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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.
//
// --------------------------------------------------------------------------
// $Maintainer: Alexandra Zerck$
// $Authors: Alexandra Zerck $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelectionPreprocessing.h>
#include <OpenMS/ANALYSIS/TARGETED/PrecursorIonSelection.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(PrecursorIonSelection, "$Id: PrecursorIonSelection_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
PrecursorIonSelection* ptr = 0;
PrecursorIonSelection* nullPointer = 0;
START_SECTION(PrecursorIonSelection())
ptr = new PrecursorIonSelection();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PrecursorIonSelection())
delete ptr;
END_SECTION
ptr = new PrecursorIonSelection();
START_SECTION(PrecursorIonSelection(const PrecursorIonSelection& source))
ptr->setMaxScore(23.5);
PrecursorIonSelection copy(*ptr);
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
TEST_REAL_SIMILAR(copy.getMaxScore(), ptr->getMaxScore())
END_SECTION
START_SECTION(const DoubleReal& getMaxScore() const)
TEST_REAL_SIMILAR(ptr->getMaxScore(),23.5)
END_SECTION
START_SECTION(void setMaxScore(const DoubleReal& max_score))
ptr->setMaxScore(24.5);
TEST_REAL_SIMILAR(ptr->getMaxScore(),24.5)
END_SECTION
std::vector<ProteinIdentification> prot_ids;
std::vector<PeptideIdentification> pep_ids;
String document_id;
IdXMLFile file;
file.load(OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelection_ids.idXML"),prot_ids,pep_ids, document_id);
FeatureMap<> features,next_features;
FeatureXMLFile f_file;
f_file.load(OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelection_features.featureXML"),features);
START_SECTION(void sortByTotalScore(FeatureMap<>& features))
ptr->sortByTotalScore(features);
TEST_REAL_SIMILAR((DoubleReal)features[0].getMetaValue("msms_score"),49485.75)
END_SECTION
START_SECTION(void getNextPrecursors(FeatureMap<>& features,FeatureMap<>& next_features,UInt number))
ptr->getNextPrecursors(features,next_features,2);
TEST_EQUAL(next_features.size(),2)
TEST_REAL_SIMILAR((DoubleReal)next_features[0].getMetaValue("msms_score"),49485.75)
TEST_REAL_SIMILAR((DoubleReal)next_features[1].getMetaValue("msms_score"),47365)
END_SECTION
PrecursorIonSelectionPreprocessing preprocessing;
Param param;
param.setValue("precursor_mass_tolerance",0.05);
param.setValue("precursor_mass_tolerance_unit","Da");
param.setValue("missed_cleavages",1);
param.setValue("preprocessed_db_path",OPENMS_GET_TEST_DATA_PATH(""));
preprocessing.setParameters(param);
preprocessing.dbPreprocessing(OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelection_db.fasta"),false);
Param param2;
param2.setValue("Preprocessing:precursor_mass_tolerance",0.05);
param2.setValue("Preprocessing:precursor_mass_tolerance_unit","Da");
param2.setValue("Preprocessing:missed_cleavages",1);
param2.setValue("max_iteration",10);
param2.setValue("type","IPS");
param2.setValue("MIPFormulation:thresholds:min_peptide_ids",2);
param2.setValue("MIPFormulation:thresholds:use_peptide_rule","true");
ptr->setParameters(param2);
next_features.clear(true);
START_SECTION(void rescore(FeatureMap<>& features,std::vector<PeptideIdentification>& new_pep_ids,std::vector<ProteinIdentification>& prot_ids,PrecursorIonSelectionPreprocessing& preprocessed_db, bool check_meta_values=true))
ptr->rescore(features,pep_ids,prot_ids,preprocessing,false);
ptr->getNextPrecursors(features,next_features,1);
TEST_REAL_SIMILAR(next_features[0].getMetaValue("msms_score"),46365.5)
END_SECTION
START_SECTION( void simulateRun(FeatureMap<>& features,std::vector<PeptideIdentification>& pep_ids,std::vector<ProteinIdentification>& prot_ids,PrecursorIonSelectionPreprocessing& preprocessed_db, String path,MSExperiment<> & experiment, String precursor_path=""))
ptr->reset();
features.clear(true);
f_file.load(OPENMS_GET_TEST_DATA_PATH("PrecursorIonSelection_features.featureXML"),features);
std::string tmp_filename;
NEW_TMP_FILE(tmp_filename);
MSExperiment<> exp;
ptr->simulateRun(features,pep_ids,prot_ids,preprocessing,tmp_filename,exp);
ptr->sortByTotalScore(features);
TEST_EQUAL(features[20].getMetaValue("shifted"),"both")
TEST_REAL_SIMILAR(features[20].getMetaValue("msms_score"),27574.40625)
END_SECTION
START_SECTION((const std::map<String,std::set<String> >& getPeptideProteinCounter()))
TEST_EQUAL(ptr->getPeptideProteinCounter().size(),1)
END_SECTION
START_SECTION((void reset()))
ptr->reset();
TEST_EQUAL(ptr->getPeptideProteinCounter().size(),0)
END_SECTION
START_SECTION(([PrecursorIonSelection::TotalScoreMore] bool operator()(Feature const &left, Feature const &right) const ))
{
Feature a,b;
a.setMetaValue("msms_score",200.0);
b.setMetaValue("msms_score",100.0);
TEST_EQUAL(PrecursorIonSelection::TotalScoreMore().operator ()(a,b), true)
TEST_EQUAL(PrecursorIonSelection::TotalScoreMore().operator ()(b,a), false)
TEST_EQUAL(PrecursorIonSelection::TotalScoreMore().operator ()(a,a), false)
}
END_SECTION
START_SECTION((void setLPSolver(LPWrapper::SOLVER solver)))
{
#if COINOR_SOLVER==1
ptr->setLPSolver(LPWrapper::SOLVER_COINOR);
TEST_EQUAL(ptr->getLPSolver(),LPWrapper::SOLVER_COINOR)
#endif
ptr->setLPSolver(LPWrapper::SOLVER_GLPK);
TEST_EQUAL(ptr->getLPSolver(),LPWrapper::SOLVER_GLPK)
}
END_SECTION
START_SECTION((LPWrapper::SOLVER getLPSolver()))
{
// was tested in previous section
NOT_TESTABLE
}
END_SECTION
START_SECTION((void getNextPrecursorsSeq(FeatureMap<> &features, FeatureMap<> &next_features, UInt number, DoubleReal &rt)))
{
NOT_TESTABLE
}
END_SECTION
START_SECTION((void getNextPrecursors(std::vector< Int > &solution_indices, std::vector< PSLPFormulation::IndexTriple > &variable_indices, std::set< Int > &measured_variables, FeatureMap<> &features, FeatureMap<> &new_features, UInt step_size, PSLPFormulation &ilp)))
{
NOT_TESTABLE
}
END_SECTION
START_SECTION(([PrecursorIonSelection::SeqTotalScoreMore] bool operator()(Feature const &left, Feature const &right) const ))
{
Feature a,b,c;
a.setRT(11.);
a.setMetaValue("msms_score",111.);
b.setRT(12.);
b.setMetaValue("msms_score",112.);
c.setRT(11.);
c.setMetaValue("msms_score",113.);
TEST_EQUAL(PrecursorIonSelection::SeqTotalScoreMore().operator()(a,b),true)
TEST_EQUAL(PrecursorIonSelection::SeqTotalScoreMore().operator()(a,c),false)
}
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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