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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: Marc Sturm $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/CONCEPT/FuzzyStringComparator.h>
///////////////////////////
START_TEST(IdXMLFile, "$Id: IdXMLFile_test.C 10915 2013-04-04 20:14:57Z aiche $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace OpenMS;
using namespace std;
IdXMLFile* ptr = 0;
IdXMLFile* nullPointer = 0;
START_SECTION((IdXMLFile()))
ptr = new IdXMLFile();
TEST_NOT_EQUAL(ptr,nullPointer)
END_SECTION
START_SECTION(void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids) )
std::vector<ProteinIdentification> protein_ids;
std::vector<PeptideIdentification> peptide_ids;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IdXMLFile_whole.idXML"), protein_ids, peptide_ids);
TEST_EQUAL(protein_ids.size(),2)
TEST_EQUAL(peptide_ids.size(),3)
END_SECTION
START_SECTION(void load(const String& filename, std::vector<ProteinIdentification>& protein_ids, std::vector<PeptideIdentification>& peptide_ids, String& document_id) )
std::vector<ProteinIdentification> protein_ids;
std::vector<PeptideIdentification> peptide_ids;
String document_id;
IdXMLFile().load(OPENMS_GET_TEST_DATA_PATH("IdXMLFile_whole.idXML"), protein_ids, peptide_ids,document_id);
TEST_STRING_EQUAL(document_id,"LSID1234")
TEST_EQUAL(protein_ids.size(),2)
TEST_EQUAL(peptide_ids.size(),3)
/////////////// protein id 1 //////////////////
TEST_EQUAL(protein_ids[0].getScoreType(),"MOWSE")
TEST_EQUAL(protein_ids[0].isHigherScoreBetter(),true)
TEST_EQUAL(protein_ids[0].getSearchEngine(),"Mascot")
TEST_EQUAL(protein_ids[0].getSearchEngineVersion(),"2.1.0")
TEST_EQUAL(protein_ids[0].getDateTime().getDate(),"2006-01-12")
TEST_EQUAL(protein_ids[0].getDateTime().getTime(),"12:13:14")
TEST_EQUAL(protein_ids[0].getIdentifier(),"Mascot_2006-01-12T12:13:14")
TEST_EQUAL(protein_ids[0].getSearchParameters().db,"MSDB")
TEST_EQUAL(protein_ids[0].getSearchParameters().db_version,"1.0")
TEST_EQUAL(protein_ids[0].getSearchParameters().enzyme,ProteinIdentification::TRYPSIN)
TEST_EQUAL(protein_ids[0].getSearchParameters().charges,"+1, +2")
TEST_EQUAL(protein_ids[0].getSearchParameters().mass_type,ProteinIdentification::AVERAGE)
TEST_REAL_SIMILAR(protein_ids[0].getSearchParameters().peak_mass_tolerance,0.3)
TEST_REAL_SIMILAR(protein_ids[0].getSearchParameters().precursor_tolerance,1.0)
TEST_EQUAL((String)(protein_ids[0].getMetaValue("name")),"ProteinIdentification")
TEST_EQUAL(protein_ids[0].getProteinGroups().size(), 1);
TEST_EQUAL(protein_ids[0].getProteinGroups()[0].probability, 0.88);
TEST_EQUAL(protein_ids[0].getProteinGroups()[0].accessions.size(), 2);
TEST_EQUAL(protein_ids[0].getProteinGroups()[0].accessions[0], "PROT1");
TEST_EQUAL(protein_ids[0].getProteinGroups()[0].accessions[1], "PROT2");
