private void ExportGroupNode(PeptideDocNode peptideNode,
TransitionGroupDocNode groupNode,
ChromatogramSet chromatograms,
ICollection <string> filesToExport,
ICollection <ChromSource> chromSources,
TextWriter writer,
CultureInfo cultureInfo)
{
string peptideModifiedSequence = _settings.GetDisplayName(peptideNode);
var precursorCharge = groupNode.TransitionGroup.PrecursorAdduct;
string labelType = groupNode.TransitionGroup.LabelType.Name;
var filesInChrom = chromatograms.MSDataFilePaths.Select(path => path.GetFileName()).ToList();
// Don't load the chromatogram group if none of its files are being exported
if (!filesInChrom.Where(filesToExport.Contains).Any())
{
return;
}
ChromatogramGroupInfo[] arrayChromInfo;
if (!_measuredResults.TryLoadChromatogram(chromatograms, peptideNode, groupNode,
_matchTolerance, true, out arrayChromInfo))
{
// TODO: Determine if this is a real error or just a missing node for this file
// If the former throw an exception, if the latter continue
return;
}
if (arrayChromInfo.Length != chromatograms.FileCount)
{
throw new InvalidDataException(string.Format(Resources.ChromatogramExporter_ExportGroupNode_One_or_more_missing_chromatograms_at_charge_state__0__of__1_,
precursorCharge, peptideModifiedSequence));
}
foreach (var chromGroupInfo in arrayChromInfo)
{
string fileName = chromGroupInfo.FilePath.GetFileName();
// Skip the files that have not been selected for export
if (!filesToExport.Contains(fileName))
{
continue;
}
foreach (var nodeTran in groupNode.Transitions)
{
// TODO: Check a source attribute on the transition chrom info
bool isMs1 = nodeTran.Transition.IsPrecursor() && !nodeTran.HasLoss;
if (isMs1 && !chromSources.Contains(ChromSource.ms1))
{
continue;
}
if (!isMs1 && !chromSources.Contains(ChromSource.fragment))
{
continue;
}
int productCharge = nodeTran.Transition.Charge;
float productMz = (float)nodeTran.Mz;
var chromInfo = chromGroupInfo.GetTransitionInfo(nodeTran, _matchTolerance, chromatograms.OptimizationFunction);
// Sometimes a transition in the transition group does not have results for a particular file
// If this happens just skip it for that file
if (chromInfo == null)
{
continue;
}
IList <float> times = chromInfo.Times;
IList <float> intensities = chromInfo.Intensities;
if (times.Count != intensities.Count || intensities.Count == 0)
{
throw new InvalidDataException(string.Format(Resources.ChromatogramExporter_Export_Bad_chromatogram_data_for_charge__0__state_of_peptide__1_,
precursorCharge, peptideModifiedSequence));
}
float tic = CalculateTic(times, intensities);
string[] fieldArray =
{
fileName,
peptideModifiedSequence,
System.Convert.ToString(precursorCharge, cultureInfo),
System.Convert.ToString(productMz, cultureInfo),
nodeTran.GetFragmentIonName(CultureInfo.InvariantCulture),
System.Convert.ToString(productCharge, cultureInfo),
labelType,
System.Convert.ToString(tic, cultureInfo)
};
FormatChromLine(writer, fieldArray, times, intensities, cultureInfo);
}
}
}