本文整理汇总了C#中SrmDocument.ChangeChildrenChecked方法的典型用法代码示例。如果您正苦于以下问题：C# SrmDocument.ChangeChildrenChecked方法的具体用法？C# SrmDocument.ChangeChildrenChecked怎么用？C# SrmDocument.ChangeChildrenChecked使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类SrmDocument的用法示例。
在下文中一共展示了SrmDocument.ChangeChildrenChecked方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C#代码示例。
示例1: LookupProteinMetadata
//.........这里部分代码省略.........
progressStatus =
progressStatus.ChangePercentComplete(100*nResolved++/nUnresolved));
}
}
if (progressMonitor.IsCanceled)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
}
}
}
// ReSharper disable once EmptyGeneralCatchClause
catch
{
// The protDB file is busy, or some other issue - just go directly to web
}
}
}
if (nResolved != nUnresolved)
{
try
{
// Now go to the web for more protein metadata (or pretend to, depending on WebEnabledFastaImporter.DefaultWebAccessMode)
var docNodesWithUnresolvedProteinMetadata = new Dictionary<ProteinSearchInfo,PeptideGroupDocNode>();
var proteinsToSearch = new List<ProteinSearchInfo>();
foreach (PeptideGroupDocNode node in docOrig.PeptideGroups)
{
if (node.ProteinMetadata.NeedsSearch() && !_processedNodes.ContainsKey(node.Id.GlobalIndex)) // Did we already process this?
{
var proteinMetadata = node.ProteinMetadata;
if (proteinMetadata.WebSearchInfo.IsEmpty()) // Never even been hit with regex
{
// Use Regexes to get some metadata, and a search term
var parsedProteinMetaData = FastaImporter.ParseProteinMetaData(proteinMetadata);
if ((parsedProteinMetaData == null) || Equals(parsedProteinMetaData.Merge(proteinMetadata),proteinMetadata.SetWebSearchCompleted()))
{
// That didn't parse well enough to make a search term, or didn't add any new info - just set it as searched so we don't keep trying
_processedNodes.Add(node.Id.GlobalIndex, proteinMetadata.SetWebSearchCompleted());
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved++ / nUnresolved));
proteinMetadata = null; // No search to be done
}
else
{
proteinMetadata = proteinMetadata.Merge(parsedProteinMetaData); // Fill in any gaps with parsed info
}
}
if (proteinMetadata != null)
{
// We note the sequence length because it's useful in disambiguating search results
proteinsToSearch.Add(new ProteinSearchInfo(new DbProteinName(null, proteinMetadata),
node.PeptideGroup.Sequence == null ? 0 : node.PeptideGroup.Sequence.Length));
docNodesWithUnresolvedProteinMetadata.Add(proteinsToSearch.Last(), node);
}
}
}
if (progressMonitor.IsCanceled)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved / nUnresolved));
// Now we actually hit the internet
if (proteinsToSearch.Any())
{
foreach (var result in FastaImporter.DoWebserviceLookup(proteinsToSearch, progressMonitor, false)) // Resolve them all, now
{
Debug.Assert(!result.GetProteinMetadata().NeedsSearch());
_processedNodes.Add(docNodesWithUnresolvedProteinMetadata[result].Id.GlobalIndex, result.GetProteinMetadata());
progressMonitor.UpdateProgress(progressStatus = progressStatus.ChangePercentComplete(100 * nResolved++ / nUnresolved));
}
}
}
catch (OperationCanceledException)
{
progressMonitor.UpdateProgress(progressStatus.Cancel());
return null;
}
}
// And finally write back to the document
var listProteins = new List<PeptideGroupDocNode>();
foreach (PeptideGroupDocNode node in docOrig.MoleculeGroups)
{
if (_processedNodes.ContainsKey(node.Id.GlobalIndex))
{
listProteins.Add(node.ChangeProteinMetadata(_processedNodes[node.Id.GlobalIndex]));
}
else
{
listProteins.Add(node);
}
}
var docNew = docOrig.ChangeChildrenChecked(listProteins.Cast<DocNode>().ToArray());
progressMonitor.UpdateProgress(progressStatus.Complete());
return (SrmDocument)docNew;
}
}示例2: Refine
public SrmDocument Refine(SrmDocument document, SrmSettingsChangeMonitor progressMonitor)
{
HashSet<int> outlierIds = new HashSet<int>();
if (RTRegressionThreshold.HasValue)
{
// TODO: Move necessary code into Model.
