FeatureFinderMultiplexAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Lars Nilse $
// $Authors: Lars Nilse $
// --------------------------------------------------------------------------
 
#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);
  
  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);
  
};
 
}