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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: Chris Bielow $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <iostream>
#include <OpenMS/ANALYSIS/ID/IDMapper.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/ConsensusXMLFile.h>
///////////////////////////
using namespace OpenMS;
class IDMapper2 : public IDMapper
{
public:
DoubleReal getAbsoluteMZTolerance2_(const DoubleReal mz)
{
return getAbsoluteMZTolerance_(mz);
}
bool isMatch2_(const DoubleReal rt_distance, const DoubleReal mz_theoretical, const DoubleReal mz_observed)
{
return isMatch_(rt_distance, mz_theoretical, mz_observed);
}
};
START_TEST(IDMapper, "$Id: IDMapper_test.C 11338 2013-06-05 20:48:48Z hroest $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace std;
IDMapper* ptr = 0;
IDMapper* nullPointer = 0;
START_SECTION((IDMapper()))
ptr = new IDMapper();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION((~IDMapper()))
delete ptr;
END_SECTION
START_SECTION((IDMapper(const IDMapper& cp)))
{
IDMapper mapper;
Param p = mapper.getParameters();
p.setValue("rt_tolerance", 0.5);
p.setValue("mz_tolerance", 0.05);
p.setValue("mz_measure","ppm");
mapper.setParameters(p);
IDMapper m2(mapper);
TEST_EQUAL(m2.getParameters(), p);
}
END_SECTION
START_SECTION((IDMapper& operator = (const IDMapper& rhs)))
{
IDMapper mapper;
Param p = mapper.getParameters();
p.setValue("rt_tolerance", 0.5);
p.setValue("mz_tolerance", 0.05);
p.setValue("mz_measure", "ppm");
mapper.setParameters(p);
IDMapper m2=mapper;
TEST_EQUAL(m2.getParameters(), p);
}
END_SECTION
START_SECTION((template <typename PeakType> void annotate(MSExperiment< PeakType > &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids)))
{
//load id
vector<PeptideIdentification> identifications;
vector<ProteinIdentification> protein_identifications;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_1.idXML"), protein_identifications, identifications, document_id);
TEST_EQUAL(identifications.size(),3)
TEST_EQUAL(identifications[0].getHits().size(), 2)
TEST_EQUAL(identifications[1].getHits().size(), 1)
TEST_EQUAL(identifications[2].getHits().size(), 2)
TEST_EQUAL(protein_identifications.size(),1)
TEST_EQUAL(protein_identifications[0].getHits().size(), 2)
//create experiment
MSExperiment<> experiment;
MSSpectrum<> spectrum;
Precursor precursor;
precursor.setMZ(0);
spectrum.setRT(60);
experiment.addSpectrum(spectrum);
experiment[0].getPrecursors().push_back(precursor);
precursor.setMZ(20);
spectrum.setRT(181);
experiment.addSpectrum(spectrum);
experiment[1].getPrecursors().push_back(precursor);
precursor.setMZ(11);
spectrum.setRT(120.0001);
experiment.addSpectrum(spectrum);
experiment[2].getPrecursors().push_back(precursor);
//map
IDMapper mapper;
Param p = mapper.getParameters();
p.setValue("rt_tolerance", 0.5);
p.setValue("mz_tolerance", 0.05);
p.setValue("mz_measure","Da");
p.setValue("ignore_charge", "true");
mapper.setParameters(p);
mapper.annotate(experiment, identifications, protein_identifications);
//test
TEST_EQUAL(experiment.getProteinIdentifications().size(), 1)
TEST_EQUAL(experiment.getProteinIdentifications()[0].getHits().size(),2)
TEST_EQUAL(experiment.getProteinIdentifications()[0].getHits()[0].getAccession(),"ABCDE")
TEST_EQUAL(experiment.getProteinIdentifications()[0].getHits()[1].getAccession(),"FGHIJ")
//scan 1
TEST_EQUAL(experiment[0].getPeptideIdentifications().size(), 1)
TEST_EQUAL(experiment[0].getPeptideIdentifications()[0].getHits().size(), 2)
TEST_EQUAL(experiment[0].getPeptideIdentifications()[0].getHits()[0].getSequence(), "LHASGITVTEIPVTATNFK")
TEST_EQUAL(experiment[0].getPeptideIdentifications()[0].getHits()[1].getSequence(), "MRSLGYVAVISAVATDTDK")
//scan 2