TEST_EQUAL(protein_ids[0].getIndistinguishableProteins().size(), 1);
TEST_EQUAL(protein_ids[0].getIndistinguishableProteins()[0].accessions.size(),
2);
TEST_EQUAL(protein_ids[0].getIndistinguishableProteins()[0].accessions[0],
"PROT1");
TEST_EQUAL(protein_ids[0].getIndistinguishableProteins()[0].accessions[1],
"PROT2");
TEST_EQUAL(protein_ids[0].getHits().size(),2)
//protein hit 1
TEST_REAL_SIMILAR(protein_ids[0].getHits()[0].getScore(),34.4)
TEST_EQUAL(protein_ids[0].getHits()[0].getAccession(),"PROT1")
TEST_EQUAL(protein_ids[0].getHits()[0].getSequence(),"ABCDEFG")
TEST_EQUAL((String)(protein_ids[0].getHits()[0].getMetaValue("name")),"ProteinHit")
//protein hit 2
TEST_REAL_SIMILAR(protein_ids[0].getHits()[1].getScore(),24.4)
TEST_EQUAL(protein_ids[0].getHits()[1].getAccession(),"PROT2")
TEST_EQUAL(protein_ids[0].getHits()[1].getSequence(),"ABCDEFG")
//peptide id 1
TEST_EQUAL(peptide_ids[0].getScoreType(),"MOWSE")
TEST_EQUAL(peptide_ids[0].isHigherScoreBetter(),false)
TEST_EQUAL(peptide_ids[0].getIdentifier(),"Mascot_2006-01-12T12:13:14")
TEST_REAL_SIMILAR((DoubleReal)(peptide_ids[0].getMetaValue("MZ")),675.9)
TEST_REAL_SIMILAR((DoubleReal)(peptide_ids[0].getMetaValue("RT")),1234.5)
TEST_EQUAL((UInt)(peptide_ids[0].getMetaValue("spectrum_reference")),17)
TEST_EQUAL((String)(peptide_ids[0].getMetaValue("name")),"PeptideIdentification")
TEST_EQUAL(peptide_ids[0].getHits().size(),2)
//peptide hit 1
TEST_REAL_SIMILAR(peptide_ids[0].getHits()[0].getScore(),0.9)
TEST_EQUAL(peptide_ids[0].getHits()[0].getSequence(),"PEP1")
TEST_EQUAL(peptide_ids[0].getHits()[0].getCharge(),1)
TEST_EQUAL(peptide_ids[0].getHits()[0].getAABefore(),'A')
TEST_EQUAL(peptide_ids[0].getHits()[0].getAAAfter(),'B')
TEST_EQUAL(peptide_ids[0].getHits()[0].getProteinAccessions().size(),2)
TEST_EQUAL(peptide_ids[0].getHits()[0].getProteinAccessions()[0],"PROT1")
TEST_EQUAL(peptide_ids[0].getHits()[0].getProteinAccessions()[1],"PROT2")
TEST_EQUAL((String)(peptide_ids[0].getHits()[0].getMetaValue("name")),"PeptideHit")
//peptide hit 2
TEST_REAL_SIMILAR(peptide_ids[0].getHits()[1].getScore(),1.4)
TEST_EQUAL(peptide_ids[0].getHits()[1].getSequence(),"PEP2")
TEST_EQUAL(peptide_ids[0].getHits()[1].getCharge(),1)
TEST_EQUAL(peptide_ids[0].getHits()[1].getProteinAccessions().size(),0)
TEST_EQUAL(peptide_ids[0].getHits()[1].getAABefore(),' ')
TEST_EQUAL(peptide_ids[0].getHits()[1].getAAAfter(),' ')
//peptide id 2
TEST_EQUAL(peptide_ids[1].getScoreType(),"MOWSE")
TEST_EQUAL(peptide_ids[1].isHigherScoreBetter(),true)
TEST_EQUAL(peptide_ids[1].getIdentifier(),"Mascot_2006-01-12T12:13:14")
TEST_EQUAL(peptide_ids[1].getHits().size(),2)
//peptide hit 1
TEST_REAL_SIMILAR(peptide_ids[1].getHits()[0].getScore(),44.4)
TEST_EQUAL(peptide_ids[1].getHits()[0].getSequence(),"PEP3")
TEST_EQUAL(peptide_ids[1].getHits()[0].getCharge(),2)
