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