private Dictionary <char, List <TargetVariant> > GetSubstitutionDeltaMass()
{
var result = new Dictionary <char, List <TargetVariant> >();
var aa = new Aminoacids();
var validAA = aa.GetVisibleAminoacids();
foreach (var ai in validAA)
{
foreach (var aj in validAA)
{
if (ai == aj)
{
continue;
}
if (this.IsSingleNucleotideMutationOnly && !MutationUtils.IsSingleNucleotideMutation(ai, aj))
{
continue;
}
if (this.IgnoreDeamidatedMutation && MutationUtils.IsDeamidatedMutation(ai, aj))
{
continue;
}
if (!result.ContainsKey(ai))
{
result[ai] = new List <TargetVariant>();
}
var deltaMass = aa[aj].MonoMass - aa[ai].MonoMass;
if (Math.Abs(deltaMass) < MinimumAminoacidSubstitutionDeltaMass)
{
continue;
}
result[ai].Add(new TargetVariant()
{
Source = ai.ToString(),
Target = new HashSet <string>(new[] { aj.ToString() }),
DeltaMass = deltaMass,
TargetType = VariantType.SingleAminoacidPolymorphism
});
}
}
foreach (var v in result.Values)
{
v.Sort((m1, m2) => m1.DeltaMass.CompareTo(m2.DeltaMass));
}
return(result);
}
private static bool DoIsMutationOne(IsMutationOneDelegate func, string fromPeptide, string toPeptide, ref int mutationSite, bool ignoreNtermMutation, bool ignoreDeamidatedMutation, bool ignoreMultipleNucleotideMutation)
{
if (func(fromPeptide, toPeptide, ref mutationSite))
{
if (ignoreNtermMutation && 0 == mutationSite)
{
return(false);
}
if (ignoreDeamidatedMutation && MutationUtils.IsDeamidatedMutation(fromPeptide[mutationSite], toPeptide[mutationSite]))
{
return(false);
}
if (ignoreMultipleNucleotideMutation && IsSingleNucleotideMutation(fromPeptide[mutationSite], toPeptide[mutationSite]))
{
return(false);
}
return(true);
}
return(false);
}
