public bool foundParent(string frag, ParentInfo.terminal terminal, FusionCandidate candidate, bool foundFirstSearch)
{
//localTheoreticals.AsParallel().Where(x => x.Contains(frag)).ToList();
if (notFoundSequences.Contains(frag)) //has the fragment been searched but not found before?
{
return(false);
}
List <TheoreticalProtein> matches = new List <TheoreticalProtein>();
if (foundSequences.TryGetValue(frag, out matches)) //has the fragment been searched AND found before?
{
candidate.parentInfo.Add(new ParentInfo(matches, terminal, frag));
return(true);
}
if (foundFirstSearch) //Has something smaller been found before? Well, then we can just search against those found sequences
{
string shorterFrag = terminal.Equals(ParentInfo.terminal.N) ? frag.Substring(0, frag.Length - 1) : frag.Substring(1, frag.Length - 1);
foreach (ParentInfo info in candidate.parentInfo)
{
if (info.parentType.Equals(terminal) && info.fragFound.Equals(shorterFrag))
{
List <TheoreticalProtein> tempProtList = new List <TheoreticalProtein>();
info.theoreticalProteins.ForEach(protein => tempProtList.Add(protein));
matches = tempProtList.AsParallel().Where(x => x.seq.Contains(frag)).ToList();
}
}
}
else //it hasn't been found before... we need to search against the whole database :(
{
matches = theoreticalProteins.AsParallel().Where(x => x.seq.Contains(frag)).ToList();
}
if (matches != null && matches.Count() > 0)
{
foundSequences.Add(frag, matches);
candidate.parentInfo.Add(new ParentInfo(matches, terminal, frag));
return(true);
}
else
{
notFoundSequences.Add(frag);
return(false);
}
}
public TransParent(string id, string seq, List <int> start, int length, ParentInfo.terminal terminal) : base(id, seq)
{
this.start = start;
this.peptideLength = length;
this.terminal = terminal;
}
