IsoSpecWrapper.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// 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
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// 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
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//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Rost $
// $Authors: Hannes Rost, Michał Startek, Mateusz Łącki $
// --------------------------------------------------------------------------

#pragma once

#include <vector>
#include <memory>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Constants.h>
#include <OpenMS/CONCEPT/Exception.h>

#include <OpenMS/KERNEL/Peak1D.h>

#include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>


// forward declarations
namespace IsoSpec
{
class IsoLayeredGenerator;
class IsoThresholdGenerator;
class IsoOrderedGenerator;
}

namespace OpenMS
{
  class OPENMS_DLLAPI IsoSpecGeneratorWrapper
  {

public:

    virtual bool nextConf() = 0;

    virtual Peak1D getConf() = 0;

    virtual double getMass() = 0;

    virtual double getIntensity() = 0;

    virtual double getLogIntensity() = 0;

    virtual ~IsoSpecGeneratorWrapper() = default;
  };

  class OPENMS_DLLAPI IsoSpecWrapper
  {
public:
    virtual IsotopeDistribution run() = 0;

    virtual inline ~IsoSpecWrapper() = default;
  };

  //-------------------------------------------------------------------------- 
  // IsoSpecGeneratorWrapper classes
  //-------------------------------------------------------------------------- 

  class OPENMS_DLLAPI IsoSpecTotalProbGeneratorWrapper : public IsoSpecGeneratorWrapper
  {
public:
    IsoSpecTotalProbGeneratorWrapper(const std::vector<int>& isotopeNumbers,
             const std::vector<int>& atomCounts,
             const std::vector<std::vector<double> >& isotopeMasses,
             const std::vector<std::vector<double> >& isotopeProbabilities,
             double p);

    IsoSpecTotalProbGeneratorWrapper(const IsoSpecTotalProbGeneratorWrapper&) = delete;
    IsoSpecTotalProbGeneratorWrapper(const EmpiricalFormula& formula, double p);

    ~IsoSpecTotalProbGeneratorWrapper();

    bool nextConf() final;
    Peak1D getConf() final;
    double getMass() final;
    double getIntensity() final;
    double getLogIntensity() final;

protected:
    std::unique_ptr<IsoSpec::IsoLayeredGenerator> ILG;
  };

  class OPENMS_DLLAPI IsoSpecThresholdGeneratorWrapper : public IsoSpecGeneratorWrapper
  {

public:
  IsoSpecThresholdGeneratorWrapper(const std::vector<int>& isotopeNumbers,
             const std::vector<int>& atomCounts,
             const std::vector<std::vector<double> >& isotopeMasses,
             const std::vector<std::vector<double> >& isotopeProbabilities,
             double threshold,
             bool absolute);

  // delete copy constructor
  IsoSpecThresholdGeneratorWrapper(const IsoSpecThresholdGeneratorWrapper&) = delete;

  IsoSpecThresholdGeneratorWrapper(const EmpiricalFormula& formula, double threshold, bool absolute);

  ~IsoSpecThresholdGeneratorWrapper();

  bool nextConf() final;
  Peak1D getConf() final;
  double getMass() final;
  double getIntensity() final;
  double getLogIntensity() final;


protected:
  std::unique_ptr<IsoSpec::IsoThresholdGenerator> ITG;
  };

  class OPENMS_DLLAPI IsoSpecOrderedGeneratorWrapper : public IsoSpecGeneratorWrapper
  {
public:
  IsoSpecOrderedGeneratorWrapper(const std::vector<int>& isotopeNumbers,
             const std::vector<int>& atomCounts,
             const std::vector<std::vector<double> >& isotopeMasses,
             const std::vector<std::vector<double> >& isotopeProbabilities);

  // delete copy constructor
  IsoSpecOrderedGeneratorWrapper(const IsoSpecOrderedGeneratorWrapper&) = delete;
  IsoSpecOrderedGeneratorWrapper(const EmpiricalFormula& formula);

  ~IsoSpecOrderedGeneratorWrapper();

  inline bool nextConf() final;
  inline Peak1D getConf() final;
  inline double getMass() final;
  inline double getIntensity() final;
  inline double getLogIntensity() final;

protected:
  std::unique_ptr<IsoSpec::IsoOrderedGenerator> IOG;
  };

  //-------------------------------------------------------------------------- 
  // IsoSpecWrapper classes
  //-------------------------------------------------------------------------- 

  class OPENMS_DLLAPI IsoSpecTotalProbWrapper : public IsoSpecWrapper
  {
public:
    IsoSpecTotalProbWrapper(const std::vector<int>& isotopeNumbers,
             const std::vector<int>& atomCounts,
             const std::vector<std::vector<double> >& isotopeMasses,
             const std::vector<std::vector<double> >& isotopeProbabilities,
             double p,
             bool do_p_trim = false);
    
    // delete copy constructor
    IsoSpecTotalProbWrapper(const IsoSpecTotalProbWrapper&) = delete;

    IsoSpecTotalProbWrapper(const EmpiricalFormula& formula, double p, bool do_p_trim = false);

    ~IsoSpecTotalProbWrapper();

    IsotopeDistribution run() final;

protected:
    std::unique_ptr<IsoSpec::IsoLayeredGenerator> ILG;
    const double target_prob;
    const bool do_p_trim;
  };

  class OPENMS_DLLAPI IsoSpecThresholdWrapper : public IsoSpecWrapper
  {

public:
    IsoSpecThresholdWrapper(const std::vector<int>& isotopeNumbers,
             const std::vector<int>& atomCounts,
             const std::vector<std::vector<double> >& isotopeMasses,
             const std::vector<std::vector<double> >& isotopeProbabilities,
             double threshold,
             bool absolute);
    
    // delelte copy constructor
    IsoSpecThresholdWrapper(const IsoSpecThresholdWrapper&) = delete;
    IsoSpecThresholdWrapper(const EmpiricalFormula& formula, double threshold, bool absolute);

    ~IsoSpecThresholdWrapper();

    IsotopeDistribution run() final;

protected:
    std::unique_ptr<IsoSpec::IsoThresholdGenerator> ITG;

  };

}