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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: Oliver Kohlbacher, Stephan Aiche $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/FORMAT/MzDataFile.h>
#include <OpenMS/FORMAT/ParamXMLFile.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPicked.h>
#include <OpenMS/KERNEL/RichPeak1D.h>
///////////////////////////
START_TEST(FeatureFinderAlgorithmPicked, "$Id: FeatureFinderAlgorithmPicked_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace OpenMS::Math;
using namespace std;
typedef FeatureFinderAlgorithmPicked<Peak1D,Feature> FFPP;
FFPP* ptr = 0;
FFPP* nullPointer = 0;
FeatureFinderAlgorithm<Peak1D,Feature>* ffA_nullPointer = 0;
START_SECTION((FeatureFinderAlgorithmPicked()))
ptr = new FFPP;
TEST_NOT_EQUAL(ptr,nullPointer)
END_SECTION
START_SECTION((~FeatureFinderAlgorithmPicked()))
delete ptr;
END_SECTION
START_SECTION([EXTRA] FeatureFinderAlgorithmPicked() - with RichPeak1D)
FeatureFinderAlgorithmPicked<RichPeak1D,Feature> ffa;
NOT_TESTABLE
END_SECTION
START_SECTION((static FeatureFinderAlgorithm<PeakType,FeatureType>* create()))
FeatureFinderAlgorithm<Peak1D,Feature>* ptr2 = FFPP::create();
TEST_NOT_EQUAL(ptr2,ffA_nullPointer)
delete ptr2;
END_SECTION
START_SECTION((static const String getProductName()))
TEST_EQUAL(FFPP::getProductName(),"centroided")
END_SECTION
START_SECTION((virtual void run()))
//input and output
MSExperiment<> input;
MzDataFile mzdata_file;
mzdata_file.getOptions().addMSLevel(1);
mzdata_file.load(OPENMS_GET_TEST_DATA_PATH("FeatureFinderAlgorithmPicked.mzData"),input);
input.updateRanges(1);
FeatureMap<> output;
//parameters
Param param;
ParamXMLFile paramFile;
paramFile.load(OPENMS_GET_TEST_DATA_PATH("FeatureFinderAlgorithmPicked.ini"), param);
param = param.copy("FeatureFinder:1:algorithm:",true);
//Dummy featurefinder
FeatureFinder ff;
FFPP ffpp;
ffpp.setParameters(param);
ffpp.setData(input, output, ff);
ffpp.run();
TEST_EQUAL(output.size(),8);
TOLERANCE_ABSOLUTE(0.001);
TEST_REAL_SIMILAR(output[0].getOverallQuality(),0.8819);
TEST_REAL_SIMILAR(output[1].getOverallQuality(),0.8673);
TEST_REAL_SIMILAR(output[2].getOverallQuality(),0.9079);
TEST_REAL_SIMILAR(output[3].getOverallQuality(),0.9271);
TEST_REAL_SIMILAR(output[4].getOverallQuality(),0.9401);
TEST_REAL_SIMILAR(output[5].getOverallQuality(),0.9094);
TEST_REAL_SIMILAR(output[6].getOverallQuality(),0.9403);
TEST_REAL_SIMILAR(output[7].getOverallQuality(),0.9243);
TOLERANCE_ABSOLUTE(20.0);
TEST_REAL_SIMILAR(output[0].getIntensity(),51260.0);
TEST_REAL_SIMILAR(output[1].getIntensity(),44667.3);
TEST_REAL_SIMILAR(output[2].getIntensity(),34613.3);
TEST_REAL_SIMILAR(output[3].getIntensity(),19428.9);
TEST_REAL_SIMILAR(output[4].getIntensity(),12513.9);
TEST_REAL_SIMILAR(output[5].getIntensity(),8512.71);
TEST_REAL_SIMILAR(output[6].getIntensity(),7295.3);
TEST_REAL_SIMILAR(output[7].getIntensity(),5024.74);
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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