KroenikFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
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#ifndef OPENMS_FORMAT_KROENIKFILE_H
#define OPENMS_FORMAT_KROENIKFILE_H

#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/FORMAT/TextFile.h>

#include <fstream>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI KroenikFile
  {
public:
    KroenikFile();
    virtual ~KroenikFile();

    template <typename FeatureMapType>
    void load(const String & filename, FeatureMapType & feature_map)
    {
      // load input
      TextFile input(filename);

      // reset map
      FeatureMapType fmap;
      feature_map = fmap;

      for (Size i = 1; i < input.size(); ++i)
      {
        String line = input[i];

        //split lines: File,  First Scan,  Last Scan,  Num of Scans,  Charge,  Monoisotopic Mass,  Base Isotope Peak,  Best Intensity,  Summed Intensity,  First RTime,  Last RTime,  Best RTime,  Best Correlation,  Modifications
        std::vector<String> parts;
        line.split('\t', parts);

        if (parts.size() != 14)
        {
          throw Exception::ParseError(__FILE__, __LINE__, __PRETTY_FUNCTION__, "",
                                      String("Failed parsing in line ") + String(i + 1) + ": missing 14 tab-separated entries (got " + String(parts.size()) + ")\nLine was: '" + line + "'");
        }
        //create feature
        Feature f;
        f.setCharge(parts[4].toInt());
        f.setMZ(parts[5].toDouble() / f.getCharge() + Constants::PROTON_MASS_U);
        f.setRT(parts[11].toDouble());
        f.setOverallQuality(parts[12].toDouble());
        f.setIntensity(parts[8].toDouble());
        ConvexHull2D hull;
        ConvexHull2D::PointType point;

        point.setX(parts[9].toDouble());
        point.setY(f.getMZ());
        hull.addPoint(point);

        point.setX(parts[9].toDouble());
        point.setY(f.getMZ() + 3.0 / (DoubleReal)f.getCharge());
        hull.addPoint(point);

        point.setX(parts[10].toDouble());
        point.setY(f.getMZ() + 3.0 / (DoubleReal)f.getCharge());
        hull.addPoint(point);

        point.setX(parts[10].toDouble());
        point.setY(f.getMZ());
        hull.addPoint(point);

        point.setX(parts[9].toDouble());
        point.setY(f.getMZ());
        hull.addPoint(point);

        std::vector<ConvexHull2D> hulls;
        hulls.push_back(hull);
        f.setConvexHulls(hulls);
        f.setMetaValue("Mass", parts[5].toDouble());
        f.setMetaValue("FirstScan", parts[1].toDouble());
        f.setMetaValue("LastScan", parts[2].toInt());
        f.setMetaValue("NumOfScans", parts[3].toDouble());
        f.setMetaValue("AveragineModifications", parts[13]);
        feature_map.push_back(f);
      }

      LOG_INFO << "Hint: The convex hulls are approximated in m/z dimension (Kroenik lacks this information)!\n";
    }

    template <typename SpectrumType>
    void store(const String & filename, const SpectrumType & spectrum) const
    {
      std::cerr << "Store() for KroenikFile not implemented. Filename was: " << filename << ", spec of size " << spectrum.size() << "\n";
      throw Exception::NotImplemented(__FILE__, __LINE__, __PRETTY_FUNCTION__);
    }

  };
} // namespace OpenMS

#endif // OPENMS_FORMAT_KROENIKFILE_H