OpenSwathOSWWriter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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.
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// 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;
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// --------------------------------------------------------------------------
// $Maintainer: George Rosenberger $
// $Authors: George Rosenberger $
// --------------------------------------------------------------------------
 
#pragma once
 
// Interfaces
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/CONCEPT/UniqueIdGenerator.h>
 
#include <OpenMS/KERNEL/FeatureMap.h>
 
#include <fstream>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI OpenSwathOSWWriter
  {
    String output_filename_;
    String input_filename_;
    OpenMS::UInt64 run_id_;
    bool doWrite_;
    bool use_ms1_traces_;
    bool sonar_;
    bool enable_uis_scoring_;
 
  public:
 
    OpenSwathOSWWriter(const String& output_filename,
                       const String& input_filename = "inputfile",
                       bool ms1_scores = false,
                       bool sonar = false,
                       bool uis_scores = false) :
      output_filename_(output_filename),
      input_filename_(input_filename),
      run_id_(OpenMS::UniqueIdGenerator::getUniqueId()),
      doWrite_(!output_filename.empty()),
      use_ms1_traces_(ms1_scores),
      sonar_(sonar),
      enable_uis_scoring_(uis_scores)
      {}
 
    bool isActive() const;
 
    void writeHeader();
 
    String getScore(const Feature& feature, std::string score_name) const;
 
    std::vector<String> getSeparateScore(const Feature& feature, std::string score_name) const;
 
    String prepareLine(const OpenSwath::LightCompound& /* pep */,
        const OpenSwath::LightTransition* /* transition */,
        FeatureMap& output, String id) const;
 
    void writeLines(const std::vector<String>& to_osw_output);
 
  };
 
}