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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/CHEMISTRY/MASSDECOMPOSITION/IMS/IntegerMassDecomposer.h>
///////////////////////////
#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/CHEMISTRY/ResidueDB.h>
#include <OpenMS/CHEMISTRY/Residue.h>
using namespace OpenMS;
using namespace ims;
using namespace std;
Weights createWeights()
{
Map<char, DoubleReal> aa_to_weight;
set<const Residue*> residues = ResidueDB::getInstance()->getResidues("Natural19WithoutI");
for (set<const Residue*>::const_iterator it = residues.begin(); it != residues.end(); ++it)
{
aa_to_weight[(*it)->getOneLetterCode()[0]] = (*it)->getMonoWeight(Residue::Internal);
}
// init mass decomposer
IMSAlphabet alphabet;
for (Map<char, DoubleReal>::ConstIterator it = aa_to_weight.begin(); it != aa_to_weight.end(); ++it)
{
alphabet.push_back(String(it->first), it->second);
}
// initializes weights
Weights weights(alphabet.getMasses(), 0.01);
// optimize alphabet by dividing by gcd
weights.divideByGCD();
return weights;
}
START_TEST(IntegerMassDecomposer, "$Id: IntegerMassDecomposer_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
IntegerMassDecomposer<>* ptr = 0;
IntegerMassDecomposer<>* null_ptr = 0;
START_SECTION((IntegerMassDecomposer(const Weights &alphabet_)))
{
ptr = new IntegerMassDecomposer<>(createWeights());
TEST_NOT_EQUAL(ptr, null_ptr)
}
END_SECTION
START_SECTION(~IntegerMassDecomposer())
{
delete ptr;
}
END_SECTION
START_SECTION((bool exist(value_type mass)))
{
// TODO
}
END_SECTION
START_SECTION((IntegerMassDecomposer< ValueType, DecompositionValueType >::decomposition_type getDecomposition(value_type mass)))
{
// TODO
}
END_SECTION
START_SECTION((IntegerMassDecomposer< ValueType, DecompositionValueType >::decompositions_type getAllDecompositions(value_type mass)))
{
// TODO
}
END_SECTION
START_SECTION((IntegerMassDecomposer< ValueType, DecompositionValueType >::decomposition_value_type getNumberOfDecompositions(value_type mass)))
{
// TODO
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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