//public static List<BYCZIons> CalculateBYCZIon(string Sequence, MassSpectrometry.SuperSpectrum spectrum, List<ModificationList> AllValidationModifications = null, double MatchTolerance = 0.00, SortedList<char, double> aa = null, bool isauto = false, Dictionary<double, double> CurrentMonomasses = null)
//{
// return CalculateBYCZIon(Sequence, spectrum)
//}
/// <summary>
/// Calcaulate all the b and y ions using a given sequence.
/// And compare it to the Monomasses already present.
/// </summary>
/// <param name="Sequence"></param>
/// <param name="Monomasses"></param>
/// <returns></returns>
public static List <BYCZIons> CalculateBYCZIon(string Sequence, List <double> Monomasses, double ParentMass, string ActivationType, List <ModificationList> AllValidationModifications = null, double MatchTolerance = 0.00, SortedList <char, double> aa = null, bool isauto = false, Dictionary <double, double> CurrentMonomasses = null)
{
List <BYCZIons> AllIons = new List <BYCZIons>();
if (string.IsNullOrWhiteSpace(Sequence))
{
return(AllIons); // some simple validation. If there is no valid sequence, there are no ions, so return the empty list.
}
AminoAcids = aa ?? AminoAcids;
Monomasses = Monomasses.OrderBy(a => a).ToList();
if (AllValidationModifications == null)
{
AllValidationModifications = App.AllValidationModifications;
}
if (MatchTolerance == 0.00)
{
MatchTolerance = Properties.Settings.Default.MatchTolerancePPM;
}
double ion = new double();
double cion = new double();
cion = Molecules.Ammonia;
//if (!isauto)
{
if (ParentMass == 0.0)
{
ParentMass = LocalParentMass;
}
Monomasses.Add(ParentMass);
Monomasses = Monomasses.Where(a => a <= ParentMass).OrderBy(a => a).ToList();
}
string[] splitstring = { "[", "]" };
List <string> sequences = Sequence.Replace("(", "").Replace(")", "").Trim().Split(splitstring, StringSplitOptions.RemoveEmptyEntries).ToList();
int count = 1;
Regex regex = new Regex(@"^[0-9\.\+\-]+$");
Regex regexlwrcs = new Regex(@"[a-z]+$");
//bool number = false;
string tempseq = string.Empty;
if (regex.IsMatch(sequences[0]))
{
ion = Convert.ToDouble(sequences[0]);
cion = cion + Convert.ToDouble(sequences[0]);
}
for (int i = 0; i < sequences.Count; i++)
{
string seq = sequences[i];
if (i < sequences.Count)
{
if ((regex.IsMatch(seq)) || AllValidationModifications.Any(a => (a.Abbreviation == sequences[i]) || ("+" + a.Abbreviation == sequences[i]) || ("-" + a.Abbreviation == sequences[i])))
{
continue;
}
}
{
{
bool breaksequence = false;
for (int j = 0; j < seq.Length; j++) /// This is the individual AminoAcids
{
if (j == seq.Length - 1)
{
for (int ii = i + 1; ii < sequences.Count; ii++)
{
if ((regex.IsMatch(sequences[ii])) || AllValidationModifications.Any(a => (a.Abbreviation == sequences[ii]) || ("+" + a.Abbreviation == sequences[ii]) || ("-" + a.Abbreviation == sequences[ii])))
{
breaksequence = true;
break;
}
else
{
breaksequence = false;
break;
}
}
}
if (breaksequence)
{
for (int ii = i + 1; ii < sequences.Count; ii++)
{
{
if (AllValidationModifications.Any(a => a.Abbreviation == sequences[ii]))
{
tempseq = "+" + sequences[ii] + " " + tempseq;
ion = ion + Convert.ToDouble(AllValidationModifications.First(a => a.Abbreviation == sequences[ii]).Mass);
cion = cion + Convert.ToDouble(AllValidationModifications.First(a => a.Abbreviation == sequences[ii]).Mass);
}
else if (AllValidationModifications.Any(a => "+" + a.Abbreviation == sequences[ii]))
{
tempseq = sequences[ii] + " " + tempseq;
ion = ion + Convert.ToDouble(AllValidationModifications.First(a => "+" + a.Abbreviation == sequences[ii]).Mass);
cion = cion + Convert.ToDouble(AllValidationModifications.First(a => "+" + a.Abbreviation == sequences[ii]).Mass);
}
else if (AllValidationModifications.Any(a => "-" + a.Abbreviation == sequences[ii]))
{
tempseq = sequences[ii] + " " + tempseq;
