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#define BAD_VALIDATOR #define TESTPOPPHYMUTECO(seh, entry) #define TESTWGS(seh, entry) #define START_CODON_AND_INT_STOP_ERR #define INTERNAL_STOP_ERR #define NO_STOP_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "NoStop", "Missing stop codon")); #define NO_PUB_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "NoPubFound", "No publications anywhere on this entire record.")); #define PROT_LEN_ERR #define NO_SUB_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Info, "MissingPubRequirement", "No submission citation anywhere on this entire record.")); #define EXCEPTION_PROBLEM_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "ExceptionProblem", "unclassified translation discrepancy is not a legal exception explanation")); #define NO_SRC_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "NoSourceDescriptor", "No source information included on this record.")); #define test_gene_syn(name) #define test_undesired_protein_name(name) void WriteErrors (const CValidError &eval, bool debug_mode) void CheckErrors (const CValidError &eval, vector< CExpectedError * > &expected_errors) void CheckStrings (const vector< string > &seen, const vector< string > &expected) template<typename T > static string ToAsn1 (const T &entry) USING_SCOPE (objects) NCBITEST_INIT_TREE () static void SetErrorsAccessions (vector< CExpectedError * > &expected_errors, string accession) NCBITEST_INIT_CMDLINE (arg_desc) NCBITEST_AUTO_INIT () void AddChromosomeNoLocation (vector< CExpectedError * > &expected_errors, const string &id) void AddChromosomeNoLocation (vector< CExpectedError * > &expected_errors, CRef< CSeq_entry > entry) BOOST_AUTO_TEST_CASE (Test_Descr_MissingKeyword) BOOST_AUTO_TEST_CASE (Test_Descr_LatLonValue) void TestOneLatLonCountry (const string &country, const string &lat_lon, const string &error, bool use_state=false, const string &err_code="LatLonCountry") BOOST_AUTO_TEST_CASE (Test_VR_840) BOOST_AUTO_TEST_CASE (Test_Descr_LatLonCountry) BOOST_AUTO_TEST_CASE (Test_ValidError_Format) BOOST_AUTO_TEST_CASE (Test_ValidError_Format1) BOOST_AUTO_TEST_CASE (Test_GB_6395) BOOST_AUTO_TEST_CASE (Test_Descr_LatLonState) CRef< CSeq_entry > s_BuildBadEcNumberEntry () BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadEcNumberValue) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_InvalidQualifierValue) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_ExtNotAllowed) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_ReprInvalid) BOOST_AUTO_TEST_CASE (Test_CollidingLocusTags) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_CircularProtein) BOOST_AUTO_TEST_CASE (Test_BadProteinMoltype) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_MolNotSet) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_FuzzyLen) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_InvalidAlphabet) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_InvalidResidue) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_StopInProtein) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_PartialInconsistent) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_ShortSeq) static bool IsProteinTech (CMolInfo::TTech tech) static void AddRefGeneTrackingUserObject (CRef< CSeq_entry > entry) static void SetRefGeneTrackingStatus (CRef< CSeq_entry > entry, string status) static void SetTitle (CRef< CSeq_entry > entry, string title) static void AddGenbankKeyword (CRef< CSeq_entry > entry, string keyword) void TestDeltaTechAllowed (CMolInfo::TTech tech) void TestDeltaTechNotAllowed (CMolInfo::TTech tech) void TestStartGapSeg (CMolInfo::TTech tech) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_BadDeltaSeq) void AdjustGap (CSeq_gap &gap, CSeq_gap::EType gap_type, bool is_linked, vector< CLinkage_evidence::EType > linkage_evidence) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_SeqGapBadLinkage) void ChangeErrorAcc (vector< CExpectedError * > expected_errors, const string &acc) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_ConflictingIdsOnBioseq) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_MolNuclAcid) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_ConflictingBiomolTech) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_SeqIdNameHasSpace) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_DuplicateSegmentReferences) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_TrailingX) void TestBadProtId (const string &id_str) void TestGoodProtId (const string &id_str) void