private TransitionGroupDocNode CreateChoice(Identity childId, ExplicitMods mods)
{
TransitionGroup tranGroup = (TransitionGroup)childId;
TransitionDocNode[] transitions = DocNode.GetMatchingTransitions(
tranGroup, DocSettings, mods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
return(nodeGroup.ChangeSettings(DocSettings, DocNode, mods, SrmSettingsDiff.ALL));
}
public PeptideDocNode PermuteModificationsOnPeptide(SrmDocument document, PeptideGroupDocNode peptideGroupDocNode,
PeptideDocNode peptideDocNode, List <IsotopeLabelType> partialLabelTypes)
{
if (SkipPeptide(peptideDocNode))
{
return(peptideDocNode);
}
var potentiallyModifiedResidues = PotentiallyModifiedResidues(peptideDocNode, IsotopeModification);
if (potentiallyModifiedResidues.Count == 0)
{
return(peptideDocNode);
}
// Create a document containing only one peptide so that "ChangePeptideMods" does not have to walk
// over a long list of peptides to see which modifications are in use.
var smallDocument = (SrmDocument)document.ChangeChildren(new DocNode[]
{ peptideGroupDocNode.ChangeChildren(new DocNode[] { peptideDocNode }) });
var newTypedExplicitModifications = PermuteTypedExplicitModifications(partialLabelTypes, peptideDocNode, potentiallyModifiedResidues);
var newExplicitMods = new ExplicitMods(peptideDocNode.Peptide, peptideDocNode.ExplicitMods?.StaticModifications, newTypedExplicitModifications);
var identityPath = new IdentityPath(peptideGroupDocNode.PeptideGroup, peptideDocNode.Peptide);
smallDocument = smallDocument.ChangePeptideMods(identityPath, newExplicitMods, false, GlobalStaticMods,
GlobalIsotopeMods);
peptideDocNode = (PeptideDocNode)smallDocument.FindPeptideGroup(peptideGroupDocNode.PeptideGroup).FindNode(peptideDocNode.Peptide);
var lightChargeStates = peptideDocNode.TransitionGroups.Where(tg => tg.IsLight).Select(tg => tg.PrecursorCharge).Distinct().ToList();
var chargeStatesByLabel =
peptideDocNode.TransitionGroups.ToLookup(tg => tg.LabelType, tg => tg.PrecursorCharge);
var transitionGroupsToAdd = new List <TransitionGroupDocNode>();
foreach (var typedExplicitModifications in newExplicitMods.GetHeavyModifications())
{
var labelType = typedExplicitModifications.LabelType;
foreach (var chargeState in lightChargeStates.Except(chargeStatesByLabel[labelType]))
{
var tranGroup = new TransitionGroup(peptideDocNode.Peptide, Adduct.FromChargeProtonated(chargeState), labelType);
TransitionDocNode[] transitions = peptideDocNode.GetMatchingTransitions(tranGroup, smallDocument.Settings, newExplicitMods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(smallDocument.Settings, peptideDocNode, newExplicitMods, SrmSettingsDiff.ALL);
transitionGroupsToAdd.Add(nodeGroup);
}
}
if (transitionGroupsToAdd.Any())
{
var newChildren = peptideDocNode.TransitionGroups.Concat(transitionGroupsToAdd).ToList();
newChildren.Sort(Peptide.CompareGroups);
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeChildren(newChildren.Cast <DocNode>().ToList());
}
return(peptideDocNode);
}
public void AddRemoveExplicitModTest()
{
SrmDocument docStudy7 = CreateStudy7Doc();
string transitionList = ExportCsv(docStudy7);
Assert.AreEqual(69, transitionList.Split('\n').Length); // Special test mode may add an extra doc node
var modifications = docStudy7.Settings.PeptideSettings.Modifications;
var listStaticMods = modifications.StaticModifications;
var listHeavyMods = modifications.AllHeavyModifications.ToList();