ion = ion - Math.Abs(Convert.ToDouble(AllValidationModifications.First(a => "-" + a.Abbreviation == sequences[ii]).Mass));
cion = cion - Math.Abs(Convert.ToDouble(AllValidationModifications.First(a => "-" + a.Abbreviation == sequences[ii]).Mass));
}
else if (regex.IsMatch(sequences[ii]))
{
if (sequences[ii].StartsWith("+"))
{
ion = ion + Convert.ToDouble(sequences[ii]);
cion = cion + Convert.ToDouble(sequences[ii]);
tempseq += "+ " + sequences[ii].Remove(sequences[ii].IndexOf("+"), 1) + " ";
}
else if (sequences[ii].StartsWith("-"))
{
ion = ion - Math.Abs(Convert.ToDouble(sequences[ii]));
cion = cion - Math.Abs(Convert.ToDouble(sequences[ii]));
tempseq += "- " + sequences[ii].Remove(sequences[ii].IndexOf("-"), 1) + " ";
}
else
{
ion = ion + Convert.ToDouble(sequences[ii]);
cion = cion + Convert.ToDouble(sequences[ii]);
tempseq += "+ " + sequences[ii] + " ";
}
}
else
{
break;
}
}
}
}
if (j != seq.Length - 1)
{
if (regexlwrcs.IsMatch(Convert.ToString(seq[j + 1])))
{
ion = ion + sequencelengthwithmods((Convert.ToString(seq[j]) + Convert.ToString(seq[j + 1])));
cion = cion + sequencelengthwithmods((Convert.ToString(seq[j]) + Convert.ToString(seq[j + 1])));
tempseq = Convert.ToString(seq[j]) + Convert.ToString(seq[j + 1]) + " " + tempseq;
j = j + 1;
}
else
{
ion = ion + sequencelength(Convert.ToString(seq[j]));
cion = cion + sequencelength(Convert.ToString(seq[j]));
tempseq = seq[j] + " " + tempseq;
}
}
else
{
ion = ion + sequencelength(Convert.ToString(seq[j]));
cion = cion + sequencelength(Convert.ToString(seq[j]));
tempseq = seq[j] + " " + tempseq;
}
//if (isauto)
//{
// double bionerror = Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100;
// AllIons.Add(new BYIons()
// {
// Bion = ion,
// //Yion = 0,
// //AminoAcid = tempseq.TrimEnd(),
// //BionNumber = count,
// //BorYIon = count,
// bioncolor = bionerror == 100 ? false : (((PPM.CalculatePPM(ion, bionerror) <= Properties.Settings.Default.FragementIonTolerance) && (PPM.CalculatePPM(ion, bionerror) >= -(Properties.Settings.Default.FragementIonTolerance)))), /// Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)),
// Intensity = CurrentMonomasses.Any(a => Math.Abs(a.Key - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? CurrentMonomasses.First(a => Math.Abs(a.Key - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Value : 0,
// bnh3ioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Ammonia), MatchTolerance)),
// bh2oioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Water), MatchTolerance)),
// bionerror = bionerror,/// Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100,
// //bh2oion = Math.Round(ion - Molecules.Water, 5),
// //bh2oioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Water), MatchTolerance)),
// //bionerror = Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100,
// //BionDescription = "B" + Convert.ToString(count) + " " + PPM.CalculatePPM(ion, Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100),
// //BionDaltonDescription = "B" + Convert.ToString(count) + " " + (Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100)
// });
//}
//else
{
double bionerror = Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100;
double cionerror = Monomasses.Any(a => Math.Abs(a - cion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - cion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)).Select(a => a - cion).First() : 100;
AllIons.Add(new BYCZIons()
{
Bion = ion,
Yion = 0,
Cion = cion,
Zion = 0,
AminoAcid = tempseq.TrimEnd(),
BionNumber = count,
ActivationType = ActivationType,
BorYIon = count,
CionNumber = count,
CorZIon = count,
Intensity = CurrentMonomasses != null ? (CurrentMonomasses.Any(a => Math.Abs(a.Key - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? CurrentMonomasses.First(a => Math.Abs(a.Key - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Value : 0) : 0,
