public static int[] GetSequenceCoverage(this IAminoAcidSequence baseSequence, IEnumerable <IAminoAcidSequence> sequences, bool useLeucineSequence = true)
{
int[] bits = new int[baseSequence.Length];
string masterSequence = useLeucineSequence ? baseSequence.GetLeucineSequence() : baseSequence.Sequence;
foreach (IAminoAcidSequence sequence in sequences)
{
string seq = useLeucineSequence ? sequence.GetLeucineSequence() : sequence.Sequence;
int startIndex = 0;
while (true)
{
int index = masterSequence.IndexOf(seq, startIndex, StringComparison.InvariantCulture);
if (index < 0)
{
break;
}
for (int aa = index; aa < index + sequence.Length; aa++)
{
bits[aa]++;
}
startIndex = index + 1;
}
}
return(bits);
}
public static double GetSequenceCoverageFraction(this IAminoAcidSequence baseSequence, IEnumerable <IAminoAcidSequence> sequences, bool useLeucineSequence = true)
{
int[] counts = baseSequence.GetSequenceCoverage(sequences, useLeucineSequence);
return(((double)counts.Count(x => x > 0)) / baseSequence.Length);
}
public IEnumerable <int> GetDigestionSites(IAminoAcidSequence aminoacidpolymer)
{
return(GetDigestionSites(aminoacidpolymer.Sequence));
}
public int MissedCleavages(IAminoAcidSequence aminoAcidSequence)
{
return(MissedCleavages(aminoAcidSequence.Sequence));
}
public void AddPeptide(IAminoAcidSequence peptide)
{
Peptides.Add(peptide);
}
public int MissedCleavages(IAminoAcidSequence aminoAcidSequence)
{
return MissedCleavages(aminoAcidSequence.Sequence);
}
public IEnumerable<int> GetDigestionSites(IAminoAcidSequence aminoacidpolymer)
{
return GetDigestionSites(aminoacidpolymer.Sequence);
}