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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 <iostream>
#include <OpenMS/ANALYSIS/ID/PILISModel.h>
#include <OpenMS/FORMAT/DTAFile.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
///////////////////////////
START_TEST(PILISModel_test.C, "$Id: PILISModel_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace std;
PILISModel* ptr = 0;
PILISModel* nullPointer = 0;
const AASequence peptide("DFPIANGER");
START_SECTION(PILISModel())
ptr = new PILISModel();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PILISModel())
delete ptr;
END_SECTION
ptr = new PILISModel();
START_SECTION(PILISModel(const PILISModel& model))
PILISModel copy(*ptr);
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(PILISModel& operator = (const PILISModel& mode))
PILISModel copy;
copy = *ptr;
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(void writeGraphMLFile(const String& filename))
NOT_TESTABLE // will be tested in the next section, to avoid time consuming instantiation
END_SECTION
START_SECTION(void writeToFile(const String& filename))
String filename;
NEW_TMP_FILE(filename)
PILISModel model;
Param p(model.getParameters());
p.setValue("model_depth", 2);
p.setValue("visible_model_depth", 3);
model.setParameters(p);
model.init(true);
model.writeToFile(filename);
String graphml_filename;
NEW_TMP_FILE(graphml_filename)
model.writeGraphMLFile(graphml_filename);
//TEST_FILE_SIMILAR(graphml_filename, OPENMS_GET_TEST_DATA_PATH("PILISModel_test.graphML"))
PILISModel model2;
model2.readFromFile(filename);
TEST_EQUAL(model.getParameters() == model2.getParameters(), true)
//model.getParameters().store("p.param");
//model2.getParameters().store("p2.param");
RichPeakSpectrum spec, spec2;
model.getSpectrum(spec, "DER", 1);
model2.getSpectrum(spec2, "DER", 1);
TOLERANCE_ABSOLUTE(0.1) // arithmetic with small numbers...
TEST_EQUAL(spec.size(), spec2.size())
for (Size i = 0; i != spec.size(); ++i)
{
TEST_REAL_SIMILAR(spec[i].getMZ(), spec2[i].getMZ())
TEST_REAL_SIMILAR(spec[i].getIntensity(), spec2[i].getIntensity())
}
END_SECTION
START_SECTION(void readFromFile(const String& filename))
NOT_TESTABLE // tested in previous section
END_SECTION
START_SECTION(void getSpectrum(RichPeakSpectrum& spec, const AASequence& peptide, UInt charge))
RichPeakSpectrum spec;
PILISModel model;
model.init(true);
model.getSpectrum(spec, "DER", 1);
TEST_EQUAL(spec.size(), 18)
END_SECTION
START_SECTION(void train(const RichPeakSpectrum&, const AASequence& peptide, UInt charge))
RichPeakSpectrum spec1, spec2, spec3;
PILISModel model;
model.init(true);
model.getSpectrum(spec1, "DER", 1);
model.getSpectrum(spec2, "DEK", 1);
model.getSpectrum(spec3, "DQK", 1);
TEST_EQUAL(spec1.size(), 18);
TEST_EQUAL(spec2.size(), 19);
TEST_EQUAL(spec3.size(), 21);
model.train(spec1, "DER", 1);
model.train(spec2, "DEK", 1);
model.train(spec3, "DQK", 1);
// before calling evaluate the generated spectra should not change!
RichPeakSpectrum spec4, spec5, spec6;
model.getSpectrum(spec4, "DER", 1);
model.getSpectrum(spec5, "DEK", 1);
model.getSpectrum(spec6, "DQK", 1);
TEST_EQUAL(spec1.size(), spec4.size())
TEST_EQUAL(spec2.size(), spec5.size())
TEST_EQUAL(spec3.size(), spec6.size())
for (Size i = 0; i != spec1.size(); ++i)
{
TEST_REAL_SIMILAR(spec1[i].getMZ(), spec4[i].getMZ())
TEST_REAL_SIMILAR(spec1[i].getIntensity(), spec4[i].getIntensity())
}
for (Size i = 0; i != spec2.size(); ++i)
{
TEST_REAL_SIMILAR(spec2[i].getMZ(), spec5[i].getMZ())
TEST_REAL_SIMILAR(spec2[i].getIntensity(), spec5[i].getIntensity())
}
for (Size i = 0; i != spec3.size(); ++i)
{
TEST_REAL_SIMILAR(spec3[i].getMZ(), spec6[i].getMZ())
TEST_REAL_SIMILAR(spec3[i].getIntensity(), spec6[i].getIntensity())
}
model.evaluate();
RichPeakSpectrum spec;
model.getSpectrum(spec, "DER", 1);
/*
for (Size i = 0; i != spec.size(); ++i)
{
cout << i << " " << spec[i].getMZ() << " " << spec[i].getIntensity() << " " << spec[i].getMetaValue("IonName") << endl;
}
for (Size i = 0; i != spec1.size(); ++i)
{
cout << i << " " << spec1[i].getMZ() << " " << spec1[i].getIntensity() << " " << spec1[i].getMetaValue("IonName") << endl;
}
*/
TEST_NOT_EQUAL(spec == spec1, true)
END_SECTION
START_SECTION(void evaluate())
NOT_TESTABLE // tested above
END_SECTION
START_SECTION((void init(bool generate_models=true)))
NOT_TESTABLE // tested implicetely above
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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