ConsensusMap.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   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:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/UniqueIdInterface.h>
#include <OpenMS/CONCEPT/UniqueIdIndexer.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <OpenMS/METADATA/DocumentIdentifier.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Utils/MapUtilities.h>
#include <OpenMS/OpenMSConfig.h>
 
#include <map>
#include <vector>
 
namespace OpenMS
{
  class PeptideIdentification;
  class PeptideHit;
  class ProteinIdentification;
  class DataProcessing;
  namespace Logger
  {
    class LogStream;
  }
 
  class ConsensusMap : // no OPENMS_DLLAPI here, since the class is derived from an STL class - we do not want parts of the STL lib in OpenMS.lib, since it will cause linker errors
    private std::vector<ConsensusFeature>,
    public MetaInfoInterface,
    public RangeManager<2>,
    public DocumentIdentifier,
    public UniqueIdInterface,
    public UniqueIdIndexer<ConsensusMap>,
    public MapUtilities<ConsensusMap>
  {
 
public:
    typedef std::vector<ConsensusFeature> privvec;
 
    // types
    using privvec::value_type;
    using privvec::iterator;
    using privvec::const_iterator;
    using privvec::size_type;
    using privvec::pointer; // ConstRefVector
    using privvec::reference; // ConstRefVector
    using privvec::const_reference; // ConstRefVector
    using privvec::difference_type; // ConstRefVector
 
    // functions
    using privvec::begin;
    using privvec::end;
 
    using privvec::size;
    using privvec::resize;
    using privvec::empty;
    using privvec::reserve;
    using privvec::operator[];
    using privvec::at;
    using privvec::back;
    using privvec::push_back;
    using privvec::emplace_back;
    using privvec::erase;
 
    enum class SplitMeta
    {
      DISCARD,                 
      COPY_ALL,               
      COPY_FIRST              
    };
    
    struct OPENMS_DLLAPI ColumnHeader :
      public MetaInfoInterface
    {
      ColumnHeader();
 
      ColumnHeader(const ColumnHeader&);
 
      String filename;
      String label;
      Size size;
      UInt64 unique_id;
 
      unsigned getLabelAsUInt(const String& experiment_type) const
      {
        if (metaValueExists("channel_id"))
        {
          return static_cast<unsigned int>(getMetaValue("channel_id")) + 1;
        }
        else
        {
          if (experiment_type != "label-free")
          {
            // TODO There seem to be files in our test data from the Multiplex toolset that do not annotate
            //  a channel id but only add the "label" attribute with the SILAC modification. Add a fall-back here?
            OPENMS_LOG_WARN << "No channel id annotated in labelled consensusXML. Assuming only a single channel was used." << std::endl;
          }
          return 1;
        }
      }
    };
 
 
    typedef std::vector<ConsensusFeature> Base;
    typedef RangeManager<2> RangeManagerType;
    typedef std::map<UInt64, ColumnHeader> ColumnHeaders;
    typedef std::vector<ConsensusFeature>::iterator Iterator;
    typedef std::vector<ConsensusFeature>::const_iterator ConstIterator;
    typedef std::vector<ConsensusFeature>::reverse_iterator ReverseIterator;
    typedef std::vector<ConsensusFeature>::const_reverse_iterator ConstReverseIterator;
 
    OPENMS_DLLAPI ConsensusMap();
 
    OPENMS_DLLAPI ConsensusMap(const ConsensusMap& source);
 
    OPENMS_DLLAPI ~ConsensusMap() override;
 
    OPENMS_DLLAPI explicit ConsensusMap(Base::size_type n);
 
    OPENMS_DLLAPI ConsensusMap& operator=(const ConsensusMap& source);
 
    OPENMS_DLLAPI ConsensusMap& appendRows(const ConsensusMap& rhs);
 
    OPENMS_DLLAPI ConsensusMap& appendColumns(const ConsensusMap& rhs);
 
 
    OPENMS_DLLAPI void clear(bool clear_meta_data = true);
 
