public PeptideDocNode MatchSinglePeptide(ViewLibraryPepInfo pepInfo)
{
_chargeSettingsMap = new AdductMap <SrmSettings>();
var nodePep = AssociateMatchingPeptide(pepInfo, pepInfo.Key.Adduct).PeptideNode;
if (nodePep == null)
{
return(null);
}
IList <ProteinInfo> matchedProteins = null;
var target = nodePep.Peptide.Target;
if (pepInfo.Target.IsProteomic)
{
// This is only set if the user has checked the associate peptide box.
if (_backgroundProteome != null)
{
using (var proteomeDb = _backgroundProteome.OpenProteomeDb())
{
var digestion = _backgroundProteome.GetDigestion(proteomeDb, Settings.PeptideSettings);
if (digestion != null)
{
matchedProteins = digestion.GetProteinsWithSequence(target.Sequence)
.Select(protein => new ProteinInfo(protein)).ToArray();
}
}
}
}
PeptideMatches = new Dictionary <PeptideSequenceModKey, PeptideMatch>
{
{ nodePep.SequenceKey, new PeptideMatch(nodePep, matchedProteins,
pepInfo.LibInfo,
MatchesFilter(target, pepInfo.Key.Adduct)) }
};
return(nodePep);
}
/// <summary>
/// Tries to match each library peptide to document settings.
/// </summary>
public void MatchAllPeptides(ILongWaitBroker broker)
{
_chargeSettingsMap = new SrmSettings[128];
// Build a dictionary mapping sequence to proteins because getting this information is slow.
var dictSequenceProteins = new Dictionary <string, IList <ProteinInfo> >();
var dictNewNodePeps = new Dictionary <PeptideSequenceModKey, PeptideMatch>();
PeptideMatches = null;
MatchedPeptideCount = 0;
int peptides = 0;
int totalPeptides = _libraryPepInfos.Length;
foreach (ViewLibraryPepInfo pepInfo in _libraryPepInfos)
{
if (broker.IsCanceled)
{
return;
}
int charge = pepInfo.Key.Charge;
// Find the matching peptide.
var nodePepMatched = AssociateMatchingPeptide(pepInfo, charge).PeptideNode;
if (nodePepMatched != null)
{
MatchedPeptideCount++;
PeptideMatch peptideMatchInDict;
// If peptide is already in the dictionary of peptides to add, merge the children.
if (!dictNewNodePeps.TryGetValue(nodePepMatched.SequenceKey, out peptideMatchInDict))
{
IList <ProteinInfo> matchedProteins = null;
var sequence = nodePepMatched.Peptide.Sequence;
// This is only set if the user has checked the associate peptide box.
if (_backgroundProteome != null)
{
// We want to query the background proteome as little as possible,
// so sequences are mapped to protein lists in a dictionary.
if (!dictSequenceProteins.TryGetValue(sequence, out matchedProteins))
{
using (var proteomeDb = _backgroundProteome.OpenProteomeDb())
{
var digestion = _backgroundProteome.GetDigestion(proteomeDb, Settings.PeptideSettings);
if (digestion != null)
{
matchedProteins = digestion.GetProteinsWithSequence(sequence).Select(protein => new ProteinInfo(protein)).ToList();
dictSequenceProteins.Add(sequence, matchedProteins);
}
}
}
}
dictNewNodePeps.Add(nodePepMatched.SequenceKey,
new PeptideMatch(nodePepMatched, matchedProteins,
MatchesFilter(sequence, charge)));
}
else
{
PeptideDocNode nodePepInDictionary = peptideMatchInDict.NodePep;
if (!nodePepInDictionary.HasChildCharge(charge))
{
List <DocNode> newChildren = nodePepInDictionary.Children.ToList();
newChildren.AddRange(nodePepMatched.Children);
newChildren.Sort(Peptide.CompareGroups);
var key = nodePepMatched.SequenceKey;
dictNewNodePeps.Remove(key);
dictNewNodePeps.Add(key,
new PeptideMatch((PeptideDocNode)nodePepInDictionary.ChangeChildren(newChildren),
peptideMatchInDict.Proteins, peptideMatchInDict.MatchesFilterSettings));
}
}
}
peptides++;
int progressValue = (int)((peptides + 0.0) / totalPeptides * PERCENT_PEPTIDE_MATCH);
broker.ProgressValue = progressValue;
}
PeptideMatches = dictNewNodePeps;
}