docStudy7 = docStudy7.ChangeSettings(docStudy7.Settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(false)));
// Remove all modifications
int i = 0;
// But save them for later
var removedMods = new Dictionary <int, ExplicitMods>();
foreach (var peptide in docStudy7.Peptides)
{
if (peptide.HasExplicitMods)
{
removedMods.Add(i, peptide.ExplicitMods);
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, i);
docStudy7 = docStudy7.ChangePeptideMods(path, null, listStaticMods, listHeavyMods);
}
i++;
}
// Removes heavy from peptide with c-terminal P
AssertEx.IsDocumentState(docStudy7, 6, 7, 11, 21, 63);
modifications = docStudy7.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modifications.AllHeavyModifications.Count());
Assert.AreEqual(0, modifications.AllHeavyModifications.Count(mod => mod.IsExplicit));
Assert.AreEqual(0, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
listHeavyMods = ATOMIC_HEAVY_MODS;
foreach (var pair in removedMods)
{
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, pair.Key);
docStudy7 = docStudy7.ChangePeptideMods(path, pair.Value, listStaticMods, listHeavyMods);
}
AssertEx.IsDocumentState(docStudy7, 11, 7, 11, 21, 63);
// Replace the heavy precursor that was removed
// TODO: Yuck. Would be nice to have a way to do this without duplicating
// so much of the logic in PeptideDocNode and PeptideTreeNode
var pepPath = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, 10);
var nodePep = (PeptideDocNode)docStudy7.FindNode(pepPath);
var mods = nodePep.ExplicitMods;
var nodeGroupLight = (TransitionGroupDocNode)nodePep.Children[0];
var settings = docStudy7.Settings;
foreach (var tranGroup in nodePep.GetTransitionGroups(settings, mods, false))
{
if (tranGroup.PrecursorAdduct.Equals(nodeGroupLight.TransitionGroup.PrecursorAdduct) &&
!tranGroup.LabelType.IsLight)
{
TransitionDocNode[] transitions = nodePep.GetMatchingTransitions(tranGroup, settings, mods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(settings, nodePep, mods, SrmSettingsDiff.ALL);
docStudy7 = (SrmDocument)docStudy7.Add(pepPath, nodeGroup);
break;
}
}
AssertEx.IsDocumentState(docStudy7, 12, 7, 11, 22, 66);
modifications = docStudy7.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modifications.AllHeavyModifications.Count(mod => mod.IsExplicit && mod.Label13C));
Assert.AreEqual(2, modifications.AllHeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(3, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.StaticModifications.Count > 0 &&
peptide.ExplicitMods.StaticModifications[0].Modification.AAs[0] == 'C'));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
Assert.AreEqual(1, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'L' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
AssertEx.NoDiff(transitionList, ExportCsv(docStudy7));
}
public void AddRemoveExplicitModTest()
{
SrmDocument docStudy7 = CreateStudy7Doc();
string transitionList = ExportCsv(docStudy7);
Assert.AreEqual(69 + (TestSmallMolecules ? 2 : 0), transitionList.Split('\n').Length); // Special test mode may add an extra doc node
var modifications = docStudy7.Settings.PeptideSettings.Modifications;
var listStaticMods = modifications.StaticModifications;
var listHeavyMods = modifications.HeavyModifications;
docStudy7 = docStudy7.ChangeSettings(docStudy7.Settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(false)));
// Remove all modifications
int i = 0;
// But save them for later
var removedMods = new Dictionary<int, ExplicitMods>();
foreach (var peptide in docStudy7.Peptides)
