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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: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_COMPARISON_SPECTRA_PEAKALIGNMENT_H
#define OPENMS_COMPARISON_SPECTRA_PEAKALIGNMENT_H
#include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
#include <vector>
namespace OpenMS
{
/**
@brief make a PeakAlignment of two PeakSpectra
The alignment is done according to the Needleman-Wunsch Algorithm (local alignment considering gaps).
@htmlinclude OpenMS_PeakAlignment.parameters
@ingroup SpectraComparison
*/
class OPENMS_DLLAPI PeakAlignment :
public PeakSpectrumCompareFunctor
{
public:
/// default constructor
PeakAlignment();
/// copy constructor
PeakAlignment(const PeakAlignment & source);
/// destructor
virtual ~PeakAlignment();
/// assignment operator
PeakAlignment & operator=(const PeakAlignment & source);
/** function call operator, calculates the similarity of the given arguments
@param spec1 First spectrum given in a binned representation
@param spec2 Second spectrum ginve in a binned representation
*/
double operator()(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const;
/// function call operator, calculates self similarity
double operator()(const PeakSpectrum & spec) const;
///
static PeakSpectrumCompareFunctor * create() { return new PeakAlignment(); }
/// get the identifier for this DefaultParamHandler
static const String getProductName()
{
return "PeakAlignment";
}
/// make alignment and get the traceback
std::vector<std::pair<Size, Size> > getAlignmentTraceback(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const;
private:
/// calculates the score for aligning two peaks
double peakPairScore_(double & pos1, double & intens1, double & pos2, double & intens2, const double & sigma) const;
};
}
#endif //OPENMS_COMPARISON_SPECTRA_PEAKALIGNMENT_H
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