public PeptideDocNode ChangeSettings(SrmSettings settingsNew, SrmSettingsDiff diff, bool recurse = true)
{
if (diff.Monitor != null)
diff.Monitor.ProcessMolecule(this);
// If the peptide has explicit modifications, and the modifications have
// changed, see if any of the explicit modifications have changed
var explicitMods = ExplicitMods;
if (HasExplicitMods &&
!diff.IsUnexplainedExplicitModificationAllowed &&
diff.SettingsOld != null &&
!ReferenceEquals(settingsNew.PeptideSettings.Modifications,
diff.SettingsOld.PeptideSettings.Modifications))
{
explicitMods = ExplicitMods.ChangeGlobalMods(settingsNew);
if (explicitMods == null || !ArrayUtil.ReferencesEqual(explicitMods.GetHeavyModifications().ToArray(),
ExplicitMods.GetHeavyModifications().ToArray()))
{
diff = new SrmSettingsDiff(diff, SrmSettingsDiff.ALL);
}
else if (!ReferenceEquals(explicitMods.StaticModifications, ExplicitMods.StaticModifications))
{
diff = new SrmSettingsDiff(diff, SrmSettingsDiff.PROPS);
}
}
TransitionSettings transitionSettings = settingsNew.TransitionSettings;
PeptideDocNode nodeResult = this;
if (!ReferenceEquals(explicitMods, ExplicitMods))
nodeResult = nodeResult.ChangeExplicitMods(explicitMods);
nodeResult = nodeResult.UpdateModifiedSequence(settingsNew);
if (diff.DiffPeptideProps)
{
var rt = settingsNew.PeptideSettings.Prediction.RetentionTime;
bool isStandard = Equals(nodeResult.GlobalStandardType, STANDARD_TYPE_IRT);
if (rt != null)
{
bool isStandardNew = rt.IsStandardPeptide(nodeResult);
if (isStandard ^ isStandardNew)
nodeResult = nodeResult.ChangeStandardType(isStandardNew ? STANDARD_TYPE_IRT : null);
}
else if (isStandard)
{
nodeResult = nodeResult.ChangeStandardType(null);
}
}
if (diff.DiffTransitionGroups && settingsNew.TransitionSettings.Filter.AutoSelect && AutoManageChildren)
{
IList<DocNode> childrenNew = new List<DocNode>();
PeptideRankId rankId = settingsNew.PeptideSettings.Libraries.RankId;
bool useHighestRank = (rankId != null && settingsNew.PeptideSettings.Libraries.PeptideCount.HasValue);
bool isPickedIntensityRank = useHighestRank &&
ReferenceEquals(rankId, LibrarySpec.PEP_RANK_PICKED_INTENSITY);
Dictionary<Identity, DocNode> mapIdToChild = CreateIdContentToChildMap();
foreach (TransitionGroup tranGroup in GetTransitionGroups(settingsNew, explicitMods, true))
{
TransitionGroupDocNode nodeGroup;
SrmSettingsDiff diffNode = diff;
DocNode existing;
// Add values that existed before the change, unless using picked intensity ranking,
// since this could bias the ranking, otherwise.
if (!isPickedIntensityRank && mapIdToChild.TryGetValue(tranGroup, out existing))
nodeGroup = (TransitionGroupDocNode)existing;
// Add new node
else
{
TransitionDocNode[] transitions = !isPickedIntensityRank
? GetMatchingTransitions(tranGroup, settingsNew, explicitMods)
: null;
nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
// If not recursing, then ChangeSettings will not be called on nodeGroup. So, make
// sure its precursor m/z is set correctly.
if (!recurse)
nodeGroup = nodeGroup.ChangePrecursorMz(settingsNew, explicitMods);
diffNode = SrmSettingsDiff.ALL;
}
if (nodeGroup != null)
{
TransitionGroupDocNode nodeChanged = recurse
? nodeGroup.ChangeSettings(settingsNew, nodeResult, explicitMods, diffNode)
: nodeGroup;
if (transitionSettings.IsMeasurablePrecursor(nodeChanged.PrecursorMz))
childrenNew.Add(nodeChanged);
}
}
// If only using rank limited peptides, then choose only the single
// highest ranked precursor charge.
if (useHighestRank)
{
childrenNew = FilterHighestRank(childrenNew, rankId);
// If using picked intensity, make sure original nodes are replaced
if (isPickedIntensityRank)
{
for (int i = 0; i < childrenNew.Count; i++)
{
var nodeNew = (TransitionGroupDocNode) childrenNew[i];
DocNode existing;
if (mapIdToChild.TryGetValue(nodeNew.TransitionGroup, out existing))
childrenNew[i] = existing;
}
}
}
nodeResult = (PeptideDocNode) nodeResult.ChangeChildrenChecked(childrenNew);
}
else
{
// Even with auto-select off, transition groups for which there is
// no longer a precursor calculator must be removed.
if (diff.DiffTransitionGroups && nodeResult.HasHeavyTransitionGroups)
{
IList<DocNode> childrenNew = new List<DocNode>();
foreach (TransitionGroupDocNode nodeGroup in nodeResult.Children)
{
if (settingsNew.HasPrecursorCalc(nodeGroup.TransitionGroup.LabelType, explicitMods))
childrenNew.Add(nodeGroup);
}
nodeResult = (PeptideDocNode)nodeResult.ChangeChildrenChecked(childrenNew);
}
// Update properties and children, if necessary
if (diff.DiffTransitionGroupProps ||
diff.DiffTransitions || diff.DiffTransitionProps ||
diff.DiffResults)
{
IList<DocNode> childrenNew = new List<DocNode>();
// Enumerate the nodes making necessary changes.
foreach (TransitionGroupDocNode nodeGroup in nodeResult.Children)
{
TransitionGroupDocNode nodeChanged = nodeGroup.ChangeSettings(settingsNew, nodeResult, explicitMods, diff);
// Skip if the node can no longer be measured on the target instrument
if (!transitionSettings.IsMeasurablePrecursor(nodeChanged.PrecursorMz))
continue;
// Skip this node, if it is heavy and the update caused it to have the
// same m/z value as the light value.
if (!nodeChanged.TransitionGroup.LabelType.IsLight &&
!Peptide.IsCustomIon) // No mods on customs
{
double precursorMassLight = settingsNew.GetPrecursorMass(
IsotopeLabelType.light, Peptide.Sequence, explicitMods);
double precursorMzLight = SequenceMassCalc.GetMZ(precursorMassLight,
nodeChanged.TransitionGroup.PrecursorCharge);
if (nodeChanged.PrecursorMz == precursorMzLight)
continue;
}
childrenNew.Add(nodeChanged);
}
nodeResult = (PeptideDocNode)nodeResult.ChangeChildrenChecked(childrenNew);
}
}
if (diff.DiffResults || ChangedResults(nodeResult))
nodeResult = nodeResult.UpdateResults(settingsNew /*, diff*/);
return nodeResult;
}