TheoreticalSpectrumGenerator.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, Eugen Netz $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/Residue.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/DataArrays.h>
 
namespace OpenMS
{
  class AASequence;
 
  class OPENMS_DLLAPI TheoreticalSpectrumGenerator :
    public DefaultParamHandler
  {
    public:
 
    TheoreticalSpectrumGenerator();
 
    TheoreticalSpectrumGenerator(const TheoreticalSpectrumGenerator& source);
 
    ~TheoreticalSpectrumGenerator() override;
 
    TheoreticalSpectrumGenerator& operator=(const TheoreticalSpectrumGenerator& tsg);
 
    virtual void getSpectrum(PeakSpectrum& spec, const AASequence& peptide, Int min_charge, Int max_charge) const;
 
    void updateMembers_() override;
 
    protected:
 
    virtual void addPeaks_(PeakSpectrum& spectrum, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Residue::ResidueType res_type, Int charge = 1) const;
 
    virtual void addPrecursorPeaks_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Int charge = 1) const;
 
    void addAbundantImmoniumIons_(PeakSpectrum& spec, const AASequence& peptide, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges) const;
 
    void addIsotopeCluster_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, Residue::ResidueType res_type, Int charge, double intensity) const;
 
    static char residueTypeToIonLetter_(Residue::ResidueType res_type);
 
    void addLosses_(PeakSpectrum& spectrum, const AASequence& ion, DataArrays::StringDataArray& ion_names, DataArrays::IntegerDataArray& charges, double intensity, Residue::ResidueType res_type, int charge) const;
 
    bool add_b_ions_;
    bool add_y_ions_;
    bool add_a_ions_;
    bool add_c_ions_;
    bool add_x_ions_;
    bool add_z_ions_;
    bool add_first_prefix_ion_;
    bool add_losses_;
    bool add_metainfo_;
    bool add_isotopes_;
    int isotope_model_;
    bool add_precursor_peaks_;
    bool add_all_precursor_charges_ ;
    bool add_abundant_immonium_ions_;
    bool sort_by_position_;
    double a_intensity_;
    double b_intensity_;
    double c_intensity_;
    double x_intensity_;
    double y_intensity_;
    double z_intensity_;
 
    Int max_isotope_;
    double rel_loss_intensity_;
    double max_isotope_probability_;
    double pre_int_;
    double pre_int_H2O_;
    double pre_int_NH3_;
  };
}