{
if (peptide.HasExplicitMods)
{
removedMods.Add(i, peptide.ExplicitMods);
IdentityPath path = docStudy7.GetPathTo((int) SrmDocument.Level.Molecules, i);
docStudy7 = docStudy7.ChangePeptideMods(path, null, listStaticMods, listHeavyMods);
}
i++;
}
// Removes heavy from peptide with c-terminal P
AssertEx.IsDocumentState(docStudy7, 6, 7, 11, 21, 63);
modifications = docStudy7.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modifications.HeavyModifications.Count);
Assert.AreEqual(0, modifications.HeavyModifications.Count(mod => mod.IsExplicit));
Assert.AreEqual(0, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
listHeavyMods = ATOMIC_HEAVY_MODS;
foreach (var pair in removedMods)
{
IdentityPath path = docStudy7.GetPathTo((int)SrmDocument.Level.Molecules, pair.Key);
docStudy7 = docStudy7.ChangePeptideMods(path, pair.Value, listStaticMods, listHeavyMods);
}
AssertEx.IsDocumentState(docStudy7, 11, 7, 11, 21, 63);
// Replace the heavy precursor that was removed
// TODO: Yuck. Would be nice to have a way to do this without duplicating
// so much of the logic in PeptideDocNode and PeptideTreeNode
var pepPath = docStudy7.GetPathTo((int) SrmDocument.Level.Molecules, 10);
var nodePep = (PeptideDocNode) docStudy7.FindNode(pepPath);
var mods = nodePep.ExplicitMods;
var nodeGroupLight = (TransitionGroupDocNode) nodePep.Children[0];
var settings = docStudy7.Settings;
foreach (var tranGroup in nodePep.GetTransitionGroups(settings, mods, false))
{
if (tranGroup.PrecursorCharge == nodeGroupLight.TransitionGroup.PrecursorCharge &&
!tranGroup.LabelType.IsLight)
{
TransitionDocNode[] transitions = nodePep.GetMatchingTransitions(tranGroup, settings, mods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(settings, nodePep, mods, SrmSettingsDiff.ALL);
docStudy7 = (SrmDocument) docStudy7.Add(pepPath, nodeGroup);
break;
}
}
AssertEx.IsDocumentState(docStudy7, 12, 7, 11, 22, 66);
modifications = docStudy7.Settings.PeptideSettings.Modifications;
Assert.AreEqual(2, modifications.HeavyModifications.Count(mod => mod.IsExplicit && mod.Label13C));
Assert.AreEqual(2, modifications.HeavyModifications.Count(mod => mod.Formula != null));
Assert.AreEqual(3, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.StaticModifications.Count > 0 &&
peptide.ExplicitMods.StaticModifications[0].Modification.AAs[0] == 'C'));
Assert.AreEqual(2, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'V' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
Assert.AreEqual(1, docStudy7.Peptides.Count(peptide => peptide.HasExplicitMods &&
peptide.ExplicitMods.HeavyModifications[0].Modification.AAs[0] == 'L' &&
peptide.ExplicitMods.HeavyModifications[0].Modification.Label13C));
AssertEx.NoDiff(transitionList, ExportCsv(docStudy7));
}
private DocNode CreateChoice(Identity childId, ExplicitMods mods)
{
TransitionGroup tranGroup = (TransitionGroup)childId;
TransitionDocNode[] transitions = DocNode.GetMatchingTransitions(
tranGroup, DocSettings, mods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
return nodeGroup.ChangeSettings(DocSettings, DocNode, mods, SrmSettingsDiff.ALL);
}
private PeptideDocNode Refine(PeptideDocNode nodePep,
SrmDocument document,
int bestResultIndex,
List<int> acceptedCharges)
{
int minTrans = MinTransitionsPepPrecursor ?? 0;
bool addedGroups = false;
var listGroups = new List<TransitionGroupDocNode>();
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (acceptedCharges != null && !acceptedCharges.Contains(nodeGroup.TransitionGroup.PrecursorCharge))
