public PeptideDocNode CreateDocNodeFromSettings(LibKey key, Peptide peptide, SrmSettingsDiff diff, out TransitionGroupDocNode nodeGroupMatched)
{
if (!key.Target.IsProteomic)
{
// Scan the spectral lib entry for top N ranked (for now, that's just by intensity with high mz as tie breaker) fragments,
// add those as mass-only fragments, or with more detail if peak annotations are present.
foreach (var nodePep in peptide.CreateDocNodes(Settings, new MaxModFilter(0)))
{
SpectrumHeaderInfo libInfo;
if (nodePep != null && Settings.PeptideSettings.Libraries.TryGetLibInfo(key, out libInfo))
{
var isotopeLabelType = key.Adduct.HasIsotopeLabels ? IsotopeLabelType.heavy : IsotopeLabelType.light;
var group = new TransitionGroup(peptide, key.Adduct, isotopeLabelType);
nodeGroupMatched = new TransitionGroupDocNode(group, Annotations.EMPTY, Settings, null, libInfo, ExplicitTransitionGroupValues.EMPTY, null, null, false);
SpectrumPeaksInfo spectrum;
if (Settings.PeptideSettings.Libraries.TryLoadSpectrum(key, out spectrum))
{
// Add fragment and precursor transitions as needed
var transitionDocNodes =
Settings.TransitionSettings.Filter.SmallMoleculeIonTypes.Contains(IonType.precursor)
? nodeGroupMatched.GetPrecursorChoices(Settings, null, true) // Gives list of precursors
: new List <DocNode>();
if (Settings.TransitionSettings.Filter.SmallMoleculeIonTypes.Contains(IonType.custom))
{
GetSmallMoleculeFragments(key, nodeGroupMatched, spectrum, transitionDocNodes);
}
nodeGroupMatched = (TransitionGroupDocNode)nodeGroupMatched.ChangeChildren(transitionDocNodes);
return((PeptideDocNode)nodePep.ChangeChildren(new List <DocNode>()
{
nodeGroupMatched
}));
}
}
}
nodeGroupMatched = null;
return(null);
}
return(CreateDocNodeFromSettings(key.Target, peptide, diff, out nodeGroupMatched));
}
public static IEnumerable <PeptideDocNode> CreateAllDocNodes(SrmSettings settings, Peptide peptide)
{
return(peptide.CreateDocNodes(settings, PeptideFilter.UNFILTERED));
}