public TagSequenceMatch(string sequence, string proteinName, TagMatch tagMatch, char pre, char post)
{
Sequence = sequence;
ProteinName = proteinName;
TagMatch = tagMatch;
Pre = pre;
Post = post;
}
private IEnumerable <TagMatch> FindMatchesWithFeatureMass(MatchedTag matchedTag)
{
if (matchedTag.NTermFlankingMass == null || matchedTag.CTermFlankingMass == null)
{
yield break;
}
var featureMass = (double)matchedTag.NTermFlankingMass + matchedTag.Mass +
(double)matchedTag.CTermFlankingMass + Composition.H2O.Mass;
var shiftMass = matchedTag.Mass + (double)matchedTag.NTermFlankingMass;
var backwardGraph = new ShiftedSequenceGraph(_aaSet, shiftMass, false,
matchedTag.StartIndex, featureMass - MinSumModificationMasses);
foreach (var backwardMatch in GetBackwardMatches(matchedTag, backwardGraph, featureMass))
{
// Make a forward graph
var nTermShiftMass = backwardMatch.Mass + matchedTag.Mass;
var forwardGraph = new ShiftedSequenceGraph(_aaSet, nTermShiftMass, true,
_proteinSequence.Length - matchedTag.EndIndex, featureMass - MinSumModificationMasses);
foreach (
var forwardMatch in
GetForwardMatches(matchedTag, forwardGraph, featureMass))
{
var mass = forwardMatch.Mass + matchedTag.Mass + backwardMatch.Mass;
if (mass > _maxSequenceMass)
{
continue;
}
var offset = matchedTag.EndIndex - backwardMatch.Index - 1;
var modStr = string.Join(",", backwardMatch.Modifications.Concat(forwardMatch.Modifications.Select(m => m.GetModificationInstanceWithOffset(offset))));
var modList = new List <Modification>();
foreach (var mod in backwardMatch.Modifications)
{
modList.Add(mod.Modification);
}
foreach (var mod in forwardMatch.Modifications)
{
modList.Add(mod.Modification);
}
var tagMatch = new TagMatch(
backwardMatch.Index,
forwardMatch.Index,
matchedTag.Length,
backwardMatch.Charge,
backwardMatch.Score,
forwardMatch.Score,
mass,
new ModificationCombination(modList),
modStr);
yield return(tagMatch);
}
}
}
