private static SrmDocument AddPeptidesToLibraryGroup(SrmDocument document,
ICollection <PeptideMatch> listMatches,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = listMatches.Count;
var listPeptides = new List <PeptideDocNode>();
var hasSmallMolecules = false;
foreach (var match in listMatches)
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = null;
return(document);
}
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
listPeptides.Add(match.NodePep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL));
hasSmallMolecules |= !match.NodePep.IsProteomic;
}
bool hasVariable =
listPeptides.Contains(nodePep => nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods);
// Use existing group by this name, if present.
var nodeName = hasSmallMolecules
? Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Molecules
: Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides;
var nodePepGroupNew = FindPeptideGroupDocNode(document, nodeName);
if (nodePepGroupNew != null)
{
var newChildren = nodePepGroupNew.Children.ToList();
newChildren.AddRange(listPeptides.ConvertAll(nodePep => (DocNode)nodePep));
selectedPath = (listPeptides.Count == 1 ? new IdentityPath(nodePepGroupNew.Id, listPeptides[0].Id) : toPath);
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeChildren(newChildren);
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
return((SrmDocument)document.ReplaceChild(nodePepGroupNew));
}
else
{
nodePepGroupNew = new PeptideGroupDocNode(new PeptideGroup(),
nodeName,
string.Empty, listPeptides.ToArray());
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
IdentityPath nextAdd;
document = document.AddPeptideGroups(new[] { nodePepGroupNew }, true,
toPath, out selectedPath, out nextAdd);
selectedPath = new IdentityPath(selectedPath, nodePepGroupNew.Children[0].Id);
return(document);
}
}
private static SrmDocument AddPeptidesToLibraryGroup(SrmDocument document,
ICollection <PeptideMatch> listMatches,
ILongWaitBroker broker,
IdentityPath toPath,
out IdentityPath selectedPath)
{
// Get starting progress values
int startPercent = (broker != null ? broker.ProgressValue : 0);
int processedPercent = 0;
int processedCount = 0;
int totalMatches = listMatches.Count;
selectedPath = null;
// Some .blib files provide protein accessions (understood as Molecule List Names fro small molecules).
// If those are provided we will use them as node names.
// TODO(bspratt) for now we will do this only for small molecules since it might be a surprise to proteomics users. We should revisit that decision.
foreach (var proteinName in listMatches.Select(m => m.LibInfo.Protein).Distinct())
{
var listPeptides = new List <PeptideDocNode>();
var hasSmallMolecules = false;
foreach (var match in listMatches.Where(m => Equals(proteinName, m.LibInfo.Protein)))
{
// Show progress, if in a long wait
if (broker != null)
{
if (broker.IsCanceled)
{
selectedPath = null;
return(document);
}
processedCount++;
int processPercentNow = processedCount * (100 - startPercent) / totalMatches;
if (processedPercent != processPercentNow)
{
processedPercent = processPercentNow;
broker.ProgressValue = startPercent + processedPercent;
}
}
listPeptides.Add(match.NodePep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL));
hasSmallMolecules |= !match.NodePep.IsProteomic;
}
bool hasVariable =
listPeptides.Contains(nodePep => nodePep.HasExplicitMods && nodePep.ExplicitMods.IsVariableStaticMods);
// Use existing group by this name, if present.
// If library provides a RefSpectraProteins table, use that to name the group
// TODO(bspratt) for now we will use RefSpectraProteins names only for small molecules
var genericLibraryPeptidesGroupName = hasSmallMolecules
? Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Molecules
: Resources.ViewLibraryPepMatching_AddPeptidesToLibraryGroup_Library_Peptides;
var nodeName = string.IsNullOrEmpty(proteinName) ||
listPeptides.Any(p => p.IsProteomic) // TODO(bspratt) revisit this caution-driven decision
? genericLibraryPeptidesGroupName
: proteinName;
var nodePepGroupNew = FindPeptideGroupDocNode(document, nodeName, null);
if (nodePepGroupNew != null)
{
var newChildren = nodePepGroupNew.Children.ToList();
newChildren.AddRange(listPeptides.ConvertAll(nodePep => (DocNode)nodePep));
selectedPath = (listPeptides.Count == 1 ? new IdentityPath(nodePepGroupNew.Id, listPeptides[0].Id) : toPath);
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeChildren(newChildren);
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
document = (SrmDocument)document.ReplaceChild(nodePepGroupNew);
}
else
{
nodePepGroupNew = new PeptideGroupDocNode(new PeptideGroup(),
nodeName,
string.Empty, listPeptides.ToArray());
if (hasVariable)
{
nodePepGroupNew = (PeptideGroupDocNode)nodePepGroupNew.ChangeAutoManageChildren(false);
}
IdentityPath nextAdd;
document = document.AddPeptideGroups(new[] { nodePepGroupNew }, true,
toPath, out selectedPath, out nextAdd);
selectedPath = new IdentityPath(selectedPath, nodePepGroupNew.Children[0].Id);
}
}
return(document);
}
