SeedListGenerator.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#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 <OpenMS/METADATA/PeptideIdentificationList.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(PeptideIdentificationList & 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);
 
  };
 
}