var outliers = RTLinearRegressionGraphPane.CalcOutliers(document,
RTRegressionThreshold.Value, RTRegressionPrecision, UseBestResult);
foreach (var nodePep in outliers)
outlierIds.Add(nodePep.Id.GlobalIndex);
}
HashSet<RefinementIdentity> includedPeptides = (RemoveRepeatedPeptides ? new HashSet<RefinementIdentity>() : null);
HashSet<RefinementIdentity> repeatedPeptides = (RemoveDuplicatePeptides ? new HashSet<RefinementIdentity>() : null);
Dictionary<RefinementIdentity, List<int>> acceptedPeptides = null;
if (AcceptedPeptides != null)
{
acceptedPeptides = new Dictionary<RefinementIdentity, List<int>>();
foreach (var peptideCharge in AcceptedPeptides)
{
List<int> charges;
if (!acceptedPeptides.TryGetValue(new RefinementIdentity(peptideCharge.Sequence), out charges))
{
charges = (peptideCharge.Charge.HasValue ? new List<int> {peptideCharge.Charge.Value} : null);
acceptedPeptides.Add(new RefinementIdentity(peptideCharge.Sequence), charges);
}
else if (charges != null)
{
if (peptideCharge.Charge.HasValue)
charges.Add(peptideCharge.Charge.Value);
else
acceptedPeptides[new RefinementIdentity(peptideCharge.Sequence)] = null;
}
}
}
HashSet<string> acceptedProteins = (AcceptedProteins != null ? new HashSet<string>(AcceptedProteins) : null);
var listPepGroups = new List<PeptideGroupDocNode>();
// Excluding proteins with too few peptides, since they can impact results
// of the duplicate peptide check.
int minPeptides = MinPeptidesPerProtein ?? 0;
foreach (PeptideGroupDocNode nodePepGroup in document.Children)
{
if (progressMonitor != null)
progressMonitor.ProcessGroup(nodePepGroup);
if (acceptedProteins != null && !acceptedProteins.Contains(GetAcceptProteinKey(nodePepGroup)))
continue;
PeptideGroupDocNode nodePepGroupRefined = nodePepGroup;
// If auto-managing all peptides, make sure this flag is set correctly,
// and update the peptides list, if necessary.
if (AutoPickPeptidesAll && nodePepGroup.AutoManageChildren == AutoPickChildrenOff)
{
nodePepGroupRefined =
(PeptideGroupDocNode) nodePepGroupRefined.ChangeAutoManageChildren(!AutoPickChildrenOff);
var settings = document.Settings;
if (!AutoPickChildrenOff && !settings.PeptideSettings.Filter.AutoSelect)
settings = settings.ChangePeptideFilter(filter => filter.ChangeAutoSelect(true));
nodePepGroupRefined = nodePepGroupRefined.ChangeSettings(settings,
new SrmSettingsDiff(true, false, false, false, false, false));
}
nodePepGroupRefined = Refine(nodePepGroupRefined, document, outlierIds,
includedPeptides, repeatedPeptides, acceptedPeptides, progressMonitor);
if (nodePepGroupRefined.Children.Count < minPeptides)
continue;
listPepGroups.Add(nodePepGroupRefined);
}
// Need a second pass, if all duplicate peptides should be removed,
// and duplicates were found.
if (repeatedPeptides != null && repeatedPeptides.Count > 0)
{
var listPepGroupsFiltered = new List<PeptideGroupDocNode>();
foreach (PeptideGroupDocNode nodePepGroup in listPepGroups)
{
var listPeptides = new List<PeptideDocNode>();
foreach (PeptideDocNode nodePep in nodePepGroup.Children)
{
var identity = nodePep.Peptide.IsCustomIon
? new RefinementIdentity(nodePep.Peptide.CustomIon)
: new RefinementIdentity(document.Settings.GetModifiedSequence(nodePep));
if (!repeatedPeptides.Contains(identity))
listPeptides.Add(nodePep);
}
PeptideGroupDocNode nodePepGroupRefined = (PeptideGroupDocNode)
nodePepGroup.ChangeChildrenChecked(listPeptides.ToArray(), true);
if (nodePepGroupRefined.Children.Count < minPeptides)
continue;
listPepGroupsFiltered.Add(nodePepGroupRefined);
}
listPepGroups = listPepGroupsFiltered;
//.........这里部分代码省略.........
示例3: UpdateExistingPeptides
/// <summary>
/// Enumerate all document peptides. If a library peptide already exists in the
/// current document, update the transition groups for that document peptide and
/// remove the peptide from the list to add.
