MassTrace.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
//
// This software is released under a three-clause BSD license:
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//    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.
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// --------------------------------------------------------------------------
// $Maintainer: Erhan Kenar $
// $Authors: Erhan Kenar, Holger Franken $
// --------------------------------------------------------------------------

#ifndef OPENMS_KERNEL_MASSTRACE_H
#define OPENMS_KERNEL_MASSTRACE_H

#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/FeatureMap.h>


#include <vector>
#include <list>
#include <map>


namespace OpenMS
{
  typedef Peak2D PeakType;

  class OPENMS_DLLAPI MassTrace
  {
public:

    MassTrace();

    MassTrace(const std::list<PeakType> &, const DoubleReal & scan_time = 1.0);

    MassTrace(const std::vector<PeakType> &, const DoubleReal & scan_time = 1.0);

    ~MassTrace();

    MassTrace(const MassTrace &);

    MassTrace & operator=(const MassTrace &);

    PeakType & operator[](const Size & mt_idx);
    const PeakType & operator[](const Size & mt_idx) const;


    typedef std::vector<PeakType>::iterator iterator;
    typedef std::vector<PeakType>::const_iterator const_iterator;
    typedef std::vector<PeakType>::reverse_iterator reverse_iterator;
    typedef std::vector<PeakType>::const_reverse_iterator const_reverse_iterator;

    iterator begin()
    {
      return trace_peaks_.begin();
    }

    iterator end()
    {
      return trace_peaks_.end();
    }

    const_iterator begin() const
    {
      return trace_peaks_.begin();
    }

    const_iterator end() const
    {
      return trace_peaks_.end();
    }

    reverse_iterator rbegin()
    {
      return trace_peaks_.rbegin();
    }

    reverse_iterator rend()
    {
      return trace_peaks_.rend();
    }

    const_reverse_iterator rbegin() const
    {
      return trace_peaks_.rbegin();
    }

    const_reverse_iterator rend() const
    {
      return trace_peaks_.rend();
    }


    Size getSize() const
    {
      return trace_peaks_.size();
    }

    String getLabel() const
    {
      return label_;
    }

    void setLabel(const String & label)
    {
      label_ = label;
    }

    DoubleReal getCentroidMZ()
    {
      return centroid_mz_;
    }

    DoubleReal getCentroidMZ() const
    {
      return centroid_mz_;
    }

    DoubleReal getCentroidRT()
    {
      return centroid_rt_;
    }

    DoubleReal getCentroidRT() const
    {
      return centroid_rt_;
    }

    DoubleReal getCentroidSD()
    {
      return centroid_sd_;
    }

    DoubleReal getCentroidSD() const
    {
      return centroid_sd_;
    }

    void setCentroidSD(const DoubleReal & tmp_sd)
    {
      centroid_sd_ = tmp_sd;
    }

    DoubleReal getFWHM()
    {
        return fwhm_;
    }

    DoubleReal getFWHM() const
    {
        return fwhm_;
    }

    DoubleReal getTraceLength()
    {
        DoubleReal length(0.0);

        if (trace_peaks_.size() > 1)
        {
            length = std::fabs(trace_peaks_.rbegin()->getRT() - trace_peaks_.begin()->getRT());
        }

        return length;
    }

    DoubleReal getTraceLength() const
    {
        DoubleReal length(0.0);

        if (trace_peaks_.size() > 1)
        {
            length = std::fabs(trace_peaks_.rbegin()->getRT() - trace_peaks_.begin()->getRT());
        }

        return length;
    }

    std::pair<Size, Size> getFWHMborders()
    {
      return std::make_pair(fwhm_start_idx_, fwhm_end_idx_);
    }

    std::pair<Size, Size> getFWHMborders() const
    {
      return std::make_pair(fwhm_start_idx_, fwhm_end_idx_);
    }

    std::vector<DoubleReal> getSmoothedIntensities()
    {
      return smoothed_intensities_;
    }

    std::vector<DoubleReal> getSmoothedIntensities() const
    {
      return smoothed_intensities_;
    }

    void setSmoothedIntensities(const std::vector<DoubleReal> & db_vec)
    {
      if (trace_peaks_.size() != db_vec.size())
      {
        throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Number of smoothed intensities deviates from mass trace size! Aborting...", String(db_vec.size()));
      }

      smoothed_intensities_ = db_vec;
    }

    DoubleReal getScanTime()
    {
      return scan_time_;
    }


    DoubleReal computeSmoothedPeakArea();

    DoubleReal computePeakArea();
    DoubleReal computePeakArea() const;


    Size findMaxByIntPeak(bool) const;

    DoubleReal estimateFWHM(bool);

    DoubleReal computeFwhmAreaSmooth();
    DoubleReal computeFwhmArea();
    DoubleReal computeFwhmAreaSmoothRobust();
    DoubleReal computeFwhmAreaRobust();

    DoubleReal getIntensity(bool);
    DoubleReal getMaxIntensity(bool);
    DoubleReal getMaxIntensity(bool) const;

    ConvexHull2D getConvexhull() const;


    void updateSmoothedMaxRT();

    void updateWeightedMeanRT();

    void updateSmoothedWeightedMeanRT();

    void updateMedianRT();

    void updateMedianMZ();

    void updateMeanMZ();

    void updateWeightedMeanMZ();

    void updateWeightedMZsd();

private:
    std::vector<PeakType> trace_peaks_;

    DoubleReal centroid_mz_;

    DoubleReal centroid_sd_;

    DoubleReal centroid_rt_;

    String label_;

    std::vector<DoubleReal> smoothed_intensities_;

    DoubleReal fwhm_;

    DoubleReal scan_time_;

    Size fwhm_start_idx_;
    Size fwhm_end_idx_;


    // Size fwhm_num_scans_;
  };

}

#endif // OPENMS_KERNEL_MASSTRACE_H