// -------------------------------------------------------------------------- // 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 /////////////////////////// #include #include #include 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& peptides, SeedList& seeds, bool use_peptide_mass = false))) { vector 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& seed_lists))) { ConsensusMap consensus; String path = OPENMS_GET_TEST_DATA_PATH("ConsensusXMLFile_1.consensusXML"); ConsensusXMLFile().load(path, consensus); Map 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