeutralFormula, name), Adduct);
}
catch (InvalidDataException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else
{
SetResult(new CustomMolecule(monoMass, averageMass, textName.Text), Adduct);
}
// Did user change the list of heavy labels?
if (_driverLabelType != null)
{
PeptideModifications modifications = new PeptideModifications(
_peptideSettings.Modifications.StaticModifications,
_peptideSettings.Modifications.MaxVariableMods,
_peptideSettings.Modifications.MaxNeutralLosses,
_driverLabelType.GetHeavyModifications(), // This is the only thing the user may have altered
_peptideSettings.Modifications.InternalStandardTypes);
var settings = _peptideSettings.ChangeModifications(modifications);
// Only update if anything changed
if (!Equals(settings, _peptideSettings))
{
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (!_parent.ChangeSettings(newSettings, true))
{
return;
}
_peptideSettings = newSettings.PeptideSettings;
}
}
// See if this combination of charge and label would conflict with any existing transition groups
if (_existingIds != null && _existingIds.Any(t =>
{
var transitionGroup = t as TransitionGroup;
return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) &&
Equals(transitionGroup.PrecursorAdduct.AsFormula(),
Adduct
.AsFormula()) && // Compare AsFormula so proteomic and non-proteomic protonation are seen as same thing
!ReferenceEquals(t, _initialId));
}))
{
helper.ShowTextBoxError(textName,
Resources
.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_adduct_and_label_type_already_exists_,
textName.Text);
return;
}
// See if this would conflict with any existing transitions
if (_existingIds != null && (_existingIds.Any(t =>
{
var transition = t as Transition;
return(transition != null && (Equals(transition.Adduct.AsFormula(), Adduct.AsFormula()) &&
Equals(transition.CustomIon, ResultCustomMolecule)) &&
!ReferenceEquals(t, _initialId));
})))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text);
return;
}
DialogResult = DialogResult.OK;
}
private static void TestEditingTransitionAsMasses()
{
double massPrecisionTolerance = Math.Pow(10, -SequenceMassCalc.MassPrecision);
var doc = SkylineWindow.Document;
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode;
});
var editMoleculeDlg =
ShowDialog <EditCustomMoleculeDlg>(
() => SkylineWindow.ModifyTransition((TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode));
var monoMass = new TypedMass(805, MassType.Monoisotopic);
RunUI(() =>
{
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.CalculateIonMz(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12), editMoleculeDlg.Adduct), double.Parse(editMoleculeDlg.FormulaBox.MonoText), massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.CalculateIonMz(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12), editMoleculeDlg.Adduct), double.Parse(editMoleculeDlg.FormulaBox.AverageText), massPrecisionTolerance);
Assert.AreEqual(Adduct.M_PLUS.AdductFormula, editMoleculeDlg.FormulaBox.Adduct.AdductFormula);
editMoleculeDlg.FormulaBox.AverageMass = 800;
editMoleculeDlg.FormulaBox.MonoMass = monoMass.Value;
editMoleculeDlg.NameText = "Fragment";
});
OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
var newdoc = WaitForDocumentChange(doc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsFalse(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id)); // Changing the mass changes the Id
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
// And test undo/redo
RunUI(() => SkylineWindow.Undo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreNotEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreNotEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsTrue(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id));
