IOTest.cpp File Reference

#include "IO.hpp"
#include "Diff.hpp"
#include "TextWriter.hpp"
#include "examples.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "pwiz/utility/misc/Std.hpp"

Go to the source code of this file.

Functions
template<typename object_type >
void	testObject (const object_type &a)
void	testIdentifiable ()
void	testIdentifiableParamContainer ()
void	testCV ()
void	testBibliographicReference ()
void	testPerson ()
void	testOrganization ()
void	testContactRole ()
void	testProvider ()
void	testSample ()
void	testAnalysisSoftware ()
void	testAnalysisSampleCollection ()
void	testDBSequence ()
void	testModification ()
void	testSubstitutionModification ()
void	testPeptide ()
void	testSequenceCollection ()
void	testSpectrumIdentification ()
void	testProteinDetection ()
void	testAnalysisCollection ()
void	testSearchModification ()
void	testEnzyme ()
void	testEnzymes ()
void	testResidue ()
void	testAmbiguousResidue ()
void	testMassTable ()
void	testFilter ()
void	testSpectrumIdentificationProtocol ()
void	testProteinDetectionProtocol ()
void	testAnalysisProtocolCollection ()
void	testSpectraData ()
void	testSearchDatabase ()
void	testSourceFile ()
void	testInputs ()
void	testMeasure ()
void	testFragmentArray ()
void	testIonType ()
void	testPeptideEvidence ()
void	testSpectrumIdentificationItem ()
void	testSpectrumIdentificationResult ()
PeptideHypothesis	testPeptideHypothesis ()
void	testProteinDetectionHypothesis ()
void	testProteinAmbiguityGroup ()
void	testSpectrumIdentificationList ()
void	testProteinDetectionList ()
void	testAnalysisData ()
void	testDataCollection ()
void	testIdentData ()
void	test ()
int	main (int argc, char *argv[])

Variables
ostream *	os_ = 0

---

Function Documentation

template<typename object_type >

void testObject

(

const object_type &

a

)

Definition at line 41 of file IOTest.cpp.

References diff(), os_, pwiz::identdata::IO::read(), unit_assert, and write().

Referenced by testAmbiguousResidue(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisSampleCollection(), testAnalysisSoftware(), testBibliographicReference(), testComponent(), testComponentList(), testContactRole(), testCV(), testCVParam(), testDataCollection(), testDataProcessing(), testDBSequence(), testEnzyme(), testEnzymes(), testFileDescription(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testInputs(), testInstrumentConfiguration(), testIonType(), testMassTable(), testMeasure(), testModification(), testNamedParamContainer(), testOrganization(), testParamGroup(), testPeptide(), testPeptideEvidence(), testPeptideHypothesis(), testPerson(), testPrecursor(), testProcessingMethod(), testProduct(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProvider(), testResidue(), testSample(), testScanSettings(), testSearchDatabase(), testSearchModification(), testSequenceCollection(), testSoftware(), testSourceFile(), testSpectraData(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), testSubstitutionModification(), and testUserParam().

{
    if (os_) *os_ << "testObject(): " << typeid(a).name() << endl;

    // write 'a' out to a stream

    ostringstream oss;
    XMLWriter writer(oss);
    IO::write(writer, a);
    if (os_) *os_ << oss.str() << endl;

    // read 'b' in from stream

    object_type b; 
    istringstream iss(oss.str());
    IO::read(iss, b);

    // compare 'a' and 'b'

    Diff<object_type, DiffConfig> diff(a,b);
    if (diff && os_) *os_ << "diff:\n" << diff_string<TextWriter>(diff) << endl;
    unit_assert(!diff);
}

void testIdentifiable

(

)

Definition at line 66 of file IOTest.cpp.

References pwiz::identdata::Identifiable::id, pwiz::identdata::Identifiable::name, os_, and testObject().

{
    if (os_) *os_ << "testIdentifiable\n" ;

    Identifiable a;
    a.id = "id";
    a.name = "name";

    testObject(a);
}

void testIdentifiableParamContainer

(

)

Definition at line 78 of file IOTest.cpp.

References pwiz::identdata::IdentifiableParamContainer::id, MS_TIC, pwiz::identdata::IdentifiableParamContainer::name, os_, pwiz::data::ParamContainer::set(), testObject(), and pwiz::data::ParamContainer::userParams.

Referenced by test().

{
    if (os_) *os_ << "testIdentifiableParamContainer\n" ;

    IdentifiableParamContainer a;
    a.id = "id";
    a.name = "name";

    a.set(MS_TIC, 123);
    a.userParams.push_back(UserParam("abc", "123", "!@#"));

    testObject(a);
}

void testCV

(

)

Definition at line 93 of file IOTest.cpp.

References pwiz::cv::CV::fullName, pwiz::cv::CV::id, os_, testObject(), pwiz::cv::CV::URI, and pwiz::cv::CV::version.

{
    if (os_) *os_ << "testCV\n" ;

    CV a;
    a.URI = "abcd";
    a.id = "efgh";
    a.fullName = "ijkl";
    a.version = "mnop";

    testObject(a);
}

void testBibliographicReference

(

)

Definition at line 107 of file IOTest.cpp.

