private static List<TransitionGroupDocNode> GetDecoyGroups(PeptideDocNode nodePep, Peptide decoyPeptide,
ExplicitMods mods, IEnumerable<TransitionGroupDocNode> comparableGroups, SrmDocument document, bool shiftMass)
{
var decoyNodeTranGroupList = new List<TransitionGroupDocNode>();
var chargeToPrecursor = new Tuple<int, TransitionGroupDocNode>[TransitionGroup.MAX_PRECURSOR_CHARGE+1];
foreach (TransitionGroupDocNode nodeGroup in comparableGroups)
{
var transGroup = nodeGroup.TransitionGroup;
int precursorMassShift;
TransitionGroupDocNode nodeGroupPrimary = null;
var primaryPrecursor = chargeToPrecursor[nodeGroup.TransitionGroup.PrecursorCharge];
if (primaryPrecursor != null)
{
precursorMassShift = primaryPrecursor.Item1;
nodeGroupPrimary = primaryPrecursor.Item2;
}
else if (shiftMass)
{
precursorMassShift = GetPrecursorMassShift();
}
else
{
precursorMassShift = TransitionGroup.ALTERED_SEQUENCE_DECOY_MZ_SHIFT;
}
var decoyGroup = new TransitionGroup(decoyPeptide, transGroup.PrecursorCharge,
transGroup.LabelType, false, precursorMassShift);
var decoyNodeTranList = nodeGroupPrimary != null
? decoyGroup.GetMatchingTransitions(document.Settings, nodeGroupPrimary, mods)
: GetDecoyTransitions(nodeGroup, decoyGroup, shiftMass);
var nodeGroupDecoy = new TransitionGroupDocNode(decoyGroup,
Annotations.EMPTY,
document.Settings,
mods,
nodeGroup.LibInfo,
nodeGroup.ExplicitValues,
nodeGroup.Results,
decoyNodeTranList,
false);
decoyNodeTranGroupList.Add(nodeGroupDecoy);
if (primaryPrecursor == null)
{
chargeToPrecursor[transGroup.PrecursorCharge] =
new Tuple<int, TransitionGroupDocNode>(precursorMassShift, nodeGroupDecoy);
}
}
return decoyNodeTranGroupList;
}
public TransitionDocNode[] GetMatchingTransitions(TransitionGroup tranGroup, SrmSettings settings, ExplicitMods explicitMods)
{
int iMatch = Children.IndexOf(nodeGroup =>
((TransitionGroupDocNode)nodeGroup).TransitionGroup.PrecursorCharge == tranGroup.PrecursorCharge);
if (iMatch == -1)
return null;
TransitionGroupDocNode nodeGroupMatching = (TransitionGroupDocNode) Children[iMatch];
// If the matching node is auto-managed, and auto-select is on in the settings,
// then returning no transitions should allow transitions to be chosen correctly
// automatically.
if (nodeGroupMatching.AutoManageChildren && settings.TransitionSettings.Filter.AutoSelect &&
// Having disconnected libraries can mess up automatic picking
settings.PeptideSettings.Libraries.DisconnectedLibraries == null)
return null;
return tranGroup.GetMatchingTransitions(settings, nodeGroupMatching, explicitMods);
}