public PeptideDocNode UpdateMolecule(IdentityPath parent, PeptideDocNode peptideDocNode)
{
CheckCancelled();
AnnotationUpdater updater;
_annotationUpdaters.TryGetValue(AnnotationDef.AnnotationTarget.peptide, out updater);
var identityPath = new IdentityPath(parent, peptideDocNode.Peptide);
if (updater != null)
{
var peptide = new Databinding.Entities.Peptide(SkylineDataSchema, new IdentityPath(parent, peptideDocNode.Peptide));
var annotations = updater.UpdateAnnotations(peptideDocNode.Annotations, peptide);
if (!Equals(annotations, peptideDocNode.Annotations))
{
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeAnnotations(annotations);
}
}
if (!RecursePrecursors)
{
return(peptideDocNode);
}
var newChildren = peptideDocNode.TransitionGroups.Select(tg => UpdatePrecursor(identityPath, tg)).ToArray();
if (!ArrayUtil.ReferencesEqual(peptideDocNode.Children, newChildren))
{
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeChildren(newChildren);
}
return(peptideDocNode);
}
private PeptideDocNode RemoveTransition(PeptideDocNode nodePep)
{
var precursors = nodePep.TransitionGroups.ToList();
precursors[0] = (TransitionGroupDocNode)precursors[0].ChangeChildren(precursors[0].Children.Skip(1).ToList());
return((PeptideDocNode)nodePep.ChangeChildren(precursors.Cast <DocNode>().ToList()));
}
public PeptideDocNode PermuteModificationsOnPeptide(SrmDocument document, PeptideGroupDocNode peptideGroupDocNode,
PeptideDocNode peptideDocNode, List <IsotopeLabelType> partialLabelTypes)
{
if (SkipPeptide(peptideDocNode))
{
return(peptideDocNode);
}
var potentiallyModifiedResidues = PotentiallyModifiedResidues(peptideDocNode, IsotopeModification);
if (potentiallyModifiedResidues.Count == 0)
{
return(peptideDocNode);
}
// Create a document containing only one peptide so that "ChangePeptideMods" does not have to walk
// over a long list of peptides to see which modifications are in use.
var smallDocument = (SrmDocument)document.ChangeChildren(new DocNode[]
{ peptideGroupDocNode.ChangeChildren(new DocNode[] { peptideDocNode }) });
var newTypedExplicitModifications = PermuteTypedExplicitModifications(partialLabelTypes, peptideDocNode, potentiallyModifiedResidues);
var newExplicitMods = new ExplicitMods(peptideDocNode.Peptide, peptideDocNode.ExplicitMods?.StaticModifications, newTypedExplicitModifications);
var identityPath = new IdentityPath(peptideGroupDocNode.PeptideGroup, peptideDocNode.Peptide);
smallDocument = smallDocument.ChangePeptideMods(identityPath, newExplicitMods, false, GlobalStaticMods,
GlobalIsotopeMods);
peptideDocNode = (PeptideDocNode)smallDocument.FindPeptideGroup(peptideGroupDocNode.PeptideGroup).FindNode(peptideDocNode.Peptide);
var lightChargeStates = peptideDocNode.TransitionGroups.Where(tg => tg.IsLight).Select(tg => tg.PrecursorCharge).Distinct().ToList();
var chargeStatesByLabel =
peptideDocNode.TransitionGroups.ToLookup(tg => tg.LabelType, tg => tg.PrecursorCharge);
var transitionGroupsToAdd = new List <TransitionGroupDocNode>();
foreach (var typedExplicitModifications in newExplicitMods.GetHeavyModifications())
{
var labelType = typedExplicitModifications.LabelType;
foreach (var chargeState in lightChargeStates.Except(chargeStatesByLabel[labelType]))
{
var tranGroup = new TransitionGroup(peptideDocNode.Peptide, Adduct.FromChargeProtonated(chargeState), labelType);
TransitionDocNode[] transitions = peptideDocNode.GetMatchingTransitions(tranGroup, smallDocument.Settings, newExplicitMods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(smallDocument.Settings, peptideDocNode, newExplicitMods, SrmSettingsDiff.ALL);
transitionGroupsToAdd.Add(nodeGroup);
}
}
if (transitionGroupsToAdd.Any())
{
var newChildren = peptideDocNode.TransitionGroups.Concat(transitionGroupsToAdd).ToList();
newChildren.Sort(Peptide.CompareGroups);
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeChildren(newChildren.Cast <DocNode>().ToList());
}
return(peptideDocNode);
}
/// <summary>
/// Tries to match each library peptide to document settings.
/// </summary>
public void MatchAllPeptides(ILongWaitBroker broker)
{
_chargeSettingsMap = new AdductMap <SrmSettings>();
// 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.Count;
ProteomeDb proteomeDb = null;
IStatelessSession session = null;
try
{
foreach (ViewLibraryPepInfo pepInfo in _libraryPepInfos)
{
if (broker.IsCanceled)
{
return;
}
var charge = pepInfo.Key.Adduct;
// 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 target = nodePepMatched.Peptide.Target;
// This is only set if the user has checked the associate peptide box.
if (target.IsProteomic && _backgroundProteome != null)
{
var sequence = target.Sequence;
// 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))
{
if (proteomeDb == null)
{
proteomeDb = _backgroundProteome.OpenProteomeDb(broker.CancellationToken);
session = proteomeDb.OpenStatelessSession(false);
}
var digestion = proteomeDb.GetDigestion();
if (sequence.Length >= MIN_PEPTIDE_LENGTH)
{
matchedProteins = digestion.GetProteinsWithSequence(session, sequence)
.Select(protein => new ProteinInfo(protein)).ToList();
}
if (matchedProteins == null || matchedProteins.Count > MAX_PROTEIN_MATCHES)
{
// If the peptide was too short, or matched too many proteins, then
// treat it as if it was not found in any proteins.
matchedProteins = new List <ProteinInfo>();
}
dictSequenceProteins.Add(sequence, matchedProteins);
}
}
dictNewNodePeps.Add(nodePepMatched.SequenceKey,
new PeptideMatch(nodePepMatched, matchedProteins,
MatchesFilter(target, 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;
}
finally
{
using (proteomeDb)
using (session)
{
}
}
}
/// <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;
}