private IEnumerable<FlankingMassMatch> GetBackwardMatches(
MatchedTag matchedTag,
ShiftedSequenceGraph backwardGraph,
double? featureMass = null
)
{
for (var j = matchedTag.StartIndex - 1; j >= -1; j--)
{
var residue = j >= 0 ? _proteinSequence[j] : AminoAcid.ProteinNTerm.Residue;
var location = j > 0 ? SequenceLocation.Everywhere : SequenceLocation.ProteinNTerm;
if(!backwardGraph.AddAminoAcid(residue, location)) yield break;
if (j == 0) continue;
var backwardMatch = GetBestMatchInTheGraph(backwardGraph, _spec, featureMass);
if (backwardMatch != null)
{
backwardMatch.Index = Math.Max(j, 0);
yield return backwardMatch;
}
}
}
// private readonly int _minProductIonCharge;
// private readonly int _maxProductIonCharge;
private IEnumerable<FlankingMassMatch> GetForwardMatches(
MatchedTag matchedTag,
ShiftedSequenceGraph forwardGraph,
double? featureMass = null
)
{
for (var i = matchedTag.EndIndex; i <= _proteinSequence.Length; i++)
{
var residue = i < _proteinSequence.Length ? _proteinSequence[i] : AminoAcid.ProteinCTerm.Residue;
var location = i < _proteinSequence.Length - 1
? SequenceLocation.Everywhere
: SequenceLocation.ProteinCTerm;
if (!forwardGraph.AddAminoAcid(residue, location)) yield break;
if (i == _proteinSequence.Length - 1) continue;
var forwardMatch = GetBestMatchInTheGraph(forwardGraph, _spec, featureMass);
if (forwardMatch != null)
{
forwardMatch.Index = Math.Min(i + 1, _proteinSequence.Length);
yield return forwardMatch;
}
}
}