ConsensusMapNormalizerAlgorithmMedian.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: Johannes Veit $
// $Authors: Johannes Junker $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/ConsensusMapNormalizerAlgorithmThreshold.h>

namespace OpenMS
{

  class OPENMS_DLLAPI ConsensusMapNormalizerAlgorithmMedian
  {
    friend class ConsensusMapNormalizerAlgorithmThreshold;

private:
    ConsensusMapNormalizerAlgorithmMedian(const ConsensusMapNormalizerAlgorithmMedian & copyin);

    ConsensusMapNormalizerAlgorithmMedian & operator=(const ConsensusMapNormalizerAlgorithmMedian & rhs);

public:
    ConsensusMapNormalizerAlgorithmMedian();

    virtual ~ConsensusMapNormalizerAlgorithmMedian();

    enum NormalizationMethod { NM_SCALE, NM_SHIFT };

    static void normalizeMaps(ConsensusMap & map, NormalizationMethod method, const String& acc_filter, const String& desc_filter);

    static Size computeMedians(const ConsensusMap & map, std::vector<double> & medians, const String& acc_filter, const String& desc_filter);

    static bool passesFilters_(ConsensusMap::ConstIterator cf_it, const ConsensusMap& map, const String& acc_filter, const String& desc_filter);
  };

} // namespace OpenMS