References pwiz::identdata::BibliographicReference::authors, pwiz::identdata::BibliographicReference::editor, pwiz::identdata::Identifiable::id, pwiz::identdata::BibliographicReference::issue, os_, pwiz::identdata::BibliographicReference::pages, pwiz::identdata::BibliographicReference::publication, pwiz::identdata::BibliographicReference::publisher, testObject(), pwiz::identdata::BibliographicReference::title, pwiz::identdata::BibliographicReference::volume, and pwiz::identdata::BibliographicReference::year.

{
    if (os_) *os_ << "testBibliographicReference\n" ;

    BibliographicReference br;

    br.id = "id";
    br.authors = "abcd";
    br.publication = "efg";
    br.publisher = "hijk";
    br.editor = "lmnop";
    br.year = 1984;
    br.volume = "qrs";
    br.issue = "tuv";
    br.pages = "wx";
    br.title = "yz";

    testObject(br);
}

void testPerson

(

)

Definition at line 128 of file IOTest.cpp.

References pwiz::identdata::Person::affiliations, pwiz::identdata::Person::firstName, pwiz::identdata::Person::lastName, pwiz::identdata::Person::midInitials, MS_contact_address, MS_contact_email, MS_contact_fax_number, MS_contact_phone_number, MS_contact_toll_free_phone_number, os_, pwiz::data::ParamContainer::set(), and testObject().

{
    if (os_) *os_ << "testPerson\n" ;

    Person a;

    a.set(MS_contact_address, "123 abc");
    a.set(MS_contact_phone_number, "456");
    a.set(MS_contact_email, "efg@hijk.op");
    a.set(MS_contact_fax_number, "789");
    a.set(MS_contact_toll_free_phone_number, "012-345-678");

    a.lastName = "tuv";
    a.firstName = "wx";
    a.midInitials = "yz";

    a.affiliations.push_back(OrganizationPtr(new Organization("ref")));

    testObject(a);
}

void testOrganization

(

)

Definition at line 150 of file IOTest.cpp.

References MS_contact_address, MS_contact_email, MS_contact_fax_number, MS_contact_phone_number, MS_contact_toll_free_phone_number, os_, pwiz::identdata::Organization::parent, pwiz::data::ParamContainer::set(), and testObject().

{
    if (os_) *os_ << "testOrganization\n" ;
    
    Organization a;

    a.set(MS_contact_address, "123 abc");
    a.set(MS_contact_phone_number, "456");
    a.set(MS_contact_email, "efg@hijk.op");
    a.set(MS_contact_fax_number, "789");
    a.set(MS_contact_toll_free_phone_number, "012-345-678");

    a.parent = OrganizationPtr(new Organization("ref"));

    testObject(a);
}

void testContactRole

(

)

Definition at line 168 of file IOTest.cpp.

References pwiz::identdata::ContactRole::contactPtr, pwiz::data::CVParam::cvid, MS_software_vendor, os_, and testObject().

{
    if (os_) *os_ << "testContactRole\n" ;
    
    ContactRole a;
    a.contactPtr = ContactPtr(new Contact("ref"));
    a.cvid = MS_software_vendor;

    testObject(a);
}

void testProvider

(

)

Definition at line 180 of file IOTest.cpp.

References pwiz::identdata::Provider::contactRolePtr, MS_role_type, os_, and testObject().

{
    if (os_) *os_ << "testProvider\n" ;
    
    Provider a;

    // Reduced to a previously tested object.
    a.contactRolePtr.reset(new ContactRole(MS_role_type, ContactPtr(new Contact("abc"))));

    testObject(a);
}

void testSample

(

)

Definition at line 193 of file IOTest.cpp.

References pwiz::identdata::Sample::contactRole, MS_programmer, MS_septum, MS_software_vendor, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::Sample::subSamples, and testObject().

{
    if (os_) *os_ << "testSample\n" ;
    
    Sample a;

    // Reduced to a previously tested object.
    a.contactRole.push_back(ContactRolePtr(new ContactRole(MS_software_vendor, ContactPtr(new Contact("abc")))));
    a.contactRole.push_back(ContactRolePtr(new ContactRole(MS_programmer, ContactPtr(new Contact("def")))));
    a.set(MS_septum);

    a.subSamples.push_back(SamplePtr(new Sample("subSample_ref")));

    testObject(a);
}

void testAnalysisSoftware

(

)

Definition at line 210 of file IOTest.cpp.

References pwiz::identdata::AnalysisSoftware::contactRolePtr, pwiz::identdata::AnalysisSoftware::customizations, MS_Mascot, MS_software_vendor, os_, pwiz::data::ParamContainer::set(), pwiz::identdata::AnalysisSoftware::softwareName, testObject(), pwiz::identdata::AnalysisSoftware::URI, and pwiz::identdata::AnalysisSoftware::version.

{
    if (os_) *os_ << "testAnalysisSoftware\n" ;

    AnalysisSoftware a;
    a.version = "abcd";
    a.URI = "efg";
    a.customizations = "hijk";
    ContactRolePtr cont = ContactRolePtr(new ContactRole());
    cont->contactPtr = ContactPtr(new Contact("ref"));
    cont->cvid = MS_software_vendor;
    a.contactRolePtr = cont;
    a.softwareName.set(MS_Mascot);

    testObject(a);
}

void testAnalysisSampleCollection

(

)

Definition at line 228 of file IOTest.cpp.

References os_, and testObject().

