SeedListGenerator.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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//  * 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
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DPosition.h>
#include <OpenMS/DATASTRUCTURES/Map.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,
                           Map<UInt64, SeedList> & seed_lists);
 
 
    void convertSeedList(const SeedList & seeds, FeatureMap & features);
 
 
    void convertSeedList(const FeatureMap & features, SeedList & seeds);
 
  };
 
}