public IList <DocNode> RankChildren(SrmSettings settingsNew, IList <DocNode> childrenNew)
{
if (PeptideGroup.Sequence != null)
{
childrenNew = PeptideGroup.RankPeptides(childrenNew, settingsNew, false);
}
return(childrenNew);
}
public PeptideGroupDocNode ChangeSettings(SrmSettings settingsNew, SrmSettingsDiff diff)
{
if (diff.Monitor != null)
{
diff.Monitor.ProcessGroup(this);
}
if (diff.DiffPeptides && settingsNew.PeptideSettings.Filter.AutoSelect && AutoManageChildren)
{
IList <DocNode> childrenNew = new List <DocNode>();
int countPeptides = 0;
int countIons = 0;
Dictionary <int, DocNode> mapIndexToChild = CreateGlobalIndexToChildMap();
Dictionary <PeptideModKey, DocNode> mapIdToChild = CreatePeptideModToChildMap();
foreach (PeptideDocNode nodePep in GetPeptideNodes(settingsNew, true))
{
PeptideDocNode nodePepResult = nodePep;
SrmSettingsDiff diffNode = SrmSettingsDiff.ALL;
DocNode existing;
// Add values that existed before the change. First check for exact match by
// global index, which will happen when explicit modifications are added,
// and then by content identity.
if (mapIndexToChild.TryGetValue(nodePep.Id.GlobalIndex, out existing) ||
mapIdToChild.TryGetValue(nodePep.Key, out existing))
{
nodePepResult = (PeptideDocNode)existing;
diffNode = diff;
}
if (nodePepResult != null)
{
// Materialize children of the peptide.
nodePepResult = nodePepResult.ChangeSettings(settingsNew, diffNode);
childrenNew.Add(nodePepResult);
// Make sure a single peptide group does not exceed document limits.
countPeptides++;
countIons += nodePepResult.TransitionCount;
if (countIons > SrmDocument.MAX_TRANSITION_COUNT)
{
throw new InvalidDataException(String.Format(
Resources.PeptideGroupDocNode_ChangeSettings_The_current_document_settings_would_cause_the_number_of_targeted_transitions_to_exceed__0_n0___The_document_settings_must_be_more_restrictive_or_add_fewer_proteins_,
SrmDocument.MAX_TRANSITION_COUNT));
}
if (countPeptides > SrmDocument.MAX_PEPTIDE_COUNT)
{
throw new InvalidDataException(String.Format(
Resources.PeptideGroupDocNode_ChangeSettings_The_current_document_settings_would_cause_the_number_of_peptides_to_exceed__0_n0___The_document_settings_must_be_more_restrictive_or_add_fewer_proteins_,
SrmDocument.MAX_PEPTIDE_COUNT));
}
}
}
if (PeptideGroup.Sequence != null)
{
childrenNew = PeptideGroup.RankPeptides(childrenNew, settingsNew, true);
}
return((PeptideGroupDocNode)ChangeChildrenChecked(childrenNew));
}
else
{
var nodeResult = this;
if (diff.DiffPeptides && diff.SettingsOld != null)
{
// If variable modifications changed, remove all peptides with variable
// modifications which are no longer possible.
var modsNew = settingsNew.PeptideSettings.Modifications;
var modsVarNew = modsNew.VariableModifications.ToArray();
var modsOld = diff.SettingsOld.PeptideSettings.Modifications;
var modsVarOld = modsOld.VariableModifications.ToArray();
if (modsNew.MaxVariableMods < modsOld.MaxVariableMods ||
!ArrayUtil.EqualsDeep(modsVarNew, modsVarOld))
{
IList <DocNode> childrenNew = new List <DocNode>();
foreach (PeptideDocNode nodePeptide in nodeResult.Children)
{
if (nodePeptide.AreVariableModsPossible(modsNew.MaxVariableMods, modsVarNew))
{
childrenNew.Add(nodePeptide);
}
}
nodeResult = (PeptideGroupDocNode)nodeResult.ChangeChildrenChecked(childrenNew);
}
}
// Check for changes affecting children
if (diff.DiffPeptideProps || diff.DiffExplicit ||
diff.DiffTransitionGroups || diff.DiffTransitionGroupProps ||
diff.DiffTransitions || diff.DiffTransitionProps ||
diff.DiffResults)
{
IList <DocNode> childrenNew = new List <DocNode>();
// Enumerate the nodes making necessary changes.
foreach (PeptideDocNode nodePeptide in nodeResult.Children)
{
childrenNew.Add(nodePeptide.ChangeSettings(settingsNew, diff));
}
childrenNew = RankChildren(settingsNew, childrenNew);
nodeResult = (PeptideGroupDocNode)nodeResult.ChangeChildrenChecked(childrenNew);
}
return(nodeResult);
}
}
public PeptideGroupDocNode ChangeSettings(SrmSettings settingsNew, SrmSettingsDiff diff,
DocumentSettingsContext context = null)
{
if (diff.Monitor != null)
{
diff.Monitor.ProcessGroup(this);
}
if (diff.DiffPeptides && settingsNew.PeptideSettings.Filter.AutoSelect && AutoManageChildren)
{
IList <DocNode> childrenNew = new List <DocNode>();
int countPeptides = 0;
int countIons = 0;
Dictionary <int, DocNode> mapIndexToChild = CreateGlobalIndexToChildMap();
Dictionary <PeptideModKey, DocNode> mapIdToChild = CreatePeptideModToChildMap();
IEnumerable <PeptideDocNode> peptideDocNodes;
if (settingsNew.PeptideSettings.Filter.PeptideUniqueness == PeptideFilter.PeptideUniquenessConstraint.none ||
settingsNew.PeptideSettings.NeedsBackgroundProteomeUniquenessCheckProcessing)
{
peptideDocNodes = GetPeptideNodes(settingsNew, true).ToList();
}
else
{
// Checking peptide uniqueness against the background proteome can be expensive.
