OpenPepXLAlgorithm.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: Eugen Netz $
// $Authors: Timo Sachsenberg, Eugen Netz $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>

namespace OpenMS
{

//-------------------------------------------------------------
//Doxygen docu
//-------------------------------------------------------------

  class OPENMS_DLLAPI OpenPepXLAlgorithm :
   public DefaultParamHandler, public ProgressLogger
  {
public:

    enum ExitCodes
    {
      EXECUTION_OK,
      ILLEGAL_PARAMETERS,
      UNEXPECTED_RESULT
    };

    OpenPepXLAlgorithm();

    ~OpenPepXLAlgorithm() override;

    ExitCodes run(PeakMap& unprocessed_spectra, ConsensusMap& cfeatures, std::vector<FASTAFile::FASTAEntry>& fasta_db, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, OPXLDataStructs::PreprocessedPairSpectra& preprocessed_pair_spectra, std::vector< std::pair<Size, Size> >& spectrum_pairs, std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms, PeakMap& spectra);

private:
    void updateMembers_() override;

    static OPXLDataStructs::PreprocessedPairSpectra preprocessPairs_(const PeakMap& spectra, const std::vector< std::pair<Size, Size> >& spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm, bool deisotope);

    String decoy_string_;
    bool decoy_prefix_;

    Int min_precursor_charge_;
    Int max_precursor_charge_;
    double precursor_mass_tolerance_;
    bool precursor_mass_tolerance_unit_ppm_;
    IntList precursor_correction_steps_;

    double fragment_mass_tolerance_;
    double fragment_mass_tolerance_xlinks_;
    bool fragment_mass_tolerance_unit_ppm_;

    StringList cross_link_residue1_;
    StringList cross_link_residue2_;
    double cross_link_mass_light_;
    double cross_link_mass_iso_shift_;
    DoubleList cross_link_mass_mono_link_;
    String cross_link_name_;

    StringList fixedModNames_;
    StringList varModNames_;
    Size max_variable_mods_per_peptide_;
    Size peptide_min_size_;
    Size missed_cleavages_;
    String enzyme_name_;

    Int number_top_hits_;
    String deisotope_mode_;

    String add_y_ions_;
    String add_b_ions_;
    String add_x_ions_;
    String add_a_ions_;
    String add_c_ions_;
    String add_z_ions_;
    String add_losses_;
  };
}