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