public int[] GetSequenceCoverage(IEnumerable <Peptide> peptides, bool includePSMcounts = false)
{
int[] bits = new int[Length];
foreach (Peptide pep in peptides)
{
int start_index = 0;
while (true)
{
int index = LeucineSequence.IndexOf(pep.LeucineSequence, start_index);
start_index = index + 1;
if (index < 0)
{
break;
}
for (int aa = index; aa < index + pep.Length; aa++)
{
if (includePSMcounts)
{
bits[aa] += pep.PSMs.Count;
}
else
{
bits[aa]++;
}
}
}
}
return(bits);
}
public bool Equals(Peptide other)
{
return(ReferenceEquals(this, other) || LeucineSequence.Equals(other.LeucineSequence));
}
public int FindStopResidue(string sequence)
{
return(LeucineSequence.IndexOf(sequence) + sequence.Length);
}
public int FindStartResidue(string sequence)
{
return(LeucineSequence.IndexOf(sequence) + 1);
}
