36 using boost::iostreams::stream_offset;
40 template <
typename object_type>
43 if (
os_) *
os_ <<
"testObject(): " <<
typeid(a).name() << endl;
50 if (
os_) *
os_ << oss.str() << endl;
55 istringstream iss(oss.str());
61 if (diff &&
os_) *
os_ <<
"diff:\n" << diff_string<TextWriter>(
diff) << endl;
68 if (
os_) *
os_ <<
"testIdentifiable\n" ;
80 if (
os_) *
os_ <<
"testIdentifiableParamContainer\n" ;
95 if (
os_) *
os_ <<
"testCV\n" ;
109 if (
os_) *
os_ <<
"testBibliographicReference\n" ;
130 if (
os_) *
os_ <<
"testPerson\n" ;
152 if (
os_) *
os_ <<
"testOrganization\n" ;
170 if (
os_) *
os_ <<
"testContactRole\n" ;
182 if (
os_) *
os_ <<
"testProvider\n" ;
195 if (
os_) *
os_ <<
"testSample\n" ;
212 if (
os_) *
os_ <<
"testAnalysisSoftware\n" ;
218 ContactRolePtr cont = ContactRolePtr(
new ContactRole());
230 if (
os_) *
os_ <<
"testAnalysisSampleCollection\n" ;
322 if (
os_) *
os_ <<
"testSpectrumIdentification\n" ;
339 if (
os_) *
os_ <<
"testProteinDetection\n" ;
355 if (
os_) *
os_ <<
"testAnalysisCollection\n" ;
360 b->activityDate =
"abc";
370 if (
os_) *
os_ <<
"testSearchModification\n" ;
387 if (
os_) *
os_ <<
"testEnzyme\n" ;
407 if (
os_) *
os_ <<
"testEnzymes\n" ;
413 a.
enzymes.back()->siteRegexp =
"pxegeRetiS";
421 if (
os_) *
os_ <<
"testResidue\n" ;
434 if (
os_) *
os_ <<
"testAmbiguousResidue\n" ;
489 a.
massTable.back()->msLevel.push_back(1);
490 a.
massTable.back()->msLevel.push_back(2);
495 FilterPtr b(
new Filter());
508 a.
id=
"PDP_MascotParser_1";
586 b->location =
"blah";
594 d->location =
"bleh";
630 a.
index.push_back(0);
631 a.
index.push_back(1);
632 a.
index.push_back(2);
633 a.
index.push_back(3);
742 b->dbSequencePtr = DBSequencePtr(
new DBSequence(
"dbs_ref"));
763 c->spectrumID =
"sID";
790 b->numSequencesSearched = 5;
809 c->numSequencesSearched = 5;
831 if (
os_) *
os_ << oss.str() << endl;
836 istringstream iss(oss.str());
846 si->spectrumIdentificationListPtr.reset();
854 if (diff &&
os_) *
os_ <<
"diff:\n" << diff << endl;
910 int main(
int argc,
char* argv[])
916 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
MS_contact_address
contact address: Postal address of the contact person or organization.
std::string id
the short label to be used as a reference tag with which to refer to this particular Controlled Vocab...
SpectrumIdentificationProtocolPtr spectrumIdentificationProtocolPtr
void testAmbiguousResidue()
void testObject(const object_type &a)
MS_TIC
TIC (total ion current): The sum of all the separate ion currents carried by the ions of different m/...
std::vector< OrganizationPtr > affiliations
ParamContainer analysisParams
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
The XMLWriter class provides simple, tag-level XML syntax writing.
void testProteinDetectionHypothesis()
MS_peptide
peptide: A compound of low molecular weight that is composed of two or more amino acids...
boost::logic::tribool independent
Implementation of AnalysisCollectionType from the mzIdentML schema.
Implementation of AnalysisSampleCollectionType from mzIdentML schema.
MS_DB_MW_filter
DB MW filter: Filtering applied specifically by protein molecular weight, specified as either a range...
std::vector< PeptideEvidencePtr > peptideEvidence
MS_contact_phone_number
contact phone number: Phone number of the contact person or organization.
Implementation of PeptideEvidenceType from the mzIdentML schema.
MS_parent_mass_type_mono
parent mass type mono: Mass type setting for parent mass was monoisotopic.
Implementation of MeasureType from the mzIdentML schema.
Implementation of TranslationTableType from the mzIdentML schema.