RunUI(() => SkylineWindow.Redo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
}
public static TransitionQuantInfo GetTransitionQuantInfo(Transition transition, TransitionLosses losses, IsotopeDistInfo isotopeDist, TypedMass massH, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> ranks)
{
var transitionIsotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
return(GetLibTransitionQuantInfo(transition, losses, massH, ranks).ChangeIsotopeDistInfo(transitionIsotopeDistInfo));
}
public static TransitionQuantInfo GetLibTransitionQuantInfo(Transition transition, TransitionLosses losses, TypedMass massH,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> ranks)
{
LibraryRankedSpectrumInfo.RankedMI rmi = null;
if (ranks != null)
{
ranks.TryGetValue(SequenceMassCalc.GetMZ(massH, transition.Adduct), out rmi);
}
TransitionLibInfo transitionLibInfo = null;
if (rmi != null)
{
transitionLibInfo = new TransitionLibInfo(rmi.Rank, rmi.Intensity);
}
return(new TransitionQuantInfo(null, transitionLibInfo,
rmi == null || rmi.Quantitative));
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double? minDelta = null;
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMasses[type, offset];
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
private TransitionDocNode CreateTransitionNode(IonType type, int cleavageOffset, Adduct charge, TypedMass massH,
TransitionLosses losses, IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks, CustomMolecule customMolecule = null)
{
Transition transition = new Transition(this, type, cleavageOffset, 0, charge, null, customMolecule);
var info = TransitionDocNode.TransitionQuantInfo.GetLibTransitionQuantInfo(transition, losses, Transition.CalcMass(massH, losses), transitionRanks);
return(new TransitionDocNode(transition, losses, massH, info));
}
public void OkDialog()
{
var helper = new MessageBoxHelper(this);
var charge = 0;
if (textCharge.Visible &&
!helper.ValidateSignedNumberTextBox(textCharge, _minCharge, _maxCharge, out charge))
{
return;
}
var adduct = Adduct.NonProteomicProtonatedFromCharge(charge);
if (RetentionTimeWindow.HasValue && !RetentionTime.HasValue)
{
helper.ShowTextBoxError(textRetentionTimeWindow,
Resources
.Peptide_ExplicitRetentionTimeWindow_Explicit_retention_time_window_requires_an_explicit_retention_time_value_);
return;
}
if (Adduct.IsEmpty || Adduct.AdductCharge != adduct.AdductCharge)
{
Adduct =
adduct; // Note: order matters here, this settor indirectly updates _formulaBox.MonoMass when formula is empty
}
if (string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
// Can the text fields be understood as mz?
if (!_formulaBox.ValidateAverageText(helper))
{
return;
}
if (!_formulaBox.ValidateMonoText(helper))
{
return;
}
}
var monoMass = new TypedMass(_formulaBox.MonoMass ?? 0, MassType.Monoisotopic);
var averageMass = new TypedMass(_formulaBox.AverageMass ?? 0, MassType.Average);
if (monoMass < CustomMolecule.MIN_MASS || averageMass < CustomMolecule.MIN_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_greater_than_or_equal_to__0__,
CustomMolecule.MIN_MASS));
return;
}
if (monoMass > CustomMolecule.MAX_MASS || averageMass > CustomMolecule.MAX_MASS)
{
_formulaBox.ShowTextBoxErrorFormula(helper,
string.Format(
Resources
.EditCustomMoleculeDlg_OkDialog_Custom_molecules_must_have_a_mass_less_than_or_equal_to__0__,
CustomMolecule.MAX_MASS));
return;
}
if ((_transitionSettings != null) &&
(!_transitionSettings.IsMeasurablePrecursor(
adduct.MzFromNeutralMass(monoMass, MassType.Monoisotopic)) ||
!_transitionSettings.IsMeasurablePrecursor(adduct.MzFromNeutralMass(averageMass, MassType.Average))))
{
_formulaBox.ShowTextBoxErrorFormula(helper,
Resources
