MassTraceDetection.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 2002-2012.
//
// 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: Erhan Kenar $
// $Authors: Erhan Kenar, Holger Franken $
// --------------------------------------------------------------------------

#ifndef OPENMS_FILTERING_DATAREDUCTION_MASSTRACEDETECTION_H
#define OPENMS_FILTERING_DATAREDUCTION_MASSTRACEDETECTION_H

#include <OpenMS/KERNEL/MassTrace.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MassTraceDetection :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MassTraceDetection();

    virtual ~MassTraceDetection();


    void updateIterativeWeightedMeanMZ(const DoubleReal &, const DoubleReal &, DoubleReal &, DoubleReal &, DoubleReal &);

    // void filterByPeakWidth(std::vector<MassTrace>&, std::vector<MassTrace>&);


    void run(const MSExperiment<Peak1D> &, std::vector<MassTrace> &);

    void run(MSExperiment<Peak1D>::ConstAreaIterator & begin, MSExperiment<Peak1D>::ConstAreaIterator & end, std::vector<MassTrace> & found_masstraces);

protected:
    virtual void updateMembers_();

private:
    // parameter stuff
    DoubleReal mass_error_ppm_;
    DoubleReal noise_threshold_int_;
    DoubleReal chrom_peak_snr_;

    DoubleReal min_sample_rate_;
    DoubleReal min_trace_length_;

    bool reestimate_mt_sd_;
  };
}

#endif // OPENMS_FILTERING_DATAREDUCTION_MASSTRACEDETECTION_H