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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: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/ID/PILISIdentification.h>
#include <OpenMS/FORMAT/DTAFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
///////////////////////////
START_TEST(PILISIdentification, "$Id: PILISIdentification_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace std;
PILISIdentification* ptr = 0;
PILISIdentification* nullPointer = 0;
RichPeakSpectrum spec;
DTAFile().load(OPENMS_GET_TEST_DATA_PATH("PILISSequenceDB_DFPIANGER_1.dta"), spec);
spec.setMSLevel(2);
START_SECTION(PILISIdentification())
ptr = new PILISIdentification();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PILISIdentification())
delete ptr;
END_SECTION
ptr = new PILISIdentification();
START_SECTION(PILISIdentification(const PILISIdentification& source))
PILISIdentification copy(*ptr);
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(PILISIdentification& operator = (const PILISIdentification& source))
PILISIdentification copy;
copy = *ptr;
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(void setModel(PILISModel* hmm_model))
PILISModel* model = new PILISModel();
model->readFromFile("PILIS/PILIS_default_model.dat");
ptr->setModel(model);
END_SECTION
START_SECTION(void getIdentification(const std::map<String, UInt>& candidates, PeptideIdentification& id, const RichPeakSpectrum& spectrum))
map<String, UInt> candidates;
candidates["DDFPIVIVGNKADIENQR"] = 2;
candidates["DFPIANGER"] = 1;
candidates["DFPIADGER"] = 1;
PeptideIdentification id;
ptr->getIdentification(candidates, id, spec);
TEST_EQUAL(id.getHits().size(), 3)
TEST_EQUAL(id.getHits().begin()->getSequence(), "DFPIANGER")
END_SECTION
START_SECTION(void getIdentifications(const std::vector<std::map<String, UInt> >& candidates, std::vector<PeptideIdentification>& ids, const RichPeakMap& exp))
map<String, UInt> cand;
cand["DDFPIVIVGNKADIENQR"] = 2;
cand["DFPIANGER"] = 1;
cand["DFPIADGER"] = 1;
vector<map<String, UInt> > candidates;
candidates.push_back(cand);
vector<PeptideIdentification> ids;
RichPeakMap map;
map.push_back(spec);
ptr->getIdentifications(candidates, ids, map);
TEST_EQUAL(ids.size(), map.size())
TEST_EQUAL(ids.begin()->getHits().size(), 3)
TEST_EQUAL(ids.begin()->getHits().begin()->getSequence(), "DFPIANGER")
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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