private void AddPeptideGroup(ICollection<PeptideGroupDocNode> listGroups,
PeptideGroupBuilder builder,
List<MeasuredRetentionTime> irtPeptides,
List<SpectrumMzInfo> librarySpectra,
List<TransitionImportErrorInfo> errorList)
{
PeptideGroupDocNode nodeGroup = builder.ToDocNode();
listGroups.Add(nodeGroup);
irtPeptides.AddRange(builder.IrtPeptides);
librarySpectra.AddRange(builder.LibrarySpectra);
if (builder.PeptideGroupErrorInfo.Count > 0)
errorList.AddRange(builder.PeptideGroupErrorInfo);
_countPeptides += nodeGroup.MoleculeCount;
_countIons += nodeGroup.TransitionCount;
}
private PeptideGroupBuilder AddRow(PeptideGroupBuilder seqBuilder,
MassListRowReader rowReader,
IDictionary<string, FastaSequence> dictNameSeq,
ICollection<PeptideGroupDocNode> peptideGroupsNew,
long lineNum,
List<MeasuredRetentionTime> irtPeptides,
List<SpectrumMzInfo> librarySpectra,
List<TransitionImportErrorInfo> errorList)
{
var info = rowReader.TransitionInfo;
var irt = rowReader.Irt;
var libraryIntensity = rowReader.LibraryIntensity;
var productMz = rowReader.ProductMz;
if (irt == null && rowReader.IrtColumn != -1)
{
var error = new TransitionImportErrorInfo(string.Format(Resources.MassListImporter_AddRow_Invalid_iRT_value_at_precusor_m_z__0__for_peptide__1_,
rowReader.TransitionInfo.PrecursorMz,
rowReader.TransitionInfo.ModifiedSequence),
rowReader.IrtColumn,
lineNum);
errorList.Add(error);
return seqBuilder;
}
if (libraryIntensity == null && rowReader.LibraryColumn != -1)
{
var error = new TransitionImportErrorInfo(string.Format(Resources.MassListImporter_AddRow_Invalid_library_intensity_at_precursor__0__for_peptide__1_,
rowReader.TransitionInfo.PrecursorMz,
rowReader.TransitionInfo.ModifiedSequence),
rowReader.LibraryColumn,
lineNum);
errorList.Add(error);
return seqBuilder;
}
string name = info.ProteinName;
if (info.TransitionExps.Any(t => t.IsDecoy))
name = PeptideGroup.DECOYS;
if (seqBuilder == null || (name != null && !Equals(name, seqBuilder.BaseName)))
{
if (seqBuilder != null)
{
AddPeptideGroup(peptideGroupsNew, seqBuilder, irtPeptides, librarySpectra, errorList);
}
FastaSequence fastaSeq;
if (name != null && dictNameSeq.TryGetValue(name, out fastaSeq) && fastaSeq != null)
seqBuilder = new PeptideGroupBuilder(fastaSeq, Document.Settings);
else
{
string safeName = name != null ?
Helpers.GetUniqueName(name, dictNameSeq.Keys) :
Document.GetPeptideGroupId(true);
seqBuilder = new PeptideGroupBuilder(">>" + safeName, true, Document.Settings) {BaseName = name}; // Not L10N
}
}
try
{
seqBuilder.AppendTransition(info, irt, libraryIntensity, productMz, lineNum);
}
catch (InvalidDataException x)
{
throw new LineColNumberedIoException(x.Message, lineNum, -1, x);
}
return seqBuilder;
}
private void AddPeptideGroup(List<PeptideGroupDocNode> listGroups,
ICollection<FastaSequence> set, PeptideGroupBuilder builder)
{
PeptideGroupDocNode nodeGroup = builder.ToDocNode();
FastaSequence fastaSeq = nodeGroup.Id as FastaSequence;
if (fastaSeq != null && set.Contains(fastaSeq))
return;
if (nodeGroup.MoleculeCount == 0)
{
EmptyPeptideGroupCount++;
// If more than MaxEmptyPeptideGroupCount, then don't keep the empty peptide groups
// This is not useful and is likely to cause memory and performance issues
if (EmptyPeptideGroupCount > MaxEmptyPeptideGroupCount)
{
if (EmptyPeptideGroupCount == MaxEmptyPeptideGroupCount + 1)
{
var nonEmptyGroups = listGroups.Where(g => g.MoleculeCount > 0).ToArray();
listGroups.Clear();
listGroups.AddRange(nonEmptyGroups);
}
return;
}
}
listGroups.Add(nodeGroup);
_countPeptides += nodeGroup.MoleculeCount;
_countIons += nodeGroup.TransitionCount;
}