{
    if (os_) *os_ << "testAnalysisSampleCollection\n" ;

    AnalysisSampleCollection a;
    SamplePtr b(new Sample());
    b->subSamples.push_back(SamplePtr(new Sample("ref")));

    testObject(a);
}

void testDBSequence

(

)

Definition at line 240 of file IOTest.cpp.

References pwiz::identdata::DBSequence::accession, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::DBSequence::length, MS_protein_description, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::DBSequence::searchDatabasePtr, pwiz::identdata::DBSequence::seq, pwiz::data::ParamContainer::set(), and testObject().

{
    DBSequence a;

    a.id = "id";
    a.name = "name";
    a.length = 3;
    a.accession = "abc";
    a.searchDatabasePtr = SearchDatabasePtr(new SearchDatabase("def"));
    a.seq = "ghi";
    a.set(MS_protein_description, "blahbitty blah blah");

    testObject(a);
}

void testModification

(

)

Definition at line 256 of file IOTest.cpp.

References pwiz::identdata::Modification::avgMassDelta, pwiz::identdata::Modification::location, pwiz::identdata::Modification::monoisotopicMassDelta, pwiz::identdata::Modification::residues, pwiz::data::ParamContainer::set(), testObject(), and UNIMOD_Gln__pyro_Glu.

{
    Modification a;

    a.location = 1;
    a.avgMassDelta = 1.001001;
    a.residues.push_back('A');
    a.residues.push_back('C');
    a.monoisotopicMassDelta = 100.1001;

    a.set(UNIMOD_Gln__pyro_Glu);

    testObject(a);
}

void testSubstitutionModification

(

)

Definition at line 272 of file IOTest.cpp.

References pwiz::identdata::SubstitutionModification::avgMassDelta, pwiz::identdata::SubstitutionModification::location, pwiz::identdata::SubstitutionModification::monoisotopicMassDelta, pwiz::identdata::SubstitutionModification::originalResidue, pwiz::identdata::SubstitutionModification::replacementResidue, and testObject().

{
    SubstitutionModification a;

    a.originalResidue = 'L';
    a.replacementResidue = 'V';
    a.location = 1;
    a.avgMassDelta = 2.;
    a.monoisotopicMassDelta = 3.;

    testObject(a);
}

void testPeptide

(

)

Definition at line 286 of file IOTest.cpp.

References pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::Peptide::modification, MS_peptide, pwiz::identdata::IdentifiableParamContainer::name, pwiz::identdata::Peptide::peptideSequence, pwiz::data::ParamContainer::set(), pwiz::identdata::Peptide::substitutionModification, and testObject().

{
    Peptide a;

    a.id = "id";
    a.name = "name";
    a.peptideSequence = "abc";

    ModificationPtr mod(new Modification);
    mod->location = 1;
    a.modification.push_back(mod);

    SubstitutionModificationPtr sub(new SubstitutionModification);
    sub->location = 2;
    a.substitutionModification.push_back(sub);
    
    a.set(MS_peptide);

    testObject(a);
}

void testSequenceCollection

(

)

Definition at line 308 of file IOTest.cpp.

References pwiz::identdata::SequenceCollection::dbSequences, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, and testObject().

{
    SequenceCollection a;

    a.dbSequences.push_back(DBSequencePtr(new DBSequence("db_id")));
    a.peptides.push_back(PeptidePtr(new Peptide("pep_id")));
    a.peptideEvidence.push_back(PeptideEvidencePtr(new PeptideEvidence("pe1")));
    
    testObject(a);
}

void testSpectrumIdentification

(

)

Definition at line 320 of file IOTest.cpp.

References pwiz::identdata::SpectrumIdentification::activityDate, pwiz::identdata::SpectrumIdentification::inputSpectra, os_, pwiz::identdata::SpectrumIdentification::searchDatabase, pwiz::identdata::SpectrumIdentification::spectrumIdentificationListPtr, pwiz::identdata::SpectrumIdentification::spectrumIdentificationProtocolPtr, and testObject().

{
    if (os_) *os_ << "testSpectrumIdentification\n" ;

    SpectrumIdentification a;
    a.spectrumIdentificationProtocolPtr =
        SpectrumIdentificationProtocolPtr( new SpectrumIdentificationProtocol("sip"));
    a.spectrumIdentificationListPtr =
        SpectrumIdentificationListPtr(new SpectrumIdentificationList("sil"));
    a.activityDate = "123";
    a.inputSpectra.push_back(SpectraDataPtr(new SpectraData("is_sd")));
    a.searchDatabase.push_back(SearchDatabasePtr(new SearchDatabase("sd_sd")));

    testObject(a);
}

void testProteinDetection

(

)

Definition at line 337 of file IOTest.cpp.

References pwiz::identdata::ProteinDetection::activityDate, pwiz::identdata::Identifiable::id, pwiz::identdata::Identifiable::name, os_, pwiz::identdata::ProteinDetection::proteinDetectionListPtr, pwiz::identdata::ProteinDetection::proteinDetectionProtocolPtr, and testObject().

{
    if (os_) *os_ << "testProteinDetection\n" ;

    ProteinDetection a;

    a.id = "id";
    a.name = "name";
    a.proteinDetectionProtocolPtr = ProteinDetectionProtocolPtr(new ProteinDetectionProtocol("abc"));
    a.proteinDetectionListPtr = ProteinDetectionListPtr(new ProteinDetectionList("def"));
    a.activityDate = "ghi";

    testObject(a);
}

void testAnalysisCollection

(

)

Definition at line 353 of file IOTest.cpp.

