Example #1
0
  void MapAlignmentTransformer::transformSinglePeakMap(MSExperiment<> & msexp,
                                                       const TransformationDescription & trafo)
  {
    msexp.clearRanges();

    // Transform spectra
    for (MSExperiment<>::iterator mse_iter = msexp.begin(); mse_iter != msexp.end(); ++mse_iter)
    {
      DoubleReal rt = mse_iter->getRT();
      mse_iter->setRT(trafo.apply(rt));
    }

    // Also transform chromatograms
    DoubleReal rt;
    std::vector<MSChromatogram<ChromatogramPeak> > chromatograms;
    for (Size i = 0; i < msexp.getChromatograms().size(); i++)
    {
      MSChromatogram<ChromatogramPeak> chromatogram = msexp.getChromatograms()[i];
      for (Size j = 0; j < chromatogram.size(); j++)
      {
        rt = chromatogram[j].getRT();
        chromatogram[j].setRT(trafo.apply(rt));
      }
      chromatograms.push_back(chromatogram);
    }
    msexp.setChromatograms(chromatograms);

    msexp.updateRanges();
  }
  void MapAlignmentTransformer::transformRetentionTimes(
    MSExperiment<>& msexp, const TransformationDescription& trafo,
    bool store_original_rt)
  {
    msexp.clearRanges();

    // Transform spectra
    for (MSExperiment<>::iterator mse_iter = msexp.begin();
         mse_iter != msexp.end(); ++mse_iter)
    {
      double rt = mse_iter->getRT();
      if (store_original_rt) storeOriginalRT_(*mse_iter, rt);
      mse_iter->setRT(trafo.apply(rt));
    }

    // Also transform chromatograms
    for (Size i = 0; i < msexp.getNrChromatograms(); ++i)
    {
      MSChromatogram<ChromatogramPeak>& chromatogram = msexp.getChromatogram(i);
      vector<double> original_rts;
      if (store_original_rt) original_rts.reserve(chromatogram.size());
      for (Size j = 0; j < chromatogram.size(); j++)
      {
        double rt = chromatogram[j].getRT();
        if (store_original_rt) original_rts.push_back(rt);
        chromatogram[j].setRT(trafo.apply(rt));
      }
      if (store_original_rt && !chromatogram.metaValueExists("original_rt"))
      {
        chromatogram.setMetaValue("original_rt", original_rts);
      }
    }

    msexp.updateRanges();
  }