protected override void DoRealGo()
{
Aminoacids aas = Aminoacids.ParseModificationFromOutFileLine(modification.Text);
IPeptideMassCalculator calc;
if (isMonoisotopic.Checked)
{
calc = new MonoisotopicPeptideMassCalculator(aas);
}
else
{
calc = new AveragePeptideMassCalculator(aas);
}
string seq = PeptideUtils.GetMatchedSequence(sequence.Text);
double value;
if (isMH.Checked)
{
value = calc.GetMz(seq, 1);
}
else
{
value = calc.GetMass(seq);
}
txtResult.Text = value.ToString();
}
public IPeptideMassCalculator GetPeptideMassCalculator()
{
bool isMono = IsPrecursorMonoisotopic();
var aas = new Aminoacids();
Dictionary <char, double> staticModifications = GetStaticAminoacidModification();
foreach (char aa in staticModifications.Keys)
{
aas[aa].ResetMass(aas[aa].MonoMass + staticModifications[aa], aas[aa].AverageMass + staticModifications[aa]);
}
var diff = new[] { '*', '#', '@', '^', '~', '$' };
int i = 0;
foreach (double mod in Diff_search_options.Values)
{
aas[diff[i++]].ResetMass(mod, mod);
}
double nterm = isMono ? Atom.H.MonoMass : Atom.H.AverageMass;
double cterm = isMono ? Atom.H.MonoMass + Atom.O.MonoMass : Atom.H.AverageMass + Atom.O.AverageMass;
if (this.term_diff_search_options.First != 0.0 || this.term_diff_search_options.Second != 0.0)
{
throw new Exception(
"Term dynamic modification has not been implemented into this function, call author to fix it.");
}
IPeptideMassCalculator result;
if (isMono)
{
result = new MonoisotopicPeptideMassCalculator(aas, nterm, cterm);
}
else
{
result = new AveragePeptideMassCalculator(aas, nterm, cterm);
}
return(result);
}
public IIdentifiedResult Build(List <IIdentifiedProteinGroup> groups)
{
IdentifiedResult result = new IdentifiedResult();
result.AddRange(groups);
result.Sort();
result.BuildGroupIndex();
if (FillSequence(result))
{
AveragePeptideMassCalculator massCalc = new AveragePeptideMassCalculator(new Aminoacids(), Atom.H.AverageMass, Atom.H.AverageMass + Atom.O.AverageMass);
Progress.SetMessage("Calculating coverage and mass weight ...");
foreach (IIdentifiedProteinGroup group in result)
{
foreach (IIdentifiedProtein protein in group)
{
if (!string.IsNullOrEmpty(protein.Sequence))
{
try
{
protein.CalculateCoverage();
protein.MolecularWeight = massCalc.GetMass(protein.Sequence);
}
catch (Exception ex)
{
var error = "Calculating coverage and mass weight error:" + ex.Message;
Progress.SetMessage(error);
Console.Error.WriteLine(error);
}
}
}
}
}
return(result);
}