References pwiz::identdata::ProteinDetection::activityDate, os_, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisCollection::spectrumIdentification, and testObject().

{
    if (os_) *os_ << "testAnalysisCollection\n" ;

    AnalysisCollection a;

    SpectrumIdentificationPtr b(new SpectrumIdentification());
    b->activityDate = "abc";
    a.spectrumIdentification.push_back(b);
    a.proteinDetection.activityDate = "def";

    testObject(a);
}

void testSearchModification

(

)

Definition at line 368 of file IOTest.cpp.

References pwiz::data::CVParam::cvid, pwiz::identdata::SearchModification::fixedMod, pwiz::identdata::SearchModification::massDelta, MS_modification_specificity_N_term, os_, pwiz::identdata::SearchModification::residues, pwiz::data::ParamContainer::set(), pwiz::identdata::SearchModification::specificityRules, testObject(), and UNIMOD_Gln__pyro_Glu.

{
    if (os_) *os_ << "testSearchModification\n" ;

    SearchModification a;

    a.fixedMod = true;
    a.massDelta = 3.14;
    a.residues.push_back('Q');
    a.residues.push_back('E');
    a.set(UNIMOD_Gln__pyro_Glu);
    a.specificityRules.cvid = MS_modification_specificity_N_term;

    testObject(a);
}

void testEnzyme

(

)

Definition at line 385 of file IOTest.cpp.

References pwiz::identdata::Enzyme::cTermGain, pwiz::identdata::Enzyme::enzymeName, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzyme::minDistance, pwiz::identdata::Enzyme::missedCleavages, MS_Trypsin, pwiz::identdata::Enzyme::nTermGain, os_, SemiSpecific, pwiz::data::ParamContainer::set(), pwiz::identdata::Enzyme::siteRegexp, pwiz::identdata::Enzyme::terminalSpecificity, and testObject().

{
    if (os_) *os_ << "testEnzyme\n" ;

    Enzyme a;

    a.id = "id";
    a.nTermGain = "n";
    a.cTermGain = "c";
    a.terminalSpecificity = proteome::Digestion::SemiSpecific;
    a.missedCleavages = 1;
    a.minDistance = 2;
    
    a.siteRegexp = "tyrannosaurus regex";
    a.enzymeName.set(MS_Trypsin);
    
    testObject(a);
}

void testEnzymes

(

)

Definition at line 405 of file IOTest.cpp.

References pwiz::identdata::Enzymes::enzymes, pwiz::identdata::Enzymes::independent, os_, and testObject().

{
    if (os_) *os_ << "testEnzymes\n" ;

    Enzymes a;

    a.independent = "yes";
    a.enzymes.push_back(EnzymePtr(new Enzyme()));
    a.enzymes.back()->siteRegexp = "pxegeRetiS";

    testObject(a);
}

void testResidue

(

)

Definition at line 419 of file IOTest.cpp.

References pwiz::identdata::Residue::code, pwiz::identdata::Residue::mass, os_, and testObject().

{
    if (os_) *os_ << "testResidue\n" ;

    Residue a;

    a.code = 'A';
    a.mass = 2;

    testObject(a);
}

void testAmbiguousResidue

(

)

Definition at line 432 of file IOTest.cpp.

References pwiz::identdata::AmbiguousResidue::code, MS_alternate_single_letter_codes, os_, pwiz::data::ParamContainer::set(), and testObject().

{
    if (os_) *os_ << "testAmbiguousResidue\n" ;

    AmbiguousResidue a;

    a.code = 'B';
    a.set(MS_alternate_single_letter_codes, "D N");

    testObject(a);
}

void testMassTable

(

)

Definition at line 445 of file IOTest.cpp.

References pwiz::identdata::MassTable::ambiguousResidue, pwiz::identdata::MassTable::id, pwiz::identdata::MassTable::msLevel, pwiz::identdata::MassTable::residues, and testObject().

{
    MassTable a;
    
    a.id = "id";
    a.msLevel.push_back(1);

    ResiduePtr b(new Residue());
    b->code = 'B';
    a.residues.push_back(b);
    
    AmbiguousResiduePtr c(new AmbiguousResidue());
    c->code = 'C';
    a.ambiguousResidue.push_back(c);

    testObject(a);
}

void testFilter

(

)

Definition at line 464 of file IOTest.cpp.

References pwiz::identdata::Filter::exclude, pwiz::identdata::Filter::filterType, pwiz::identdata::Filter::include, MS_DB_filter_on_accession_numbers, MS_DB_filter_taxonomy, MS_DB_MW_filter, pwiz::data::ParamContainer::set(), and testObject().

{
    Filter a;

    a.filterType.set(MS_DB_filter_taxonomy);
    a.include.set(MS_DB_filter_on_accession_numbers);
    a.exclude.set(MS_DB_MW_filter);

    testObject(a);
}

void testSpectrumIdentificationProtocol

(

)

Definition at line 476 of file IOTest.cpp.