TestGoodNucId (const string &id_str) BOOST_FIXTURE_TEST_CASE (Test_SEQ_INST_BadSeqIdFormat, CGenBankFixture) void TestOneGeneralSeqId (const string &db, const string &tag, const string &errmsg) BOOST_AUTO_TEST_CASE (Test_VR_748) void TestOneLongGeneral (bool emb, bool err) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_LongGeneralSeqId) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_BadSecondaryAccn) BOOST_AUTO_TEST_CASE (Test_SEQ_INST_ZeroGiNumber) BOOST_AUTO_TEST_CASE (Test_HistoryGiCollision) BOOST_AUTO_TEST_CASE (Test_GiWithoutAccession) void TestOneOtherAcc (CRef< CSeq_id > other_acc, bool id_change, bool conflict, bool need_hist=false) BOOST_FIXTURE_TEST_CASE (Test_MultipleAccessions, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_HistAssemblyMissing) BOOST_AUTO_TEST_CASE (Test_TerminalNs) BOOST_FIXTURE_TEST_CASE (Test_UnexpectedIdentifierChange, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_InternalNsInSeqLit) BOOST_AUTO_TEST_CASE (Test_SeqLitGapLength0) static void AddTpaAssemblyUserObject (CRef< CSeq_entry > entry) BOOST_FIXTURE_TEST_CASE (Test_TpaAssemblyProblem, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SeqLocLength, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_MissingGaps) BOOST_AUTO_TEST_CASE (Test_CompleteTitleProblem) BOOST_AUTO_TEST_CASE (Test_CompleteCircleProblem) BOOST_AUTO_TEST_CASE (Test_BadHTGSeq) BOOST_AUTO_TEST_CASE (Test_GapInProtein_and_BadProteinStart) BOOST_AUTO_TEST_CASE (Test_TerminalGap) BOOST_FIXTURE_TEST_CASE (Test_OverlappingDeltaRange, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_LeadingX) BOOST_AUTO_TEST_CASE (Test_InternalNsInSeqRaw) BOOST_AUTO_TEST_CASE (Test_InternalNsAdjacentToGap) BOOST_AUTO_TEST_CASE (Test_DeltaComponentIsGi0) BOOST_AUTO_TEST_CASE (Test_InternalGapsInSeqRaw) BOOST_AUTO_TEST_CASE (Test_SelfReferentialSequence) BOOST_FIXTURE_TEST_CASE (Test_WholeComponent, CGenBankFixture) void s_AddGeneralAndLocal (CBioseq &seq) BOOST_AUTO_TEST_CASE (Test_ProteinsHaveGeneralID) BOOST_AUTO_TEST_CASE (Test_HighNContentPercent_and_HighNContentStretch) BOOST_AUTO_TEST_CASE (Test_SeqLitDataLength0) static CRef< CSeq_entry > BuildGapFuzz100DeltaSeq (void) BOOST_AUTO_TEST_CASE (Test_UnknownLengthGapNot100) BOOST_AUTO_TEST_CASE (Test_DSmRNA) BOOST_AUTO_TEST_CASE (Test_BioSourceMissing) BOOST_AUTO_TEST_CASE (Test_Descr_InvalidForType) BOOST_AUTO_TEST_CASE (Test_Descr_Unknown) static CRef< CSeq_entry > MakeGps (CRef< CSeq_entry > member) BOOST_AUTO_TEST_CASE (Test_Descr_NoPubFound) BOOST_AUTO_TEST_CASE (Test_Descr_NoOrgFound) BOOST_AUTO_TEST_CASE (Test_Descr_MultipleBioSources) BOOST_AUTO_TEST_CASE (Test_Descr_NoMolInfoFound) BOOST_AUTO_TEST_CASE (Test_Descr_NoTaxonID) BOOST_AUTO_TEST_CASE (Test_Descr_InconsistentBiosources) BOOST_AUTO_TEST_CASE (Test_Descr_MissingLineage) BOOST_AUTO_TEST_CASE (Test_Descr_SerialInComment) BOOST_AUTO_TEST_CASE (Test_Descr_BioSourceNeedsFocus) BOOST_AUTO_TEST_CASE (Test_Descr_BadOrganelle) BOOST_AUTO_TEST_CASE (Test_Descr_MultipleChromosomes) BOOST_AUTO_TEST_CASE (Test_Descr_BadSubSource) void ShowOrgRef (const COrg_ref &org) void ShowOrgRef (const CSeq_entry &entry) BOOST_AUTO_TEST_CASE (Test_Descr_BadOrgMod) BOOST_AUTO_TEST_CASE (Test_BadVariety) BOOST_AUTO_TEST_CASE (Test_Descr_InconsistentProteinTitle) BOOST_FIXTURE_TEST_CASE (Test_Descr_Inconsistent, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_Descr_ObsoleteSourceLocation) BOOST_AUTO_TEST_CASE (Test_Descr_ObsoleteSourceQual) BOOST_AUTO_TEST_CASE (Test_Descr_StructuredSourceNote) BOOST_AUTO_TEST_CASE (Test_Descr_UnnecessaryBioSourceFocus) BOOST_AUTO_TEST_CASE (Test_Descr_RefGeneTrackingWithoutStatus) BOOST_AUTO_TEST_CASE (Test_Descr_UnwantedCompleteFlag) BOOST_AUTO_TEST_CASE (Test_Descr_CollidingPublications) BOOST_AUTO_TEST_CASE (Test_Descr_TransgenicProblem) BOOST_AUTO_TEST_CASE (Test_Descr_TaxonomyLookupProblem) void TestConsultRequired (const string &taxname) BOOST_AUTO_TEST_CASE (Test_VR_857) BOOST_AUTO_TEST_CASE (Test_Descr_MultipleTitles) BOOST_AUTO_TEST_CASE (Test_Descr_RefGeneTrackingOnNonRefSeq) BOOST_AUTO_TEST_CASE (Test_OrgModMissingValue) BOOST_AUTO_TEST_CASE (Test_BadTextInSourceQualifier) BOOST_AUTO_TEST_CASE (Test_InvalidSexQualifier) BOOST_AUTO_TEST_CASE (Test_HIVMolType) BOOST_AUTO_TEST_CASE (Test_MissingPlasmid) BOOST_AUTO_TEST_CASE (Test_BadPlastidName) BOOST_AUTO_TEST_CASE (Test_BadBioSourceFrequencyValue) BOOST_AUTO_TEST_CASE (Test_Descr_BioSourceInconsistency) BOOST_AUTO_TEST_CASE (Test_VR_173) BOOST_AUTO_TEST_CASE (Test_InconsistentVirusMoltype) BOOST_AUTO_TEST_CASE (Test_SingleStrandViruses) BOOST_AUTO_TEST_CASE (Test_Descr_FastaBracketTitle) BOOST_AUTO_TEST_CASE (Test_Descr_MissingText) BOOST_AUTO_TEST_CASE (Test_Descr_BadCollectionDate) BOOST_AUTO_TEST_CASE (Test_Descr_BadPCRPrimerSequence) BOOST_AUTO_TEST_CASE (Test_Descr_ModifyPCRPrimer) BOOST_AUTO_TEST_CASE (Test_Descr_BadPunctuation) BOOST_AUTO_TEST_CASE (Test_Descr_BadPCRPrimerName) BOOST_AUTO_TEST_CASE (Test_Descr_BioSourceOnProtein) BOOST_AUTO_TEST_CASE (Test_Descr_BioSourceDbTagConflict) bool s_ArePrimersUnique (const CPCRReactionSet &rset) BOOST_AUTO_TEST_CASE (Test_Descr_DuplicatePCRPrimerSequence) BOOST_AUTO_TEST_CASE (Test_Descr_MultipleNames) BOOST_AUTO_TEST_CASE (Test_Descr_MultipleComments) BOOST_AUTO_TEST_CASE (Test_Descr_LatLonFormat) BOOST_AUTO_TEST_CASE (Test_Descr_LatLonRange) BOOST_AUTO_TEST_CASE (Test_Descr_BadAltitude) BOOST_AUTO_TEST_CASE (Test_IsLikelyTaxname) void TestSpecificHostNoError (const string &host) BOOST_AUTO_TEST_CASE (Test_Descr_BadSpecificHost) BOOST_AUTO_TEST_CASE (Test_Validity_SpecificHost) BOOST_AUTO_TEST_CASE (Test_FixSpecificHost) BOOST_AUTO_TEST_CASE (Test_Descr_RefGeneTrackingIllegalStatus) BOOST_AUTO_TEST_CASE (Test_Descr_ReplacedCountryCode) BOOST_AUTO_TEST_CASE (Test_Descr_BadInstitutionCode) BOOST_AUTO_TEST_CASE (Test_Descr_BadCollectionCode) BOOST_AUTO_TEST_CASE (Test_Descr_IncorrectlyFormattedVoucherID) BOOST_AUTO_TEST_CASE (Test_Descr_UnstructuredVoucher) BOOST_AUTO_TEST_CASE (Test_Descr_ChromosomeLocation) BOOST_AUTO_TEST_CASE (Test_Descr_MultipleSourceQualifiers) static bool SubSourceHasOtherRules (CSubSource::TSubtype subtype) static bool OrgModHasOtherRules (COrgMod::TSubtype subtype) void CheckUnbalancedParenthesesSubSource (CSubSource::TSubtype subtype, const string &val) void CheckUnbalancedParenthesesOrgMod (COrgMod::TSubtype subtype, const string &val) BOOST_AUTO_TEST_CASE (Test_Descr_UnbalancedParentheses) BOOST_AUTO_TEST_CASE (Test_Descr_IdenticalInstitutionCode) BOOST_AUTO_TEST_CASE (Test_Descr_BadCountryCapitalization) BOOST_AUTO_TEST_CASE (Test_Descr_WrongVoucherType) BOOST_AUTO_TEST_CASE (Test_Descr_TitleHasPMID) BOOST_AUTO_TEST_CASE (Test_Descr_BadKeyword) BOOST_AUTO_TEST_CASE (Test_Descr_NoOrganismInTitle) BOOST_AUTO_TEST_CASE (Test_Descr_MissingChromosome) BOOST_AUTO_TEST_CASE (Test_Descr_BadStructuredCommentFormat) CRef< CUser_field > MkField (const string &label, const string &val) BOOST_AUTO_TEST_CASE (Test_VR_709) BOOST_AUTO_TEST_CASE (Test_Descr_BioSourceNeedsChromosome) BOOST_AUTO_TEST_CASE (Test_Descr_MolInfoConflictsWithBioSource) BOOST_AUTO_TEST_CASE (Test_Descr_FakeStructuredComment) BOOST_AUTO_TEST_CASE (Test_Descr_StructuredCommentPrefixOrSuffixMissing) BOOST_AUTO_TEST_CASE (Test_Generic_NonAsciiAsn) BOOST_AUTO_TEST_CASE (Test_SEQ_DESCR_MissingPersonalCollectionName) BOOST_AUTO_TEST_CASE (Test_Generic_AuthorListHasEtAl) BOOST_AUTO_TEST_CASE (Test_Generic_MissingPubRequirement) BOOST_AUTO_TEST_CASE (Test_Generic_UnnecessaryPubEquiv) BOOST_AUTO_TEST_CASE (Test_Generic_BadPageNumbering) BOOST_AUTO_TEST_CASE (Test_Generic_MedlineEntryPub) static void MakeBadSeasonDate (CDate &date) BOOST_AUTO_TEST_CASE (Test_Generic_BadDate) BOOST_AUTO_TEST_CASE (Test_Generic_StructuredCitGenCit) BOOST_AUTO_TEST_CASE (Test_Generic_CollidingSerialNumbers) BOOST_AUTO_TEST_CASE (Test_Generic_EmbeddedScript) BOOST_AUTO_TEST_CASE (Test_Generic_PublicationInconsistency) void AddSgmlError (vector< CExpectedError * > &expected_errors, const string &valtype, const string &val) BOOST_AUTO_TEST_CASE (Test_Generic_SgmlPresentInText) BOOST_AUTO_TEST_CASE (Test_Generic_UnexpectedPubStatusComment) BOOST_AUTO_TEST_CASE (Test_PKG_NoCdRegionPtr) BOOST_AUTO_TEST_CASE (Test_PKG_NucProtProblem) BOOST_AUTO_TEST_CASE (Test_PKG_SegSetProblem) BOOST_AUTO_TEST_CASE (Test_PKG_EmptySet) BOOST_AUTO_TEST_CASE (Test_PKG_NucProtNotSegSet) BOOST_AUTO_TEST_CASE (Test_PKG_GenomicProductPackagingProblem) BOOST_AUTO_TEST_CASE (Test_PKG_InconsistentMolInfoBiomols) BOOST_AUTO_TEST_CASE (Test_PKG_GraphPackagingProblem) BOOST_AUTO_TEST_CASE (Test_PKG_InternalGenBankSet) BOOST_AUTO_TEST_CASE (Test_PKG_ConSetProblem) BOOST_AUTO_TEST_CASE (Test_PKG_NoBioseqFound) BOOST_AUTO_TEST_CASE (Test_PKG_INSDRefSeqPackaging) BOOST_AUTO_TEST_CASE (Test_PKG_GPSnonGPSPackaging) BOOST_AUTO_TEST_CASE (Test_PKG_RefSeqPopSet) BOOST_AUTO_TEST_CASE (Test_PKG_BioseqSetClassNotSet) BOOST_AUTO_TEST_CASE (Test_PKG_OrphanedProtein) BOOST_AUTO_TEST_CASE (Test_PKG_MisplacedMolInfo) BOOST_AUTO_TEST_CASE (Test_PKG_ImproperlyNestedSets) BOOST_AUTO_TEST_CASE (Test_FEAT_InvalidForType) CRef< CUser_field > MakeStructuredCommentField (const string &label, const string &value) BOOST_AUTO_TEST_CASE (Test_VR_828) BOOST_AUTO_TEST_CASE (Test_VR_829) static CRef< CSeq_entry > BuildGoodSpliceNucProtSet () BOOST_AUTO_TEST_CASE (Test_FEAT_PartialProblem) void SetUpMiscForPartialTest (CSeq_feat &feat, TSeqPos start, TSeqPos stop, bool pseudo) void CheckMiscPartialErrors (CRef< CSeq_entry > entry, bool expect_bad_5, bool expect_bad_3) void TestOneMiscPartial (CRef< CSeq_entry > entry, TSeqPos good_start, TSeqPos bad_start, TSeqPos good_stop, TSeqPos bad_stop, bool is_mrna) BOOST_AUTO_TEST_CASE (Test_VR_763) BOOST_AUTO_TEST_CASE (Test_FEAT_InvalidType) BOOST_AUTO_TEST_CASE (Test_FEAT_Range) BOOST_AUTO_TEST_CASE (Test_tRNA_Mixed_Loc) BOOST_AUTO_TEST_CASE (Test_FEAT_MixedStrand) BOOST_AUTO_TEST_CASE (Test_FEAT_SeqLocOrder) BOOST_AUTO_TEST_CASE (Test_FEAT_CdTransFail) BOOST_AUTO_TEST_CASE (Test_FEAT_StartCodon) BOOST_AUTO_TEST_CASE (Test_FEAT_InternalStop) BOOST_AUTO_TEST_CASE (Test_FEAT_NoProtein) BOOST_AUTO_TEST_CASE (Test_FEAT_MisMatchAA) BOOST_AUTO_TEST_CASE (Test_FEAT_TransLen) BOOST_AUTO_TEST_CASE (Test_FEAT_NoStop) BOOST_AUTO_TEST_CASE (Test_FEAT_TranslExcept) BOOST_AUTO_TEST_CASE (Test_FEAT_NoProtRefFound) BOOST_AUTO_TEST_CASE (Test_FEAT_OrfCdsHasProduct) BOOST_AUTO_TEST_CASE (Test_FEAT_GeneRefHasNoData) BOOST_AUTO_TEST_CASE (Test_FEAT_ExceptInconsistent) BOOST_AUTO_TEST_CASE (Test_FEAT_ProtRefHasNoData) BOOST_AUTO_TEST_CASE (Test_FEAT_GenCodeMismatch) BOOST_AUTO_TEST_CASE (Test_FEAT_RNAtype0) BOOST_AUTO_TEST_CASE (Test_FEAT_UnknownImpFeatKey) BOOST_AUTO_TEST_CASE (Test_FEAT_UnknownImpFeatQual) BOOST_AUTO_TEST_CASE (Test_FEAT_MissingQualOnImpFeat) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PseudoCdsHasProduct) static string MakeWrongCap (const string &str) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_IllegalDbXref) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FarLocation) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_DuplicateFeat) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UnnecessaryGeneXref) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TranslExceptPhase) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TrnaCodonWrong) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BothStrands) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSmRNArange) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_OverlappingPeptideFeat) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SerialInComment) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultipleCDSproducts) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FocusOnBioSourceFeature) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PeptideFeatOutOfFrame) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSgeneRange) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultipleMRNAproducts) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_mRNAgeneRange) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TranscriptLen) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TranscriptMismatches) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSproductPackagingProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_DuplicateInterval) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PolyAsiteNotPoint) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ImpFeatBadLoc) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UnnecessaryCitPubEquiv) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ImpCDShasTranslation) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ImpCDSnotPseudo) BOOST_FIXTURE_TEST_CASE (Test_SEQ_FEAT_MissingMRNAproduct, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_AbuttingIntervals) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CollidingGeneNames) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultiIntervalGene) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatContentDup) static void ChangeGoodNucProtSetIdToGenbankName (CRef< CSeq_entry > entry, string name) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadProductSeqId) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_RnaProductMismatch) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MissingCDSproduct) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadTrnaCodon) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadTrnaAA) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_OnlyGeneXrefs) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UTRdoesNotAbutCDS) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ExceptionProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SeqDataLenWrong) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadConflictFlag) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ConflictFlagSet) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_LocusTagProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_AltStartCodonException) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GenesInconsistent) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_DuplicateTranslExcept) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TranslExceptAndRnaEditing) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_NoNameForProtein) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSmRNAmismatch) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UnnecessaryException) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_LocusTagProductMismatch) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PseudoCdsViaGeneHasProduct) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MissingGeneXref) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatureCitationProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_NestedSeqLocMix) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CodonQualifierUsed) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadCharInAuthorName) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PolyATail) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSwithMultipleMRNAs) void TestMultipleEquivBioSources (const string &lineage, TSeqPos first_end, TSeqPos second_start, bool expected) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultipleEquivBioSources) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultipleEquivPublications) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadFullLengthFeature) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_RedundantFields) static void AddCDSAndProtForBigGoodNucProtSet (CRef< CSeq_entry > entry, string nuc_id, string prot_id, TSeqPos offset) static CRef< CSeq_entry > BuildBigGoodNucProtSet (void) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSwithNoMRNA) BOOST_FIXTURE_TEST_CASE (Test_SEQ_FEAT_FeatureProductInconsistency, CGenBankFixture) static void SetFeatureLocationBond (CRef< CSeq_feat > feat, string id, TSeqPos pt1, TSeqPos pt2) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ImproperBondLocation) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GeneXrefWithoutGene) void CreateReciprocalLinks (CSeq_feat &f1, CSeq_feat &f2) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SeqFeatXrefProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MissingTrnaAA) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CollidingFeatureIDs) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PolyAsignalNotRange) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_OldLocusTagMismtach) static CRef< CUser_field > MakeGoTerm (string text="something", string evidence="some evidence") void CheckGeneOntologyTermDuplicate (CRef< CSeq_feat > feat) void CheckGeneOntologyTermNotDuplicate (CRef< CSeq_feat > feat) CRef< CSeq_feat > MakeGeneOntologyFeat (CRef< CUser_field > term1, CRef< CUser_field > term2) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_DuplicateGeneOntologyTerm) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_InvalidInferenceValue) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_HypotheticalProteinMismatch) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SelfReferentialProduct) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ITSdoesNotAbutRRNA) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatureSeqIDCaseDifference) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatureLocationIsGi0) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GapFeatureProblem) static CRef< CSeq_entry > BuildGenProdSetBigNucProtSet (CRef< CSeq_id > nuc_id, CRef< CSeq_id > prot_id) static CRef< CSeq_entry > BuildGenProdSetWithBigProduct () BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ErroneousException) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_WholeLocation) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_EcNumberProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_VectorContamination) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MinusStrandProtein) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadProteinName) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GeneXrefWithoutLocus) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UTRdoesNotExtendToEnd) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDShasTooManyXs) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SuspiciousFrame) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TerminalXDiscrepancy) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UnnecessaryTranslExcept) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_InvalidMatchingReplace) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_NotSpliceConsensusDonor) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_NotSpliceConsensusAcceptor) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_RareSpliceConsensusDonor) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_RareSpliceConsensusDonor_VR_65) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SeqFeatXrefNotReciprocal) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_SeqFeatXrefFeatureMissing) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatureInsideGap) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatureCrossesGap) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadAuthorSuffix) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadAnticodonAA) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadAnticodonCodon) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadAnticodonStrand) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UndesiredGeneSynonym) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UndesiredProteinName) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_FeatureBeginsOrEndsInGap) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GeneOntologyTermMissingGOID) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PseudoRnaHasProduct) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_VR_803) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadRRNAcomponentOrder) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MissingGeneLocusTag) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultipleProtRefs) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadInternalCharacter) BOOST_AUTO_TEST_CASE (Test_VR_746) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadTrailingCharacter) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadTrailingHyphen) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_MultipleGeneOverlap) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadCharInAuthorLastName) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PseudoCDSmRNArange) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GeneXrefNeeded) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_RubiscoProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_UnqualifiedException) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ProteinNameHasPMID) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadGeneOntologyFormat) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_InconsistentGeneOntologyTermAndId) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_DuplicateGeneConflictingLocusTag) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ReplicatedGeneSequence) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_GeneXrefStrandProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_CDSmRNAXrefLocationProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_IdenticalGeneSymbolAndSynonym) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_PartialProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ProteinNameEndsInBracket) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ShortIntron) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_NeedsNote) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_RptUnitRangeProblem) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_TooManyInferenceAccessions) static CRef< CSeq_align > BuildSetAlign (CRef< CSeq_entry > entry) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_SeqIdProblem, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_DensegLenStart, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_SumLenStart, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_AlignDimSeqIdNotMatch, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_FastaLike, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_NullSegs, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_SegmentGap, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_AlignDimOne, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_Segtype, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_BlastAligns, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_PercentIdentity, CGenBankFixture) static