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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/SpectrumAddition.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(SpectrumAddition, "$Id: SpectrumAddition_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
START_SECTION((static OpenSwath::SpectrumPtr addUpSpectra(std::vector< OpenSwath::SpectrumPtr > all_spectra, double sampling_rate, double filter_zeros)) )
{
OpenSwath::SpectrumPtr spec1(new OpenSwath::Spectrum());
OpenSwath::BinaryDataArrayPtr mass1(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity1(new OpenSwath::BinaryDataArray);
OpenSwath::SpectrumPtr spec2(new OpenSwath::Spectrum());
OpenSwath::BinaryDataArrayPtr mass2(new OpenSwath::BinaryDataArray);
OpenSwath::BinaryDataArrayPtr intensity2(new OpenSwath::BinaryDataArray);
static const double arr1[] = {
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
};
std::vector<double> intensity1_ (arr1, arr1 + sizeof(arr1) / sizeof(arr1[0]) );
intensity1->data = intensity1_;
static const double arr2[] = {
1, 3, 5, 7, 9, 11, 9, 7, 5, 3, 1
};
std::vector<double> intensity2_ (arr2, arr2 + sizeof(arr2) / sizeof(arr2[0]) );
intensity2->data = intensity2_;
static const double arr3[] = {
100, 101.5, 101.9, 102.0, 102.1, 102.11, 102.2, 102.25, 102.3, 102.4, 102.45
};
std::vector<double> mass3 (arr3, arr3 + sizeof(arr3) / sizeof(arr3[0]) );
mass1->data = mass3;
static const double arr4[] = {
100, 101.6, 101.95, 102.0, 102.05, 102.1, 102.12, 102.15, 102.2, 102.25, 102.30
};
std::vector<double> mass4 (arr4, arr4 + sizeof(arr4) / sizeof(arr4[0]) );
mass2->data = mass4;
spec1->setMZArray( mass1);
spec1->setIntensityArray(intensity1);
spec2->setMZArray( mass2);
spec2->setIntensityArray(intensity2);
std::vector<OpenSwath::SpectrumPtr> all_spectra;
//MRMFeatureFinderScoring ff;
OpenSwath::SpectrumPtr empty_result = SpectrumAddition::addUpSpectra(all_spectra, 0.1, false);
TEST_EQUAL(empty_result->getMZArray()->data.size(), 0);
all_spectra.push_back(spec1);
all_spectra.push_back(spec2);
OpenSwath::SpectrumPtr result = SpectrumAddition::addUpSpectra(all_spectra, 0.1, false);
TEST_EQUAL(result->getMZArray()->data.size(), 25);
OpenSwath::SpectrumPtr result_filtered = SpectrumAddition::addUpSpectra(all_spectra, 0.1, true);
TEST_EQUAL(result_filtered->getMZArray()->data.size(), 9);
TEST_REAL_SIMILAR(result_filtered->getMZArray()->data[0], 100.0);
TEST_REAL_SIMILAR(result_filtered->getIntensityArray()->data[0], 2);
TEST_REAL_SIMILAR(result_filtered->getMZArray()->data[3], 101.9);
TEST_REAL_SIMILAR(result_filtered->getIntensityArray()->data[3], 3 + 5/2.0); // 3 @ 101.9 and 5 @ 101.95
std::cout << " result size " << result->getMZArray()->data.size() << " and result m/z" << std::endl;
std::copy(result_filtered->getMZArray()->data.begin(), result_filtered->getMZArray()->data.end(),
std::ostream_iterator<double>(std::cout, " "));
std::cout << std::endl << "and result intensity " << std::endl;
std::copy(result_filtered->getIntensityArray()->data.begin(), result_filtered->getIntensityArray()->data.end(),
std::ostream_iterator<double>(std::cout, " "));
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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