FeatureFinderMultiplexAlgorithm.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: Lars Nilse $
// $Authors: Lars Nilse $
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#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexDeltaMasses.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexIsotopicPeakPattern.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/MultiplexFilteredMSExperiment.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SplinePackage.h>
#include <OpenMS/COMPARISON/CLUSTERING/GridBasedCluster.h>

#include <vector>
#include <fstream>
#include <map>

namespace OpenMS
{

class OPENMS_DLLAPI FeatureFinderMultiplexAlgorithm :
  public DefaultParamHandler, public ProgressLogger
{
public:
  FeatureFinderMultiplexAlgorithm();

  void run(MSExperiment& exp, bool progress);

  FeatureMap& getFeatureMap();
  ConsensusMap& getConsensusMap();
  MSExperiment& getBlacklist();

protected:

  // experimental data
  MSExperiment exp_profile_;
  MSExperiment exp_centroid_;

  bool centroided_;

  ProgressLogger prog_log_;

  bool progress_;

  unsigned charge_min_;
  unsigned charge_max_;

  unsigned isotopes_per_peptide_min_;
  unsigned isotopes_per_peptide_max_;


  // mass shift names and their values
  std::map<String, double> label_mass_shift_;

  // final results, maps of detected features
  FeatureMap feature_map_;
  ConsensusMap consensus_map_;

  // blacklist
  MSExperiment exp_blacklist_;

  std::vector<MultiplexIsotopicPeakPattern> generatePeakPatterns_(int charge_min, int charge_max, int peaks_per_peptide_max, const std::vector<MultiplexDeltaMasses>& mass_pattern_list);

  void correctPeptideIntensities_(const MultiplexIsotopicPeakPattern& pattern, std::map<size_t, SplinePackage>& spline_chromatograms, const std::vector<double>& rt_peptide, std::vector<double>& intensity_peptide) const;

  std::vector<double> determinePeptideIntensitiesCentroided_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteCentroided >& satellites);

  std::vector<double> determinePeptideIntensitiesProfile_(const MultiplexIsotopicPeakPattern& pattern, const std::multimap<size_t, MultiplexSatelliteProfile >& satellites);

  void generateMapsCentroided_(const std::vector<MultiplexIsotopicPeakPattern>& patterns, const std::vector<MultiplexFilteredMSExperiment>& filter_results, std::vector<std::map<int, GridBasedCluster> >& cluster_results);

  void generateMapsProfile_(const std::vector<MultiplexIsotopicPeakPattern>& patterns, const std::vector<MultiplexFilteredMSExperiment>& filter_results, const std::vector<std::map<int, GridBasedCluster> >& cluster_results);

};

}