    OPENMS_DLLAPI const ColumnHeaders& getColumnHeaders() const;
 
    OPENMS_DLLAPI ColumnHeaders& getColumnHeaders();
 
    OPENMS_DLLAPI void setColumnHeaders(const ColumnHeaders& column_description);
 
    OPENMS_DLLAPI const String& getExperimentType() const;
 
    OPENMS_DLLAPI void setExperimentType(const String& experiment_type);
 
    OPENMS_DLLAPI void sortByIntensity(bool reverse = false);
 
    OPENMS_DLLAPI void sortByRT();
 
    OPENMS_DLLAPI void sortByMZ();
 
    OPENMS_DLLAPI void sortByPosition();
 
    OPENMS_DLLAPI void sortByQuality(bool reverse = false);
 
    OPENMS_DLLAPI void sortBySize();
 
    OPENMS_DLLAPI void sortByMaps();
 
    OPENMS_DLLAPI void sortPeptideIdentificationsByMapIndex();
 
    // Docu in base class
    OPENMS_DLLAPI void updateRanges() override;
 
    OPENMS_DLLAPI void swap(ConsensusMap& from);
 
    OPENMS_DLLAPI const std::vector<ProteinIdentification>& getProteinIdentifications() const;
 
    OPENMS_DLLAPI std::vector<ProteinIdentification>& getProteinIdentifications();
 
    OPENMS_DLLAPI void setProteinIdentifications(const std::vector<ProteinIdentification>& protein_identifications);
 
    OPENMS_DLLAPI void setProteinIdentifications(std::vector<ProteinIdentification>&& protein_identifications);
 
    OPENMS_DLLAPI const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications() const;
 
    OPENMS_DLLAPI std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications();
 
    OPENMS_DLLAPI void setUnassignedPeptideIdentifications(const std::vector<PeptideIdentification>& unassigned_peptide_identifications);
 
    OPENMS_DLLAPI const std::vector<DataProcessing>& getDataProcessing() const;
 
    OPENMS_DLLAPI std::vector<DataProcessing>& getDataProcessing();
 
    OPENMS_DLLAPI void setDataProcessing(const std::vector<DataProcessing>& processing_method);
 
    OPENMS_DLLAPI void setPrimaryMSRunPath(const StringList& s);
 
    OPENMS_DLLAPI void setPrimaryMSRunPath(const StringList& s, MSExperiment & e);
 
    OPENMS_DLLAPI void getPrimaryMSRunPath(StringList& toFill) const;
 
    OPENMS_DLLAPI bool operator==(const ConsensusMap& rhs) const;
 
    OPENMS_DLLAPI bool operator!=(const ConsensusMap& rhs) const;
 
    template <typename Type>
    Size applyMemberFunction(Size (Type::* member_function)())
    {
      Size assignments = 0;
      assignments += ((*this).*member_function)();
      for (Iterator iter = this->begin(); iter != this->end(); ++iter)
      {
        assignments += ((*iter).*member_function)();
      }
      return assignments;
    }
 
    template <typename Type>
    Size applyMemberFunction(Size (Type::* member_function)() const) const
    {
      Size assignments = 0;
      assignments += ((*this).*member_function)();
      for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
      {
        assignments += ((*iter).*member_function)();
      }
      return assignments;
    }
 
    OPENMS_DLLAPI bool isMapConsistent(Logger::LogStream* stream = nullptr) const;
 
    OPENMS_DLLAPI std::vector<FeatureMap> split(SplitMeta mode = SplitMeta::DISCARD) const;
 
protected:
 
    ColumnHeaders column_description_;
 
    String experiment_type_ = "label-free";
 
    std::vector<ProteinIdentification> protein_identifications_;
 
    std::vector<PeptideIdentification> unassigned_peptide_identifications_;
 
    std::vector<DataProcessing> data_processing_;
 
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusMap& cons_map);
 
 
 
} // namespace OpenMS