private void DoQuantify(string detailDir, List <IIdentifiedSpectrum> querys)
{
Dictionary <string, List <IIdentifiedSpectrum> > filePepMap = IdentifiedSpectrumUtils.GetRawPeptideMap(querys);
int fileCount = 0;
foreach (string experimental in filePepMap.Keys)
{
fileCount++;
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
string rawFilename = option.RawFormat.GetRawFile(option.RawDir, experimental);
Progress.SetMessage(MyConvert.Format("{0}/{1} : Processing {2} ...", fileCount, filePepMap.Keys.Count, rawFilename));
SilacQuantificationFileBuilder builder = new SilacQuantificationFileBuilder(option);
builder.Progress = this.Progress;
builder.SoftwareVersion = this.SoftwareVersion;
builder.MinScanNumber = this.MinScanNumber;
List <IIdentifiedSpectrum> peps = filePepMap[experimental];
peps.Sort((m1, m2) => m1.IsExtendedIdentification().CompareTo(m2.IsExtendedIdentification()));
builder.Quantify(rawFilename, peps, detailDir);
}
}
public override IEnumerable <string> Process(string peptidesFilename)
{
List <IIdentifiedSpectrum> peptides = new SequestPeptideTextFormat().ReadFromFile(peptidesFilename);
Dictionary <string, List <IIdentifiedSpectrum> > rawPeptideMap = IdentifiedSpectrumUtils.GetRawPeptideMap(peptides);
Progress.SetRange(1, 1, rawPeptideMap.Count);
List <string> raws = new List <string>(rawPeptideMap.Keys);
raws.Sort();
int position = 0;
int totalRaws = rawPeptideMap.Count;
foreach (string raw in raws)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetPosition(1, position++);
Progress.SetMessage(1, MyConvert.Format("{0}/{1}, Extracting {2} for {3} peptides ...", position, totalRaws, raw, rawPeptideMap[raw].Count));
if (!filePathMap.ContainsKey(raw))
{
throw new Exception("Cannot find raw dtas/outs file for " + raw);
}
if (filePathMap[raw].Count == 1)
{
ExtractSingleRaw(raw, filePathMap[raw][0], rawPeptideMap[raw]);
}
else
{
ExtractMultipleRaw(raw, filePathMap[raw], rawPeptideMap[raw]);
}
}
Progress.SetPosition(1, position);
return(new List <string>());
}
