private void LoadPsms(out List <string> errors, bool haveLoadedSpectra)
{
errors = new List <string>();
HashSet <string> fileNamesWithoutExtension = new HashSet <string>(
SpectraFilePaths.Select(p => Path.GetFileName(p.Replace(GlobalVariables.GetFileExtension(p), string.Empty))));
List <PsmFromTsv> psmsThatDontHaveMatchingSpectraFile = new List <PsmFromTsv>();
try
{
foreach (var resultsFile in PsmResultFilePaths)
{
lock (ThreadLocker)
{
foreach (PsmFromTsv psm in PsmTsvReader.ReadTsv(resultsFile, out List <string> warnings))
{
if (fileNamesWithoutExtension.Contains(psm.FileNameWithoutExtension) || !haveLoadedSpectra)
{
AllPsms.Add(psm);
}
else
{
psmsThatDontHaveMatchingSpectraFile.Add(psm);
}
if (PsmsGroupedByFile.TryGetValue(psm.FileNameWithoutExtension, out var psmsForThisFile))
{
psmsForThisFile.Add(psm);
}
else
{
PsmsGroupedByFile.Add(psm.FileNameWithoutExtension, new ObservableCollection <PsmFromTsv> {
psm
});
}
}
}
}
}
catch (Exception e)
{
errors.Add("Error reading PSM file:\n" + e.Message);
}
if (psmsThatDontHaveMatchingSpectraFile.Any())
{
foreach (var file in psmsThatDontHaveMatchingSpectraFile.GroupBy(p => p.FileNameWithoutExtension))
{
errors.Add(file.Count() + " PSMs from " + file.Key + " were not loaded because this spectra file was not found");
}
}
FilterPsms();
}
private void LoadSpectraFiles(out List <string> errors)
{
errors = new List <string>();
foreach (var filepath in SpectraFilePaths)
{
lock (ThreadLocker)
{
var fileNameWithoutExtension = filepath.Replace(GlobalVariables.GetFileExtension(filepath), string.Empty);
fileNameWithoutExtension = Path.GetFileName(fileNameWithoutExtension);
DynamicDataConnection spectraFile = null;
string extension = GlobalVariables.GetFileExtension(filepath);
if (extension.Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
spectraFile = new MzmlDynamicData(filepath);
}
else if (extension.Equals(".mgf", StringComparison.OrdinalIgnoreCase))
{
spectraFile = new MgfDynamicData(filepath);
}
else if (extension.Equals(".raw", StringComparison.OrdinalIgnoreCase))
{
spectraFile = new ThermoDynamicData(filepath);
}
else
{
errors.Add("Unrecognized spectra file type: " + extension);
continue;
}
if (!MsDataFiles.TryAdd(fileNameWithoutExtension, spectraFile))
{
spectraFile.CloseDynamicConnection();
// print warning? but probably unnecessary. this means the data file was loaded twice.
// which is an error but not an important one because the data is loaded
}
}
}
}
