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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: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SeedListGenerator.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
using namespace OpenMS;
using namespace std;
///////////////////////////
START_TEST(SeedListGenerator, "$Id: SeedListGenerator_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
SeedListGenerator* slg_ptr = 0;
SeedListGenerator* slg_nullPointer = 0;
START_SECTION((SeedListGenerator()))
{
slg_ptr = new SeedListGenerator();
TEST_NOT_EQUAL(slg_ptr, slg_nullPointer);
}
END_SECTION
START_SECTION(([EXTRA] ~SeedListGenerator()))
{
delete slg_ptr;
}
END_SECTION
START_SECTION((void generateSeedList(const MSExperiment<>& experiment, SeedList& seeds)))
{
MSExperiment<> experiment;
String path = OPENMS_GET_TEST_DATA_PATH("PepXMLFile_test.mzML");
MzMLFile().load(path, experiment);
SeedListGenerator::SeedList seeds;
SeedListGenerator().generateSeedList(experiment, seeds);
TEST_EQUAL(seeds.size(), 9);
TEST_EQUAL(seeds[0], DPosition<2>(0.5927, 538.605));
TEST_EQUAL(seeds[1], DPosition<2>(0.5927, 637.885));
TEST_EQUAL(seeds[2], DPosition<2>(0.5927, 678.384));
// ...
TEST_EQUAL(seeds[8], DPosition<2>(3.7572, 512.784));
}
END_SECTION
START_SECTION((void generateSeedList(vector<PeptideIdentification>& peptides, SeedList& seeds, bool use_peptide_mass = false)))
{
vector<PeptideIdentification> peptides(3);
peptides[0].setMetaValue("RT", 1.1);
peptides[0].setMetaValue("MZ", 111.111);
peptides[1].setMetaValue("RT", 2.2);
peptides[1].setMetaValue("MZ", 222.222);
peptides[2].setMetaValue("RT", 3.3);
peptides[2].setMetaValue("MZ", 333.333);
SeedListGenerator::SeedList seeds;
SeedListGenerator().generateSeedList(peptides, seeds);
TEST_EQUAL(seeds.size(), 3);
TEST_EQUAL(seeds[0], DPosition<2>(1.1, 111.111));
TEST_EQUAL(seeds[1], DPosition<2>(2.2, 222.222));
TEST_EQUAL(seeds[2], DPosition<2>(3.3, 333.333));
PeptideHit hit;
hit.setSequence("TEST");
hit.setCharge(2);
peptides[0].insertHit(hit);
peptides.resize(1);
SeedListGenerator().generateSeedList(peptides, seeds, true);
TEST_EQUAL(seeds.size(), 1);
TEST_REAL_SIMILAR(seeds[0][1], 219.09755);
}
END_SECTION
START_SECTION((void generateSeedLists(const ConsensusMap& consensus, Map<UInt64, SeedList>& seed_lists)))
{
ConsensusMap consensus;
String path = OPENMS_GET_TEST_DATA_PATH("ConsensusXMLFile_1.consensusXML");
ConsensusXMLFile().load(path, consensus);
Map<UInt64, SeedListGenerator::SeedList> seed_lists;
SeedListGenerator().generateSeedLists(consensus, seed_lists);
TEST_EQUAL(seed_lists.size(), 2);
TEST_EQUAL(seed_lists[0].size(), 0);
TEST_EQUAL(seed_lists[1].size(), 2);
TEST_EQUAL(seed_lists[1][0], DPosition<2>(1273.27, 904.47));
TEST_EQUAL(seed_lists[1][1], DPosition<2>(1184.46, 953.368));
}
END_SECTION
START_SECTION((void convertSeedList(const SeedList& seeds, FeatureMap<>& features)))
{
SeedListGenerator::SeedList seeds(3);
seeds[0] = DPosition<2>(1.1, 111.111);
seeds[1] = DPosition<2>(2.2, 222.222);
seeds[2] = DPosition<2>(3.3, 333.333);
FeatureMap<> features;
SeedListGenerator().convertSeedList(seeds, features);
TEST_EQUAL(features.size(), 3);
TEST_EQUAL(features[0].getRT(), 1.1);
TEST_EQUAL(features[0].getMZ(), 111.111);
TEST_EQUAL(features[1].getRT(), 2.2);
TEST_EQUAL(features[1].getMZ(), 222.222);
TEST_EQUAL(features[2].getRT(), 3.3);
TEST_EQUAL(features[2].getMZ(), 333.333);
}
END_SECTION
START_SECTION((void convertSeedList(const FeatureMap<>& features, SeedList& seeds)))
{
FeatureMap<> features;
features.resize(3);
features[0].setRT(1.1);
features[0].setMZ(111.111);
features[1].setRT(2.2);
features[1].setMZ(222.222);
features[2].setRT(3.3);
features[2].setMZ(333.333);
SeedListGenerator::SeedList seeds;
SeedListGenerator().convertSeedList(features, seeds);
TEST_EQUAL(seeds.size(), 3);
TEST_EQUAL(seeds[0], DPosition<2>(1.1, 111.111));
TEST_EQUAL(seeds[1], DPosition<2>(2.2, 222.222));
TEST_EQUAL(seeds[2], DPosition<2>(3.3, 333.333));
}
END_SECTION
END_TEST
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