IsotopeModel.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: Clemens Groepl, Chris Bielow $
// --------------------------------------------------------------------------
 
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/IsotopeDistribution.h>
 
namespace OpenMS
{
  class EmpiricalFormula;
 
  class OPENMS_DLLAPI IsotopeModel :
    public InterpolationModel
  {
 
public:
    typedef InterpolationModel::CoordinateType CoordinateType;
    typedef InterpolationModel::CoordinateType IntensityType;
 
    enum Averagines {C = 0, H, N, O, S, AVERAGINE_NUM};
 
    IsotopeModel();
 
    IsotopeModel(const IsotopeModel & source);
 
    ~IsotopeModel() override;
 
    virtual IsotopeModel & operator=(const IsotopeModel & source);
 
    UInt getCharge();
 
    static BaseModel<1> * create()
    {
      return new IsotopeModel();
    }
 
    static const String getProductName()
    {
      return "IsotopeModel";
    }
 
    void setOffset(CoordinateType offset) override;
 
    CoordinateType getOffset();
 
    EmpiricalFormula getFormula();
 
    virtual void setSamples(const EmpiricalFormula & formula);
 
    using InterpolationModel::setSamples;
 
    CoordinateType getCenter() const override;
 
    const IsotopeDistribution & getIsotopeDistribution() const;
 
 
protected:
    CoordinateType isotope_stdev_;
    CoordinateType isotope_lorentz_fwhm_;
 
    UInt charge_;
    CoordinateType mean_;
    CoordinateType monoisotopic_mz_;
    double averagine_[AVERAGINE_NUM];
    Int max_isotope_;
    double trim_right_cutoff_;
    double isotope_distance_;
    IsotopeDistribution isotope_distribution_;
 
    void updateMembers_() override;
 
  };
}