bioncolor = bionerror == 100 ? false : ((Math.Abs(PPM.CalculatePPM(ParentMass, bionerror)) < Properties.Settings.Default.FragementIonTolerance)), ///Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)),
//bioncolor = bionerror == 100 ? false : (((PPM.CalculatePPM(ion, bionerror) < Properties.Settings.Default.FragementIonTolerance) && (PPM.CalculatePPM(ion, bionerror) > -(Properties.Settings.Default.FragementIonTolerance)))), ///Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)),
bh2oion = Math.Round(ion - Molecules.Water, 5),
bh2oioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Water), MatchTolerance)),
bionerror = bionerror,/// Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100,
BionDescription = "B" + Convert.ToString(count) + " " + PPM.CalculatePPM(ion, Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100),
BionDaltonDescription = "B" + Convert.ToString(count) + " " + (Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100),
bnh3ion = Math.Round(ion - Molecules.Ammonia, 5),
bnh3ioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Ammonia), MatchTolerance)),
cioncolor = cionerror == 100 ? false : ((Math.Abs(PPM.CalculatePPM(ParentMass, cionerror)) < Properties.Settings.Default.FragementIonTolerance)), //Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)),
//bioncolor = bionerror == 100 ? false : (((PPM.CalculatePPM(ion, bionerror) < Properties.Settings.Default.FragementIonTolerance) && (PPM.CalculatePPM(ion, bionerror) > -(Properties.Settings.Default.FragementIonTolerance)))), ///Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)),
ch2oion = Math.Round(cion - Molecules.Water, 5),
ch2oioncolor = Monomasses.Any(a => Math.Abs(a - (cion - Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((cion - Molecules.Water), MatchTolerance)),
cionerror = cionerror, // Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100,
CionDescription = "C" + Convert.ToString(count) + " " + PPM.CalculatePPM(cion, Monomasses.Any(a => Math.Abs(a - cion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - cion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)).Select(a => a - cion).First() : 100),
CionDaltonDescription = "C" + Convert.ToString(count) + " " + (Monomasses.Any(a => Math.Abs(a - cion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - cion) <= PPM.CurrentPPMbasedonMatchList(cion, MatchTolerance)).Select(a => a - cion).First() : 100),
cnh3ion = Math.Round(cion - Molecules.Ammonia, 5),
cnh3ioncolor = Monomasses.Any(a => Math.Abs(a - (cion - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((cion - Molecules.Ammonia), MatchTolerance)),
});
}
//{
// double cionerror = Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100;
// AllIons.Add(new BYIons()
// {
// Cion = ion,
// Zion = 0,
// AminoAcid = tempseq.TrimEnd(),
// CionNumber = count,
// CorZIon = count,
// Intensity = CurrentMonomasses != null ? (CurrentMonomasses.Any(a => Math.Abs(a.Key - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? CurrentMonomasses.First(a => Math.Abs(a.Key - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Value : 0) : 0,
// cioncolor = cionerror == 100 ? false : ((Math.Abs(PPM.CalculatePPM(ion, cionerror)) < Properties.Settings.Default.FragementIonTolerance)), ///Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)),
// //bioncolor = bionerror == 100 ? false : (((PPM.CalculatePPM(ion, bionerror) < Properties.Settings.Default.FragementIonTolerance) && (PPM.CalculatePPM(ion, bionerror) > -(Properties.Settings.Default.FragementIonTolerance)))), ///Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)),
// ch2oion = Math.Round(ion - Molecules.Water, 5),
// ch2oioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Water), MatchTolerance)),
// cionerror = cionerror,/// Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100,
