IDConflictResolverAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Lucia Espona $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_ID_IDCONFLICTRESOLVERALGORITHM
#define OPENMS_ANALYSIS_ID_IDCONFLICTRESOLVERALGORITHM

#include <OpenMS/APPLICATIONS/TOPPBase.h>

#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/METADATA/PeptideIdentification.h>

#include <algorithm>

using namespace OpenMS;
using namespace std;

//-------------------------------------------------------------
// Doxygen docu
//-------------------------------------------------------------

namespace OpenMS
{

class OPENMS_DLLAPI IDConflictResolverAlgorithm
{
public:
  static void resolve(FeatureMap & features);

  static void resolve(ConsensusMap & features);

protected:
  template<class T>
  static void resolveConflict_(T & map)
  {
    // annotate as not part of the resolution
    for (PeptideIdentification & p : map.getUnassignedPeptideIdentifications())
    {
      p.setMetaValue("feature_id", "not mapped"); // not mapped to a feature
    }

    for (auto & c : map)
    {
      c.setMetaValue("feature_id", String(c.getUniqueId()));
      resolveConflict_(c.getPeptideIdentifications(), 
        map.getUnassignedPeptideIdentifications(),
        c.getUniqueId());
    }
  }

  // compare peptide IDs by score of best hit (hits must be sorted first!)
  // (note to self: the "static" is necessary to avoid cryptic "no matching
  // function" errors from gcc when the comparator is used below)
  static bool compareIDsSmallerScores_(const PeptideIdentification & left,
                          const PeptideIdentification & right);

  static void resolveConflict_(
    vector<PeptideIdentification> & peptides, 
    vector<PeptideIdentification> & removed,
    UInt64 uid);
};

}

#endif