ConsensusFeature.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 2002-2018.
//
// 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/DATASTRUCTURES/DRange.h>
#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/FeatureHandle.h>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>

#include <set>

namespace OpenMS
{
  class FeatureMap;
  class Peak2D;

  class OPENMS_DLLAPI ConsensusFeature :
    public BaseFeature
  {
public:

    typedef std::set<FeatureHandle, FeatureHandle::IndexLess> HandleSetType;
    typedef HandleSetType::const_iterator const_iterator;
    typedef HandleSetType::iterator iterator;
    typedef HandleSetType::const_reverse_iterator const_reverse_iterator;
    typedef HandleSetType::reverse_iterator reverse_iterator;

    struct SizeLess :
      std::binary_function<ConsensusFeature, ConsensusFeature, bool>
    {
      inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
      {
        return left.size() < right.size();
      }

      inline bool operator()(ConsensusFeature const& left, UInt64 const& right) const
      {
        return left.size() < right;
      }

      inline bool operator()(UInt64 const& left, ConsensusFeature const& right) const
      {
        return left < right.size();
      }

      inline bool operator()(const UInt64& left, const UInt64& right) const
      {
        return left < right;
      }

    };

    struct MapsLess :
      std::binary_function<ConsensusFeature, ConsensusFeature, bool>
    {
      inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
      {
        return std::lexicographical_compare(left.begin(), left.end(), right.begin(), right.end(), FeatureHandle::IndexLess());
      }

    };

    struct Ratio
    {
      Ratio()
      {
      }

      Ratio(const Ratio& rhs)
      {
        ratio_value_ = rhs.ratio_value_;
        denominator_ref_ = rhs.denominator_ref_;
        numerator_ref_ = rhs.numerator_ref_;
        description_ = rhs.description_;
      }

      virtual ~Ratio()
      {
      }

      Ratio& operator=(const Ratio& rhs)
      {
        if (&rhs != this)
        {
          ratio_value_ = rhs.ratio_value_;
          denominator_ref_ = rhs.denominator_ref_;
          numerator_ref_ = rhs.numerator_ref_;
          description_ = rhs.description_;
        }
        return *this;
      }

      double ratio_value_;
      String denominator_ref_;
      String numerator_ref_;
      std::vector<String> description_;
      //TODO ratio cv info
    };


    ConsensusFeature();

    ConsensusFeature(const ConsensusFeature& rhs);

    explicit ConsensusFeature(const BaseFeature& feature);

    ConsensusFeature(UInt64 map_index, const Peak2D& element, UInt64 element_index);

    ConsensusFeature(UInt64 map_index, const BaseFeature& element);

    ConsensusFeature& operator=(const ConsensusFeature& rhs);

    ~ConsensusFeature() override;




    void insert(const ConsensusFeature& cf);

    void insert(const FeatureHandle& handle);

    void insert(const HandleSetType& handle_set);

    void insert(UInt64 map_index, const Peak2D& element, UInt64 element_index);

    void insert(UInt64 map_index, const BaseFeature& element);

    const HandleSetType& getFeatures() const;

    std::vector<FeatureHandle> getFeatureList() const;


    DRange<2> getPositionRange() const;
    DRange<1> getIntensityRange() const;


    void computeConsensus();

    void computeMonoisotopicConsensus();

    void computeDechargeConsensus(const FeatureMap& fm, bool intensity_weighted_averaging = false);

    void addRatio(const Ratio& r);

    void setRatios(std::vector<Ratio>& rs);

    std::vector<Ratio> getRatios() const;

    std::vector<Ratio>& getRatios();


    Size size() const;

    const_iterator begin() const;

    iterator begin();

    const_iterator end() const;

    iterator end();

    const_reverse_iterator rbegin() const;

    reverse_iterator rbegin();

    const_reverse_iterator rend() const;

    reverse_iterator rend();

    void clear();

    bool empty() const;

private:
    HandleSetType handles_;
    std::vector<Ratio> ratios_;
  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusFeature& cons);

} // namespace OpenMS