libopenms-dev 1.11.1-5 / usr / include / OpenMS / FORMAT / KroenikFile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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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
{
  /**
      @brief File adapter for Kroenik (HardKloer sibling) files.

  The first line is the header and contains the column names:<br>
  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

  Every subsequent line is a feature.

  All properties in the file are converted to Feature properties, whereas "First Scan", "Last Scan", "Num of Scans" and "Modifications" are stored as
  metavalues with the following names "FirstScan", "LastScan", "NumOfScans" and "AveragineModifications".

  The width in m/z of the overall convex hull of each feature is set to 3 Th in lack of a value provided by the Kroenik file.

  @note Kroenik files are Tab (\\t) separated files.

  @ingroup FileIO
*/
  class OPENMS_DLLAPI KroenikFile
  {
public:
    /// Default constructor
    KroenikFile();
    /// Destructor
    virtual ~KroenikFile();

    /**
              @brief Loads a Kroenik file into a featureXML.

              The content of the file is stored in @p features.

              @exception Exception::FileNotFound is thrown if the file could not be opened
              @exception Exception::ParseError is thrown if an error occurs during parsing
    */
    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";
    }

    /**
      @brief Stores a featureXML as a Kroenik file.

      NOT IMPLEMENTED

              @exception Exception::UnableToCreateFile is thrown if the file could not be created
    */
    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