References pwiz::identdata::SpectrumIdentificationProtocol::additionalSearchParams, pwiz::identdata::SpectrumIdentificationProtocol::analysisSoftwarePtr, pwiz::data::CVParam::cvid, pwiz::identdata::SpectrumIdentificationProtocol::databaseFilters, pwiz::identdata::SpectrumIdentificationProtocol::enzymes, pwiz::identdata::SpectrumIdentificationProtocol::fragmentTolerance, pwiz::identdata::Identifiable::id, pwiz::identdata::Enzymes::independent, pwiz::identdata::SpectrumIdentificationProtocol::massTable, pwiz::identdata::SpectrumIdentificationProtocol::modificationParams, MS_DB_filter_taxonomy, MS_Mascot_SigThreshold, MS_ms_ms_search, MS_parent_mass_type_mono, MS_search_tolerance_plus_value, pwiz::identdata::SpectrumIdentificationProtocol::parentTolerance, pwiz::identdata::SpectrumIdentificationProtocol::searchType, pwiz::data::ParamContainer::set(), testObject(), pwiz::identdata::SpectrumIdentificationProtocol::threshold, and UO_dalton.

{
    SpectrumIdentificationProtocol a;

    a.id = "id";
    
    a.analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));

    a.searchType.cvid = MS_ms_ms_search;
    a.additionalSearchParams.set(MS_parent_mass_type_mono);
    a.modificationParams.push_back(SearchModificationPtr(new SearchModification()));
    a.enzymes.independent = "no";
    a.massTable.push_back(MassTablePtr(new MassTable("MT_1")));
    a.massTable.back()->msLevel.push_back(1);
    a.massTable.back()->msLevel.push_back(2);
    a.fragmentTolerance.set(MS_search_tolerance_plus_value, "0.6", UO_dalton);
    a.parentTolerance.set(MS_search_tolerance_plus_value, "3", UO_dalton);
    a.threshold.set(MS_Mascot_SigThreshold, "0.05");

    FilterPtr b(new Filter());
    b->filterType.set(MS_DB_filter_taxonomy);
    a.databaseFilters.push_back(b);

    testObject(a);
}

void testProteinDetectionProtocol

(

)

Definition at line 503 of file IOTest.cpp.

References pwiz::identdata::ProteinDetectionProtocol::analysisParams, pwiz::identdata::ProteinDetectionProtocol::analysisSoftwarePtr, CVID_Unknown, pwiz::identdata::Identifiable::id, MS_Mascot_SigThreshold, pwiz::data::ParamContainer::set(), testObject(), and pwiz::identdata::ProteinDetectionProtocol::threshold.

{
    ProteinDetectionProtocol a;

    a.id = "id";
    a.id="PDP_MascotParser_1";
    a.analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
    a.analysisParams.set(MS_Mascot_SigThreshold, "0.05");
    a.threshold.set(MS_Mascot_SigThreshold, "0.05", CVID_Unknown);

    testObject(a);
}

void testAnalysisProtocolCollection

(

)

Definition at line 517 of file IOTest.cpp.

References pwiz::identdata::AnalysisProtocolCollection::proteinDetectionProtocol, pwiz::identdata::AnalysisProtocolCollection::spectrumIdentificationProtocol, and testObject().

{
    AnalysisProtocolCollection a;

    SpectrumIdentificationProtocolPtr b(new SpectrumIdentificationProtocol());
    b->analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
    a.spectrumIdentificationProtocol.push_back(b);

    ProteinDetectionProtocolPtr c(new ProteinDetectionProtocol());
    c->analysisSoftwarePtr = AnalysisSoftwarePtr(new AnalysisSoftware("ref"));
    a.proteinDetectionProtocol.push_back(c);
    
    testObject(a);
}

void testSpectraData

(

)

Definition at line 533 of file IOTest.cpp.

References pwiz::data::CVParam::cvid, pwiz::identdata::SpectraData::externalFormatDocumentation, pwiz::identdata::SpectraData::fileFormat, pwiz::identdata::Identifiable::id, pwiz::identdata::SpectraData::location, MS_mzML_file, and testObject().

{
    SpectraData a;

    a.id = "id";

    a.location = "here";
    a.externalFormatDocumentation.push_back("there");
    a.fileFormat.cvid = MS_mzML_file;
    
    testObject(a);
}

void testSearchDatabase

(

)

Definition at line 547 of file IOTest.cpp.

References pwiz::data::CVParam::cvid, pwiz::identdata::SearchDatabase::databaseName, pwiz::identdata::SearchDatabase::fileFormat, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SearchDatabase::location, MS_FASTA_format, pwiz::identdata::SearchDatabase::numDatabaseSequences, pwiz::identdata::SearchDatabase::numResidues, pwiz::identdata::SearchDatabase::releaseDate, testObject(), pwiz::data::ParamContainer::userParams, and pwiz::identdata::SearchDatabase::version.

{
    SearchDatabase a;

    a.id = "id";
    a.location = "here";

    a.version = "1.01a";
    a.releaseDate="now";
    a.numDatabaseSequences = 1;
    a.numResidues = 2;

    a.fileFormat.cvid = MS_FASTA_format;
    a.databaseName.userParams.push_back(UserParam("5peptideMix_20090515.fasta"));
    
    testObject(a);
}

void testSourceFile

(

)

Definition at line 566 of file IOTest.cpp.

References pwiz::data::CVParam::cvid, pwiz::identdata::SourceFile::externalFormatDocumentation, pwiz::identdata::SourceFile::fileFormat, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SourceFile::location, MS_Mascot_DAT_file, MS_mzML_file, pwiz::data::ParamContainer::set(), and testObject().

