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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: Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignmentScore.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectrumAlignment.h>
#include <cmath>
#include <boost/math/special_functions/erf.hpp>
using namespace std;
namespace OpenMS
{
SpectrumAlignmentScore::SpectrumAlignmentScore() :
PeakSpectrumCompareFunctor()
{
setName(SpectrumAlignmentScore::getProductName());
defaults_.setValue("tolerance", 0.3, "Defines the absolute (in Da) or relative (in ppm) tolerance");
defaults_.setValue("is_relative_tolerance", "false", "if true, the tolerance value is interpreted as ppm");
defaults_.setValidStrings("is_relative_tolerance", StringList::create("true,false"));
defaults_.setValue("use_linear_factor", "false", "if true, the intensities are weighted with the relative m/z difference");
defaults_.setValidStrings("use_linear_factor", StringList::create("true,false"));
defaults_.setValue("use_gaussian_factor", "false", "if true, the intensities are weighted with the relative m/z difference using a gaussian");
defaults_.setValidStrings("use_gaussian_factor", StringList::create("true,false"));
defaultsToParam_();
}
SpectrumAlignmentScore::SpectrumAlignmentScore(const SpectrumAlignmentScore & source) :
PeakSpectrumCompareFunctor(source)
{
}
SpectrumAlignmentScore::~SpectrumAlignmentScore()
{
}
SpectrumAlignmentScore & SpectrumAlignmentScore::operator=(const SpectrumAlignmentScore & source)
{
if (this != &source)
{
PeakSpectrumCompareFunctor::operator=(source);
}
return *this;
}
DoubleReal SpectrumAlignmentScore::operator()(const PeakSpectrum & spec) const
{
return operator()(spec, spec);
}
DoubleReal SpectrumAlignmentScore::operator()(const PeakSpectrum & s1, const PeakSpectrum & s2) const
{
const DoubleReal tolerance = (DoubleReal)param_.getValue("tolerance");
bool is_relative_tolerance = param_.getValue("is_relative_tolerance").toBool();
bool use_linear_factor = param_.getValue("use_linear_factor").toBool();
bool use_gaussian_factor = param_.getValue("use_gaussian_factor").toBool();
if (use_linear_factor && use_gaussian_factor)
{
cerr << "Warning: SpectrumAlignmentScore, use either 'use_linear_factor' or 'use_gaussian_factor'!" << endl;
}
SpectrumAlignment aligner;
Param p;
p.setValue("tolerance", tolerance);
p.setValue("is_relative_tolerance", (String)param_.getValue("is_relative_tolerance"));
aligner.setParameters(p);
vector<pair<Size, Size> > alignment;
aligner.getSpectrumAlignment(alignment, s1, s2);
DoubleReal score(0), sum(0), sum1(0), sum2(0);
for (PeakSpectrum::ConstIterator it1 = s1.begin(); it1 != s1.end(); ++it1)
{
sum1 += it1->getIntensity() * it1->getIntensity();
}
for (PeakSpectrum::ConstIterator it1 = s2.begin(); it1 != s2.end(); ++it1)
{
sum2 += it1->getIntensity() * it1->getIntensity();
}
for (vector<pair<Size, Size> >::const_iterator it = alignment.begin(); it != alignment.end(); ++it)
{
//DoubleReal factor(0.0);
//factor = (epsilon - fabs(s1[it->first].getPosition()[0] - s2[it->second].getPosition()[0])) / epsilon;
DoubleReal mz_tolerance(tolerance);
if (is_relative_tolerance)
{
mz_tolerance = mz_tolerance * s1[it->first].getPosition()[0] / 1e6;
}
DoubleReal mz_difference(fabs(s1[it->first].getPosition()[0] - s2[it->second].getPosition()[0]));
DoubleReal factor = 1.0;
if (use_linear_factor || use_gaussian_factor)
{
factor = getFactor_(mz_tolerance, mz_difference, use_gaussian_factor);
}
sum += sqrt(s1[it->first].getIntensity() * s2[it->second].getIntensity() * factor);
}
score = sum / (sqrt(sum1 * sum2));
return score;
}
DoubleReal SpectrumAlignmentScore::getFactor_(DoubleReal mz_tolerance, DoubleReal mz_difference, bool is_gaussian) const
{
DoubleReal factor(0.0);
if (is_gaussian)
{
static const DoubleReal denominator = mz_tolerance * 3.0 * sqrt(2.0);
factor = boost::math::erfc(mz_difference / denominator);
//cerr << "Factor: " << factor << " " << mz_tolerance << " " << mz_difference << endl;
}
else
{
factor = (mz_tolerance - mz_difference) / mz_tolerance;
}
return factor;
}
}
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