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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: Sandro Andreotti $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/DENOVO/CompNovoIdentification.h>
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/CONCEPT/Constants.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(CompNovoIdentification, "$Id: CompNovoIdentification_test.C 11338 2013-06-05 20:48:48Z hroest $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
CompNovoIdentification* ptr = 0;
CompNovoIdentification* nullPointer = 0;
START_SECTION(CompNovoIdentification())
{
ptr = new CompNovoIdentification();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~CompNovoIdentification())
{
delete ptr;
}
END_SECTION
START_SECTION((CompNovoIdentification(const CompNovoIdentification& source)))
CompNovoIdentification cni;
Param p(cni.getParameters());
p.setValue("fragment_mass_tolerance", 0.5);
cni.setParameters(p);
TEST_EQUAL(CompNovoIdentification(cni).getParameters() == p, true)
END_SECTION
START_SECTION((void getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp)))
{
TheoreticalSpectrumGenerator tsg;
Param tsg_param(tsg.getParameters());
tsg_param.setValue("add_losses", "true");
tsg_param.setValue("add_isotopes", "true");
tsg.setParameters(tsg_param);
RichPeakSpectrum rspec;
tsg.getSpectrum(rspec, AASequence("DFPIANGER"));
PeakSpectrum spec;
for (Size i = 0; i != rspec.size(); ++i)
{
Peak1D p;
p.setMZ(rspec[i].getMZ());
p.setIntensity(rspec[i].getIntensity());
spec.push_back(p);
}
RichPeakSpectrum rspec_ETD;
tsg.addPeaks(rspec_ETD, AASequence("DFPIANGER"), Residue::ZIon, 1);
tsg.addPrecursorPeaks(rspec_ETD, AASequence("DFPIANGER"), 2);
PeakSpectrum spec_ETD;
for (Size i = 0; i != rspec_ETD.size(); ++i)
{
Peak1D p;
p.setMZ(rspec_ETD[i].getMZ());
p.setIntensity(rspec_ETD[i].getIntensity());
spec_ETD.push_back(p);
}
Precursor prec;
prec.setMZ((AASequence("DFPLANGER").getMonoWeight() + 2.0 * Constants::PROTON_MASS_U) / 2.0);
prec.setCharge(2);
vector<Precursor> precs;
precs.push_back(prec);
spec.setPrecursors(precs);
spec_ETD.setPrecursors(precs);
PeakMap exp;
exp.addSpectrum(spec);
exp.addSpectrum(spec_ETD);
vector<PeptideIdentification> ids;
CompNovoIdentification cni;
Param cni_param(cni.getParameters());
cni.setParameters(cni_param);
cni.getIdentifications(ids, exp);
TEST_EQUAL(ids.size(), 1)
TEST_EQUAL(ids.begin()->getHits().size() > 0, true)
TEST_EQUAL(ids.begin()->getHits().begin()->getSequence() == AASequence("DFPLANGER"), true)
}
END_SECTION
START_SECTION((void getIdentification(PeptideIdentification &id, const PeakSpectrum &CID_spec, const PeakSpectrum &ETD_spec)))
{
TheoreticalSpectrumGenerator tsg;
Param tsg_param(tsg.getParameters());
tsg_param.setValue("add_losses", "true");
tsg_param.setValue("add_isotopes", "true");
tsg.setParameters(tsg_param);
RichPeakSpectrum rspec;
tsg.getSpectrum(rspec, AASequence("DFPIANGER"));
PeakSpectrum spec;
for (Size i = 0; i != rspec.size(); ++i)
{
Peak1D p;
p.setMZ(rspec[i].getMZ());
p.setIntensity(rspec[i].getIntensity());
spec.push_back(p);
}
RichPeakSpectrum rspec_ETD;
tsg.addPeaks(rspec_ETD, AASequence("DFPIANGER"), Residue::ZIon, 1);
tsg.addPrecursorPeaks(rspec_ETD, AASequence("DFPIANGER"), 2);
PeakSpectrum spec_ETD;
for (Size i = 0; i != rspec_ETD.size(); ++i)
{
Peak1D p;
p.setMZ(rspec_ETD[i].getMZ());
p.setIntensity(rspec_ETD[i].getIntensity());
spec_ETD.push_back(p);
}
Precursor prec;
prec.setMZ((AASequence("DFPLANGER").getMonoWeight() + 2.0 * Constants::PROTON_MASS_U) / 2.0);
prec.setCharge(2);
vector<Precursor> precs;
precs.push_back(prec);
spec.setPrecursors(precs);
spec_ETD.setPrecursors(precs);
PeptideIdentification id;
CompNovoIdentification cni;
Param cni_param(cni.getParameters());
cni.setParameters(cni_param);
cni.getIdentification(id, spec, spec_ETD);
TEST_EQUAL(id.getHits().size() > 0, true)
TEST_EQUAL(id.getHits().begin()->getSequence() == AASequence("DFPLANGER"), true)
}
END_SECTION
START_SECTION((CompNovoIdentification& operator=(const CompNovoIdentification &source)))
{
CompNovoIdentification cni;
Param p(cni.getParameters());
p.setValue("fragment_mass_tolerance", 0.5);
cni.setParameters(p);
CompNovoIdentification cni2;
cni2 = cni;
TEST_EQUAL(cni2.getParameters() == p, true)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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