// CionDescription = "B" + Convert.ToString(count) + " " + PPM.CalculatePPM(ion, Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100),
// CionDaltonDescription = "B" + Convert.ToString(count) + " " + (Monomasses.Any(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - ion) <= PPM.CurrentPPMbasedonMatchList(ion, MatchTolerance)).Select(a => a - ion).First() : 100),
// cnh3ion = Math.Round(ion - Molecules.Ammonia, 5),
// cnh3ioncolor = Monomasses.Any(a => Math.Abs(a - (ion - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((ion - Molecules.Ammonia), MatchTolerance)),
// });
//}
count = count + 1;
tempseq = string.Empty;
}
}
}
}
count = AllIons.Count - 1;
ion = 0;
cion = 0;
//if (regex.IsMatch(sequences[0]))
//{
// ion = Convert.ToDouble(sequences[0]);
//}
int c = 1;
List <BYCZIons> intensities = new List <BYCZIons>();
intensities = AllIons.Where(a => a.bioncolor == true).ToList();
tempseq = string.Empty;
for (int i = sequences.Count - 1; i >= 0; i--)
{
string seq = sequences[i];
string sq = seq;
if (regex.IsMatch(sq))
{
if (sq.Contains("+"))
{
sq = sq.Remove(sq.IndexOf("+"), 1);
ion = ion + Convert.ToDouble(sq);
cion = cion + Convert.ToDouble(sq);
}
else if (sq.Contains("-"))
{
sq = sq.Remove(sq.IndexOf("-"), 1);
ion = ion - Math.Abs(Convert.ToDouble(sq));
cion = cion - Math.Abs(Convert.ToDouble(sq));
}
else
{
ion = ion + Convert.ToDouble(sq);
cion = cion + Convert.ToDouble(sq);
}
}
else
{
if (seq.Contains("-"))
{
if (AllValidationModifications.Any(a => ("-" + a.Abbreviation) == seq))
{
ion = ion - Math.Abs(Convert.ToDouble(AllValidationModifications.Where(a => "-" + a.Abbreviation == seq).First().Mass));
cion = cion - Math.Abs(Convert.ToDouble(AllValidationModifications.Where(a => "-" + a.Abbreviation == seq).First().Mass));
}
}
else if (seq.Contains("+"))
{
if (AllValidationModifications.Any(a => ("+" + a.Abbreviation) == seq))
{
ion = ion + Convert.ToDouble(AllValidationModifications.Where(a => "+" + a.Abbreviation == seq).First().Mass);
cion = cion + Convert.ToDouble(AllValidationModifications.Where(a => "+" + a.Abbreviation == seq).First().Mass);
}
}
else if (AllValidationModifications.Any(a => a.Abbreviation == seq))
{
ion = ion + Convert.ToDouble(AllValidationModifications.Where(a => a.Abbreviation == seq).First().Mass);
cion = cion + Convert.ToDouble(AllValidationModifications.Where(a => a.Abbreviation == seq).First().Mass);
}
else
{
string[] alltheaminoacids = seq.Select(a => a.ToString()).ToArray();
double modmass = 0.0;
string tempaminoacids = string.Empty;
bool hasaminoacidsmod = false;
foreach (string AminoAcid in alltheaminoacids.Reverse())
{
if (regexlwrcs.IsMatch(AminoAcid))
{
tempaminoacids = AminoAcid;
hasaminoacidsmod = true;
continue;
}
tempaminoacids = AminoAcid + tempaminoacids;
ion = ion + (hasaminoacidsmod ? sequencelengthwithmods(tempaminoacids) : sequencelength(AminoAcid));
cion = cion + (hasaminoacidsmod ? sequencelengthwithmods(tempaminoacids) : sequencelength(AminoAcid));
double Yion = Math.Round(ion + Molecules.Water, 4);
double Zion = Math.Round(cion, 4);
//AllIons[count].yioncolor = Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance));
AllIons[count].Yion = Yion;
AllIons[count].Zion = Zion;
//AllIons[count].in
double yionerror = Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)).Select(a => a - (ion + Molecules.Water)).First() : 100;
double zionerror = Monomasses.Any(a => Math.Abs(a - (cion)) <= PPM.CurrentPPMbasedonMatchList((cion), MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - (cion)) <= PPM.CurrentPPMbasedonMatchList((cion), MatchTolerance)).Select(a => a - (cion)).First() : 100;
//if (isauto)
//{
// //if (AllIons[count].yioncolor)
// {
// AllIons[count].Intensity += CurrentMonomasses.Any(a => Math.Abs(a.Key - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)) ?
