public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, string name, string description,
PeptideDocNode[] children, bool autoManageChildren)
: this(id, annotations, new ProteinMetadata(name, description), children, autoManageChildren)
{
}
public Annotations Merge(Annotations annotations)
{
string note = Note;
if (string.IsNullOrEmpty(note))
{
note = annotations.Note;
}
else if (!string.IsNullOrEmpty(annotations.Note))
{
// Be careful not to creat repetitive notes during document merging
var newNoteBuilder = new StringBuilder();
foreach (var notePart in SplitNotes(note).Union(SplitNotes(annotations.Note)))
{
if (newNoteBuilder.Length > 0)
{
newNoteBuilder.AppendLine().AppendLine();
}
newNoteBuilder.Append(notePart);
}
note = newNoteBuilder.ToString();
}
var annotationsNew = _annotations;
if (annotationsNew == null)
{
annotationsNew = annotations._annotations;
}
else if (annotations._annotations != null)
{
// With annotations implemented as only a set of name, value pairs
// there is no way to know in this code which annotations are full-text,
// an so no way to do annotation merging as above.
annotationsNew = new Dictionary <string, string>(annotationsNew);
foreach (var annotation in annotations._annotations)
{
if (annotationsNew.ContainsKey(annotation.Key))
{
if (Equals(annotation.Value, annotationsNew[annotation.Key]))
{
continue;
}
throw new InvalidDataException(string.Format(Resources.Annotations_Merge_Annotation_conflict_for__0__found_attempting_to_merge_annotations,
annotation.Key));
}
annotationsNew.Add(annotation);
}
}
int colorIndex = (ColorIndex != -1 ? ColorIndex : annotations.ColorIndex);
var merged = new Annotations(note, annotationsNew, colorIndex);
if (Equals(merged, this))
{
return(this);
}
if (Equals(merged, annotations))
{
return(annotations);
}
return(merged);
}
public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, string name, string description,
PeptideDocNode[] children)
: this(id, annotations, name, description, children, true)
{
}
/// <summary>
/// Removes peaks and annotations that were in the document but not in the file, so that all peptide results that were not explicitly imported as part of this file are now blank
/// </summary>
/// <param name="docNew">SrmDocument for which missing peaks should be removed</param>
/// <param name="trackAdjustedResults">List of peaks that were in the imported file</param>
/// <param name="changePeaks">If true, remove both peaks and annotations. If false, only remove annotations</param>
/// <returns></returns>
private SrmDocument RemoveMissing(SrmDocument docNew, ICollection <ResultsKey> trackAdjustedResults, bool changePeaks)
{
var measuredResults = docNew.Settings.MeasuredResults;
var chromatogramSets = measuredResults.Chromatograms;
for (int i = 0; i < chromatogramSets.Count; ++i)
{
var set = chromatogramSets[i];
var nameSet = set.Name;
for (int k = 0; k < docNew.MoleculeCount; ++k)
{
IdentityPath pepPath = docNew.GetPathTo((int)SrmDocument.Level.Molecules, k);
var pepNode = (PeptideDocNode)Document.FindNode(pepPath);
if (pepNode.IsDecoy)
{
continue;
}
if (pepNode.GlobalStandardType != null)
{
continue;
}
foreach (var groupNode in pepNode.TransitionGroups)
{
var groupPath = new IdentityPath(pepPath, groupNode.Id);
var chromInfos = groupNode.Results[i];
if (chromInfos.IsEmpty)
{
continue;
}
foreach (var groupChromInfo in chromInfos)
{
if (groupChromInfo == null)
{
continue;
}
var key = new ResultsKey(groupChromInfo.FileId.GlobalIndex, groupNode.Id);
if (!trackAdjustedResults.Contains(key))
{
CountMissing++;
var fileId = groupChromInfo.FileId;
var fileInfo = set.GetFileInfo(fileId);
var filePath = fileInfo.FilePath;
// Remove annotations for defs that were imported into the document and were on this peptide prior to import
var newAnnotationValues = groupChromInfo.Annotations.ListAnnotations().ToList();
newAnnotationValues = newAnnotationValues.Where(a => !AnnotationsAdded.Contains(a.Key)).ToList();
var newAnnotations = new Annotations(groupChromInfo.Annotations.Note, newAnnotationValues, groupChromInfo.Annotations.ColorIndex);
var newGroupNode = groupNode.ChangePrecursorAnnotations(fileId, newAnnotations);
if (!ReferenceEquals(groupNode, newGroupNode))
{
docNew = (SrmDocument)docNew.ReplaceChild(groupPath.Parent, newGroupNode);
}
// Adjust peaks to null if they weren't in the file
if (changePeaks)
{
docNew = docNew.ChangePeak(groupPath, nameSet, filePath,
null, null, null, UserSet.IMPORTED, null, false);
}
}
}
}
}
}
return(docNew);
}
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings,
TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues,
SkylineDocumentProto.Types.Transition transitionProto)
{
var stringPool = scrubber.StringPool;
IonType ionType = DataValues.FromIonType(transitionProto.FragmentType);
MeasuredIon measuredIon = null;
if (transitionProto.MeasuredIonName != null)
{
measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault(
i => i.Name.Equals(transitionProto.MeasuredIonName.Value));
if (measuredIon == null)
{
throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName));
}
ionType = IonType.custom;
}
bool isCustom = Transition.IsCustom(ionType, group);
bool isPrecursor = Transition.IsPrecursor(ionType);
CustomMolecule customIon = null;
if (isCustom)
{
