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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: Mathias Walzer $
// $Authors: Nico Pfeifer, Mathias Walzer$
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <string>
#include <OpenMS/FILTERING/ID/IDFilter.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <vector>
///////////////////////////
START_TEST(IDFilter, "$Id: IDFilter_test.C 11458 2013-07-01 14:45:09Z hroest $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace std;
///load input data
std::vector< ProteinIdentification > protein_identifications;
std::vector< PeptideIdentification > identifications;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDFilter_test.idXML"), protein_identifications, identifications, document_id);
PeptideIdentification identification = identifications[0];
ProteinIdentification protein_identification = protein_identifications[0];
/// Proteins for search
vector< FASTAFile::FASTAEntry > proteins;
proteins.push_back(FASTAFile::FASTAEntry("Q824A5", "test description 1", "LHASGITVTEIPVTATNFK"));
proteins.push_back(FASTAFile::FASTAEntry("Q872T5", "test description 2", "THPYGHAIVAGIERYPSK"));
IDFilter* ptr = 0;
IDFilter* nullPointer = 0;
START_SECTION((IDFilter()))
ptr = new IDFilter();
TEST_NOT_EQUAL(ptr, nullPointer);
END_SECTION
START_SECTION((~IDFilter()))
delete ptr;
END_SECTION
START_SECTION((void filterIdentificationsByProteins(const ProteinIdentification& identification, const std::vector<FASTAFile::FASTAEntry> &proteins, ProteinIdentification& filtered_identification)))
ProteinIdentification protein_identification2;
IDFilter().filterIdentificationsByProteins(protein_identification, proteins, protein_identification2);
TEST_EQUAL(protein_identification2.getScoreType() , "Mascot")
TEST_EQUAL(protein_identification2.getHits().size(), 2)
TEST_EQUAL(protein_identification2.getHits()[0].getAccession(), "Q824A5")
TEST_EQUAL(protein_identification2.getHits()[1].getAccession(), "Q872T5")
END_SECTION
START_SECTION((void filterIdentificationsByProteins(const PeptideIdentification &identification, const std::vector< FASTAFile::FASTAEntry > &proteins, PeptideIdentification &filtered_identification, bool no_protein_identifiers=false)))
PeptideIdentification identification2;
IDFilter().filterIdentificationsByProteins(identification, proteins, identification2);
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(identification2.getHits().size(), 2)
TEST_EQUAL(identification2.getHits()[0].getSequence(), "LHASGITVTEIPVTATNFK")
TEST_EQUAL(identification2.getHits()[1].getSequence(), "MRSLGYVAVISAVATDTDK")
END_SECTION
START_SECTION((template <class IdentificationType> void filterIdentificationsByThreshold(const IdentificationType &identification, DoubleReal threshold_fraction, IdentificationType &filtered_identification)))
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
vector<ProteinHit> protein_hits;
TEST_EQUAL(identification.getHits().size(), 10)
IDFilter().filterIdentificationsByThreshold(identification, 1.3, identification2);
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 0)
IDFilter().filterIdentificationsByThreshold(identification, 1.0, identification2);
peptide_hits = identification2.getHits();
TEST_EQUAL(peptide_hits.size(), 5)
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 40)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 40)
TEST_EQUAL(peptide_hits[1].getRank() , 1)
TEST_EQUAL(peptide_hits[2].getSequence() , "THPYGHAIVAGIERYPSK")
TEST_REAL_SIMILAR(peptide_hits[2].getScore() , 39)
TEST_EQUAL(peptide_hits[2].getRank() , 2)
TEST_EQUAL(peptide_hits[3].getSequence() , "LHASGITVTEIPVTATNFK")
TEST_REAL_SIMILAR(peptide_hits[3].getScore() , 34.85)
TEST_EQUAL(peptide_hits[3].getRank() , 3)
