45 if (
os_) *
os_ <<
"testIdentifiable()\n";
53 if (diff &&
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
60 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
73 if (
os_) *os_ << diff_string<TextWriter>(diff0) << endl;
79 if (
os_) *os_ << diff_string<TextWriter>(diff1) << endl;
85 if (
os_) *os_ << diff_string<TextWriter>(diff2) << endl;
92 if (
os_) *
os_ <<
"testFragmentArray()\n";
102 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
125 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
130 if (
os_) *
os_ <<
"testIonType()\n";
133 a.
index.push_back(1);
142 if (
os_ && diff) *os_ << diff_string<TextWriter>(
diff) << endl;
153 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
172 if (
os_) *
os_ <<
"testMeasure()\n";
184 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
197 if (
os_) *
os_ <<
"testSearchModification()\n";
216 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
235 if (
os_) *
os_ <<
"testPeptideEvidence()\n";
240 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
268 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
303 if (
os_) *
os_ <<
"testProteinAmbiguityGroup()\n";
319 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
337 if (
os_) *
os_ <<
"testPeptideHypothesis()\n";
349 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
368 if (
os_) *
os_ <<
"testProteinDetectionHypothesis()\n";
389 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
417 if (
os_) *
os_ <<
"testSpectrumIdentificationList()\n";
435 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
455 if (
os_) *
os_ <<
"testProteinDetectionList()\n";
467 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
486 if (
os_) *
os_ <<
"testAnalysisData()\n";
501 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
521 if (
os_) *
os_ <<
"testSearchDatabase()" << endl;
543 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
569 if (
os_) *
os_ <<
"testSpectraData()\n" << endl;
582 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
603 if (
os_) *
os_ <<
"testSourceFile()\n" << endl;
618 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
644 if (
os_) *
os_ <<
"testInputs()\n";
660 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
681 if (
os_) *
os_ <<
"testEnzyme()\n";
685 if (diff &&
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
688 a.
id =
"Donald Trump";
689 b.
id =
"Donald Duck";
705 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
734 if (
os_) *
os_ <<
"testEnzymes()\n";
738 if (diff &&
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
747 if (
os_) *
os_ <<
"testMassTable()\n";
787 if (
os_) *
os_ <<
"testResidue()\n";
802 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
815 if (
os_) *
os_ <<
"testAmbiguousResidue()\n";
830 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
843 if (
os_) *
os_ <<
"testFilter()\n";
863 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
878 if (
os_) *
os_ <<
"testDatabaseTranslation()\n";
897 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
910 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
923 if (
os_) *
os_ <<
"testSpectrumIdentificationProtocol()\n";
932 smp->fixedMod =
true;
933 a.modificationParams.push_back(smp);
934 a.enzymes.enzymes.push_back(EnzymePtr(
new Enzyme(
"a_enzyme")));
935 a.massTable.push_back(MassTablePtr(
new MassTable(
"mt_id")));
941 a.databaseFilters.push_back(filter);
952 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
970 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
978 if (
os_) *
os_ <<
"testProteinDetectionProtocol()\n";
996 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1004 if (
os_) *
os_ <<
"testAnalysisProtocolCollection()\n";
1010 if (
os_) *
os_ <<
"testContact()\n";
1012 Contact a(
"a_id",
"a_name"), b;
1029 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1041 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1049 if (
os_) *
os_ <<
"testPerson()\n";
1086 if (
os_) *
os_ <<
"testOrganization()\n";
1092 if (
os_) *
os_ <<
"testBibliographicReference()\n";
1098 if (
os_) *
os_ <<
"testProteinDetection()\n";
1104 if (
os_) *
os_ <<
"testSpectrumIdentification()\n";
1110 if (
os_) *
os_ <<
"testAnalysisCollection()\n";
1117 if (
os_) *
os_ <<
"testDBSequence()\n";
1123 if (
os_) *
os_ <<
"testModification()\n";
1129 if (
os_) *
os_ <<
"testSubstitutionModification()\n";
1135 if (
os_) *
os_ <<
"testPeptide()\n";
1141 if (
os_) *
os_ <<
"testSequenceCollection()\n";
1147 if (
os_) *
os_ <<
"testSampleComponent()\n";
1153 if (
os_) *
os_ <<
"testSample()\n";
1161 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1168 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1190 if (
os_) *
os_ <<
"testSpectrumIdentificationItem()\n";
1196 if (
os_) *
os_ <<
"testSpectrumIdentificationResult()\n";
1202 if (
os_) *
os_ <<
"testAnalysisSampleCollection()\n";
1208 if (
os_) *
os_ <<
"testProvider()\n";
1214 if (
os_) *
os_ <<
"testContactRole()\n";
1224 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1231 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1245 if (
os_) *
os_ <<
"testAnalysisSoftware()\n";
1267 if (
os_) *
os_ <<
"testDataCollection()\n";
1282 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1289 if (
os_) *
os_ <<
"testIdentData()\n";
1299 a.