if (measuredIon != null)
{
customIon = measuredIon.SettingsCustomIon;
}
else if (isPrecursor)
{
customIon = group.CustomMolecule;
}
else
{
var formula = DataValues.FromOptional(transitionProto.Formula);
var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc
var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH);
var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH);
var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH;
var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH;
customIon = new CustomMolecule(formula,
new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic),
new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average),
DataValues.FromOptional(transitionProto.CustomIonName), moleculeID);
}
}
Transition transition;
var adductString = DataValues.FromOptional(transitionProto.Adduct);
var adduct = string.IsNullOrEmpty(adductString)
? Adduct.FromChargeProtonated(transitionProto.Charge)
: Adduct.FromStringAssumeChargeOnly(adductString);
if (isCustom)
{
transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType);
}
else if (isPrecursor)
{
transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex,
group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
else
{
int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal,
group.Peptide.Length);
transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses);
var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist);
var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null)
{
throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift);
}
TransitionLibInfo libInfo = null;
if (transitionProto.LibInfo != null)
{
libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity);
}
var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition);
var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results);
var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create(
DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy),
DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset),
DataValues.FromOptional(transitionProto.ExplicitSLens),
DataValues.FromOptional(transitionProto.ExplicitConeVoltage),
DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential));
return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results));
}
public SkylineDocumentProto.Types.Transition ToTransitionProto(SrmSettings settings)
{
var transitionProto = new SkylineDocumentProto.Types.Transition
{
FragmentType = DataValues.ToIonType(Transition.IonType),
NotQuantitative = !ExplicitQuantitative
};
if (Transition.IsCustom() && !Transition.IsPrecursor())
{
SetCustomIonFragmentInfo(transitionProto);
}
transitionProto.DecoyMassShift = DataValues.ToOptional(Transition.DecoyMassShift);
transitionProto.MassIndex = Transition.MassIndex;
if (HasDistInfo)
{
transitionProto.IsotopeDistRank = DataValues.ToOptional(IsotopeDistInfo.Rank);
transitionProto.IsotopeDistProportion = DataValues.ToOptional(IsotopeDistInfo.Proportion);
}
if (!Transition.IsPrecursor())
{
if (!Transition.IsCustom())
{
transitionProto.FragmentOrdinal = Transition.Ordinal;
transitionProto.CalcNeutralMass = GetMoleculePersistentNeutralMass();
}
transitionProto.Charge = Transition.Charge;
if (!Transition.Adduct.IsProteomic)
{
transitionProto.Adduct = DataValues.ToOptional(Transition.Adduct.AsFormulaOrSignedInt());
}
if (!Transition.IsCustom())
{
transitionProto.CleavageAa = Transition.AA;
transitionProto.LostMass = LostMass;
}
}
if (Annotations != null)
{
transitionProto.Annotations = Annotations.ToProtoAnnotations();
}
transitionProto.ProductMz = Mz;
if (Losses != null)
{
foreach (var loss in Losses.Losses)
{
var neutralLoss = new SkylineDocumentProto.Types.TransitionLoss();
if (loss.PrecursorMod == null)
{
neutralLoss.Formula = loss.Loss.Formula;
neutralLoss.MonoisotopicMass = loss.Loss.MonoisotopicMass;
neutralLoss.AverageMass = loss.Loss.AverageMass;
neutralLoss.LossInclusion = DataValues.ToLossInclusion(loss.Loss.Inclusion);
neutralLoss.Charge = loss.Loss.Charge;
}
else
{
neutralLoss.ModificationName = loss.PrecursorMod.Name;
neutralLoss.LossIndex = loss.LossIndex;
}
transitionProto.Losses.Add(neutralLoss);
}
}
if (HasLibInfo)
{
transitionProto.LibInfo = new SkylineDocumentProto.Types.TransitionLibInfo
{
Intensity = LibInfo.Intensity,
Rank = LibInfo.Rank
};
}
if (Results != null)
{
transitionProto.Results = new SkylineDocumentProto.Types.TransitionResults();
transitionProto.Results.Peaks.AddRange(GetTransitionPeakProtos(settings.MeasuredResults));
}
if (!Equals(ExplicitValues, ExplicitTransitionValues.EMPTY))
{
transitionProto.ExplicitCollisionEnergy = DataValues.ToOptional(ExplicitValues.CollisionEnergy);
transitionProto.ExplicitConeVoltage = DataValues.ToOptional(ExplicitValues.ConeVoltage);
transitionProto.ExplicitDeclusteringPotential = DataValues.ToOptional(ExplicitValues.DeclusteringPotential);
transitionProto.ExplicitIonMobilityHighEnergyOffset = DataValues.ToOptional(ExplicitValues.IonMobilityHighEnergyOffset);
transitionProto.ExplicitSLens = DataValues.ToOptional(ExplicitValues.SLens);
}
return(transitionProto);
}
public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, ProteinMetadata proteinMetadata,
PeptideDocNode[] children, bool autoManageChildren)
: this(id, annotations, proteinMetadata, children, autoManageChildren, null)
{
}