TEST_EQUAL(peptide_ids[1].getHits()[0].getProteinAccessions().size(),0)
TEST_EQUAL(peptide_ids[1].getHits()[0].getAABefore(),' ')
TEST_EQUAL(peptide_ids[1].getHits()[0].getAAAfter(),' ')
//peptide hit 2
TEST_REAL_SIMILAR(peptide_ids[1].getHits()[1].getScore(),33.3)
TEST_EQUAL(peptide_ids[1].getHits()[1].getSequence(),"PEP4")
TEST_EQUAL(peptide_ids[1].getHits()[1].getCharge(),2)
TEST_EQUAL(peptide_ids[1].getHits()[1].getProteinAccessions().size(),0)
TEST_EQUAL(peptide_ids[1].getHits()[1].getAABefore(),' ')
TEST_EQUAL(peptide_ids[1].getHits()[1].getAAAfter(),' ')
/////////////// protein id 2 //////////////////
TEST_EQUAL(protein_ids[1].getScoreType(),"MOWSE")
TEST_EQUAL(protein_ids[1].isHigherScoreBetter(),true)
TEST_EQUAL(protein_ids[1].getSearchEngine(),"Mascot")
TEST_EQUAL(protein_ids[1].getSearchEngineVersion(),"2.1.1")
TEST_EQUAL(protein_ids[1].getDateTime().getDate(),"2007-01-12")
TEST_EQUAL(protein_ids[1].getDateTime().getTime(),"12:13:14")
TEST_EQUAL(protein_ids[1].getIdentifier(),"Mascot_2007-01-12T12:13:14")
TEST_EQUAL(protein_ids[1].getSearchParameters().db,"MSDB")
TEST_EQUAL(protein_ids[1].getSearchParameters().db_version,"1.1")
TEST_EQUAL(protein_ids[1].getSearchParameters().enzyme,ProteinIdentification::UNKNOWN_ENZYME)
TEST_EQUAL(protein_ids[1].getSearchParameters().charges,"+1, +2, +3")
TEST_EQUAL(protein_ids[1].getSearchParameters().mass_type,ProteinIdentification::MONOISOTOPIC)
TEST_REAL_SIMILAR(protein_ids[1].getSearchParameters().peak_mass_tolerance,0.3)
TEST_REAL_SIMILAR(protein_ids[1].getSearchParameters().precursor_tolerance,1.0)
TEST_EQUAL(protein_ids[1].getSearchParameters().fixed_modifications.size(),2)
TEST_EQUAL(protein_ids[1].getSearchParameters().fixed_modifications[0],"Fixed")
TEST_EQUAL(protein_ids[1].getSearchParameters().fixed_modifications[1],"Fixed2")
TEST_EQUAL(protein_ids[1].getSearchParameters().variable_modifications.size(),2)
TEST_EQUAL(protein_ids[1].getSearchParameters().variable_modifications[0],"Variable")
TEST_EQUAL(protein_ids[1].getSearchParameters().variable_modifications[1],"Variable2")
TEST_EQUAL(protein_ids[1].getHits().size(),1)
//protein hit 1
TEST_REAL_SIMILAR(protein_ids[1].getHits()[0].getScore(),100.0)
TEST_EQUAL(protein_ids[1].getHits()[0].getAccession(),"PROT3")
TEST_EQUAL(protein_ids[1].getHits()[0].getSequence(),"")
//peptide id 3
TEST_EQUAL(peptide_ids[2].getScoreType(),"MOWSE")
TEST_EQUAL(peptide_ids[2].isHigherScoreBetter(),true)
TEST_EQUAL(peptide_ids[2].getIdentifier(),"Mascot_2007-01-12T12:13:14")
TEST_EQUAL(peptide_ids[2].getHits().size(),1)
//peptide hit 1
TEST_REAL_SIMILAR(peptide_ids[2].getHits()[0].getScore(),1.4)
TEST_EQUAL(peptide_ids[2].getHits()[0].getSequence(),"PEP5")
TEST_EQUAL(peptide_ids[2].getHits()[0].getCharge(),1)
TEST_EQUAL(peptide_ids[2].getHits()[0].getProteinAccessions().size(),1)