TEST_EQUAL(peptide_hits[4].getSequence() , "MRSLGYVAVISAVATDTDK")
TEST_REAL_SIMILAR(peptide_hits[4].getScore() , 33.85)
TEST_EQUAL(peptide_hits[4].getRank() , 4)
END_SECTION
START_SECTION((template <class IdentificationType> void filterIdentificationsByScore(const IdentificationType &identification, DoubleReal threshold_score, IdentificationType &filtered_identification)))
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
TEST_EQUAL(identification.getHits().size(), 10)
IDFilter().filterIdentificationsByScore(identification, 41, identification2);
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 0)
IDFilter().filterIdentificationsByScore(identification, 33, identification2);
peptide_hits = identification2.getHits();
TEST_EQUAL(peptide_hits.size(), 5)
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 40)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 40)
TEST_EQUAL(peptide_hits[1].getRank() , 1)
TEST_EQUAL(peptide_hits[2].getSequence() , "THPYGHAIVAGIERYPSK")
TEST_REAL_SIMILAR(peptide_hits[2].getScore() , 39)
TEST_EQUAL(peptide_hits[2].getRank() , 2)
TEST_EQUAL(peptide_hits[3].getSequence() , "LHASGITVTEIPVTATNFK")
TEST_REAL_SIMILAR(peptide_hits[3].getScore() , 34.85)
TEST_EQUAL(peptide_hits[3].getRank() , 3)
TEST_EQUAL(peptide_hits[4].getSequence() , "MRSLGYVAVISAVATDTDK")
TEST_REAL_SIMILAR(peptide_hits[4].getScore() , 33.85)
TEST_EQUAL(peptide_hits[4].getRank() , 4)
END_SECTION
START_SECTION((void filterIdentificationsByLength(const PeptideIdentification &identification, PeptideIdentification &filtered_identification, Size min_length, Size max_length)))
PeptideIdentification identification_len(identification);
AASequence eighter("OKTAMERR");
AASequence niner("NONAMERRR");
AASequence tener("DECAMERRRR");
identification_len.insertHit(PeptideHit (99.99, 1, 2, eighter));
identification_len.insertHit(PeptideHit (99.99, 1, 2, niner));
identification_len.insertHit(PeptideHit (99.99, 1, 2, tener)) ;
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
TEST_EQUAL(identification_len.getHits().size(), 13)
IDFilter().filterIdentificationsByLength(identification_len,identification2, 10);
peptide_hits = identification2.getHits();
TEST_EQUAL(peptide_hits.size(), 11)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
for (Size i = 0; i < peptide_hits.size(); ++i)
{
TEST_EQUAL(peptide_hits[i].getSequence().size()>=10,true)
}
PeptideIdentification identification3;
IDFilter().filterIdentificationsByLength(identification_len,identification3, 9,10);
peptide_hits = identification3.getHits();
TEST_EQUAL(peptide_hits.size(), 2)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
for (Size i = 0; i < peptide_hits.size(); ++i)
{
TEST_EQUAL(peptide_hits[i].getSequence().size()<=10,true)
}
for (Size i = 0; i < peptide_hits.size(); ++i)
{
TEST_EQUAL(peptide_hits[i].getSequence().size()>=9,true)
}
PeptideIdentification identification4;
IDFilter().filterIdentificationsByLength(identification_len,identification4, 9,8);
peptide_hits = identification4.getHits();
TEST_EQUAL(peptide_hits.size(), 12)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
for (Size i = 0; i < peptide_hits.size(); ++i)
{
TEST_EQUAL(peptide_hits[i].getSequence().size()>=9,true)
}
END_SECTION
START_SECTION((void filterIdentificationsByExclusionPeptides(const PeptideIdentification &identification, const std::set< String > &peptides, PeptideIdentification &filtered_identification)))
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
vector<ProteinHit> protein_hits;
set<String> peptides;
peptides.insert("LHASGITVTEIPVTATNFK");
peptides.insert("MRSLGYVAVISAVATDTDK");
peptides.insert("EGASTDFAALRTFLAEDGK");
peptides.insert("DLEPGTDYEVTVSTLFGR");
peptides.insert("FINFGVNVEVLSRFQTK");
peptides.insert("MSLLSNMISIVKVGYNAR");
