public override string ToString()
{
var sb = new StringBuilder();
sb.Append("Precursor Mass Only");
sb.AppendLine("Index partitions: " + CurrentPartition + "/" + commonParameters.TotalPartitions);
sb.AppendLine("Search Decoys: " + DecoyType);
sb.AppendLine("Number of proteins: " + ProteinList.Count);
sb.AppendLine("Number of fixed mods: " + FixedModifications.Count);
sb.AppendLine("Number of variable mods: " + VariableModifications.Count);
sb.AppendLine("lp: " + string.Join(",", ProductTypes));
foreach (var digestionParams in CollectionOfDigestionParams)
{
sb.AppendLine("protease: " + digestionParams.Protease);
sb.AppendLine("initiatorMethionineBehavior: " + digestionParams.InitiatorMethionineBehavior);
sb.AppendLine("maximumMissedCleavages: " + digestionParams.MaxMissedCleavages);
sb.AppendLine("minPeptideLength: " + digestionParams.MinPeptideLength);
sb.AppendLine("maxPeptideLength: " + digestionParams.MaxPeptideLength);
sb.AppendLine("maximumVariableModificationIsoforms: " + digestionParams.MaxModificationIsoforms);
}
sb.Append("Localizeable mods: " + ProteinList.Select(b => b.OneBasedPossibleLocalizedModifications.Count).Sum());
return(sb.ToString());
}
/// <summary>
/// This function removes protein clusters that do not have a
/// required number of additional unique peptides.
/// </summary>
/// <param name="minAdditionalPeptides"></param>
public void filterByMinimumCoveringSet(int minAdditionalPeptides, ProteinList proteins)
{
if (minAdditionalPeptides == 0)
return;
if (statusOutput == null)
{
// Get the minimum protein set that can explain all the peptides
List<ProteinInfo> proteinsToRemove = new List<ProteinInfo>();
foreach (ProteinList.MapPair proItr in proteins)
{
// Remove the protein cluster if it doesn't have the required number
// of unique peptides
if (proItr.Value.proteinGroup.uniquePeptideCount < minAdditionalPeptides)
{
proteinsToRemove.Add(proItr.Value);
}
else
{
proItr.Value.proteinGroup = null;
foreach (ResultInfo r in proItr.Value.results)
r.peptideGroup = null;
}
}
foreach (ProteinInfo pro in proteinsToRemove)
removeProtein(pro);
}
else
{
// Same as above with status reporting.
List<ProteinInfo> proteinsToRemove = new List<ProteinInfo>();
ProteinList.Enumerator itr = proteins.GetEnumerator(); itr.MoveNext();
for (int i = 0; i < proteins.Count; ++i, itr.MoveNext())
{
ProteinInfo pro = itr.Current.Value;
reportStatus("testing protein " + (i + 1) + " of " + proteins.Count, i + 1 == proteins.Count);
if (pro.proteinGroup.uniquePeptideCount < minAdditionalPeptides)
proteinsToRemove.Add(pro);
else
{
pro.proteinGroup = null;
foreach (ResultInfo r in pro.results)
r.peptideGroup = null;
}
}
for (int i = 0; i < proteinsToRemove.Count; ++i)
{
reportStatus("removing protein " + (i + 1) + " of " + proteinsToRemove.Count, i + 1 == proteinsToRemove.Count);
removeProtein(proteinsToRemove[i]);
}
}
assembleProteinGroups();
assemblePeptideGroups();
assembleClusters();
// we lost the actual value by regrouping, but we know the minimum
foreach (ProteinGroupInfo proGroup in proteinGroups)
proGroup.uniquePeptideCount = minAdditionalPeptides;
}