/// </summary>
/// <param name="document">The starting document</param>
/// <param name="dictCopy">A dictionary of peptides to peptide matches. All added
/// peptides are removed</param>
/// <param name="toPath">Currently selected path.</param>
/// <param name="selectedPath">Selected path after the nodes have been added</param>
/// <returns>A new document with precursors for existing petides added</returns>
private SrmDocument UpdateExistingPeptides(SrmDocument document,
Dictionary<PeptideSequenceModKey, PeptideMatch> dictCopy,
IdentityPath toPath, out IdentityPath selectedPath)
{
selectedPath = toPath;
IList<DocNode> nodePepGroups = new List<DocNode>();
foreach (PeptideGroupDocNode nodePepGroup in document.PeptideGroups)
{
IList<DocNode> nodePeps = new List<DocNode>();
foreach (PeptideDocNode nodePep in nodePepGroup.Children)
{
var key = nodePep.SequenceKey;
PeptideMatch peptideMatch;
// If this peptide is not in our list of peptides to add,
// or if we are in a peptide list and this peptide has been matched to protein(s),
// then we don't touch this particular node.
if (!dictCopy.TryGetValue(key, out peptideMatch) ||
(nodePepGroup.IsPeptideList &&
(peptideMatch.Proteins != null && peptideMatch.Proteins.Any())))
nodePeps.Add(nodePep);
else
{
var proteinName = nodePepGroup.PeptideGroup.Name;
int indexProtein = -1;
if (peptideMatch.Proteins != null)
{
indexProtein =
peptideMatch.Proteins.IndexOf(protein => Equals(protein.ProteinMetadata.Name, proteinName));
// If the user has opted to filter duplicate peptides, remove this peptide from the list to
// add and continue.
if(FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.NoDuplicates && peptideMatch.Proteins.Count > 1)
{
dictCopy.Remove(key);
nodePeps.Add(nodePep);
continue;
}
// [1] If this protein is not the first match, and the user has opted to add only the first occurence,
// [2] or if this protein is not one of the matches, and [2a] we are either not in a peptide list
// [2b] or the user has opted to filter unmatched peptides, ignore this particular node.
if((indexProtein > 0 && FilterMultipleProteinMatches == BackgroundProteome.DuplicateProteinsFilter.FirstOccurence) ||
(indexProtein == -1 &&
(!nodePepGroup.IsPeptideList || !Properties.Settings.Default.LibraryPeptidesAddUnmatched)))
{
nodePeps.Add(nodePep);
continue;
}
}
// Update the children of the peptide in the document to include the charge state of the peptide we are adding.
PeptideDocNode nodePepMatch = peptideMatch.NodePep;
PeptideDocNode nodePepSettings = null;
var newChildren = nodePep.Children.ToList();
Identity nodeGroupChargeId = newChildren.Count > 0 ? newChildren[0].Id : null;
foreach (TransitionGroupDocNode nodeGroup in nodePepMatch.Children)
{
int chargeGroup = nodeGroup.TransitionGroup.PrecursorCharge;
if (nodePep.HasChildCharge(chargeGroup))
SkippedPeptideCount++;
else
{
if (nodePepSettings == null)
nodePepSettings = nodePepMatch.ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
TransitionGroupDocNode nodeGroupCharge = (TransitionGroupDocNode) nodePepSettings.FindNode(nodeGroup.TransitionGroup);
if (nodeGroupCharge == null)
{
continue;
}
if(peptideMatch.Proteins != null && peptideMatch.Proteins.Count() > 1)
{
// If we may be adding this specific node to the document more than once, create a copy of it so that
// we don't have two nodes with the same global id.
nodeGroupCharge = (TransitionGroupDocNode) nodeGroupCharge.CopyId();
nodeGroupCharge = (TransitionGroupDocNode) nodeGroupCharge.ChangeChildren(
nodeGroupCharge.Children.ToList().ConvertAll(child => child.CopyId()));
}
nodeGroupChargeId = nodeGroupCharge.Id;
newChildren.Add(nodeGroupCharge);
}
}
// Sort the new peptide children.
newChildren.Sort(Peptide.CompareGroups);
var nodePepAdd = nodePep.ChangeChildrenChecked(newChildren);
// If we have changed the children, need to set automanage children to false.
if (nodePep.AutoManageChildren && !ReferenceEquals(nodePep, nodePepAdd))
nodePepAdd = nodePepAdd.ChangeAutoManageChildren(false);
// Change the selected path.
if (PeptideMatches.Count == 1)
{
selectedPath = nodeGroupChargeId == null
? new IdentityPath(new[] { nodePepGroup.Id, nodePepAdd.Id })
//.........这里部分代码省略.........