{
    SourceFile a;

    a.id = "id";

    a.location = "there";
    a.fileFormat.cvid = MS_mzML_file;
    a.externalFormatDocumentation.push_back("somewhere else");
    a.set(MS_Mascot_DAT_file);
    
    testObject(a);
}

void testInputs

(

)

Definition at line 581 of file IOTest.cpp.

References pwiz::identdata::Inputs::searchDatabase, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::Inputs::spectraData, and testObject().

{
    Inputs a;

    SourceFilePtr b(new SourceFile());
    b->location = "blah";
    a.sourceFile.push_back(b);

    SearchDatabasePtr c(new SearchDatabase());
    c->version = "1.0b";
    a.searchDatabase.push_back(c);

    SpectraDataPtr d(new SpectraData());
    d->location = "bleh";
    a.spectraData.push_back(d);

    testObject(a);
}

void testMeasure

(

)

Definition at line 601 of file IOTest.cpp.

References pwiz::identdata::IdentifiableParamContainer::id, MS_product_ion_m_z, pwiz::data::ParamContainer::set(), and testObject().

{
    Measure a;

    a.id = "id";
    a.set(MS_product_ion_m_z);

    testObject(a);
}

void testFragmentArray

(

)

Definition at line 612 of file IOTest.cpp.

References pwiz::identdata::FragmentArray::measurePtr, testObject(), and pwiz::identdata::FragmentArray::values.

{
    FragmentArray a;

    a.values.push_back(1.);
    a.values.push_back(2.);
    a.values.push_back(3.);
    a.values.push_back(4.);
    a.measurePtr = MeasurePtr(new Measure("ref"));

    testObject(a);
}

void testIonType

(

)

Definition at line 626 of file IOTest.cpp.

References pwiz::identdata::IonType::charge, pwiz::data::CVParam::cvid, pwiz::identdata::IonType::fragmentArray, pwiz::identdata::IonType::index, MS_frag__a_ion, and testObject().

{
    IonType a;

    a.index.push_back(0);
    a.index.push_back(1);
    a.index.push_back(2);
    a.index.push_back(3);
    a.charge = 2;

    a.cvid = MS_frag__a_ion;
    FragmentArrayPtr b(new FragmentArray());
    a.fragmentArray.push_back(b);
    
    testObject(a);
}

void testPeptideEvidence

(

)

Definition at line 644 of file IOTest.cpp.

References pwiz::identdata::PeptideEvidence::dbSequencePtr, pwiz::identdata::PeptideEvidence::end, pwiz::identdata::PeptideEvidence::frame, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::PeptideEvidence::isDecoy, MS_Mascot_score, pwiz::identdata::PeptideEvidence::post, pwiz::identdata::PeptideEvidence::pre, pwiz::data::ParamContainer::set(), pwiz::identdata::PeptideEvidence::start, testObject(), and pwiz::identdata::PeptideEvidence::translationTablePtr.

{
    PeptideEvidence a;

    a.id = "id";
    a.dbSequencePtr = DBSequencePtr(new DBSequence("dbs_ref"));
    a.start = 1;
    a.end = 2;
    a.pre = 'A';
    a.post = 'C';
    a.translationTablePtr = TranslationTablePtr(new TranslationTable("tranny_ref"));
    a.frame = 3;
    a.isDecoy = true;
    
    a.set(MS_Mascot_score, "15.71");

    testObject(a);
}

void testSpectrumIdentificationItem

(

)

Definition at line 664 of file IOTest.cpp.

References pwiz::identdata::SpectrumIdentificationItem::calculatedMassToCharge, pwiz::identdata::SpectrumIdentificationItem::calculatedPI, pwiz::identdata::SpectrumIdentificationItem::chargeState, pwiz::identdata::SpectrumIdentificationItem::experimentalMassToCharge, pwiz::identdata::SpectrumIdentificationItem::fragmentation, pwiz::identdata::IdentifiableParamContainer::id, pwiz::identdata::SpectrumIdentificationItem::massTablePtr, MS_Mascot_score, pwiz::identdata::SpectrumIdentificationItem::passThreshold, pwiz::identdata::SpectrumIdentificationItem::peptideEvidencePtr, pwiz::identdata::SpectrumIdentificationItem::peptidePtr, pwiz::identdata::SpectrumIdentificationItem::rank, pwiz::identdata::SpectrumIdentificationItem::samplePtr, pwiz::data::ParamContainer::set(), and testObject().

{
    SpectrumIdentificationItem a;

    a.id = "id";
    
    a.chargeState = 1;
    a.experimentalMassToCharge = 1.1;
    a.calculatedMassToCharge = 2.2;
    a.calculatedPI = 3.3;
    a.peptidePtr = PeptidePtr(new Peptide("pep_ref"));
    a.rank = 4;
    a.passThreshold = true;
    a.massTablePtr = MassTablePtr(new MassTable("mt_ref"));
    a.samplePtr = SamplePtr(new Sample("s_ref"));
    a.peptideEvidencePtr.push_back(PeptideEvidencePtr(new PeptideEvidence("pe_ref")));

    IonTypePtr c(new IonType());
    c->charge = 5;
    a.fragmentation.push_back(c);

    a.set(MS_Mascot_score, "15.71");
    
    testObject(a);
}

void testSpectrumIdentificationResult

(

)

Definition at line 691 of file IOTest.cpp.