SpectraDataPtr spectraDataPtr
SearchDatabasePtr searchDatabasePtr
MS_alternate_single_letter_codes
alternate single letter codes: List of standard residue one letter codes which are used to replace a ...
double monoisotopicMassDelta
std::vector< PeptideEvidencePtr > peptideEvidencePtr
void testAnalysisCollection()
MS_software_vendor
software vendor: Software vendor role.
AnalysisCollection analysisCollection
void testSpectrumIdentification()
Implementation of EnzymeType from the mzIdentML schema.
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of SpectraDataType from the mzIdentML schema.
void testSubstitutionModification()
MS_mzML_format
mzML format: Proteomics Standards Inititative mzML file format.
MS_Trypsin
Trypsin: Enzyme trypsin.
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
std::string customizations
Implementation of PersonType from the mzIdentML schema.
Calculate diffs of objects in a ProteoWizard data model hierarchy.
std::vector< SpectrumIdentificationListPtr > spectrumIdentificationList
std::string peptideSequence
MS_Mascot_score
Mascot:score: The Mascot result 'Score'.
ParamContainer parentTolerance
std::vector< IonTypePtr > fragmentation
Implementation of SpectrumIdentificationResultType from the mzIdentML schema.
Implementation of ProteinDetectionHypothesisType from the mzIdentML schema.
MS_contact_fax_number
contact fax number: Fax number for the contact person or organization.
std::vector< SpectrumIdentificationProtocolPtr > spectrumIdentificationProtocol
Information about an ontology or CV source and a short 'lookup' tag to refer to.
std::vector< PeptideHypothesis > peptideHypothesis
MS_contact_toll_free_phone_number
contact toll-free phone number: Toll-free phone number of the contact person or organization.
long numDatabaseSequences
std::vector< ProteinDetectionProtocolPtr > proteinDetectionProtocol
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
ParamContainer filterType
std::vector< ResiduePtr > residues
std::vector< SpectraDataPtr > inputSpectra
Implementation of FilterType from the mzIdentML schema.
Implementation of PeptideType from the mzIdentML schema.
void testSpectrumIdentificationItem()
MS_contact_email
contact email: Email address of the contact person or organization.
void testIdentifiableParamContainer()
Implementation of AnalysisDataType from the mzIdentML schema.
double experimentalMassToCharge
DataCollection dataCollection
std::vector< EnzymePtr > enzymes
TranslationTablePtr translationTablePtr
std::vector< double > values
void diff(const string &filename1, const string &filename2)
MS_protein_description
protein description: The protein description line from the sequence entry in the source database FAST...
boost::shared_ptr< Organization > parent
std::string fullName
the usual name for the resource (e.g. The PSI-MS Controlled Vocabulary).
std::vector< SearchDatabasePtr > searchDatabase
Implementation of ProviderType from the mzIdentML schema.
std::vector< PeptidePtr > peptides
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
MS_frag__a_ion
frag: a ion: Fragmentation information, type of product: a ion.
void testPeptideEvidence()
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
void testAnalysisSampleCollection()
void testBibliographicReference()
SemiSpecific
neither termini must match digestion motif(s)
std::vector< MassTablePtr > massTable
std::vector< UserParam > userParams
a collection of uncontrolled user terms
std::vector< SubstitutionModificationPtr > substitutionModification
Implementation of MassTableType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
void testAnalysisProtocolCollection()
ProteinDetection proteinDetection
std::vector< boost::shared_ptr< Sample > > subSamples
void testSearchDatabase()
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
Implementation of SequenceCollectionType from the mzIdentML schema.
boost::shared_ptr< Contact > ContactPtr
std::string URI
the URI for the resource.
Implementation of the MzIdentMLType from the mzIdentML schema.
std::vector< int > msLevel
AnalysisSoftwarePtr analysisSoftwarePtr
DBSequencePtr dbSequencePtr
Implementation of EnzymesType from the mzIdentML schema.
Implementation of ProteinDetectionListType from the mzIdentML schema.
MS_FASTA_format
FASTA format: The sequence database was stored in the FASTA format.
boost::shared_ptr< Peptide > PeptidePtr
void testSpectrumIdentificationList()
std::vector< SearchModificationPtr > modificationParams
UO_dalton
dalton: An independently to the base SI units defined mass unit which is equal to one twelfth of the ...
long numSequencesSearched
Implementation of IonTypeType from the mzIdentML schema.
MS_search_tolerance_plus_value
search tolerance plus value:
double monoisotopicMassDelta
ParamContainer enzymeName
Implementation of SearchModificationType from the mzIdentML schema.