peptides.insert("THPYGHAIVAGIERYPSK");
peptides.insert("AITSDFANQAKTVLQNFK");
IDFilter().filterIdentificationsByExclusionPeptides(identification, peptides, identification2);
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 2)
TEST_EQUAL(peptide_hits[0].getSequence() , "TGCDTWGQGTLVTVSSASTK")
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 10.93)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL(peptide_hits[1].getSequence() , "TLCHHDATFDNLVWTPK")
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 10.37)
TEST_EQUAL(peptide_hits[1].getRank() , 2)
protein_hits = protein_identification.getHits();
END_SECTION
START_SECTION((template<class PeakT> void filterIdentificationsByProteins(MSExperiment< PeakT > &experiment, const std::vector<FASTAFile::FASTAEntry> &proteins)))
MSExperiment<> experiment;
vector< FASTAFile::FASTAEntry > proteins;
vector< PeptideIdentification > ids;
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
vector<ProteinHit> protein_hits;
ids.push_back(identification);
proteins.push_back(FASTAFile::FASTAEntry("Q824A5", "first desription", "LHASGITVTEIPVTATNFK"));
proteins.push_back(FASTAFile::FASTAEntry("Q872T5", "second description", "THPYGHAIVAGIERYPSK"));
for (Size i = 0; i < 5; ++i)
{
experiment.addSpectrum(MSSpectrum<>());
}
experiment[3].setMSLevel(2);
experiment[3].setPeptideIdentifications(ids);
IDFilter().filterIdentificationsByProteins(experiment, proteins);
identification2 = experiment[3].getPeptideIdentifications()[0];
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 2)
TEST_EQUAL(peptide_hits[0].getSequence() , "LHASGITVTEIPVTATNFK")
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 34.85)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL(peptide_hits[1].getSequence() , "MRSLGYVAVISAVATDTDK")
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 33.85)
TEST_EQUAL(peptide_hits[1].getRank() , 2)
END_SECTION
START_SECTION((void filterIdentificationsByBestHits(const PeptideIdentification& identification, PeptideIdentification& filtered_identification, bool strict = false)))
PeptideIdentification identification2;
//strict
IDFilter().filterIdentificationsByBestHits(identification, identification2, true);
TEST_EQUAL(identification2.getHits().size(), 0)
TEST_EQUAL(identification2.getScoreType() , "Mascot")
//not strict
IDFilter().filterIdentificationsByBestHits(identification, identification2);
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(identification2.getHits().size(), 2)
TEST_REAL_SIMILAR(identification2.getHits()[0].getScore() , 40)
TEST_EQUAL(identification2.getHits()[0].getRank() , 1)
TEST_REAL_SIMILAR(identification2.getHits()[1].getScore() , 40)
TEST_EQUAL(identification2.getHits()[1].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
END_SECTION
START_SECTION((template <class PeakT> void filterIdentificationsByThresholds(MSExperiment< PeakT > &experiment, DoubleReal peptide_threshold_fraction, DoubleReal protein_threshold_fraction)))
MSExperiment<> experiment;
vector< PeptideIdentification > ids;
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
vector<ProteinHit> protein_hits;
ids.push_back(identification);
for (Size i = 0; i < 5; ++i)
{
experiment.addSpectrum(MSSpectrum<>());
}
experiment[3].setMSLevel(2);
experiment[3].setPeptideIdentifications(ids);
IDFilter().filterIdentificationsByThresholds(experiment, 1.0, 1.0);
identification2 = experiment[3].getPeptideIdentifications()[0];
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 5)
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 40)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 40)
TEST_EQUAL(peptide_hits[1].getRank() , 1)
TEST_EQUAL(peptide_hits[2].getSequence() , "THPYGHAIVAGIERYPSK")
