public override IEnumerable <DocNode> GetChoices(bool useFilter)
{
SrmSettings settings = DocSettings;
List <DocNode> listPeptides = new List <DocNode>();
foreach (var nodePep in DocNode.GetPeptideNodes(settings, useFilter))
{
var nodePepMaterialized = nodePep.ChangeSettings(settings, SrmSettingsDiff.ALL);
if (!useFilter || settings.TransitionSettings.Libraries.MinIonCount == 0 || nodePepMaterialized.Children.Count != 0)
{
listPeptides.Add(nodePepMaterialized);
}
}
PeptideRankId rankId = DocSettings.PeptideSettings.Libraries.RankId;
if (rankId != null && !DocNode.IsPeptideList)
{
listPeptides = PeptideGroup.RankPeptides(listPeptides, settings, useFilter).ToList();
}
MergeChosen(listPeptides, useFilter, node => ((PeptideDocNode)node).Key);
return(listPeptides);
}
void GroupProteinsOrPeptides(
IDictionary <string, Node> entities,
IReadOnlyList <string> entityNames,
Type entityType,
GlobalIDContainer globalIDTracker)
{
for (var count = 0; count != entityNames.Count; count++)
{
// Is the key there?
if (!entities.ContainsKey(entityNames[count]))
{
continue;
}
// Get the protein or peptide
var entity = entities[entityNames[count]];
// Only proceed if the correct type
if (entity.GetType() != entityType)
{
continue;
}
var duplicates = new NodeChildren <Node>();
// Look for duplicates and add to a duplicate list
duplicates.AddRange(FindDuplicates(entity));
if (duplicates.Count <= 1)
{
continue;
}
// Create a protein or peptide group from the duplicates
Group newGroup;
if (entityType == typeof(Protein))
{
newGroup = new ProteinGroup(duplicates, globalIDTracker);
}
else if (entityType == typeof(Peptide))
{
newGroup = new PeptideGroup(duplicates, globalIDTracker);
}
else
{
throw new Exception("Invalid type: must be Protein or Peptide");
}
foreach (var duplicateItem in duplicates)
{
// Remove entities from the library, add the new group
entities.Remove(duplicateItem.NodeName);
}
entities.Add(newGroup.NodeName, newGroup);
}
}
public override IEnumerable <DocNode> GetChoices(bool useFilter)
{
SrmSettings settings = DocSettings;
List <DocNode> listPeptides = new List <DocNode>();
foreach (var nodePep in DocNode.GetPeptideNodes(settings, useFilter))
{
listPeptides.Add(nodePep.ChangeSettings(settings, SrmSettingsDiff.ALL));
}
PeptideRankId rankId = DocSettings.PeptideSettings.Libraries.RankId;
if (rankId != null && !DocNode.IsPeptideList)
{
listPeptides = PeptideGroup.RankPeptides(listPeptides, settings, useFilter).ToList();
}
MergeChosen(listPeptides, useFilter, node => ((PeptideDocNode)node).Key);
return(listPeptides);
}