// CurrentMonomasses.First(a => Math.Abs(a.Key - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)).Value : 0;
// AllIons[count].yh2oioncolor = Monomasses.Any(a => Math.Abs(a - (ion)) <= PPM.CurrentPPMbasedonMatchList((ion), MatchTolerance));
// AllIons[count].ynh3ioncolor = Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water - Molecules.Ammonia), MatchTolerance));
// AllIons[count].yionerror = yionerror;/// Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)).Select(a => a - (ion + Molecules.Water)).First() : 100;
// AllIons[count].yioncolor = yionerror == 100 ? false : (((PPM.CalculatePPM(Yion, yionerror) <= Properties.Settings.Default.FragementIonTolerance) && (PPM.CalculatePPM(Yion, yionerror) >= -(Properties.Settings.Default.FragementIonTolerance)))); //Checking if the PPM ion tolerance is between the limits
// //CurrentMonomasses.ContainsKey(AllIons[count].Yion) ? CurrentMonomasses[AllIons[count].Yion] : 0;
// //AllIons[count].Intensity += CurrentMonomasses.ContainsKey(AllIons[count].Yion) ? CurrentMonomasses[AllIons[count].Yion] : 0;
// }
//}
//if (!isauto)
{
AllIons[count].Yion = Yion;/// Math.Round(ion + Molecules.Water, 4);
AllIons[count].Zion = Zion;
AllIons[count].YionNumber = -c;
AllIons[count].ZionNumber = -c;
AllIons[count].Intensity += CurrentMonomasses != null ? (CurrentMonomasses.Any(a => Math.Abs(a.Key - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)) ?
CurrentMonomasses.First(a => Math.Abs(a.Key - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)).Value : 0) : 0;
AllIons[count].ActivationType = ActivationType;
AllIons[count].NewYIonNumber = c;
AllIons[count].NewZIonNumber = c;
AllIons[count].yh2oion = Math.Round(ion, 4);
AllIons[count].zh2oion = Math.Round(Zion + Molecules.Water, 4);
AllIons[count].ynh3ion = Math.Round(ion + Molecules.Water - Molecules.Ammonia, 4);
AllIons[count].znh3ion = Math.Round(Zion - Molecules.Ammonia, 4);
AllIons[count].yh2oioncolor = Monomasses.Any(a => Math.Abs(a - (ion)) <= PPM.CurrentPPMbasedonMatchList((ion), MatchTolerance));
//AllIons[count].zh2oioncolor = Monomasses.Any(a => Math.Abs(a - (Zion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion), MatchTolerance));
AllIons[count].ynh3ioncolor = Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water - Molecules.Ammonia), MatchTolerance));
AllIons[count].znh3ioncolor = Monomasses.Any(a => Math.Abs(a - (Zion - Molecules.Ammonia)) <= PPM.CurrentPPMbasedonMatchList((Zion - Molecules.Ammonia), MatchTolerance));
AllIons[count].yionerror = yionerror; /// Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)) ? Monomasses.Where(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)).Select(a => a - (ion + Molecules.Water)).First() : 100;
AllIons[count].zionerror = zionerror;
AllIons[count].yioncolor = yionerror == 100 ? false : ((Math.Abs(PPM.CalculatePPM(ParentMass, yionerror)) <= Properties.Settings.Default.FragementIonTolerance));
AllIons[count].zioncolor = zionerror == 100 ? false : ((Math.Abs(PPM.CalculatePPM(ParentMass, zionerror)) <= Properties.Settings.Default.FragementIonTolerance));
//AllIons[count].yioncolor = yionerror == 100 ? false : (((PPM.CalculatePPM(Yion, yionerror) <= Properties.Settings.Default.FragementIonTolerance) && (PPM.CalculatePPM(Yion, yionerror) >= -(Properties.Settings.Default.FragementIonTolerance))));
if (Monomasses.Any(a => Math.Abs(a - (ion + Molecules.Water)) <= PPM.CurrentPPMbasedonMatchList((ion + Molecules.Water), MatchTolerance)))
{
AllIons[count].YionDescription = "Y" + Convert.ToString(c) + " " + Convert.ToString(AllIons[count].yionPPM);
AllIons[count].YionDaltonDescription = "Y" + Convert.ToString(c) + " " + Convert.ToString(AllIons[count].yionerror);
}
if (Monomasses.Any(a => Math.Abs(a - (Zion)) <= PPM.CurrentPPMbasedonMatchList((Zion), MatchTolerance)))
{
AllIons[count].ZionDescription = "Y" + Convert.ToString(c) + " " + Convert.ToString(AllIons[count].zionPPM);
AllIons[count].ZionDaltonDescription = "Y" + Convert.ToString(c) + " " + Convert.ToString(AllIons[count].zionerror);
}
}
c = c + 1;
count = count - 1;
tempaminoacids = string.Empty;
hasaminoacidsmod = false;
}
}
}
}
return(AllIons);
}