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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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
#include <OpenMS/FORMAT/TraMLFile.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/DataAccessHelper.h>
#include <OpenMS/ANALYSIS/OPENSWATH/DATAACCESS/SimpleOpenMSSpectraAccessFactory.h>
///////////////////////////
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
typedef std::map<String, MRMTransitionGroup< MSSpectrum <ChromatogramPeak>, OpenSwath::LightTransition > > TransitionGroupMapType;
START_TEST(MRMFeatureFinderScoring, "$Id: MRMFeatureFinderScoring_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
MRMFeatureFinderScoring* ptr = 0;
MRMFeatureFinderScoring* nullPointer = 0;
START_SECTION(MRMFeatureFinderScoring())
{
ptr = new MRMFeatureFinderScoring();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~MRMFeatureFinderScoring())
{
delete ptr;
}
END_SECTION
START_SECTION(void pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map))
{
MRMFeatureFinderScoring ff;
MRMFeature feature;
FeatureMap<> featureFile;
TransformationDescription trafo;
PeakMap swath_map;
TransitionGroupMapType transition_group_map;
MRMFeatureFinderScoring::MRMTransitionGroupType transition_group;
// Load the chromatograms (mzML) and the meta-information (TraML)
PeakMap exp;
OpenSwath::LightTargetedExperiment transitions;
MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("OpenSwath_generic_input.mzML"), exp);
{
TargetedExperiment transition_exp_;
TraMLFile().load(OPENMS_GET_TEST_DATA_PATH("OpenSwath_generic_input.TraML"), transition_exp_);
OpenSwathDataAccessHelper::convertTargetedExp(transition_exp_, transitions);
}
// Pick features in the experiment
#ifdef USE_SP_INTERFACE
OpenSwath::SpectrumAccessPtr swath_ptr = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(swath_map);
OpenSwath::SpectrumAccessPtr chromatogram_ptr = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp);
ff.pickExperiment(chromatogram_ptr, featureFile, transitions, trafo, swath_ptr, transition_group_map);
#else
ff.pickExperiment(exp, featureFile, transitions, trafo, swath_map, transition_group_map);
#endif
// Test the number of features found
TEST_EQUAL(transition_group_map.size(), 2)
///////////////////////////////////////////////////////////////////////////
//// Scores for the first group
transition_group = transition_group_map["tr_gr1"];
TEST_EQUAL(transition_group.size(), 2)
TEST_EQUAL(transition_group.getFeatures().size(), 1)
// Look closely at the feature we found in the first group
feature = transition_group.getFeatures()[0];
TOLERANCE_ABSOLUTE(0.1);
TEST_REAL_SIMILAR (feature.getRT(), 3119.092);
TEST_REAL_SIMILAR (feature.getIntensity(), 3574.23);
// feature attributes
TEST_REAL_SIMILAR(feature.getMetaValue("leftWidth" ), 3096.28);
TEST_REAL_SIMILAR(feature.getMetaValue("rightWidth"), 3147.68);
TEST_REAL_SIMILAR(feature.getMetaValue("total_xic"), 3680.16);
// feature scores
TEST_REAL_SIMILAR(feature.getMetaValue("var_xcorr_coelution"), 0);
TEST_REAL_SIMILAR(feature.getMetaValue("var_xcorr_shape"), 0.9981834605);
TEST_REAL_SIMILAR(feature.getMetaValue("var_library_rmsd"), 0.108663236);
TEST_REAL_SIMILAR(feature.getMetaValue("var_library_corr"), 1);
TEST_REAL_SIMILAR(feature.getMetaValue("var_elution_model_fit_score"), 0.9854);
TEST_REAL_SIMILAR(feature.getMetaValue("var_intensity_score"), 0.971);
TEST_REAL_SIMILAR(feature.getMetaValue("sn_ratio"), 86.0);
TEST_REAL_SIMILAR(feature.getMetaValue("var_log_sn_score"), 4.45439541136954);
TOLERANCE_RELATIVE(1.001);
TEST_REAL_SIMILAR(feature.getMetaValue("rt_score"), 3118.651968);
TOLERANCE_ABSOLUTE(0.1);
///////////////////////////////////////////////////////////////////////////
//// Scores for the second group
