private static double GetDeltaMass(Modification2 mod, string sequence, bool isNterm, bool isCterm)
{
ModificationPosition pos = mod.Position;
double deltaMass = 0;
for (int i = 0; i < mod.AaCount; i++)
{
for (int j = 0; j < sequence.Length; j++)
{
if ((pos == ModificationPosition.notNterm || pos == ModificationPosition.notTerm) && j == 0)
{
continue;
}
if ((pos == ModificationPosition.notCterm || pos == ModificationPosition.notTerm) && j == sequence.Length - 1)
{
continue;
}
if (sequence[j] == mod.GetAaAt(i))
{
deltaMass += mod.DeltaMass;
}
}
}
if (pos == ModificationPosition.anyNterm)
{
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.anyCterm)
{
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.proteinNterm && isNterm)
{
deltaMass += mod.DeltaMass;
}
if (pos == ModificationPosition.proteinCterm && isCterm)
{
deltaMass += mod.DeltaMass;
}
return(deltaMass);
}
public void SetPosition(ModificationPosition pos)
{
position = pos;
}
private void Fill(Modification m)
{
DeltaMass = m.DeltaMass;
Position = m.Position;
IsProteinTerminal = m.IsProteinTerminal;
IsInternal = m.IsInternal;
IsNterminal = m.IsNterminal;
IsCterminal = m.IsCterminal;
IsIsotopicLabel = m.IsIsotopicLabel;
IsIsotopicMod = m.IsIsotopicMod;
ModificationType = m.ModificationType;
HasNeutralLoss = m.HasNeutralLoss;
aas = new char[m.AaCount];
for (int i = 0; i < aas.Length; i++){
aas[i] = m.GetAaAt(i);
}
Index = m.Index;
Name = m.Name;
}