// Do all the regular processing, then filter those results at the end when we
// can do it in aggregate for best speed.
IEnumerable <PeptideDocNode> peptideDocNodesUnique;
var peptideDocNodesPrecalculatedForUniquenessCheck = context == null ? null : context.PeptideDocNodesPrecalculatedForUniquenessCheck;
var uniquenessDict = context == null ? null : context.UniquenessDict;
if (peptideDocNodesPrecalculatedForUniquenessCheck != null)
{
// Already processed, and a global list of peptides provided
Assume.IsNotNull(uniquenessDict);
peptideDocNodesUnique = peptideDocNodesPrecalculatedForUniquenessCheck;
}
else
{
// We'll have to do the processing for this node, and work with
// just the peptides on this node. With luck the background proteome
// will already have those cached for uniqueness checks.
var settingsNoUniquenessFilter =
settingsNew.ChangePeptideFilter(f => f.ChangePeptideUniqueness(PeptideFilter.PeptideUniquenessConstraint.none));
var nodes = GetPeptideNodes(settingsNoUniquenessFilter, true).ToList();
var sequences = new List <string>(from p in nodes select p.Peptide.Sequence);
peptideDocNodesUnique = nodes; // Avoid ReSharper multiple enumeration warning
uniquenessDict = settingsNew.PeptideSettings.Filter.CheckPeptideUniqueness(settingsNew, sequences, diff.Monitor);
}
// ReSharper disable once PossibleNullReferenceException
peptideDocNodes = peptideDocNodesUnique.Where(p =>
{
// It's possible during document load for uniqueness dict to get out of synch, so be
// cautious with lookup and just return false of not found. Final document change will clean that up.
bool isUnique;
return(uniquenessDict.TryGetValue(p.Peptide.Sequence, out isUnique) && isUnique);
});
}
foreach (var nodePep in peptideDocNodes)
{
PeptideDocNode nodePepResult = nodePep;
SrmSettingsDiff diffNode = SrmSettingsDiff.ALL;
DocNode existing;
// Add values that existed before the change. First check for exact match by
// global index, which will happen when explicit modifications are added,
// and then by content identity.
if (mapIndexToChild.TryGetValue(nodePep.Id.GlobalIndex, out existing) ||
mapIdToChild.TryGetValue(nodePep.Key, out existing))
{
nodePepResult = (PeptideDocNode)existing;
diffNode = diff;
}
if (nodePepResult != null)
{
// Materialize children of the peptide.
nodePepResult = nodePepResult.ChangeSettings(settingsNew, diffNode);
childrenNew.Add(nodePepResult);
// Make sure a single peptide group does not exceed document limits.
countPeptides++;
countIons += nodePepResult.TransitionCount;
if (countIons > SrmDocument.MAX_TRANSITION_COUNT)
{
throw new InvalidDataException(String.Format(
Resources.PeptideGroupDocNode_ChangeSettings_The_current_document_settings_would_cause_the_number_of_targeted_transitions_to_exceed__0_n0___The_document_settings_must_be_more_restrictive_or_add_fewer_proteins_,
SrmDocument.MAX_TRANSITION_COUNT));
}
if (countPeptides > SrmDocument.MAX_PEPTIDE_COUNT)
{
throw new InvalidDataException(String.Format(
Resources.PeptideGroupDocNode_ChangeSettings_The_current_document_settings_would_cause_the_number_of_peptides_to_exceed__0_n0___The_document_settings_must_be_more_restrictive_or_add_fewer_proteins_,
SrmDocument.MAX_PEPTIDE_COUNT));
}
}
}
if (PeptideGroup.Sequence != null)
{
childrenNew = PeptideGroup.RankPeptides(childrenNew, settingsNew, true);
}
return((PeptideGroupDocNode)ChangeChildrenChecked(childrenNew));
}
else
{
var nodeResult = this;
if (diff.DiffPeptides && diff.SettingsOld != null)
{
// If variable modifications changed, remove all peptides with variable
// modifications which are no longer possible.
var modsNew = settingsNew.PeptideSettings.Modifications;
var modsVarNew = modsNew.VariableModifications.ToArray();
var modsOld = diff.SettingsOld.PeptideSettings.Modifications;
var modsVarOld = modsOld.VariableModifications.ToArray();
if (modsNew.MaxVariableMods < modsOld.MaxVariableMods ||
!ArrayUtil.EqualsDeep(modsVarNew, modsVarOld))
{
IList <DocNode> childrenNew = new List <DocNode>();
foreach (PeptideDocNode nodePeptide in nodeResult.Children)
{
if (nodePeptide.AreVariableModsPossible(modsNew.MaxVariableMods, modsVarNew))
{
childrenNew.Add(nodePeptide);
}
}
nodeResult = (PeptideGroupDocNode)nodeResult.ChangeChildrenChecked(childrenNew);
}
}
// Check for changes affecting children
if (diff.DiffPeptideProps || diff.DiffExplicit ||
diff.DiffTransitionGroups || diff.DiffTransitionGroupProps ||
diff.DiffTransitions || diff.DiffTransitionProps ||
diff.DiffResults)
{
IList <DocNode> childrenNew = new List <DocNode>();
// Enumerate the nodes making necessary changes.
foreach (PeptideDocNode nodePeptide in nodeResult.Children)
{
childrenNew.Add(nodePeptide.ChangeSettings(settingsNew, diff));
}
childrenNew = RankChildren(settingsNew, childrenNew);
nodeResult = (PeptideGroupDocNode)nodeResult.ChangeChildrenChecked(childrenNew);
}
return(nodeResult);
}
}