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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche$
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/QUANTITATION/ItraqFourPlexQuantitationMethod.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(ItraqFourPlexQuantitationMethod, "$Id: ItraqFourPlexQuantitationMethod_test.C 11266 2013-05-21 08:12:56Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
ItraqFourPlexQuantitationMethod* ptr = 0;
ItraqFourPlexQuantitationMethod* null_ptr = 0;
START_SECTION(ItraqFourPlexQuantitationMethod())
{
ptr = new ItraqFourPlexQuantitationMethod();
TEST_NOT_EQUAL(ptr, null_ptr)
}
END_SECTION
START_SECTION(~ItraqFourPlexQuantitationMethod())
{
delete ptr;
}
END_SECTION
START_SECTION((const String& getName() const ))
{
ItraqFourPlexQuantitationMethod quant_meth;
TEST_STRING_EQUAL(quant_meth.getName(), "itraq4plex")
}
END_SECTION
START_SECTION((ItraqFourPlexQuantitationMethod(const ItraqFourPlexQuantitationMethod &other)))
{
ItraqFourPlexQuantitationMethod qm;
Param p = qm.getParameters();
p.setValue("channel_114_description", "new_description");
p.setValue("reference_channel", 116);
qm.setParameters(p);
ItraqFourPlexQuantitationMethod qm2(qm);
IsobaricQuantitationMethod::IsobaricChannelList channel_list = qm2.getChannelInformation();
TEST_STRING_EQUAL(channel_list[0].description, "new_description")
TEST_EQUAL(qm2.getReferenceChannel(), 2)
}
END_SECTION
START_SECTION((ItraqFourPlexQuantitationMethod& operator=(const ItraqFourPlexQuantitationMethod &rhs)))
{
ItraqFourPlexQuantitationMethod qm;
Param p = qm.getParameters();
p.setValue("channel_114_description", "new_description");
p.setValue("reference_channel", 116);
qm.setParameters(p);
ItraqFourPlexQuantitationMethod qm2;
qm2 = qm;
IsobaricQuantitationMethod::IsobaricChannelList channel_list = qm2.getChannelInformation();
TEST_STRING_EQUAL(channel_list[0].description, "new_description")
TEST_EQUAL(qm2.getReferenceChannel(), 2)
}
END_SECTION
START_SECTION((const IsobaricChannelList& getChannelInformation() const ))
{
ItraqFourPlexQuantitationMethod quant_meth;
IsobaricQuantitationMethod::IsobaricChannelList channel_list = quant_meth.getChannelInformation();
TEST_EQUAL(channel_list.size(), 4)
ABORT_IF(channel_list.size() != 4)
// descriptions are empty by default
TEST_STRING_EQUAL(channel_list[0].description, "")
TEST_STRING_EQUAL(channel_list[1].description, "")
TEST_STRING_EQUAL(channel_list[2].description, "")
TEST_STRING_EQUAL(channel_list[3].description, "")
// check masses&co
TEST_EQUAL(channel_list[0].name, 114)
TEST_EQUAL(channel_list[0].id, 0)
TEST_EQUAL(channel_list[0].center, 114.1112)
TEST_EQUAL(channel_list[1].name, 115)
TEST_EQUAL(channel_list[1].id, 1)
TEST_EQUAL(channel_list[1].center, 115.1082)
TEST_EQUAL(channel_list[2].name, 116)
TEST_EQUAL(channel_list[2].id, 2)
TEST_EQUAL(channel_list[2].center, 116.1116)
TEST_EQUAL(channel_list[3].name, 117)
TEST_EQUAL(channel_list[3].id, 3)
TEST_EQUAL(channel_list[3].center, 117.1149)
}
END_SECTION
START_SECTION((Size getNumberOfChannels() const ))
{
ItraqFourPlexQuantitationMethod quant_meth;
TEST_EQUAL(quant_meth.getNumberOfChannels(), 4)
}
END_SECTION
START_SECTION((virtual Matrix<double> getIsotopeCorrectionMatrix() const ))
{
ItraqFourPlexQuantitationMethod quant_meth;
// we only check the default matrix here
Matrix<double> m = quant_meth.getIsotopeCorrectionMatrix();
TEST_EQUAL(m.rows(), 4)
TEST_EQUAL(m.cols(), 4)
ABORT_IF(m.rows() != 4)
ABORT_IF(m.cols() != 4)
/**
0.929 0.02 0 0
0.059 0.923 0.03 0.001
0.002 0.056 0.924 0.04
0 0.001 0.045 0.923
*/
double real_m[4][4] = {{0.929, 0.02, 0, 0},
{0.059, 0.923, 0.03, 0.001},
{0.002, 0.056, 0.924, 0.04},
{0, 0.001, 0.045, 0.923}};
for(Matrix<double>::SizeType i = 0; i < m.rows(); ++i)
{
for(Matrix<double>::SizeType j = 0; j < m.cols(); ++j)
{
TEST_REAL_SIMILAR(m(i,j), real_m[i][j])
}
}
}
END_SECTION
START_SECTION((virtual Size getReferenceChannel() const ))
{
ItraqFourPlexQuantitationMethod quant_meth;
TEST_EQUAL(quant_meth.getReferenceChannel(), 0)
Param p;
p.setValue("reference_channel",115);
quant_meth.setParameters(p);
TEST_EQUAL(quant_meth.getReferenceChannel(), 1)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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