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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/ANALYSIS/OPENSWATH/OpenSwathHelper.h>
#include <boost/assign/std/vector.hpp>
#include <boost/assign/list_of.hpp>
///////////////////////////
START_TEST(OpenSwathHelper, "$Id: OpenSwathHelper_test.C 11338 2013-06-05 20:48:48Z hroest $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace std;
using namespace OpenMS;
using namespace OpenSwath;
OpenSwathHelper* ptr = 0;
OpenSwathHelper* nullPointer = 0;
START_SECTION(OpenSwathHelper())
{
ptr = new OpenSwathHelper();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~OpenSwathHelper())
{
delete ptr;
}
END_SECTION
START_SECTION(static void selectSwathTransitions(const OpenMS::TargetedExperiment &targeted_exp, OpenMS::TargetedExperiment &transition_exp_used, double min_upper_edge_dist, double lower, double upper))
{
TargetedExperiment exp1;
TargetedExperiment exp2;
ReactionMonitoringTransition tr1;
ReactionMonitoringTransition tr2;
ReactionMonitoringTransition tr3;
tr1.setPrecursorMZ(100.0);
tr2.setPrecursorMZ(200.0);
tr3.setPrecursorMZ(300.0);
std::vector<ReactionMonitoringTransition> transitions;
transitions.push_back(tr1);
transitions.push_back(tr2);
transitions.push_back(tr3);
exp1.setTransitions(transitions);
// select all transitions between 200 and 500
OpenSwathHelper::selectSwathTransitions(exp1, exp2, 1.0, 199.9, 500);
TEST_EQUAL(exp2.getTransitions().size(), 2)
}
END_SECTION
START_SECTION(static void selectSwathTransitions(const OpenSwath::LightTargetedExperiment &targeted_exp, OpenSwath::LightTargetedExperiment &transition_exp_used, double min_upper_edge_dist, double lower, double upper))
{
LightTargetedExperiment exp1;
LightTargetedExperiment exp2;
LightTransition tr1;
LightTransition tr2;
LightTransition tr3;
tr1.precursor_mz = 100.0;
tr2.precursor_mz = 200.0;
tr3.precursor_mz = 300.0;
std::vector<LightTransition> transitions;
transitions.push_back(tr1);
transitions.push_back(tr2);
transitions.push_back(tr3);
exp1.transitions = transitions;
// select all transitions between 200 and 500
OpenSwathHelper::selectSwathTransitions(exp1, exp2, 1.0, 199.9, 500);
TEST_EQUAL(exp2.getTransitions().size(), 2)
}
END_SECTION
START_SECTION( (template < class TargetedExperimentT > static bool checkSwathMapAndSelectTransitions(const OpenMS::MSExperiment< Peak1D > &exp, const TargetedExperimentT &targeted_exp, TargetedExperimentT &transition_exp_used, double min_upper_edge_dist)))
{
// tested above already
NOT_TESTABLE
}
END_SECTION
START_SECTION(static void checkSwathMap(const OpenMS::MSExperiment< Peak1D > &swath_map, double &lower, double &upper))
{
OpenMS::MSExperiment<Peak1D> swath_map;
OpenMS::MSSpectrum<Peak1D> spectrum;
OpenMS::Precursor prec;
std::vector<Precursor> precursors;
prec.setIsolationWindowLowerOffset(200);
prec.setIsolationWindowUpperOffset(300);
precursors.push_back(prec);
spectrum.setPrecursors(precursors);
swath_map.addSpectrum(spectrum);
double lower, upper;
OpenSwathHelper::checkSwathMap(swath_map, lower, upper);
TEST_REAL_SIMILAR(lower, 200);
TEST_REAL_SIMILAR(upper, 300);
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