transition_group = transition_group_map["tr_gr2"];
TEST_EQUAL(transition_group.size(), 3)
TEST_EQUAL(transition_group.getFeatures().size(), 2)
TEST_EQUAL(featureFile.size(), 3)
// Look closely at the feature we found in the second group
feature = transition_group.getFeatures()[0];
TOLERANCE_ABSOLUTE(0.1);
TEST_REAL_SIMILAR(feature.getRT(), 3119.092);
TEST_REAL_SIMILAR(feature.getIntensity(), 1034.55);
// feature attributes
TEST_REAL_SIMILAR(feature.getMetaValue("leftWidth" ), 3099.7);
TEST_REAL_SIMILAR(feature.getMetaValue("rightWidth"), 3147.68);
TEST_REAL_SIMILAR(feature.getMetaValue("total_xic"), 1610.27);
// feature scores
TEST_REAL_SIMILAR(feature.getMetaValue("var_xcorr_coelution"), 2.265);
TEST_REAL_SIMILAR(feature.getMetaValue("var_xcorr_shape"), 0.7245);
TEST_REAL_SIMILAR(feature.getMetaValue("var_library_rmsd"), 0.43566);
TEST_REAL_SIMILAR(feature.getMetaValue("var_library_corr"), -0.784);
TEST_REAL_SIMILAR(feature.getMetaValue("var_elution_model_fit_score"), 0.902);
TEST_REAL_SIMILAR(feature.getMetaValue("var_intensity_score"), 0.642);
TEST_REAL_SIMILAR(feature.getMetaValue("sn_ratio"), 30.18);
TEST_REAL_SIMILAR(feature.getMetaValue("var_log_sn_score"), 3.40718216971789);
}
END_SECTION
START_SECTION(void mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window))
{
MRMFeatureFinderScoring ff;
MRMFeature feature;
FeatureMap<> featureFile;
TransformationDescription trafo;
PeakMap swath_map;
TransitionGroupMapType transition_group_map;
MRMFeatureFinderScoring::MRMTransitionGroupType transition_group;
// Load the chromatograms (mzML) and the meta-information (TraML)
PeakMap exp;
OpenSwath::LightTargetedExperiment transitions;
MzMLFile().load(OPENMS_GET_TEST_DATA_PATH("OpenSwath_generic_input.mzML"), exp);
{
TargetedExperiment transition_exp_;
TraMLFile().load(OPENMS_GET_TEST_DATA_PATH("OpenSwath_generic_input.TraML"), transition_exp_);
OpenSwathDataAccessHelper::convertTargetedExp(transition_exp_, transitions);
}
// Pick features in the experiment
#ifdef USE_SP_INTERFACE
OpenSwath::SpectrumAccessPtr chromatogram_ptr = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp);
ff.mapExperimentToTransitionList(chromatogram_ptr, transitions, transition_group_map, trafo, -1);
#else
ff.mapExperimentToTransitionList(exp, transitions, transition_group_map, trafo, -1);
#endif
// Test the number of features found
TEST_EQUAL(transition_group_map.size(), 2)
///////////////////////////////////////////////////////////////////////////
//// The first group
transition_group = transition_group_map["tr_gr1"];
TEST_EQUAL(transition_group.size(), 2)
TEST_EQUAL(transition_group.getTransitions().size(), 2)
TEST_EQUAL(transition_group.getChromatograms().size(), 2)
TEST_EQUAL(transition_group.hasChromatogram("tr1"), true)
TEST_EQUAL(transition_group.hasChromatogram("tr2"), true)
TEST_EQUAL(transition_group.getChromatogram("tr2").getNativeID(), "tr2")
TEST_EQUAL(transition_group.getTransition("tr2").getNativeID(), "tr2")
///////////////////////////////////////////////////////////////////////////
//// The second group
transition_group = transition_group_map["tr_gr2"];
TEST_EQUAL(transition_group.size(), 3)
TEST_EQUAL(transition_group.getTransitions().size(), 3)
TEST_EQUAL(transition_group.getChromatograms().size(), 3)
TEST_EQUAL(transition_group.hasChromatogram("tr3"), true)
TEST_EQUAL(transition_group.hasChromatogram("tr4"), true)
TEST_EQUAL(transition_group.hasChromatogram("tr5"), true)
TEST_EQUAL(transition_group.getChromatogram("tr5").getNativeID(), "tr5")
TEST_EQUAL(transition_group.getTransition("tr5").getNativeID(), "tr5")
}
END_SECTION
START_SECTION(void setStrictFlag(bool f))
NOT_TESTABLE
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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