TEST_REAL_SIMILAR(peptide_hits[2].getScore() , 39)
TEST_EQUAL(peptide_hits[2].getRank() , 2)
TEST_EQUAL(peptide_hits[3].getSequence() , "LHASGITVTEIPVTATNFK")
TEST_REAL_SIMILAR(peptide_hits[3].getScore() , 34.85)
TEST_EQUAL(peptide_hits[3].getRank() , 3)
TEST_EQUAL(peptide_hits[4].getSequence() , "MRSLGYVAVISAVATDTDK")
TEST_REAL_SIMILAR(peptide_hits[4].getScore() , 33.85)
TEST_EQUAL(peptide_hits[4].getRank() , 4)
END_SECTION
START_SECTION((template <class PeakT> void filterIdentificationsByScores(MSExperiment< PeakT > &experiment, DoubleReal peptide_threshold_score, DoubleReal protein_threshold_score)))
MSExperiment<> experiment;
vector< PeptideIdentification > ids;
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
vector<ProteinHit> protein_hits;
ids.push_back(identification);
for (Size i = 0; i < 5; ++i)
{
experiment.addSpectrum(MSSpectrum<>());
}
experiment[3].setMSLevel(2);
experiment[3].setPeptideIdentifications(ids);
IDFilter().filterIdentificationsByScores(experiment, 31.8621, 0);
identification2 = experiment[3].getPeptideIdentifications()[0];
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 5)
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 40)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 40)
TEST_EQUAL(peptide_hits[1].getRank() , 1)
TEST_EQUAL(peptide_hits[2].getSequence() , "THPYGHAIVAGIERYPSK")
TEST_REAL_SIMILAR(peptide_hits[2].getScore() , 39)
TEST_EQUAL(peptide_hits[2].getRank() , 2)
TEST_EQUAL(peptide_hits[3].getSequence() , "LHASGITVTEIPVTATNFK")
TEST_REAL_SIMILAR(peptide_hits[3].getScore() , 34.85)
TEST_EQUAL(peptide_hits[3].getRank() , 3)
TEST_EQUAL(peptide_hits[4].getSequence() , "MRSLGYVAVISAVATDTDK")
TEST_REAL_SIMILAR(peptide_hits[4].getScore() , 33.85)
TEST_EQUAL(peptide_hits[4].getRank() , 4)
END_SECTION
START_SECTION((template < class PeakT > void filterIdentificationsByBestNHits(MSExperiment< PeakT > &experiment, Size n)))
MSExperiment<> experiment;
vector< PeptideIdentification > ids;
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
vector<ProteinHit> protein_hits;
ids.push_back(identification);
for (Size i = 0; i < 5; ++i)
{
experiment.addSpectrum(MSSpectrum<>());
}
experiment[3].setMSLevel(2);
experiment[3].setPeptideIdentifications(ids);
IDFilter().filterIdentificationsByBestNHits(experiment, 3);
identification2 = experiment[3].getPeptideIdentifications()[0];
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 3)
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 40)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 40)
TEST_EQUAL(peptide_hits[1].getRank() , 1)
TEST_EQUAL(peptide_hits[2].getSequence() , "THPYGHAIVAGIERYPSK")
TEST_REAL_SIMILAR(peptide_hits[2].getScore() , 39)
TEST_EQUAL(peptide_hits[2].getRank() , 2)
END_SECTION
START_SECTION((template < class IdentificationType > void filterIdentificationsByBestNHits(const IdentificationType &identification, Size n, IdentificationType &filtered_identification)))
PeptideIdentification identification2;
vector<PeptideHit> peptide_hits;
IDFilter().filterIdentificationsByBestNHits(identification, 3, identification2);
peptide_hits = identification2.getHits();
TEST_EQUAL(identification2.getScoreType() , "Mascot")
TEST_EQUAL(peptide_hits.size(), 3)
TEST_REAL_SIMILAR(peptide_hits[0].getScore() , 40)
TEST_EQUAL(peptide_hits[0].getRank() , 1)
TEST_EQUAL((identification2.getHits()[0].getSequence()=="FINFGVNVEVLSRFQTK" && identification2.getHits()[1].getSequence()=="MSLLSNMISIVKVGYNAR") || (identification2.getHits()[0].getSequence()=="MSLLSNMISIVKVGYNAR" && identification2.getHits()[1].getSequence()=="FINFGVNVEVLSRFQTK") , true)
TEST_REAL_SIMILAR(peptide_hits[1].getScore() , 40)
TEST_EQUAL(peptide_hits[1].getRank() , 1)
TEST_EQUAL(peptide_hits[2].getSequence() , "THPYGHAIVAGIERYPSK")
