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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Erhan Kenar$
// $Authors: Erhan Kenar$
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>
#include <OpenMS/FILTERING/DATAREDUCTION/ElutionPeakDetection.h>
///////////////////////////
#include <OpenMS/FILTERING/DATAREDUCTION/FeatureFindingMetabo.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(FeatureFindingMetabo, "$Id: FeatureFindingMetabo_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
FeatureFindingMetabo* ptr = 0;
FeatureFindingMetabo* null_ptr = 0;
START_SECTION(FeatureFindingMetabo())
{
ptr = new FeatureFindingMetabo();
TEST_NOT_EQUAL(ptr, null_ptr)
}
END_SECTION
START_SECTION(~FeatureFindingMetabo())
{
delete ptr;
}
END_SECTION
// load a mzML file for testing the algorithm
MSExperiment<Peak1D> input;
MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("FeatureFindingMetabo_input1.mzML"), input);
FeatureMap<> exp_fm, test_fm;
FeatureXMLFile().load(OPENMS_GET_TEST_DATA_PATH("FeatureFindingMetabo_output1.featureXML"), exp_fm);
// exp_fm.sortByMZ();
std::vector<MassTrace> output_mt, splitted_mt, filtered_mt;
MassTraceDetection test_mtd;
test_mtd.run(input, output_mt);
ElutionPeakDetection test_epd;
test_epd.detectPeaks(output_mt, splitted_mt);
// test_epd.filterByPeakWidth(splitted_mt, filtered_mt);
START_SECTION((void run(std::vector< MassTrace > &, FeatureMap<> &)))
{
FeatureFindingMetabo test_ffm;
test_ffm.run(splitted_mt, test_fm);
test_fm.sortByMZ();
TEST_EQUAL(exp_fm.size(), test_fm.size());
if (exp_fm.size() == test_fm.size())
{
for (Size i = 0; i < exp_fm.size(); ++i)
{
TEST_EQUAL(exp_fm[i].getMetaValue(3), test_fm[i].getMetaValue(3));
TEST_REAL_SIMILAR(exp_fm[i].getRT(), test_fm[i].getRT());
TEST_REAL_SIMILAR(exp_fm[i].getMZ(), test_fm[i].getMZ());
TEST_REAL_SIMILAR(exp_fm[i].getIntensity(), test_fm[i].getIntensity());
}
}
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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