text: // --------------------------------------------------------------------------
  //                   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: Mathias Walzer $
  // $Authors: Timo Sachsenberg $
  // --------------------------------------------------------------------------
  //
  
  #include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>
  
  using namespace std;
  
  namespace OpenMS
  {
    // Empty vector initialized to maximum supported dimensionality.
    const BinnedSpectrum::SparseVectorType BinnedSpectrum::EmptySparseVector(numeric_limits<BinnedSpectrum::SparseVectorIndexType>::max());
  
    BinnedSpectrum::BinnedSpectrum(const PeakSpectrum& ps, float size, bool unit_ppm, UInt spread, float offset) :
      bin_spread_(spread), 
      bin_size_(size),
      unit_ppm_(unit_ppm),
      offset_(offset),
      bins_()
    {
      precursors_ = ps.getPrecursors();
      binSpectrum_(ps);
    }
  
    BinnedSpectrum::~BinnedSpectrum()
    {
    }
  
    const BinnedSpectrum::SparseVectorType& BinnedSpectrum::getBins() const
    {
      return bins_;
    }
  
    BinnedSpectrum::SparseVectorType& BinnedSpectrum::getBins()
    {
      return bins_;
    }
  
    const std::vector<Precursor>& BinnedSpectrum::getPrecursors() const
    {
      return precursors_;
    }
  
    std::vector<Precursor>& BinnedSpectrum::getPrecursors()
    {
      return precursors_;
    }
  
    void BinnedSpectrum::binSpectrum_(const PeakSpectrum& ps)
    {
      OPENMS_PRECONDITION(ps.isSorted(), "Spectrum needs to be sorted by m/z.");
  
      if (ps.empty()) { return; }
  
      bins_ = EmptySparseVector;
  
      for (auto const & p : ps)
      {
        // if bin size is in relative units (ppm), check if minimum value is >= 1 (otherwise we might get numerical problems with the negative log)
        OPENMS_PRECONDITION(!unit_ppm_ || p.getMZ() >= BinnedSpectrum::MIN_MZ_, "Spectrum with relative bin size contains peaks with m/z < 1");
  
        // e.g.: bin_size_ = 1.5: first bin covers range [0, 1.5) so peak at 1.5 falls in second bin (index 1)
        const size_t idx = getBinIndex(p.getMZ());
  
        // add peak to corresponding bin
        bins_.coeffRef(idx) += p.getIntensity();
  
        // add peak to neighboring bins
        for (Size j = 0; j < bin_spread_; ++j)
        {
           bins_.coeffRef(idx + j + 1) +=  p.getIntensity();
          
          // prevent spreading over left boundaries
          if (static_cast<int>(idx - j - 1) >= 0)
          {
            bins_.coeffRef(idx - j - 1) += p.getIntensity();
          }
        }
      }
    }
  
    bool BinnedSpectrum::operator==(const BinnedSpectrum& rhs) const
    {
      // first compare bin layout and precursors
      if (std::tie(unit_ppm_, bin_size_, bin_spread_, precursors_)
          != std::tie(rhs.unit_ppm_, rhs.bin_size_, rhs.bin_spread_, rhs.precursors_)) 
      {
        return false; 
      }
  
      // efficient look-up of number of non-zero entries, so we use this as-well
      if (bins_.nonZeros() != rhs.bins_.nonZeros()) { return false; }
  
      // test non-sparse (non-zero) elements for equality
      SparseVectorIteratorType it(bins_);
      SparseVectorIteratorType rhs_it(rhs.bins_);  
      while (it)      
      {
        if (it.index() != rhs_it.index()
         || it.value() != rhs_it.value()) { return false; }
        ++it;
        ++rhs_it;
      }
      return true;
    }
  
    // static
    bool BinnedSpectrum::isCompatible(const BinnedSpectrum& a, const BinnedSpectrum& b)
    {
      // check if bin size, offset (and unit) are equal
      return std::tie(a.unit_ppm_, a.bin_size_, a.offset_) 
          == std::tie(b.unit_ppm_, b.bin_size_, b.offset_);
    }
  
    bool BinnedSpectrum::operator!=(const BinnedSpectrum& rhs) const
    {
      return !(operator==(rhs));
    }
  
  }
  
  