FeatureDeconvolution.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 2002-2021.
//
// 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: Chris Bielow $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
// OpenMS
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/ANALYSIS/DECHARGING/ILPDCWrapper.h>
#include <OpenMS/DATASTRUCTURES/DPosition.h>
#include <OpenMS/DATASTRUCTURES/MassExplainer.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
namespace OpenMS
{
 
  class Compomer;
 
  class OPENMS_DLLAPI FeatureDeconvolution :
    public DefaultParamHandler
  {
public:
 
    enum CHARGEMODE {QFROMFEATURE = 1, QHEURISTIC, QALL};
 
    typedef FeatureMap FeatureMapType;
    typedef Feature FeatureType;
    typedef DPosition<2> ClusterPointType;
    typedef FeatureMapType::FeatureType::CoordinateType CoordinateType;
    typedef ILPDCWrapper::PairsType PairsType;
 
    FeatureDeconvolution();
 
    FeatureDeconvolution(const FeatureDeconvolution& source);
 
    FeatureDeconvolution& operator=(const FeatureDeconvolution& source);
 
    ~FeatureDeconvolution() override;
 
    void compute(const FeatureMapType& fm_in, FeatureMapType& fm_out, ConsensusMap& cons_map, ConsensusMap& cons_map_p);
 
protected:
 
    void updateMembers_() override;
 
    struct CmpInfo_;
 
    /*
      @brief test for obviously wrong parameter settings and warn
 
      Currently supports the following scenarios:
      * If the lower charge bound is too high, consensus features with gapped, even charges will occur (e.g. 30,32,34), instead of the true (15,16,17)
      When more than 5% of the cf's look like this, we report it.
 
    */
    void checkSolution_(const ConsensusMap& cons_map) const;
 
    void inferMoreEdges_(PairsType& edges, Map<Size, std::set<CmpInfo_> >& feature_adducts);
 
    void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType& feature_relation);
 
    inline bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer& cmp, const FeatureType& f1, const FeatureType& f2);
 
    bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const;
 
    MassExplainer::AdductsType potential_adducts_;
    Map<Size, String> map_label_;
    Map<String, Size> map_label_inverse_;
    bool enable_intensity_filter_;
    CHARGEMODE q_try_;
    Int verbose_level_;
 
  };
} // namespace OpenMS