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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: Lars Nilse $
// $Authors: Lars Nilse, Holger Plattfaut $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SILACFilter.h>
#include <OpenMS/FILTERING/DATAREDUCTION/SILACFiltering.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/PeakWidthEstimator.h>
using namespace OpenMS;
using namespace std;
START_TEST(SILACFiltering, "$Id: SILACFiltering_test.C 10915 2013-04-04 20:14:57Z aiche $")
MSExperiment<> input;
MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("SILACFiltering_test.mzML"), input);
const PeakWidthEstimator::Result peak_width(PeakWidthEstimator::estimateFWHM(input));
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
std::vector<DoubleReal> mass_separations;
mass_separations.push_back(8.0142);
SILACFiltering filtering(input, peak_width, 0);
SILACFilter filter(mass_separations, 2, 2, 3, 0, .9, false);
START_SECTION((SILACFiltering(MSExperiment< Peak1D > &exp, const PeakWidthEstimator::Result &, const DoubleReal intensity_cutoff, const String debug_filebase_="")))
{
TEST_EQUAL(filtering.filters_.size(), 0);
TEST_EQUAL(filtering.blacklist.size(), 0);
}
END_SECTION
START_SECTION((void addFilter(SILACFilter &filter)))
{
filtering.addFilter(filter);
TEST_EQUAL(filtering.filters_.size(), 1);
}
END_SECTION
START_SECTION((void filterDataPoints()))
{
filtering.filterDataPoints();
SILACFiltering::Filters::iterator filter_it = filtering.filters_.begin();
std::vector<SILACPattern> &p = filter_it->getElements();
TEST_EQUAL(p.size(), 3);
TEST_REAL_SIMILAR(p[0].rt, 830);
TEST_REAL_SIMILAR(p[0].mz, 670.84);
TEST_REAL_SIMILAR(p[1].rt, 830);
TEST_REAL_SIMILAR(p[1].mz, 670.84);
TEST_REAL_SIMILAR(p[2].rt, 833);
TEST_REAL_SIMILAR(p[2].mz, 670.84);
}
END_SECTION
START_SECTION([SILACFiltering::SpectrumInterpolation] SpectrumInterpolation(const MSSpectrum<> &, const SILACFiltering &))
SILACFiltering::SpectrumInterpolation si(input[0], filtering);
END_SECTION
START_SECTION([SILACFiltering::SpectrumInterpolation] ~SpectrumInterpolation())
SILACFiltering::SpectrumInterpolation si(input[0], filtering);
END_SECTION
START_SECTION([SILACFiltering::SpectrumInterpolation] DoubleReal operator()(DoubleReal mz) const)
SILACFiltering::SpectrumInterpolation si(input[0], filtering);
TEST_REAL_SIMILAR(si(670.5), 0)
TEST_REAL_SIMILAR(si(671.1), 0)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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