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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// 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: Andreas Bertsch $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_COMPARISON_SPECTRA_SPECTRUMCHEAPDPCORR_H
#define OPENMS_COMPARISON_SPECTRA_SPECTRUMCHEAPDPCORR_H
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
namespace OpenMS
{
/**
@brief SpectrumCheapDPCorr calculates an optimal alignment on stick spectra
to save computing time only Peak Pairs that could get a score > 0 are considered
which Peak Pairs could get scores > 0 ? <br>
Peaks get a score depending on the difference in position and the heights of the peaks <br>
pairs with positions that differ more than some limit get score 0
@htmlinclude OpenMS_SpectrumCheapDPCorr.parameters
@ingroup SpectraComparison
*/
class OPENMS_DLLAPI SpectrumCheapDPCorr :
public PeakSpectrumCompareFunctor
{
public:
// @name Constructors and Destructors
// @{
/// default constructor
SpectrumCheapDPCorr();
/// copy constructor
SpectrumCheapDPCorr(const SpectrumCheapDPCorr & source);
/// destructor
virtual ~SpectrumCheapDPCorr();
// @}
// @name Operators
// @{
/// assignment operator
SpectrumCheapDPCorr & operator=(const SpectrumCheapDPCorr & source);
double operator()(const PeakSpectrum & a, const PeakSpectrum & b) const;
double operator()(const PeakSpectrum & a) const;
// @}
// @name Accessors
// @{
///
static PeakSpectrumCompareFunctor * create() { return new SpectrumCheapDPCorr(); }
///
static const String getProductName()
{
return "SpectrumCheapDPCorr";
}
/// return consensus spectrum from last funtion call operator
const PeakSpectrum & lastconsensus() const;
///
Map<UInt, UInt> getPeakMap() const;
/// set weighting of the second spectrum for consensus from next function call operator
void setFactor(double f);
// @}
private:
/// O(n^2) dynamical programming
double dynprog_(const PeakSpectrum &, const PeakSpectrum &, int, int, int, int) const;
/// similarity of two peaks
double comparepeaks_(double posa, double posb, double inta, double intb) const;
static const String info_;
/// consensus spectrum of the last comparison
mutable PeakSpectrum lastconsensus_;
/// should peaks with no alignment partner be kept in the consensus?
bool keeppeaks_;
/// weighting factor for the next consensus spectrum
mutable double factor_;
/// last peak map
mutable Map<UInt, UInt> peak_map_;
};
}
#endif //OPENMS_COMPARISON_SPECTRA_SPECTRUMCHEAPDPCORR_H
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