public List <int> GetDigestionSiteIndices(AminoAcidPolymer aminoAcidPolymer)
{
List <int> indices = new List <int>();
for (int i = 0; i < aminoAcidPolymer.Length - 1; i++)
{
foreach (string c in SequencesInducingCleavage)
{
if ((CleavageTerminus != Terminus.N && i - c.Length + 1 >= 0 && aminoAcidPolymer.BaseSequence.Substring(i - c.Length + 1, c.Length).Equals(c, StringComparison.InvariantCultureIgnoreCase)) ||
(CleavageTerminus == Terminus.N && i + 1 + c.Length <= aminoAcidPolymer.Length && aminoAcidPolymer.BaseSequence.Substring(i + 1, c.Length).Equals(c, StringComparison.InvariantCultureIgnoreCase)))
{
bool cleave = true;
foreach (string nc in SequencesPreventingCleavage)
{
if ((CleavageTerminus != Terminus.N && i + 1 + nc.Length <= aminoAcidPolymer.Length && aminoAcidPolymer.BaseSequence.Substring(i + 1, nc.Length).Equals(nc, StringComparison.InvariantCultureIgnoreCase)) ||
(CleavageTerminus == Terminus.N && i - nc.Length + 1 >= 0 && aminoAcidPolymer.BaseSequence.Substring(i - nc.Length + 1, nc.Length).Equals(nc, StringComparison.InvariantCultureIgnoreCase)))
{
cleave = false;
break;
}
}
if (cleave)
{
indices.Add(i);
}
}
}
}
return(indices);
}
public List<int> GetDigestionSiteIndices(AminoAcidPolymer aminoAcidPolymer)
{
List<int> indices = new List<int>();
for(int i = 0; i < aminoAcidPolymer.Length - 1; i++)
{
foreach(string c in SequencesInducingCleavage)
{
if((CleavageTerminus != Terminus.N && i - c.Length + 1 >= 0 && aminoAcidPolymer.BaseSequence.Substring(i - c.Length + 1, c.Length).EqualsIgnoringCase(c))
|| (CleavageTerminus == Terminus.N && i + 1 + c.Length <= aminoAcidPolymer.Length && aminoAcidPolymer.BaseSequence.Substring(i + 1, c.Length).EqualsIgnoringCase(c)))
{
bool cleave = true;
foreach(string nc in SequencesPreventingCleavage)
{
if((CleavageTerminus != Terminus.N && i + 1 + nc.Length <= aminoAcidPolymer.Length && aminoAcidPolymer.BaseSequence.Substring(i + 1, nc.Length).EqualsIgnoringCase(nc))
|| (CleavageTerminus == Terminus.N && i - nc.Length + 1 >= 0 && aminoAcidPolymer.BaseSequence.Substring(i - nc.Length + 1, nc.Length).EqualsIgnoringCase(nc)))
{
cleave = false;
break;
}
}
if(cleave)
{
indices.Add(i);
}
}
}
}
return indices;
}