/// <summary>
/// Adds a list of PeptideDocNodes found in the library to the current document.
/// </summary>
public SrmDocument AddPeptides(SrmDocument document, ILongWaitBroker broker, IdentityPath toPath, out IdentityPath selectedPath)
{
if (toPath != null &&
toPath.Depth == (int)SrmDocument.Level.MoleculeGroups &&
ReferenceEquals(toPath.GetIdentity((int)SrmDocument.Level.MoleculeGroups), SequenceTree.NODE_INSERT_ID))
{
toPath = null;
}
SkippedPeptideCount = 0;
var dictCopy = new Dictionary <PeptideSequenceModKey, PeptideMatch>();
// Make heavy mods explicit
if (PeptideMatches.Values.Contains(match => match.NodePep.HasExplicitMods &&
match.NodePep.ExplicitMods.HeavyModifications != null))
{
_matcher.ConvertAllHeavyModsExplicit();
}
// Call ensure mods on all peptides to be added to the document.
var listDefStatMods = new MappedList <string, StaticMod>();
listDefStatMods.AddRange(Properties.Settings.Default.StaticModList);
listDefStatMods.AddRange(document.Settings.PeptideSettings.Modifications.StaticModifications);
var listDefHeavyMods = new MappedList <string, StaticMod>();
listDefHeavyMods.AddRange(Properties.Settings.Default.HeavyModList);
listDefHeavyMods.AddRange(document.Settings.PeptideSettings.Modifications.AllHeavyModifications);
foreach (var key in PeptideMatches.Keys)
{
var match = PeptideMatches[key];
var nodePepDocSet = match.NodePep;
if (_matcher.MatcherPepMods != null)
{
nodePepDocSet = match.NodePep.EnsureMods(_matcher.MatcherPepMods,
document.Settings.PeptideSettings.Modifications,
listDefStatMods, listDefHeavyMods);
}
if (!dictCopy.ContainsKey(nodePepDocSet.SequenceKey))
{
dictCopy.Add(nodePepDocSet.SequenceKey,
new PeptideMatch(nodePepDocSet, match.Proteins,
match.MatchesFilterSettings));
}
}
if (!Properties.Settings.Default.LibraryPeptidesKeepFiltered)
{
// TODO: This removes entire peptides where only a single
// precursor does not match. e.g. the library contains
// a singly charged precursor match, but also doubly charged
dictCopy = dictCopy.Where(match => match.Value.MatchesFilterSettings)
.ToDictionary(match => match.Key, match => match.Value);
}
SrmDocument newDocument = UpdateExistingPeptides(document, dictCopy, toPath, out selectedPath);
toPath = selectedPath;
// If there is an associated background proteome, add peptides that can be
// matched to the proteins from the background proteom.
if (_backgroundProteome != null)
{
newDocument = AddProteomePeptides(newDocument, dictCopy, broker,
toPath, out selectedPath);
}
toPath = selectedPath;
// Add all remaining peptides as a peptide list.
if (_backgroundProteome == null || Properties.Settings.Default.LibraryPeptidesAddUnmatched)
{
var listPeptidesToAdd = dictCopy.Values.ToList();
listPeptidesToAdd.RemoveAll(match => match.Proteins != null && match.Proteins.Count > 0);
if (listPeptidesToAdd.Count > 0)
{
newDocument = AddPeptidesToLibraryGroup(newDocument, listPeptidesToAdd, broker,
toPath, out selectedPath);
if (listPeptidesToAdd.Count > 1000)
{
selectedPath = selectedPath.Parent; // Don't force Skyline to open a massive peptide list, if it wouldn't otherwise
}
}
}
return(newDocument);
}
