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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Alexandra Zerck$
// $Authors: $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/FILTERING/CALIBRATION/InternalCalibration.h>
#include <OpenMS/FORMAT/MzDataFile.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(InternalCalibration, "$Id: InternalCalibration_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
InternalCalibration* ptr = 0;
InternalCalibration* nullPointer = 0;
START_SECTION(InternalCalibration())
{
ptr = new InternalCalibration();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~InternalCalibration())
{
delete ptr;
}
END_SECTION
ptr = new InternalCalibration();
MSExperiment<> exp;
MzDataFile file;
file.load(OPENMS_GET_TEST_DATA_PATH("InternalCalibration_test.mzData"),exp);
std::vector<double> ref_masses;
ref_masses.push_back(1296.68476942);
ref_masses.push_back(2465.19833942);
Param param;
param.setValue("mz_tolerance",100.);
param.setValue("mz_tolerance_unit","ppm");
START_SECTION((template < typename InputPeakType > void calibrateMapSpectrumwise(const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< DoubleReal > &ref_masses)))
{
TOLERANCE_ABSOLUTE(0.000001)
MSExperiment<> calibrated_exp;
ptr->setParameters(param);
ptr->calibrateMapSpectrumwise(exp,calibrated_exp,ref_masses);
TEST_REAL_SIMILAR(calibrated_exp[0][14].getMZ(),1296.68476942)
TEST_REAL_SIMILAR(calibrated_exp[0][77].getMZ(),2465.19833942)
}
END_SECTION
START_SECTION((template < typename InputPeakType > void calibrateMapGlobally(const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< DoubleReal > &ref_masses, String trafo_file_name="")))
{
TOLERANCE_ABSOLUTE(0.000001)
MSExperiment<> calibrated_exp;
ptr->setParameters(param);
ptr->calibrateMapGlobally(exp,calibrated_exp,ref_masses);
TEST_REAL_SIMILAR(calibrated_exp[0][14].getMZ(),1296.68476942)
TEST_REAL_SIMILAR(calibrated_exp[1][40].getMZ(),1296.68476942)
TEST_REAL_SIMILAR(calibrated_exp[0][77].getMZ(),2465.19833942)
TEST_REAL_SIMILAR(calibrated_exp[1][90].getMZ(),2465.19833942)
}
END_SECTION
IdXMLFile id_file;
std::vector<ProteinIdentification> prot_ids;
std::vector<PeptideIdentification> pep_ids;
id_file.load(OPENMS_GET_TEST_DATA_PATH("InternalCalibration_1.idXML"),prot_ids,pep_ids);
START_SECTION((template < typename InputPeakType > void calibrateMapGlobally(const MSExperiment< InputPeakType > &exp, MSExperiment< InputPeakType > &calibrated_exp, std::vector< PeptideIdentification > &ref_ids, String trafo_file_name="")))
{
TOLERANCE_ABSOLUTE(0.000001)
MSExperiment<> calibrated_exp;
ptr->setParameters(param);
ptr->calibrateMapGlobally(exp,calibrated_exp,pep_ids);
TEST_REAL_SIMILAR(calibrated_exp[0][14].getMZ(),1296.68476942)
TEST_REAL_SIMILAR(calibrated_exp[1][40].getMZ(),1296.68476942)
TEST_REAL_SIMILAR(calibrated_exp[0][77].getMZ(),2465.19833942)
TEST_REAL_SIMILAR(calibrated_exp[1][90].getMZ(),2465.19833942)
}
END_SECTION
FeatureMap<> f_map;
FeatureXMLFile f_file;
f_file.load(OPENMS_GET_TEST_DATA_PATH("InternalCalibration_annotated.featureXML"),f_map);
START_SECTION((void calibrateMapGlobally(const FeatureMap<> &feature_map, FeatureMap<> &calibrated_feature_map, String trafo_file_name="")))
{
FeatureMap<> calibrated_f_map;
ptr->calibrateMapGlobally(f_map,calibrated_f_map);
TEST_REAL_SIMILAR(calibrated_f_map[0].getMZ(),687.841430243171)
TEST_REAL_SIMILAR(calibrated_f_map[1].getMZ(),720.005082366204)
TEST_REAL_SIMILAR(calibrated_f_map[2].getMZ(),927.493444113771)
TEST_REAL_SIMILAR(calibrated_f_map[3].getMZ(),1052.06529617992)
TEST_REAL_SIMILAR(calibrated_f_map[4].getMZ(),1224.59976809287)
TEST_REAL_SIMILAR(calibrated_f_map[5].getMZ(),998.486309862771)
}
END_SECTION
id_file.load(OPENMS_GET_TEST_DATA_PATH("InternalCalibration_2.idXML"),prot_ids,pep_ids);
START_SECTION((void calibrateMapGlobally(const FeatureMap<> &feature_map, FeatureMap<> &calibrated_feature_map, std::vector< PeptideIdentification > &ref_ids, String trafo_file_name="")))
{
FeatureMap<> calibrated_f_map;
ptr->calibrateMapGlobally(f_map,calibrated_f_map,pep_ids);
TEST_REAL_SIMILAR(calibrated_f_map[0].getMZ(),687.841430243171)
TEST_REAL_SIMILAR(calibrated_f_map[1].getMZ(),720.005082366204)
TEST_REAL_SIMILAR(calibrated_f_map[2].getMZ(),927.493444113771)
TEST_REAL_SIMILAR(calibrated_f_map[3].getMZ(),1052.06529617992)
TEST_REAL_SIMILAR(calibrated_f_map[4].getMZ(),1224.59976809287)
TEST_REAL_SIMILAR(calibrated_f_map[5].getMZ(),998.486309862771)
}
END_SECTION
START_SECTION((template < typename InputPeakType > void calibrateMapList(std::vector< MSExperiment< InputPeakType > > &exp_list, std::vector< MSExperiment< InputPeakType > > &calibrated_exp_list, std::vector< DoubleReal > &ref_masses, std::vector< DoubleReal > &detected_background_masses)))
{
NOT_TESTABLE // not yet existing
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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