TEST_EQUAL(peptide_ids[2].getHits()[0].getProteinAccessions()[0],"PROT3")
TEST_EQUAL(peptide_ids[2].getHits()[0].getAABefore(),' ')
TEST_EQUAL(peptide_ids[2].getHits()[0].getAAAfter(),' ')
END_SECTION
START_SECTION(void store(String filename, const std::vector<ProteinIdentification>& protein_ids, const std::vector<PeptideIdentification>& peptide_ids, const String& document_id="") )
//store and load data
std::vector<ProteinIdentification> protein_ids, protein_ids2;
std::vector<PeptideIdentification> peptide_ids, peptide_ids2;
String document_id, document_id2;
String input_path = OPENMS_GET_TEST_DATA_PATH("IdXMLFile_whole.idXML");
IdXMLFile().load(input_path, protein_ids2, peptide_ids2, document_id2);
String filename;
NEW_TMP_FILE(filename)
IdXMLFile().store(filename, protein_ids2, peptide_ids2, document_id2);
FuzzyStringComparator fuzzy;
fuzzy.setWhitelist(StringList::create("<?xml-stylesheet"));
fuzzy.setAcceptableAbsolute(0.0001);
bool result = fuzzy.compareFiles(input_path, filename);
TEST_EQUAL(result, true);
END_SECTION
START_SECTION([EXTRA] static bool isValid(const String& filename))
std::vector<ProteinIdentification> protein_ids, protein_ids2;
std::vector<PeptideIdentification> peptide_ids, peptide_ids2;
String filename;
IdXMLFile f;
//test if empty file is valid
NEW_TMP_FILE(filename)
f.store(filename, protein_ids2, peptide_ids2);
TEST_EQUAL(f.isValid(filename),true);
//test if full file is valid
NEW_TMP_FILE(filename);
String document_id;
f.load(OPENMS_GET_TEST_DATA_PATH("IdXMLFile_whole.idXML"), protein_ids2, peptide_ids2, document_id);
protein_ids2[0].setMetaValue("stringvalue",String("bla"));
protein_ids2[0].setMetaValue("intvalue",4711);
protein_ids2[0].setMetaValue("floatvalue",5.3);
f.store(filename, protein_ids2, peptide_ids2);
TEST_EQUAL(f.isValid(filename),true);
//check if meta information can be loaded
f.load(filename, protein_ids2, peptide_ids2, document_id);
END_SECTION
START_SECTION(([EXTRA] No protein identification bug))
IdXMLFile id_xmlfile;
vector<ProteinIdentification> protein_ids;
vector<PeptideIdentification> peptide_ids;
id_xmlfile.load(OPENMS_GET_TEST_DATA_PATH("IdXMLFile_no_proteinhits.idXML"), protein_ids, peptide_ids);
TEST_EQUAL(protein_ids.size(), 1)
TEST_EQUAL(protein_ids[0].getHits().size(), 0)
TEST_EQUAL(peptide_ids.size(), 10)
TEST_EQUAL(peptide_ids[0].getHits().size(), 1)
String filename;
NEW_TMP_FILE(filename)
id_xmlfile.store(filename , protein_ids, peptide_ids);
vector<ProteinIdentification> protein_ids2;
vector<PeptideIdentification> peptide_ids2;
id_xmlfile.load(filename, protein_ids2, peptide_ids2);
TEST_EQUAL(protein_ids == protein_ids2, true)
TEST_EQUAL(peptide_ids == peptide_ids2, true)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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