Implementation of the SampleType from the mzIdentML schema.
void testProteinDetectionList()
MS_DB_filter_taxonomy
DB filter taxonomy: A taxonomy filter was to the database search.
proteome::Digestion::Specificity terminalSpecificity
Implementation of PeptideHypothesisType from the mzIdentML schema.
std::vector< SpectrumIdentificationPtr > spectrumIdentification
Implementation of AbstractOrganizationType from the mzIdentML schema.
MS_septum
septum: A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber.
MS_Mascot_DAT_format
Mascot DAT format: Source file for this mzIdentML was in Mascot DAT file format.
ParamContainer softwareName
void testProteinAmbiguityGroup()
std::vector< MeasurePtr > fragmentationTable
Implementation of DataCollectionType from the mzIdentML schema.
std::vector< FilterPtr > databaseFilters
ParamContainer databaseName
ParamContainer fragmentTolerance
Implementation of SourceFileType from the mzIdentML schema.
#define TEST_PROLOG_EX(argc, argv, suffix)
PWIZ_API_DECL void read(std::istream &is, CV &cv)
MS_programmer
programmer: Programmer role.
std::vector< char > residues
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
AnalysisSoftwarePtr analysisSoftwarePtr
std::vector< DBSequencePtr > dbSequences
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
MS_Mascot
Mascot: The name of the Mascot search engine.
Implementation of FragmentArrayType from the mzIdentML schema.
MS_modification_specificity_peptide_N_term
modification specificity peptide N-term: As parameter for search engine: apply the modification only ...
SequenceCollection sequenceCollection
void testProteinDetection()
Implementation of SubstitutionModificationType from the mzIdentML schema.
MS_role_type
role type: Role of a Person or Organization.
std::vector< std::string > externalFormatDocumentation
MS_ms_ms_search
ms-ms search: An MS2 search (with fragment ions).
std::vector< ModificationPtr > modification
Implementation of ModificationType from the mzIdentML schema.
ProteinDetectionProtocolPtr proteinDetectionProtocolPtr
void set(CVID cvid, const std::string &value="", CVID units=CVID_Unknown)
set/add a CVParam (not recursive)
MS_product_ion_m_z
product ion m/z: The m/z of the product ion.
Implementation of SearchDatabaseType from the mzIdentML schema.
ContactRolePtr contactRolePtr
void testSpectrumIdentificationResult()
UNIMOD_Gln__pyro_Glu
Gln->pyro-Glu: Pyro-glu from Q.
void testProteinDetectionProtocol()
ContactRolePtr contactRolePtr
MS_DB_filter_on_accession_numbers
DB filter on accession numbers: Filtering applied specifically by accession number pattern...
Implementation of AnalysisSoftwareType from the mzIdentML schema.
ParamContainer additionalSearchParams
int main(int argc, char *argv[])
PeptideEvidencePtr peptideEvidencePtr
Implementation of SpectrumIdentificationType from the mzIdentML schema.
Implementation of ResidueType from the mzIdentML schema.
void testSequenceCollection()
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
boost::shared_ptr< Sample > SamplePtr
std::string version
the version of the CV from which the referred-to terms are drawn.
Implementation of AnalysisProtocolCollectionType from the mzIdentML schema.
std::vector< ProteinAmbiguityGroupPtr > proteinAmbiguityGroup
DBSequencePtr dbSequencePtr
Implementation of DBSequenceType from the mzIdentML schema.
Implementation for the BibliographicReferenceType tag in the mzIdentML schema.
std::vector< FragmentArrayPtr > fragmentArray
double calculatedMassToCharge
void testSearchModification()
SpectrumIdentificationListPtr spectrumIdentificationListPtr
ProteinDetectionListPtr proteinDetectionListPtr
std::vector< char > residues
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
MassTablePtr massTablePtr
AnalysisData analysisData
std::vector< AmbiguousResiduePtr > ambiguousResidue
ProteinDetectionListPtr proteinDetectionListPtr
void testAnalysisSoftware()
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
void testDataCollection()
MS_Mascot_SigThreshold
Mascot:SigThreshold: Significance threshold below which the p-value of a peptide match must lie to be...
Parent class of all Identifiable objects that have ParamGroups.
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItem
void testSpectrumIdentificationProtocol()
std::vector< ContactRolePtr > contactRole
PeptideHypothesis testPeptideHypothesis()
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.
Implementation of ProteinDetectionType from the mzIdentML schema.