FLASHDeconvSpectrumFile.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: Kyowon Jeong $
// $Authors: Kyowon Jeong $
// --------------------------------------------------------------------------
#pragma once

#include <OpenMS/config.h>
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>

#include <iomanip>

namespace OpenMS
{
  class OPENMS_DLLAPI FLASHDeconvSpectrumFile
  {
  public:
    static void writeDeconvolvedMassesHeader(std::fstream& fs,
                                             uint ms_level,
                                             bool detail,
                                             bool decoy);

    static void writeDeconvolvedMasses(DeconvolvedSpectrum& dspec, std::fstream& fs,
                                       const String& file_name,
                                       const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,
                                       double tol,
                                       bool write_detail,
                                       bool decoy);

    //      @param avg averagine information to calculate monoisotopic and average mass difference
    static void writeTopFD(const DeconvolvedSpectrum& dspec, std::fstream& fs,
                           double snr_threshold = 1.0,
                           double decoy_harmonic_factor = 1.0,
                           double decoy_precursor_offset = .0);

  private:

    static const int topFD_min_peak_count_ = 3;
    static const int topFD_max_peak_count_ = 500;

  };
}// namespace OpenMS