IDConflictResolverAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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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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// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Lucia Espona, Moritz Freidank $
// --------------------------------------------------------------------------

#pragma once

#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>

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

namespace OpenMS
{

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

  static void resolve(ConsensusMap & features);

  static void resolveBetweenFeatures(FeatureMap & features);
  
  static void resolveBetweenFeatures(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_(
    std::vector<PeptideIdentification> & peptides,
    std::vector<PeptideIdentification> & removed,
    UInt64 uid);
  
  template<class T>
  static void resolveBetweenFeatures_(T & map)
  {
    // unassigned peptide identifications in this map
    std::vector<PeptideIdentification>& unassigned = map.getUnassignedPeptideIdentifications();
    
    // A std::map tracking the set of unique features.
    // Uniqueness criterion/key is a pair <charge, sequence> for each feature. The peptide sequence may be modified, i.e. is not stripped.
    typedef std::map<std::pair<Int, AASequence>, typename T::value_type*> FeatureSet;
    FeatureSet feature_set;
    
    // Create a std::map `feature_set` mapping pairs <charge, sequence> to a pointer to
    // the feature with the highest intensity for this sequence.
    for (typename T::value_type& element : map)
    {
      std::vector<PeptideIdentification>& pep_ids = element.getPeptideIdentifications();
      
      if (!pep_ids.empty())
      {
        if (pep_ids.size() != 1)
        {
          // Should never happen. In IDConflictResolverAlgorithm TOPP tool
          // IDConflictResolverAlgorithm::resolve() is called before IDConflictResolverAlgorithm::resolveBetweenFeatures().
          throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Feature does contain multiple identifications.");
        }
        
        // Make sure best hit is in front, i.e. sort hits first.
        pep_ids.front().sort();
        const std::vector<PeptideHit>& hits = pep_ids.front().getHits();
        
        if (!hits.empty())
        {
          const PeptideHit& highest_score_hit = hits.front();
          
          // Pair <charge, sequence> of charge of the new feature and the sequence of its highest scoring peptide hit.
          std::pair<Int, AASequence> pair = std::make_pair(element.getCharge(), highest_score_hit.getSequence());
          
          // If a <charge, sequence> pair is not yet in the FeatureSet or new feature `feature_in_set`
          // has higher intensity than its counterpart `feature_set[<charge, sequence>]`
          // store a pointer to `feature_in_set` in `feature_set`.
          typename FeatureSet::iterator feature_in_set = feature_set.find(pair);
          if (feature_in_set != feature_set.end())
          {
            // Identical (charge, sequence) key found. Remove annotations from either the old or new feature.
            
            if (feature_in_set->second->getIntensity() < element.getIntensity())
            {
              // Remove annotations from the old low-intensity feature. But only after moving these annotations to the unassigned list.
              std::vector<PeptideIdentification>& obsolete = feature_in_set->second->getPeptideIdentifications();
              unassigned.insert(unassigned.end(), obsolete.begin(), obsolete.end());
              std::vector<PeptideIdentification> pep_ids_empty;
              feature_in_set->second->setPeptideIdentifications(pep_ids_empty);
              
              // Replace feature in the set.
              feature_in_set->second = &(element);
            }
            else
            {
              // Remove annotations from the new low-intensity feature. But only after moving these annotations to the unassigned list.
              std::vector<PeptideIdentification>& obsolete = element.getPeptideIdentifications();
              unassigned.insert(unassigned.end(), obsolete.begin(), obsolete.end());
              std::vector<PeptideIdentification> pep_ids_empty;
              element.setPeptideIdentifications(pep_ids_empty);
            }
          }
          else
          {
            // Feature is not yet in our set -- add it.
            feature_set[pair] = &(element);
          }
        }
      }
    }
  }
  
};

}// namespace OpenMS