References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::data::ParamContainer::set(), pwiz::identdata::SpectrumIdentificationResult::spectraDataPtr, pwiz::identdata::SpectrumIdentificationResult::spectrumID, pwiz::identdata::SpectrumIdentificationResult::spectrumIdentificationItem, and testObject().

{
    SpectrumIdentificationResult a;

    a.id = "id";

    a.spectrumID = "sid";
    a.spectraDataPtr = SpectraDataPtr(new SpectraData("sd_ref"));

    SpectrumIdentificationItemPtr b(new SpectrumIdentificationItem());
    b->chargeState = 1;
    a.spectrumIdentificationItem.push_back(b);
    
    a.set(MS_Mascot_score, "15.71");

    testObject(a);
}

PeptideHypothesis testPeptideHypothesis

(

)

Definition at line 710 of file IOTest.cpp.

References pwiz::identdata::PeptideHypothesis::peptideEvidencePtr, pwiz::identdata::PeptideHypothesis::spectrumIdentificationItemPtr, and testObject().

{
    PeptideHypothesis a;

    a.peptideEvidencePtr.reset(new PeptideEvidence("pe1"));
    a.spectrumIdentificationItemPtr.push_back(SpectrumIdentificationItemPtr(new SpectrumIdentificationItem("sii1")));

    testObject(a);
    return a;
}

void testProteinDetectionHypothesis

(

)

Definition at line 722 of file IOTest.cpp.

References pwiz::identdata::ProteinDetectionHypothesis::dbSequencePtr, pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinDetectionHypothesis::passThreshold, pwiz::identdata::ProteinDetectionHypothesis::peptideHypothesis, pwiz::data::ParamContainer::set(), testObject(), and testPeptideHypothesis().

{
    ProteinDetectionHypothesis a;

    a.id = "id";
    a.dbSequencePtr = DBSequencePtr(new DBSequence("dbs_ref"));
    a.passThreshold = "pt";
    a.peptideHypothesis.push_back(testPeptideHypothesis());
    a.set(MS_Mascot_score, "164.4");

    testObject(a);
}

void testProteinAmbiguityGroup

(

)

Definition at line 736 of file IOTest.cpp.

References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinAmbiguityGroup::proteinDetectionHypothesis, pwiz::data::ParamContainer::set(), and testObject().

{
    ProteinAmbiguityGroup a;

    a.id = "id";
    ProteinDetectionHypothesisPtr b(new ProteinDetectionHypothesis());
    b->dbSequencePtr = DBSequencePtr(new DBSequence("dbs_ref"));
    a.proteinDetectionHypothesis.push_back(b);
    a.set(MS_Mascot_score, "164.4");

    testObject(a);
}

void testSpectrumIdentificationList

(

)

Definition at line 750 of file IOTest.cpp.

References pwiz::identdata::SpectrumIdentificationList::fragmentationTable, pwiz::identdata::Identifiable::id, MS_Mascot_score, pwiz::identdata::SpectrumIdentificationList::numSequencesSearched, pwiz::identdata::SpectrumIdentificationList::spectrumIdentificationResult, and testObject().

{
    SpectrumIdentificationList a;

    a.id = "id";
    a.numSequencesSearched = 1;

    MeasurePtr b(new Measure());
    b->set(MS_Mascot_score, "164.4");
    a.fragmentationTable.push_back(b);
    
    SpectrumIdentificationResultPtr c(new SpectrumIdentificationResult());
    c->id = "sid";
    c->spectrumID = "sID";
    a.spectrumIdentificationResult.push_back(c);

    testObject(a);
}

void testProteinDetectionList

(

)

Definition at line 770 of file IOTest.cpp.

References pwiz::identdata::IdentifiableParamContainer::id, MS_Mascot_score, pwiz::identdata::ProteinDetectionList::proteinAmbiguityGroup, pwiz::data::ParamContainer::set(), and testObject().

{
    ProteinDetectionList a;

    a.id = "id";
    ProteinAmbiguityGroupPtr b(new ProteinAmbiguityGroup());
    a.proteinAmbiguityGroup.push_back(b);

    a.set(MS_Mascot_score, "164.4");

    testObject(a);
}

void testAnalysisData

(

)

Definition at line 784 of file IOTest.cpp.

References MS_Mascot_score, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::AnalysisData::spectrumIdentificationList, and testObject().

{
    AnalysisData a;

    SpectrumIdentificationListPtr b(new SpectrumIdentificationList());
    b->id = "id";
    b->numSequencesSearched = 5;
    a.spectrumIdentificationList.push_back(b);

    a.proteinDetectionListPtr = ProteinDetectionListPtr(new ProteinDetectionList("id2"));
    a.proteinDetectionListPtr->set(MS_Mascot_score, "164.4");

    testObject(a);
}

void testDataCollection

(

)

Definition at line 800 of file IOTest.cpp.

References pwiz::identdata::DataCollection::analysisData, pwiz::identdata::DataCollection::inputs, pwiz::identdata::Inputs::sourceFile, pwiz::identdata::AnalysisData::spectrumIdentificationList, and testObject().