continue;
if (!AddLabelType && RefineLabelType != null && Equals(RefineLabelType, nodeGroup.TransitionGroup.LabelType))
continue;
double? peakFoundRatio = nodeGroup.GetPeakCountRatio(bestResultIndex);
if (!peakFoundRatio.HasValue)
{
if (RemoveMissingResults)
continue;
}
else
{
if (MinPeakFoundRatio.HasValue)
{
if (peakFoundRatio < MinPeakFoundRatio.Value)
continue;
}
if (MaxPeakFoundRatio.HasValue)
{
if (peakFoundRatio > MaxPeakFoundRatio.Value)
continue;
}
}
TransitionGroupDocNode nodeGroupRefined = nodeGroup;
if (AutoPickTransitionsAll && nodeGroup.AutoManageChildren == AutoPickChildrenOff)
{
nodeGroupRefined = (TransitionGroupDocNode) nodeGroupRefined.ChangeAutoManageChildren(!AutoPickChildrenOff);
var settings = document.Settings;
if (!settings.TransitionSettings.Filter.AutoSelect && !AutoPickChildrenOff)
settings = settings.ChangeTransitionFilter(filter => filter.ChangeAutoSelect(!AutoPickChildrenOff));
nodeGroupRefined = nodeGroupRefined.ChangeSettings(settings, nodePep, nodePep.ExplicitMods,
new SrmSettingsDiff(false, false, false, false, true, false));
}
nodeGroupRefined = Refine(nodeGroupRefined, bestResultIndex);
if (nodeGroupRefined.Children.Count < minTrans)
continue;
if (peakFoundRatio.HasValue)
{
if (DotProductThreshold.HasValue)
{
float? dotProduct = nodeGroupRefined.GetLibraryDotProduct(bestResultIndex);
if (dotProduct.HasValue && dotProduct.Value < DotProductThreshold.Value)
continue;
}
if (IdotProductThreshold.HasValue)
{
float? idotProduct = nodeGroupRefined.GetIsotopeDotProduct(bestResultIndex);
if (idotProduct.HasValue && idotProduct.Value < IdotProductThreshold.Value)
continue;
}
}
// If this precursor node is going to be added, check to see if it
// should be added with another matching isotope label type.
var explicitMods = nodePep.ExplicitMods;
if (IsLabelTypeRequired(nodePep, nodeGroup, listGroups) &&
document.Settings.TryGetPrecursorCalc(RefineLabelType, explicitMods) != null)
{
// CONSIDER: This is a lot like some code in PeptideDocNode.ChangeSettings
Debug.Assert(RefineLabelType != null); // Keep ReSharper from warning
var tranGroup = new TransitionGroup(nodePep.Peptide,
nodeGroup.TransitionGroup.PrecursorCharge,
RefineLabelType,
false,
nodeGroup.TransitionGroup.DecoyMassShift);
var settings = document.Settings;
// string sequence = nodePep.Peptide.Sequence;
TransitionDocNode[] transitions = nodePep.GetMatchingTransitions(
tranGroup, settings, explicitMods);
var nodeGroupMatch = new TransitionGroupDocNode(tranGroup,
Annotations.EMPTY,
settings,
explicitMods,
nodeGroup.LibInfo,
nodeGroup.ExplicitValues,
null, // results
transitions,
transitions == null);
nodeGroupMatch = nodeGroupMatch.ChangeSettings(settings, nodePep, explicitMods, SrmSettingsDiff.ALL);
// Make sure it is measurable before adding it
if (settings.TransitionSettings.IsMeasurablePrecursor(nodeGroupMatch.PrecursorMz))
{
listGroups.Add(nodeGroupMatch);
addedGroups = true;
}
}
listGroups.Add(nodeGroupRefined);
}
// If groups were added, make sure everything is in the right order.
if (addedGroups)
listGroups.Sort(Peptide.CompareGroups);
// Change the children, but only change auto-management, if the child
// identities have changed, not if their contents changed.
var childrenNew = listGroups.ToArray();
bool updateAutoManage = !PeptideDocNode.AreEquivalentChildren(nodePep.Children, childrenNew);
return (PeptideDocNode) nodePep.ChangeChildrenChecked(childrenNew, updateAutoManage);
}