public Result()
{
queries = new Queries();
precursors = new Precursors();
matchedPrecursors = new Precursors();
clusters = new GraphML_List <Cluster>();
peptides = new PeptideMatches(new PeptideMatch[0]);
peptideSequences = new PeptideMatches(new PeptideMatch[0]);
proteins = new ProteinGroupMatches();
dbOptions = new DBOptions("");
samples = new Samples();
}
public ProteinGroupMatches SearchLatest(List <PeptideMatch> peptides)//, IDictionary<string, List<Protein>> dicOfProteins)//, List<Protein> AllProteins)// Dictionary<string, List<Protein>> dicOfPeptides)
{
Dictionary <string, PeptideMatch> dicOfPeptideMatches = new Dictionary <string, PeptideMatch>();
foreach (PeptideMatch match in peptides)
{
dicOfPeptideMatches.Add(match.peptide.BaseSequence, match);
}
Dictionary <Protein, List <string> > allPossibleProteins = new Dictionary <Protein, List <string> >();
foreach (PeptideMatch match in peptides)
//foreach (string peptideSequence in dicOfProteins.Keys)
{
Protein protein = match.peptide.Parent;
//foreach (Protein protein in dicOfProteins[peptideSequence])
{
if (!allPossibleProteins.ContainsKey(protein))
{
allPossibleProteins.Add(protein, new List <string>());
}
allPossibleProteins[protein].Add(match.peptide.Sequence);
}
}
options.ConSole.WriteLine("Merging undistinguishable proteins...");
foreach (Protein protein in allPossibleProteins.Keys)
{
allPossibleProteins[protein].Sort();
}
//Merge only undistinguishable protein sequences
//Dictionary<Protein, List<Protein>> dicOfSimilarProteins = new Dictionary<Protein,List<Protein>>();
ProteinGroupMatches proteinMatches = new ProteinGroupMatches();
List <Protein> proteins = new List <Protein>(allPossibleProteins.Keys);
for (int i = 0; i < proteins.Count; i++)
{
ProteinGroupMatch groupMatch = new ProteinGroupMatch();
groupMatch.Proteins.Add(proteins[i]);
foreach (string sequence in allPossibleProteins[proteins[i]])
{
if (dicOfPeptideMatches.ContainsKey(sequence))
{
groupMatch.PeptideMatches.Add(dicOfPeptideMatches[sequence]);
}
}
for (int j = i + 1; j < proteins.Count;)
{
bool isSame = false;
if (allPossibleProteins[proteins[i]].Count == allPossibleProteins[proteins[j]].Count)
{
isSame = true;
for (int k = 0; k < allPossibleProteins[proteins[i]].Count; k++)
{
if (allPossibleProteins[proteins[i]][k].CompareTo(allPossibleProteins[proteins[j]][k]) != 0)
{
isSame = false;
}
}
}
if (isSame)
{
proteins.RemoveAt(j);
groupMatch.Proteins.Add(proteins[j]);
}
else
{
j++;
}
}
proteinMatches.Add(groupMatch);
}
options.ConSole.WriteLine("Found " + proteinMatches.Count + " protein groups.");
return(proteinMatches);
}