TEST_EQUAL(experiment[1].getPeptideIdentifications().size(), 0)
//scan 3
TEST_EQUAL(experiment[2].getPeptideIdentifications().size(), 1)
TEST_EQUAL(experiment[2].getPeptideIdentifications()[0].getHits().size(), 1)
TEST_EQUAL(experiment[2].getPeptideIdentifications()[0].getHits()[0].getSequence(), "HSKLSAK")
}
END_SECTION
START_SECTION((template < typename FeatureType > void annotate(FeatureMap< FeatureType > &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false)))
{
//load id data
vector<PeptideIdentification> identifications;
vector<ProteinIdentification> protein_identifications;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_2.idXML"), protein_identifications, identifications, document_id);
//--------------------------------------------------------------------------------------
//TEST MAPPING TO CONVEX HULLS
FeatureMap<> fm;
FeatureXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_2.featureXML"), fm);
IDMapper mapper;
Param p = mapper.getParameters();
p.setValue("rt_tolerance", 0.0);
p.setValue("mz_tolerance", 0.0);
p.setValue("mz_measure","Da");
p.setValue("ignore_charge", "true");
mapper.setParameters(p);
mapper.annotate(fm,identifications,protein_identifications);
//test protein ids
TEST_EQUAL(fm.getProteinIdentifications().size(),1)
TEST_EQUAL(fm.getProteinIdentifications()[0].getHits().size(),2)
TEST_EQUAL(fm.getProteinIdentifications()[0].getHits()[0].getAccession(),"ABCDE")
TEST_EQUAL(fm.getProteinIdentifications()[0].getHits()[1].getAccession(),"FGHIJ")
//test peptide ids
TEST_EQUAL(fm[0].getPeptideIdentifications().size(),7)
TEST_EQUAL(fm[0].getPeptideIdentifications()[0].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[1].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[2].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[3].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[4].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[5].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[6].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[0].getHits()[0].getSequence(),"A")
TEST_EQUAL(fm[0].getPeptideIdentifications()[1].getHits()[0].getSequence(),"K")
TEST_EQUAL(fm[0].getPeptideIdentifications()[2].getHits()[0].getSequence(),"C")
TEST_EQUAL(fm[0].getPeptideIdentifications()[3].getHits()[0].getSequence(),"D")
TEST_EQUAL(fm[0].getPeptideIdentifications()[4].getHits()[0].getSequence(),"E")
TEST_EQUAL(fm[0].getPeptideIdentifications()[5].getHits()[0].getSequence(),"F")
TEST_EQUAL(fm[0].getPeptideIdentifications()[6].getHits()[0].getSequence(),"I")
//test unassigned peptide ids
TEST_EQUAL(fm.getUnassignedPeptideIdentifications().size(),3)
TEST_EQUAL(fm.getUnassignedPeptideIdentifications()[0].getHits()[0].getSequence(),"G")
TEST_EQUAL(fm.getUnassignedPeptideIdentifications()[1].getHits()[0].getSequence(),"H")
TEST_EQUAL(fm.getUnassignedPeptideIdentifications()[2].getHits()[0].getSequence(),"L")
//--------------------------------------------------------------------------------------
//TEST MAPPING TO CENTROIDS
FeatureMap<> fm2;
FeatureXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_2.featureXML"), fm2);
p.setValue("rt_tolerance", 4.0);
p.setValue("mz_tolerance", 1.5);
p.setValue("mz_measure","Da");
p.setValue("ignore_charge", "true");
mapper.setParameters(p);
mapper.annotate(fm2,identifications,protein_identifications, true, true);
//test protein ids
TEST_EQUAL(fm2.getProteinIdentifications().size(),1)
TEST_EQUAL(fm2.getProteinIdentifications()[0].getHits().size(),2)
TEST_EQUAL(fm2.getProteinIdentifications()[0].getHits()[0].getAccession(),"ABCDE")
TEST_EQUAL(fm2.getProteinIdentifications()[0].getHits()[1].getAccession(),"FGHIJ")
//test peptide ids
TEST_EQUAL(fm2[0].getPeptideIdentifications().size(),2)
TEST_EQUAL(fm2[0].getPeptideIdentifications()[0].getHits().size(),1)