cvs.push_back(
CV());
1311 if (
os_) *os_ << diff_string<TextWriter>(
diff) << endl;
1377 if (argc>1 && !strcmp(argv[1],
"-v"))
os_ = &cout;
1380 catch (exception& e)
MS_contact_address
contact address: Postal address of the contact person or organization.
void testSpectrumIdentificationResult()
std::vector< OrganizationPtr > affiliations
void testPeptideHypothesis()
int main(int argc, char *argv[])
void testSampleComponent()
void testBibliographicReference()
CVParam cvParam(CVID cvid) const
finds cvid in the container:
std::vector< SpectrumIdentificationItemPtr > spectrumIdentificationItemPtr
MS_wolf
wolf (massWolf): A software for converting Waters raw directory format to mzXML or mzML...
boost::logic::tribool independent
MS_product_ion_intensity
product ion intensity: The intensity of a single product ion.
MS_DB_MW_filter
DB MW filter: Filtering applied specifically by protein molecular weight, specified as either a range...
void testSearchModification()
MS_contact_phone_number
contact phone number: Phone number of the contact person or organization.
Implementation of PeptideEvidenceType from the mzIdentML schema.
void testDataCollection()
Implementation of MeasureType from the mzIdentML schema.
MS_sample_name
sample name: A reference string relevant to the sample under study.
Implementation of TranslationTableType from the mzIdentML schema.
MS_alternate_single_letter_codes
alternate single letter codes: List of standard residue one letter codes which are used to replace a ...
MS_software_vendor
software vendor: Software vendor role.
void testProteinAmbiguityGroup()
MS_frag__b_ion
frag: b ion: Fragmentation information, type of product: b ion.
Implementation of EnzymeType from the mzIdentML schema.
Implementation of AmbiguousResidueType from the mzIdentML schema.
Implementation of SpectraDataType from the mzIdentML schema.
std::vector< TranslationTablePtr > translationTable
void testSubstitutionModification()
void testSpectrumIdentificationItem()
MS_Trypsin
Trypsin: Enzyme trypsin.
void testAmbiguousResidue()
std::vector< SpectrumIdentificationResultPtr > spectrumIdentificationResult
void testProteinDetectionProtocol()
Parent class representing extensions of the IdentifiableType from the mzIdentML schema.
Implementation of DatabaseTranslationType 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
MS_Mascot_score
Mascot:score: The Mascot result 'Score'.
ParamContainer parentTolerance
#define unit_assert_equal(x, y, epsilon)
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.
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
MS_database_filtering
database filtering: Was there filtering used on the database.
void testAnalysisSoftware()
Implementation of ProteinDetectionProtocolType from the mzIdentML schema.
ParamContainer filterType
std::vector< ResiduePtr > residues
void clear()
clears the collections
MS_search_tolerance_minus_value
search tolerance minus value:
Implementation of FilterType from the mzIdentML schema.
MS_frag__z_ion
frag: z ion: Fragmentation information, type of product: z ion.
MS_contact_email
contact email: Email address of the contact person or organization.
Implementation of AnalysisDataType from the mzIdentML schema.
std::vector< EnzymePtr > enzymes
TranslationTablePtr translationTablePtr
std::vector< double > values
void diff(const string &filename1, const string &filename2)
std::vector< int > frames
bool hasCVParam(CVID cvid) const
returns true iff cvParams contains exact cvid (recursive)
MS_frag__a_ion
frag: a ion: Fragmentation information, type of product: a ion.