{
    DataCollection a;

    SourceFilePtr b(new SourceFile());
    a.inputs.sourceFile.push_back(b);

    SpectrumIdentificationListPtr c(new SpectrumIdentificationList());
    c->id = "SIL_1";
    c->numSequencesSearched = 5;
    a.analysisData.spectrumIdentificationList.push_back(c);

    testObject(a);
}

void testIdentData

(

)

Definition at line 816 of file IOTest.cpp.

References pwiz::identdata::IdentData::analysisCollection, pwiz::identdata::DataCollection::analysisData, pwiz::identdata::IdentData::dataCollection, pwiz::identdata::SequenceCollection::dbSequences, diff(), IgnoreAnalysisData, IgnoreSequenceCollection, pwiz::identdata::examples::initializeTiny(), os_, pwiz::identdata::SequenceCollection::peptideEvidence, pwiz::identdata::SequenceCollection::peptides, pwiz::identdata::AnalysisCollection::proteinDetection, pwiz::identdata::AnalysisData::proteinDetectionListPtr, pwiz::identdata::IO::read(), pwiz::identdata::IdentData::sequenceCollection, pwiz::identdata::AnalysisCollection::spectrumIdentification, pwiz::identdata::AnalysisData::spectrumIdentificationList, testObject(), unit_assert, and write().

{
    IdentData a;

    examples::initializeTiny(a);

    testObject(a);

    // test ignoring sequence collection and analysis data
    {
        // write 'a' out to a stream

        ostringstream oss;
        XMLWriter writer(oss);
        IO::write(writer, a);
        if (os_) *os_ << oss.str() << endl;

        // read 'b' in from stream

        IdentData b; 
        istringstream iss(oss.str());
        IO::read(iss, b, 0, IO::IgnoreSequenceCollection, IO::IgnoreAnalysisData);

        // clear the original SequenceCollection
        a.sequenceCollection.dbSequences.clear();
        a.sequenceCollection.peptides.clear();
        a.sequenceCollection.peptideEvidence.clear();

        // clear the original analysis data
        BOOST_FOREACH(SpectrumIdentificationPtr& si, a.analysisCollection.spectrumIdentification)
            si->spectrumIdentificationListPtr.reset();
        a.analysisCollection.proteinDetection = b.analysisCollection.proteinDetection = ProteinDetection();
        a.dataCollection.analysisData.spectrumIdentificationList.clear();
        a.dataCollection.analysisData.proteinDetectionListPtr.reset();

        // compare 'a' and 'b'

        Diff<IdentData, DiffConfig> diff(a,b);
        if (diff && os_) *os_ << "diff:\n" << diff << endl;
        unit_assert(!diff);
    }
}

void test

(

)

Definition at line 860 of file IOTest.cpp.

References testAmbiguousResidue(), testAnalysisCollection(), testAnalysisData(), testAnalysisProtocolCollection(), testAnalysisSoftware(), testBibliographicReference(), testContactRole(), testCV(), testDataCollection(), testDBSequence(), testEnzyme(), testEnzymes(), testFilter(), testFragmentArray(), testIdentData(), testIdentifiable(), testIdentifiableParamContainer(), testInputs(), testIonType(), testMassTable(), testMeasure(), testModification(), testOrganization(), testPeptide(), testPeptideEvidence(), testPerson(), testProteinAmbiguityGroup(), testProteinDetection(), testProteinDetectionHypothesis(), testProteinDetectionList(), testProteinDetectionProtocol(), testProvider(), testResidue(), testSample(), testSearchDatabase(), testSearchModification(), testSequenceCollection(), testSourceFile(), testSpectraData(), testSpectrumIdentification(), testSpectrumIdentificationItem(), testSpectrumIdentificationList(), testSpectrumIdentificationProtocol(), testSpectrumIdentificationResult(), and testSubstitutionModification().

{
    testCV();
    testIdentifiable();
    testIdentifiableParamContainer();
    testBibliographicReference();
    testPerson();
    testOrganization();
    testContactRole();
    testProvider();
    testSample();
    testAnalysisSoftware();
    testDBSequence();
    testModification();
    testSubstitutionModification();
    testPeptide();
    testSequenceCollection();
    testSpectrumIdentification();
    testProteinDetection();
    testAnalysisCollection();
    testSearchModification();
    testEnzyme();
    testEnzymes();
    testResidue();
    testAmbiguousResidue();
    testMassTable();
    testFilter();
    testSpectrumIdentificationProtocol();
    testProteinDetectionProtocol();
    testAnalysisProtocolCollection();
    testSpectraData();
    testSearchDatabase();
    testSourceFile();
    testInputs();
    testMeasure();
    testFragmentArray();
    testIonType();
    testPeptideEvidence();
    testSpectrumIdentificationItem();
    testSpectrumIdentificationResult();
    testProteinDetectionHypothesis();
    testProteinAmbiguityGroup();
    testSpectrumIdentificationList();
    testProteinDetectionList();
    testDataCollection();
    testAnalysisData();
    testIdentData();
}

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 910 of file IOTest.cpp.

References e(), os_, test(), TEST_EPILOG, TEST_FAILED, and TEST_PROLOG_EX.

{
    TEST_PROLOG_EX(argc, argv, "_IdentData")

    try
    {
        if (argc>1 && !strcmp(argv[1],"-v")) os_ = &cout;
        test();
        if (os_) *os_ << "ok\n";
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}

---

Variable Documentation

ostream* os_ = 0

Definition at line 38 of file IOTest.cpp.