TEST_EQUAL(fm2[0].getPeptideIdentifications()[1].getHits().size(),1)
TEST_EQUAL(fm2[0].getPeptideIdentifications()[0].getHits()[0].getSequence(),"A")
TEST_EQUAL(fm2[0].getPeptideIdentifications()[1].getHits()[0].getSequence(),"K")
//test unassigned peptide ids
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications().size(),8)
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[0].getHits()[0].getSequence(),"C")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[1].getHits()[0].getSequence(),"D")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[2].getHits()[0].getSequence(),"E")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[3].getHits()[0].getSequence(),"F")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[4].getHits()[0].getSequence(),"G")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[5].getHits()[0].getSequence(),"H")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[6].getHits()[0].getSequence(),"I")
TEST_EQUAL(fm2.getUnassignedPeptideIdentifications()[7].getHits()[0].getSequence(),"L")
// ******* test charge-specific matching *******
FeatureXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_2.featureXML"), fm);
p.setValue("rt_tolerance", 0.0);
p.setValue("mz_tolerance", 0.0);
p.setValue("mz_measure", "Da");
p.setValue("ignore_charge", "false");
mapper.setParameters(p);
mapper.annotate(fm, identifications, protein_identifications);
//test protein ids
TEST_EQUAL(fm.getProteinIdentifications().size(), 1)
TEST_EQUAL(fm.getProteinIdentifications()[0].getHits().size(), 2)
TEST_EQUAL(fm.getProteinIdentifications()[0].getHits()[0].getAccession(),
"ABCDE")
TEST_EQUAL(fm.getProteinIdentifications()[0].getHits()[1].getAccession(),
"FGHIJ")
//test peptide ids
TEST_EQUAL(fm[0].getPeptideIdentifications().size(), 3)
TEST_EQUAL(fm[0].getPeptideIdentifications()[0].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[1].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[2].getHits().size(),1)
TEST_EQUAL(fm[0].getPeptideIdentifications()[0].getHits()[0].getSequence(),"A")
TEST_EQUAL(fm[0].getPeptideIdentifications()[1].getHits()[0].getSequence(),"K")
TEST_EQUAL(fm[0].getPeptideIdentifications()[2].getHits()[0].getSequence(),"C")
//test unassigned peptide ids
TEST_EQUAL(fm.getUnassignedPeptideIdentifications().size(), 7)
// ******* PPM test *******
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_4.idXML"), protein_identifications, identifications);
FeatureMap<> fm_ppm;
FeatureXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_4.featureXML"), fm_ppm);
p.setValue("rt_tolerance", 4.0);
p.setValue("mz_tolerance", 3.0);
p.setValue("mz_measure","ppm");
p.setValue("ignore_charge", "true");
mapper.setParameters(p);
mapper.annotate(fm_ppm,identifications,protein_identifications);
//test peptide ids
TEST_EQUAL(fm_ppm[0].getPeptideIdentifications().size(),1)
TEST_EQUAL(fm_ppm[0].getPeptideIdentifications()[0].getHits().size(),2)
TEST_EQUAL(fm_ppm[0].getPeptideIdentifications()[0].getHits()[0].getSequence(),"LHASGITVTEIPVTATNFK")
TEST_EQUAL(fm_ppm[1].getPeptideIdentifications().size(),0)
TEST_EQUAL(fm_ppm[2].getPeptideIdentifications().size(),1)
TEST_EQUAL(fm_ppm[2].getPeptideIdentifications()[0].getHits().size(),1)
TEST_EQUAL(fm_ppm[2].getPeptideIdentifications()[0].getHits()[0].getSequence(),"HSKLSAK")
TEST_EQUAL(fm_ppm[3].getPeptideIdentifications().size(),0)
TEST_EQUAL(fm_ppm[4].getPeptideIdentifications().size(),1)
TEST_EQUAL(fm_ppm[4].getPeptideIdentifications()[0].getHits().size(),2)
TEST_EQUAL(fm_ppm[4].getPeptideIdentifications()[0].getHits()[0].getSequence(),"RASNSPQDPQSATAHSFR")
TEST_EQUAL(fm_ppm[5].getPeptideIdentifications().size(),0)
TEST_EQUAL(fm_ppm.getUnassignedPeptideIdentifications().size(),2)
