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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 "OpenSwathTestHelper.h"
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgScoring.h>
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>
///////////////////////////
using namespace OpenMS;
START_TEST(EmgScoring, "$Id: EmgScoring_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
EmgScoring* ptr = 0;
EmgScoring* nullPointer = 0;
START_SECTION(EmgScoring())
{
ptr = new EmgScoring();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~EmgScoring())
{
delete ptr;
}
END_SECTION
START_SECTION(Param getDefaults())
{
EmgScoring emgscore;
Param p = emgscore.getDefaults();
TEST_NOT_EQUAL(&p, nullPointer)
}
END_SECTION
START_SECTION(void setFitterParam(Param param))
{
EmgScoring emgscore;
Param p = emgscore.getDefaults();
TEST_NOT_EQUAL(&p, nullPointer)
emgscore.setFitterParam(p);
}
END_SECTION
START_SECTION(( template < typename SpectrumType, class TransitionT > double calcElutionFitScore(MRMFeature &mrmfeature, MRMTransitionGroup< SpectrumType, TransitionT > &transition_group)))
{
// test a set of feature (belonging to the same peptide)
double elution_model_fit_score;
EmgScoring emgscore;
MRMFeature feature = OpenSWATH_Test::createMockFeature();
OpenSWATH_Test::MRMTransitionGroupType transition_group = OpenSWATH_Test::createMockTransitionGroup();
elution_model_fit_score = emgscore.calcElutionFitScore(feature, transition_group);
TEST_REAL_SIMILAR(elution_model_fit_score, 0.924365639)
}
END_SECTION
START_SECTION( double elutionModelFit(ConvexHull2D::PointArrayType current_section, bool smooth_data) )
{
// test a single feature
double elution_model_fit_score;
EmgScoring emgscore;
MRMFeature feature = OpenSWATH_Test::createMockFeature();
Feature f = feature.getFeature("tr1");
elution_model_fit_score = emgscore.elutionModelFit(f.getConvexHulls()[0].getHullPoints() , false);
TEST_REAL_SIMILAR(elution_model_fit_score, 0.981013417243958)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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