TEST_REAL_SIMILAR(peptide_hits[2].getScore() , 39)
TEST_EQUAL(peptide_hits[2].getRank() , 2)
END_SECTION
START_SECTION((void filterIdentificationsByRTPValues(const PeptideIdentification &identification, PeptideIdentification &filtered_identification, DoubleReal p_value=0.05)))
PeptideIdentification filtered_identification;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDFilter_test2.idXML"), protein_identifications, identifications, document_id);
PeptideIdentification identification2 = identifications[0];
ProteinIdentification protein_identification2 = protein_identifications[0];
IDFilter().filterIdentificationsByRTPValues(identification2 , filtered_identification, 0.08);
vector<PeptideHit> hits = filtered_identification.getHits();
TEST_EQUAL(hits.size(), 4)
TEST_EQUAL(hits[0].getSequence(), "LHASGITVTEIPVTATNFK")
TEST_EQUAL(hits[1].getSequence(), "DLEPGTDYEVTVSTLFGR")
TEST_EQUAL(hits[2].getSequence(), "FINFGVNVEVLSRFQTK")
TEST_EQUAL(hits[3].getSequence(), "MSLLSNMISIVKVGYNAR")
END_SECTION
START_SECTION((void filterIdentificationsByRTFirstDimPValues(const PeptideIdentification &identification, PeptideIdentification &filtered_identification, DoubleReal p_value=0.05)))
PeptideIdentification filtered_identification;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDFilter_test3.idXML"), protein_identifications, identifications, document_id);
PeptideIdentification identification2 = identifications[0];
ProteinIdentification protein_identification2 = protein_identifications[0];
IDFilter().filterIdentificationsByRTFirstDimPValues(identification2 , filtered_identification, 0.08);
vector<PeptideHit> hits = filtered_identification.getHits();
TEST_EQUAL(hits.size(), 4)
TEST_EQUAL(hits[0].getSequence(), "LHASGITVTEIPVTATNFK")
TEST_EQUAL(hits[1].getSequence(), "DLEPGTDYEVTVSTLFGR")
TEST_EQUAL(hits[2].getSequence(), "FINFGVNVEVLSRFQTK")
TEST_EQUAL(hits[3].getSequence(), "MSLLSNMISIVKVGYNAR")
END_SECTION
START_SECTION((void removeUnreferencedProteinHits(const ProteinIdentification &identification, const std::vector< PeptideIdentification > peptide_identifications, ProteinIdentification &filtered_identification)))
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IDFilter_test4.idXML"), protein_identifications, identifications, document_id);
ProteinIdentification protein_identification;
IDFilter().removeUnreferencedProteinHits(protein_identifications[0], identifications, protein_identification);
TEST_EQUAL(protein_identification.getHits().size(), 3)
TEST_EQUAL(protein_identification.getHits()[0].getAccession(), "Q824A5")
TEST_EQUAL(protein_identification.getHits()[1].getAccession(), "S53854")
TEST_EQUAL(protein_identification.getHits()[2].getAccession(), "Q872T5")
END_SECTION
START_SECTION((void filterIdentificationsUnique(const PeptideIdentification &identification, PeptideIdentification &filtered_identification)))
PeptideIdentification id, id2;
vector<PeptideHit> hits;
PeptideHit hit;
hit.setSequence("DFPIANGER");
hit.setCharge(1);
hit.setScore(0.3);
hits.push_back(hit);
hit.setCharge(2);
hits.push_back(hit);
hit.setScore(0.5);
hits.push_back(hit);
hit.setSequence("DFPIANGEK");
hits.push_back(hit);
hits.push_back(hit);
hits.push_back(hit);
hit.setCharge(5);
hits.push_back(hit);
IDFilter id_filter;
TEST_EQUAL(hits.size(), 7)
id.setHits(hits);
id_filter.filterIdentificationsUnique(id, id2);
TEST_EQUAL(id2.getHits().size(), 5)
TEST_STRING_EQUAL(id2.getHits()[3].getSequence().toString(), "DFPIANGEK")
TEST_EQUAL(id2.getHits()[3].getCharge(), 2)
TEST_STRING_EQUAL(id2.getHits()[4].getSequence().toString(), "DFPIANGEK")
TEST_EQUAL(id2.getHits()[4].getCharge(), 5)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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