SeedListGenerator.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 2002-2022.
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
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#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DPosition.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/METADATA/PeptideIdentification.h>

#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI SeedListGenerator
  {
public:

    typedef std::vector<DPosition<2> > SeedList;


    SeedListGenerator();


    void generateSeedList(const PeakMap & experiment, SeedList & seeds);


    void generateSeedList(std::vector<PeptideIdentification> & peptides,
                          SeedList & seeds, bool use_peptide_mass = false);


    void generateSeedLists(const ConsensusMap & consensus,
                           std::map<UInt64, SeedList> & seed_lists);


    void convertSeedList(const SeedList & seeds, FeatureMap & features);


    void convertSeedList(const FeatureMap & features, SeedList & seeds);

  };

}