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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche$
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/SIMULATION/DetectabilitySimulation.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(DetectabilitySimulation, "$Id: DetectabilitySimulation_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
DetectabilitySimulation* ptr = 0;
DetectabilitySimulation* nullPointer = 0;
START_SECTION(DetectabilitySimulation())
{
ptr = new DetectabilitySimulation();
TEST_NOT_EQUAL(ptr, nullPointer)
}
END_SECTION
START_SECTION(~DetectabilitySimulation())
{
delete ptr;
}
END_SECTION
START_SECTION((DetectabilitySimulation(const DetectabilitySimulation &source)))
{
DetectabilitySimulation source;
Param p = source.getParameters();
p.setValue("min_detect",0.0);
source.setParameters(p);
DetectabilitySimulation target(source);
TEST_EQUAL(source.getParameters(), target.getParameters())
}
END_SECTION
START_SECTION((DetectabilitySimulation& operator=(const DetectabilitySimulation &source)))
{
DetectabilitySimulation detect_sim1;
DetectabilitySimulation detect_sim2(detect_sim1);
Param p = detect_sim1.getParameters();
p.setValue("min_detect", 0.0);
detect_sim1.setParameters(p);
TEST_NOT_EQUAL(detect_sim1.getParameters(),detect_sim2.getParameters());
detect_sim2 = detect_sim1;
TEST_EQUAL(detect_sim2.getParameters(),detect_sim2.getParameters());
}
END_SECTION
START_SECTION((void filterDetectability(FeatureMapSim & features)))
{
// test no detect
DetectabilitySimulation detect_off;
Param p = detect_off.getParameters();
p.setValue("dt_simulation_on","false");
p.setValue("min_detect", 0.9);
detect_off.setParameters(p);
FeatureMapSim no_detect_features;
StringList peps = StringList::create("TVQMENQFVAFVDK,ACHKKKKHHACAC,AAAAHTKLRTTIPPEFG,RYCNHKTUIKL");
for (StringList::const_iterator it=peps.begin(); it!=peps.end(); ++it)
{
Feature f;
PeptideIdentification pep_id;
pep_id.insertHit(PeptideHit(1.0, 1, 1, *it));
f.getPeptideIdentifications().push_back(pep_id);
f.setIntensity(10);
no_detect_features.push_back(f);
}
detect_off.filterDetectability(no_detect_features);
TEST_EQUAL(no_detect_features.size(), 4)
for(Size i = 0 ; i < no_detect_features.size() ; ++i)
{
TEST_EQUAL(no_detect_features[i].getMetaValue("detectability"), 1.0)
}
// test svm
DetectabilitySimulation detect_svm;
Param svm_params = detect_svm.getParameters();
svm_params.setValue("dt_simulation_on","true");
svm_params.setValue("min_detect", 0.4);
svm_params.setValue("dt_model_file",OPENMS_GET_TEST_DATA_PATH("DetectabilitySimulation.svm"));
detect_svm.setParameters(svm_params);
FeatureMapSim svm_features;
for (StringList::const_iterator it=peps.begin(); it!=peps.end(); ++it)
{
Feature f;
PeptideIdentification pep_id;
pep_id.insertHit(PeptideHit(1.0, 1, 1, *it));
f.getPeptideIdentifications().push_back(pep_id);
f.setIntensity(10);
svm_features.push_back(f);
}
detect_svm.filterDetectability(svm_features);
TEST_EQUAL(svm_features.size(), 2)
TEST_EQUAL(svm_features[0].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "TVQMENQFVAFVDK")
TEST_REAL_SIMILAR(svm_features[0].getMetaValue("detectability"), 0.869237485950867)
TEST_EQUAL(svm_features[1].getPeptideIdentifications()[0].getHits()[0].getSequence().toString(), "AAAAHTKLRTTIPPEFG")
TEST_REAL_SIMILAR(svm_features[1].getMetaValue("detectability"), 0.723545391996237)
/*
for(FeatureMapSim::const_iterator it = svm_features.begin() ; it != svm_features.end();
++it)
{
std::cout << (*it).getPeptideIdentifications()[0].getHits()[0].getSequence().toString() << " " << (*it).getMetaValue("detectibility") << std::endl;
}
*/
}
END_SECTION
START_SECTION((void predictDetectabilities(std::vector<String>& peptides_vector,std::vector<DoubleReal>& labels, std::vector<DoubleReal>& detectabilities)))
{
// this method is called by "filterDetectability" so we already test it
NOT_TESTABLE
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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