TEST_EQUAL(fm_ppm.getUnassignedPeptideIdentifications()[0].getHits()[0].getSequence(),"DEAD")
TEST_EQUAL(fm_ppm.getUnassignedPeptideIdentifications()[0].getHits()[1].getSequence(),"DEADA")
TEST_EQUAL(fm_ppm.getUnassignedPeptideIdentifications()[1].getHits()[0].getSequence(),"DEADAA")
TEST_EQUAL(fm_ppm.getUnassignedPeptideIdentifications()[1].getHits()[1].getSequence(),"DEADAAA")
}
END_SECTION
START_SECTION((void annotate(ConsensusMap& map, const std::vector<PeptideIdentification>& ids, const std::vector<ProteinIdentification>& protein_ids, bool measure_from_subelements=false)))
{
IDMapper mapper;
Param p = mapper.getParameters();
p.setValue("mz_tolerance", 0.01);
p.setValue("mz_measure","Da");
p.setValue("ignore_charge", "true");
mapper.setParameters(p);
TOLERANCE_ABSOLUTE(0.01);
std::vector<ProteinIdentification> protein_ids;
std::vector<PeptideIdentification> peptide_ids;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDMapper_3.idXML"), protein_ids, peptide_ids, document_id);
ConsensusXMLFile cons_file;
{
std::string tmp_filename;
NEW_TMP_FILE(tmp_filename);
ConsensusMap cons_map;
cons_file.load(OPENMS_GET_TEST_DATA_PATH("IDMapper_3.consensusXML"), cons_map);
mapper.annotate(cons_map, peptide_ids, protein_ids);
cons_file.store(tmp_filename,cons_map);
WHITELIST("<?xml-stylesheet");
TEST_FILE_SIMILAR(tmp_filename,OPENMS_GET_TEST_DATA_PATH("IDMapper_3_out1.consensusXML"));
}
{
std::string tmp_filename;
NEW_TMP_FILE(tmp_filename);
ConsensusMap cons_map;
cons_file.load(OPENMS_GET_TEST_DATA_PATH("IDMapper_3.consensusXML"), cons_map);
mapper.annotate(cons_map, peptide_ids, protein_ids, true);
cons_file.store(tmp_filename,cons_map);
WHITELIST("<?xml-stylesheet");
TEST_FILE_SIMILAR(tmp_filename,OPENMS_GET_TEST_DATA_PATH("IDMapper_3_out2.consensusXML"));
}
// check charge-specific matching:
{
ConsensusMap cm;
cm.resize(1);
cm[0].setRT(4101.48);
cm[0].setMZ(117.1);
cm[0].setCharge(2);
mapper.annotate(cm, peptide_ids, protein_ids);
TEST_EQUAL(cm[0].getPeptideIdentifications().size(), 1);
TEST_EQUAL(cm[0].getPeptideIdentifications()[0].getHits()[0].getSequence(),
"ACSF");
TEST_EQUAL(cm.getUnassignedPeptideIdentifications().size(),
peptide_ids.size() - 1);
cm[0].getPeptideIdentifications().clear();
cm.getUnassignedPeptideIdentifications().clear();
p.setValue("ignore_charge", "false");
mapper.setParameters(p);
mapper.annotate(cm, peptide_ids, protein_ids);
TEST_EQUAL(cm[0].getPeptideIdentifications().size(), 0);
TEST_EQUAL(cm.getUnassignedPeptideIdentifications().size(),
peptide_ids.size());
}
}
END_SECTION
START_SECTION([EXTRA] DoubleReal getAbsoluteMZTolerance_(const DoubleReal mz) const)
IDMapper2 mapper;
Param p = mapper.getParameters();
p.setValue("mz_tolerance", 1.0);
mapper.setParameters(p);
TEST_REAL_SIMILAR(mapper.getAbsoluteMZTolerance2_(1000), 0.001)
p.setValue("mz_tolerance", 3.0);
mapper.setParameters(p);
TEST_REAL_SIMILAR(mapper.getAbsoluteMZTolerance2_(1000), 0.003)
p.setValue("mz_measure","Da");
mapper.setParameters(p);
TEST_REAL_SIMILAR(mapper.getAbsoluteMZTolerance2_(1000), 3)
END_SECTION
START_SECTION([EXTRA] bool isMatch_(const DoubleReal rt_distance, const DoubleReal mz_theoretical, const DoubleReal mz_observed) const)
IDMapper2 mapper;
TEST_EQUAL(mapper.isMatch2_(1, 1000, 1000.001), true)
Param p = mapper.getParameters();
p.setValue("mz_tolerance", 3.0);
mapper.setParameters(p);
TEST_EQUAL(mapper.isMatch2_(4, 1000, 1000.0028), true)
TEST_EQUAL(mapper.isMatch2_(4, 1000, 1000.004), false)
TEST_EQUAL(mapper.isMatch2_(4, 1000, 999.9972), true)
TEST_EQUAL(mapper.isMatch2_(4, 1000, 999.996), false)
p.setValue("mz_measure","Da");
mapper.setParameters(p);
TEST_EQUAL(mapper.isMatch2_(5, 999, 1002), true)
TEST_EQUAL(mapper.isMatch2_(5, 999, 1002.1), false)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
