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;
}
public IEnumerable<PeptideGroupDocNode> Import(IProgressMonitor progressMonitor,
ColumnIndices indices,
IDictionary<string, FastaSequence> dictNameSeq,
out List<MeasuredRetentionTime> irtPeptides,
out List<SpectrumMzInfo> librarySpectra,
out List<TransitionImportErrorInfo> errorList)
{
irtPeptides = new List<MeasuredRetentionTime>();
librarySpectra = new List<SpectrumMzInfo>();
errorList = new List<TransitionImportErrorInfo>();
var status = new ProgressStatus(string.Empty);
// Get the lines used to guess the necessary columns and create the row reader
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return new PeptideGroupDocNode[0];
status = status.ChangeMessage(Resources.MassListImporter_Import_Reading_transition_list);
}
var lines = new List<string>(Inputs.ReadLines());
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
return new PeptideGroupDocNode[0];
status = status.ChangeMessage(Resources.MassListImporter_Import_Inspecting_peptide_sequence_information);
}
if (indices != null)
{
_rowReader = new GeneralRowReader(FormatProvider, Separator, indices, Settings, lines);
}
else
{
// Check first line for validity
var line = lines.FirstOrDefault();
string[] fields = line.ParseDsvFields(Separator);
string[] headers = fields.All(field => GetColumnType(field.Trim(), FormatProvider) != typeof (double))
? fields
: null;
int decoyColumn = -1;
int irtColumn = -1;
int libraryColumn = -1;
var irtNames = new[] { "tr_recalibrated", "irt" }; // Not L10N
var libraryNames = new[] { "libraryintensity", "relativeintensity", "relative_intensity", "relativefragmentintensity", "library_intensity" }; // Not L10N
var decoyNames = new[] { "decoy" }; // Not L10N
if (headers != null)
{
lines.RemoveAt(0);
decoyColumn = headers.IndexOf(col => decoyNames.Contains(col.ToLowerInvariant()));
irtColumn = headers.IndexOf(col => irtNames.Contains(col.ToLowerInvariant()));
libraryColumn = headers.IndexOf(col => libraryNames.Contains(col.ToLowerInvariant()));
line = lines.FirstOrDefault();
fields = line != null ? line.ParseDsvFields(Separator) : new string[0];
}
if (fields.Length < 3)
throw new InvalidDataException(Resources.MassListImporter_Import_Invalid_transition_list_Transition_lists_must_contain_at_least_precursor_m_z_product_m_z_and_peptide_sequence);
// If no numeric columns in the first row
_rowReader = ExPeptideRowReader.Create(lines, decoyColumn, FormatProvider, Separator, Settings, irtColumn, libraryColumn);
if (_rowReader == null)
{
_rowReader = GeneralRowReader.Create(lines, headers, decoyColumn, FormatProvider, Separator, Settings, irtColumn, libraryColumn);
if (_rowReader == null && headers == null)
{
// Check for a possible header row
headers = lines[0].Split(Separator);
lines.RemoveAt(0);
_rowReader = GeneralRowReader.Create(lines, headers, decoyColumn, FormatProvider, Separator, Settings, irtColumn, libraryColumn);
}
if (_rowReader == null)
throw new LineColNumberedIoException(Resources.MassListImporter_Import_Failed_to_find_peptide_column, 1, -1);
}
}
// Set starting values for limit counters
_countPeptides = Document.PeptideCount;
_countIons = Document.PeptideTransitionCount;
List<PeptideGroupDocNode> peptideGroupsNew = new List<PeptideGroupDocNode>();
PeptideGroupBuilder seqBuilder = null;
// Process lines
long lineIndex = 0;
foreach (string row in lines)
{
lineIndex++;
var errorInfo = _rowReader.NextRow(row, lineIndex);
if (errorInfo != null)
{
errorList.Add(errorInfo);
continue;
}
if (progressMonitor != null)
{
if (progressMonitor.IsCanceled)
{
irtPeptides.Clear();
librarySpectra.Clear();
errorList.Clear();
return new PeptideGroupDocNode[0];
}
int percentComplete = (int)(lineIndex * 100 / lines.Count);
if (status.PercentComplete != percentComplete)
{
string message = string.Format(Resources.MassListImporter_Import_Importing__0__,
_rowReader.TransitionInfo.ProteinName ?? _rowReader.TransitionInfo.PeptideSequence);
status = status.ChangePercentComplete(percentComplete).ChangeMessage(message);
}
}
seqBuilder = AddRow(seqBuilder, _rowReader, dictNameSeq, peptideGroupsNew, lineIndex, irtPeptides, librarySpectra, errorList);
}
// Add last sequence.
if (seqBuilder != null)
AddPeptideGroup(peptideGroupsNew, seqBuilder, irtPeptides, librarySpectra, errorList);
return MergeEqualGroups(peptideGroupsNew);
}