Implementation of ProteinAmbiguityGroupType from the mzIdentML schema.
void testAnalysisProtocolCollection()
MS_DB_PI_filter
DB PI filter: Filtering applied specifically by predicted protein isoelectric focussing point (pI)...
SemiSpecific
neither termini must match digestion motif(s)
std::vector< MassTablePtr > massTable
void testAnalysisCollection()
#define unit_assert_operator_equal(expected, actual)
Implementation of MassTableType from the mzIdentML schema.
std::vector< std::string > externalFormatDocumentation
MS_SEQUEST_CleavesAt
SEQUEST:CleavesAt:
boost::shared_ptr< Contact > ContactPtr
Implementation of the MzIdentMLType from the mzIdentML schema.
std::vector< int > msLevel
std::vector< CVParam > cvParams
a collection of controlled vocabulary terms
AnalysisSoftwarePtr analysisSoftwarePtr
DBSequencePtr dbSequencePtr
Implementation of EnzymesType from the mzIdentML schema.
Implementation of ProteinDetectionListType from the mzIdentML schema.
void testAnalysisSampleCollection()
std::vector< SearchModificationPtr > modificationParams
long numSequencesSearched
Implementation of IonTypeType from the mzIdentML schema.
MS_translation_table
translation table: The translation table used to translate the nucleotides to amino acids...
MS_search_tolerance_plus_value
search tolerance plus value:
ParamContainer enzymeName
Implementation of SearchModificationType from the mzIdentML schema.
Implementation of the SampleType from the mzIdentML schema.
MS_DB_filter_taxonomy
DB filter taxonomy: A taxonomy filter was to the database search.
MS_FileFilter
FileFilter: Extracts or manipulates portions of data from peak, feature or consensus feature files...
proteome::Digestion::Specificity terminalSpecificity
MS_sample_number
sample number: A reference number relevant to the sample under study.
Implementation of PeptideHypothesisType from the mzIdentML schema.
Implementation of AbstractOrganizationType from the mzIdentML schema.
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)
std::vector< BibliographicReferencePtr > bibliographicReference
Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema.
MS_translation_table_description
translation table description: A URL that describes the translation table used to translate the nucle...
std::vector< ContactPtr > auditCollection
AnalysisSoftwarePtr analysisSoftwarePtr
void testSpectrumIdentificationProtocol()
PWIZ_API_DECL void initializeTiny(IdentData &mzid)
Implementation of FragmentArrayType from the mzIdentML schema.
void testPeptideEvidence()
void testSequenceCollection()
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).
MS_Mascot_expectation_value
Mascot:expectation value: The Mascot result 'expectation value'.
void testDatabaseTranslation()
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.
UNIMOD_Gln__pyro_Glu
Gln->pyro-Glu: Pyro-glu from Q.
void testProteinDetection()
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
PeptideEvidencePtr peptideEvidencePtr
Implementation of ResidueType from the mzIdentML schema.
std::vector< AnalysisSoftwarePtr > analysisSoftwareList
std::vector< ProteinDetectionHypothesisPtr > proteinDetectionHypothesis
void testSpectrumIdentification()
UNIMOD_Oxidation
Oxidation: Oxidation or Hydroxylation.
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
void testSearchDatabase()
void testProteinDetectionHypothesis()
ProteinDetectionListPtr proteinDetectionListPtr
void testProteinDetectionList()
void testSpectrumIdentificationList()
std::vector< char > residues
Implementation of SpectrumIdentificationItemType from the mzIdentML schema.
MS_low_intensity_threshold
low intensity threshold: Threshold below which some action is taken.
AnalysisData analysisData
std::vector< AmbiguousResiduePtr > ambiguousResidue
Implementation of SpectrumIdentificationListType from the mzIdentML schema.
std::vector< ContactRolePtr > contactRole
boost::shared_ptr< SourceFile > SourceFilePtr
Description of the source file, including location and type.
MS_pmf_search
pmf search: A peptide mass fingerprint search.
void filter(const TContainer &data, const TContainer &filter, TContainer &result, bool circular=false, uint32_t sides=2)
Applies linear convolution (filtering) to a univariate time series.