.SkylineWindow_AddMolecule_The_precursor_m_z_for_this_molecule_is_out_of_range_for_your_instrument_settings_);
return;
}
// Ion mobility value must have ion mobility units
if (textIonMobility.Visible && IonMobility.HasValue)
{
if (IonMobilityUnits == eIonMobilityUnits.none)
{
helper.ShowTextBoxError(textIonMobility, Resources.EditCustomMoleculeDlg_OkDialog_Please_specify_the_ion_mobility_units_);
comboBoxIonMobilityUnits.Focus();
return;
}
if (IonMobility.Value == 0 ||
(IonMobility.Value < 0 && !IonMobilityFilter.AcceptNegativeMobilityValues(IonMobilityUnits)))
{
helper.ShowTextBoxError(textIonMobility,
string.Format(Resources.SmallMoleculeTransitionListReader_ReadPrecursorOrProductColumns_Invalid_ion_mobility_value__0_, IonMobility));
textIonMobility.Focus();
return;
}
}
if (_usageMode == UsageMode.precursor)
{
// Only the adduct should be changing
SetResult(_resultCustomMolecule, Adduct);
}
else if (!string.IsNullOrEmpty(_formulaBox.NeutralFormula))
{
try
{
var name = textName.Text;
if (string.IsNullOrEmpty(name))
{
name = _formulaBox.NeutralFormula; // Clip off any adduct description
}
SetResult(new CustomMolecule(_formulaBox.NeutralFormula, name), Adduct);
}
catch (InvalidDataException x)
{
_formulaBox.ShowTextBoxErrorFormula(helper, x.Message);
return;
}
}
else
{
SetResult(new CustomMolecule(monoMass, averageMass, textName.Text), Adduct);
}
// Did user change the list of heavy labels?
if (_driverLabelType != null)
{
// This is the only thing the user may have altered
var newHeavyMods = _driverLabelType.GetHeavyModifications().ToArray();
if (!ArrayUtil.EqualsDeep(newHeavyMods, _peptideSettings.Modifications.HeavyModifications))
{
var labelTypes = _peptideSettings.Modifications.InternalStandardTypes.Where(t =>
newHeavyMods.Any(m => Equals(m.LabelType, t))).ToArray();
if (labelTypes.Length == 0)
{
labelTypes = new[] { newHeavyMods.First().LabelType }
}
;
PeptideModifications modifications = new PeptideModifications(
_peptideSettings.Modifications.StaticModifications,
_peptideSettings.Modifications.MaxVariableMods,
_peptideSettings.Modifications.MaxNeutralLosses,
newHeavyMods,
labelTypes);
var settings = _peptideSettings.ChangeModifications(modifications);
SrmSettings newSettings = _parent.DocumentUI.Settings.ChangePeptideSettings(settings);
if (!_parent.ChangeSettings(newSettings, true))
{
// Not expected, since we checked for a change before calling
// Otherwise, this is very confusing. The form just refuses to go away
// We would prefer to get an unhandled exception and fix this
Assume.Fail();
return;
}
_peptideSettings = newSettings.PeptideSettings;
}
}
// See if this combination of charge and label would conflict with any existing transition groups
if (_existingIds != null && _existingIds.Any(t =>
{
var transitionGroup = t as TransitionGroup;
return(transitionGroup != null && Equals(transitionGroup.LabelType, IsotopeLabelType) &&
Equals(transitionGroup.PrecursorAdduct.AsFormula(),
Adduct
.AsFormula()) && // Compare AsFormula so proteomic and non-proteomic protonation are seen as same thing
!ReferenceEquals(t, _initialId));
}))
{
helper.ShowTextBoxError(textName,
Resources
.EditCustomMoleculeDlg_OkDialog_A_precursor_with_that_adduct_and_label_type_already_exists_,
textName.Text);
return;
}
// See if this would conflict with any existing transitions
if (_existingIds != null && (_existingIds.Any(t =>
{
var transition = t as Transition;
return(transition != null && (Equals(transition.Adduct.AsFormula(), Adduct.AsFormula()) &&
Equals(transition.CustomIon, ResultCustomMolecule)) &&
!ReferenceEquals(t, _initialId));
})))
{
helper.ShowTextBoxError(textName,
Resources.EditCustomMoleculeDlg_OkDialog_A_similar_transition_already_exists_, textName.Text);
return;
}
DialogResult = DialogResult.OK;
}
