private bool SpectrumMatches(SpectrumDisplayInfo spectrumDisplayInfo, SpectrumIdentifier spectrumIdentifier)
{
if (!string.Equals(spectrumDisplayInfo.FilePath.ToString(), spectrumIdentifier.SourceFile.ToString(), StringComparison.OrdinalIgnoreCase))
{
return(false);
}
if (!spectrumDisplayInfo.RetentionTime.HasValue)
{
return(false);
}
return(Equals((float)spectrumDisplayInfo.RetentionTime, (float)spectrumIdentifier.RetentionTime));
}
private IList <SpectrumDisplayInfo> GetSpectra(TransitionGroupDocNode nodeGroup, Target lookupSequence, ExplicitMods lookupMods)
{
var settings = DocumentUI.Settings;
var charge = nodeGroup.PrecursorAdduct;
var spectra = settings.GetBestSpectra(lookupSequence, charge, lookupMods).Select(s => new SpectrumDisplayInfo(s)).ToList();
// Showing redundant spectra is only supported for full-scan filtering when
// the document has results files imported.
if ((!settings.TransitionSettings.FullScan.IsEnabled && !settings.PeptideSettings.Libraries.HasMidasLibrary) || !settings.HasResults)
{
return(spectra);
}
try
{
var spectraRedundant = new List <SpectrumDisplayInfo>();
var dictReplicateNameFiles = new Dictionary <string, HashSet <string> >();
foreach (var spectrumInfo in settings.GetRedundantSpectra(nodeGroup.Peptide, lookupSequence, charge, nodeGroup.TransitionGroup.LabelType, lookupMods))
{
var matchingFile = settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(spectrumInfo.FilePath));
if (matchingFile == null)
{
continue;
}
string replicateName = matchingFile.Chromatograms.Name;
spectraRedundant.Add(new SpectrumDisplayInfo(spectrumInfo,
replicateName,
matchingFile.FilePath,
matchingFile.FileOrder,
spectrumInfo.RetentionTime,
false));
// Include the best spectrum twice, once displayed in the normal
// way and once displayed with its replicate and retetion time.
if (spectrumInfo.IsBest)
{
string libName = spectrumInfo.LibName;
var labelType = spectrumInfo.LabelType;
int iBest = spectra.IndexOf(s => Equals(s.LibName, libName) &&
Equals(s.LabelType, labelType));
if (iBest != -1)
{
spectra[iBest] = new SpectrumDisplayInfo(spectra[iBest].SpectrumInfo,
replicateName,
matchingFile.FilePath,
0,
spectrumInfo.RetentionTime,
true);
}
}
HashSet <string> setFiles;
if (!dictReplicateNameFiles.TryGetValue(replicateName, out setFiles))
{
setFiles = new HashSet <string>();
dictReplicateNameFiles.Add(replicateName, setFiles);
}
setFiles.Add(spectrumInfo.FilePath);
}
// Determine if replicate name is sufficient to uniquely identify the file
foreach (var spectrumInfo in spectraRedundant)
{
string replicateName = spectrumInfo.ReplicateName;
if (replicateName != null && dictReplicateNameFiles[replicateName].Count < 2)
{
spectrumInfo.IsReplicateUnique = true;
}
}
spectraRedundant.Sort();
spectra.AddRange(spectraRedundant);
return(spectra);
}
catch (Exception)
{
return(spectra);
}
}
public SelectedSpectrumEventArgs(SpectrumDisplayInfo spectrum, bool isUserAction)
{
Spectrum = spectrum;
IsUserAction = isUserAction;
}
