TIC.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: Chris Bielow $
// $Authors: Tom Waschischeck $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/QC/QCBase.h>
 
namespace OpenMS
{
  class MzTabMetaData;
  class MSExperiment;
  class MSChromatogram;
 
  class OPENMS_DLLAPI TIC : public QCBase
  {
  public:
    TIC() = default;
 
    virtual ~TIC() = default;
 
    // stores TIC values calculated by compute function
    struct OPENMS_DLLAPI Result
    {
      std::vector<UInt> intensities;  // TIC intensities
      std::vector<float> relative_intensities;
      std::vector<float> retention_times; // TIC RTs in seconds
      UInt area = 0;  // Area under TIC
      UInt fall = 0;  // MS1 signal fall (10x) count
      UInt jump = 0;  // MS1 signal jump (10x) count
 
      bool operator==(const Result& rhs) const;
    };
 
    
    Result compute(const MSExperiment& exp, float bin_size = 0, UInt ms_level = 1);
 
    const String& getName() const override;
 
    const std::vector<MSChromatogram>& getResults() const ;
 
    QCBase::Status requires() const override;
 
    void addMetaDataMetricsToMzTab(MzTabMetaData& meta, std::vector<Result>& tics);
 
  private:
    const String name_ = "TIC";
  };
}