CRef< CSeq_align > BuildSetDendiagAlign (CRef< CSeq_entry > entry) BOOST_FIXTURE_TEST_CASE (Test_SEQ_ALIGN_UnexpectedAlignmentType, CGenBankFixture) static CRef< CSeq_graph > BuildGoodByteGraph (CRef< CSeq_entry > entry, TSeqPos offset=0, TSeqPos len=kInvalidSeqPos) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphMin) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphMax) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphByteLen) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphOutOfOrder) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphSeqLitLen) BOOST_FIXTURE_TEST_CASE (Test_SEQ_GRAPH_GraphSeqLocLen, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphStartPhase) BOOST_FIXTURE_TEST_CASE (Test_SEQ_GRAPH_GraphDiffNumber, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphACGTScore) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphNScore) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphGapScore) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphOverlap) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphBioseqId) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphACGTScoreMany) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphNScoreMany) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphLocInvalid_1) BOOST_AUTO_TEST_CASE (Test_SEQ_GRAPH_GraphLocInvalid_2) BOOST_AUTO_TEST_CASE (Test_SEQ_ANNOT_AnnotIDs) BOOST_AUTO_TEST_CASE (Test_SEQ_ANNOT_AnnotLOCs) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_WrongQualOnCDS) BOOST_AUTO_TEST_CASE (Test_FixLatLonFormat) BOOST_AUTO_TEST_CASE (Test_FixLatLonCountry) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ShortExon) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_ExtraProteinFeature) BOOST_AUTO_TEST_CASE (Test_FixFormatDate) BOOST_AUTO_TEST_CASE (Test_DetectDateFormat) static void s_USAStateTest (string before, string after, CCountries::EStateCleanup expected) BOOST_AUTO_TEST_CASE (Test_USAStateCleanup) BOOST_AUTO_TEST_CASE (Test_NewFixCountry) BOOST_AUTO_TEST_CASE (Fix_Structured_Voucher) BOOST_AUTO_TEST_CASE (Test_CheckEnds) BOOST_AUTO_TEST_CASE (Test_SQD_313) BOOST_AUTO_TEST_CASE (Test_SQD_292) BOOST_AUTO_TEST_CASE (Test_SQD_1470) BOOST_AUTO_TEST_CASE (Test_SQD_1309) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_BadCDScomment) BOOST_AUTO_TEST_CASE (Test_SEQ_FEAT_InvalidFuzz) BOOST_AUTO_TEST_CASE (Test_SQD_1532) BOOST_AUTO_TEST_CASE (Test_SexQualifiers) BOOST_AUTO_TEST_CASE (TEST_DisableStrainForwarding) BOOST_AUTO_TEST_CASE (Test_AllNs) BOOST_AUTO_TEST_CASE (Test_SubSourceAutofix) BOOST_AUTO_TEST_CASE (Test_OrgModAutofix) BOOST_AUTO_TEST_CASE (Test_RmCultureNotes) BOOST_AUTO_TEST_CASE (Test_VR_28) BOOST_AUTO_TEST_CASE (Test_GP_9919) BOOST_AUTO_TEST_CASE (Test_RemoveLineageSourceNotes) BOOST_AUTO_TEST_CASE (Test_GB_3714) BOOST_AUTO_TEST_CASE (Test_SQD_2036) BOOST_AUTO_TEST_CASE (Test_VR_146) BOOST_AUTO_TEST_CASE (Test_VR_711) BOOST_AUTO_TEST_CASE (Test_IsLocationInFrame) CRef< CTaxon3_reply > s_CreateReplyWithMessage (const string &message) BOOST_AUTO_TEST_CASE (Test_Empty_Taxon_Reply) BOOST_AUTO_TEST_CASE (Test_VR_601) BOOST_AUTO_TEST_CASE (Test_VR_612) BOOST_AUTO_TEST_CASE (Test_VR_616) BOOST_AUTO_TEST_CASE (Test_BadLocation) BOOST_AUTO_TEST_CASE (Test_VR_78) BOOST_AUTO_TEST_CASE (Test_VR_166) BOOST_AUTO_TEST_CASE (TEST_TitleNotAppropriateForSet) BOOST_AUTO_TEST_CASE (Test_VR_664) BOOST_AUTO_TEST_CASE (Test_VR_478) BOOST_AUTO_TEST_CASE (Test_VR_630) BOOST_AUTO_TEST_CASE (Test_VR_660) void AddOrgmod (COrg_ref &org, const string &val, COrgMod::ESubtype subtype) void AddOrgmodDescriptor (CRef< CSeq_entry > entry, const string &val, COrgMod::ESubtype subtype) void AddOrgmodFeat (CRef< CSeq_entry > entry, const string &val, COrgMod::ESubtype subtype) void TestBulkSpecificHostFixList (const THostStringsVector &test_values) BOOST_AUTO_TEST_CASE (Test_SQD_4354) BOOST_AUTO_TEST_CASE (Test_BulkSpecificHostFix) BOOST_AUTO_TEST_CASE (Test_VR_787) BOOST_AUTO_TEST_CASE (Test_BulkSpecificHostFixIncremental) void AddStrainDescriptor (CSeq_entry &entry, const string &taxname, const string &strain, const string &lineage, TTaxId taxID) void TestOneStrain (const string &taxname, const string &strain, const string &lineage, TTaxId taxID, bool expect_err) void AddStrainDescriptorNew (CSeq_entry &entry, const string &taxname, const string &strain, const string &lineage, TTaxId taxID) void TestOneStrainNew (const string &taxname, const string &strain, const string &lineage, TTaxId taxID, TTaxId newTaxID, bool expect_err) BOOST_AUTO_TEST_CASE (Test_BulkStrainIncremental) BOOST_AUTO_TEST_CASE (VR_762) BOOST_AUTO_TEST_CASE (TEST_VR_477) BOOST_AUTO_TEST_CASE (Test_VR_35) BOOST_AUTO_TEST_CASE (TEST_VR_15) BOOST_FIXTURE_TEST_CASE (Test_VR_433, CGenBankFixture) BOOST_FIXTURE_TEST_CASE (Test_VR_708, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_TM_145) BOOST_AUTO_TEST_CASE (Test_VR_728) BOOST_AUTO_TEST_CASE (Test_VR_733) void TestOnePlasmid (const string &plasmid_name, bool expect_error) BOOST_AUTO_TEST_CASE (Test_VR_742) BOOST_AUTO_TEST_CASE (Test_VR_751) BOOST_AUTO_TEST_CASE (Test_TripletEncodesStopCodon) BOOST_AUTO_TEST_CASE (VR_758) void CheckLocalId (const string &id, const string &badchar) BOOST_AUTO_TEST_CASE (VR_V48) BOOST_AUTO_TEST_CASE (Test_IsDateInPast) void AddYear (CDate &add_date) void AddMonth (CDate &add_date) void AddDay (CDate &add_date) BOOST_AUTO_TEST_CASE (VR_778) BOOST_AUTO_TEST_CASE (Test_InconsistentPseudogeneValue) BOOST_AUTO_TEST_CASE (Test_InvalidPseudoQualifier) BOOST_AUTO_TEST_CASE (Test_InvalidRptUnitRange) BOOST_AUTO_TEST_CASE (Test_InvalidRptUnitSeqCharacters) BOOST_AUTO_TEST_CASE (Test_MismatchedAllele) BOOST_AUTO_TEST_CASE (Test_InvalidAlleleDuplicates) BOOST_AUTO_TEST_CASE (Test_InvalidOperonMatchesGene) BOOST_AUTO_TEST_CASE (Test_InvalidCompareRefSeqAccession) BOOST_AUTO_TEST_CASE (Test_InvalidCompareMissingVersion) BOOST_AUTO_TEST_CASE (Test_InvalidCompareBadAccession) BOOST_AUTO_TEST_CASE (Test_RegulatoryClassOtherNeedsNote) BOOST_AUTO_TEST_CASE (Test_UnparsedtRNAAnticodon) BOOST_AUTO_TEST_CASE (Test_UnparsedtRNAProduct) BOOST_AUTO_TEST_CASE (Test_rRNADoesNotHaveProduct) BOOST_AUTO_TEST_CASE (Test_MobileElementInvalidQualifier) BOOST_AUTO_TEST_CASE (Test_InvalidReplace) BOOST_AUTO_TEST_CASE (Test_InvalidVariationReplace) BOOST_AUTO_TEST_CASE (Test_InvalidProductOnGene) BOOST_AUTO_TEST_CASE (Test_InvalidCodonStart) BOOST_FIXTURE_TEST_CASE (Test_InconsistentBioSources_ConLocation, CGenBankFixture) void TestOverlappingRNAFeatures (const CSeq_loc &loc1, const CSeq_loc &loc2, bool expect_err) BOOST_AUTO_TEST_CASE (Test_BADRRNAcomponentOverlapTRNA) BOOST_AUTO_TEST_CASE (Test_VR_796) CRef< CSeq_id > MakeSmallGenomeSetNucId (size_t num) void AddGeneticCode (CSeq_feat &cds, CGenetic_code::C_E::TId code_id) CRef< CSeq_entry > BuildSmallGenomeSet (size_t num_np) void AddCdregionToSmallGenomeSet (CRef< CSeq_entry > entry, size_t cdr1_num, size_t cdr2_num, size_t cdr_pos, size_t p_pos) BOOST_AUTO_TEST_CASE (Test_GB_7601) BOOST_AUTO_TEST_CASE (Test_BadKeywordUnverified) BOOST_AUTO_TEST_CASE (Test_BINDoesNotMatch) void AddStrsField (CUser_object &user, const string &label, const string &val) BOOST_AUTO_TEST_CASE (Test_BadDBLink) BOOST_AUTO_TEST_CASE (Test_DBLinkOnSet) BOOST_AUTO_TEST_CASE (Test_AssemblyGapFeatureProblem) void MakeLeft (CSeq_loc &loc) void MakeRight (CSeq_loc &loc, TSeqPos stop) void TestUTRPair (bool add_gene, bool is_minus) BOOST_AUTO_TEST_CASE (Test_NoCDSbetweenUTRs) BOOST_AUTO_TEST_CASE (Test_FormatBadSpecificHostAlternateName) BOOST_FIXTURE_TEST_CASE (Test_VR_803, CGenBankFixture) BOOST_AUTO_TEST_CASE (Test_ExceptionRequiresLocusTag) CRef< CSeq_submit > MakeGeneious () BOOST_AUTO_TEST_CASE (Test_Geneious) void TestOneReplicon (CSubSource::ESubtype subtype, const string &val, const string &err_code, EDiagSev sev, const string &msg) void TestAlwaysBadReplicon (const string &val) void TestAlwaysGoodReplicon (const string &val) void TestRepliconTaxname (CSubSource::ESubtype subtype, bool expect_errs) void TestRepliconForbiddenWords (CSubSource::ESubtype subtype, bool expect_errs) BOOST_AUTO_TEST_CASE (Test_VR_793) void CheckHost (const CBioseq &seq, const string &host) void CheckOneSpecificHost (const string &orig, const string &newval) BOOST_AUTO_TEST_CASE (Test_VR_812) BOOST_AUTO_TEST_CASE (Test_BIOS_1527) BOOST_AUTO_TEST_CASE (Test_VR_814) BOOST_AUTO_TEST_CASE (Test_VR_819) BOOST_AUTO_TEST_CASE (Test_VR_824) void TestNewAccessionOnNuc (const string &accession, bool is_prot_acc, bool is_wgs) void TestNewAccessionOnStandaloneProt (const string &accession, bool is_nuc_acc, bool is_wgs) void TestNewAccessionOnNucProt (const string &n_acc, const string &p_acc, bool is_wgs) void TestNewAccessionAsInference (const string &acc) BOOST_AUTO_TEST_CASE (Test_SQD_4560) BOOST_AUTO_TEST_CASE (Test_VR_852) BOOST_AUTO_TEST_CASE (Test_VR_875) BOOST_AUTO_TEST_CASE (Test_RW_1063) BOOST_AUTO_TEST_CASE (Test_RW_1064) BOOST_AUTO_TEST_CASE (Test_SEQ_RW_1753) ◆ BAD_VALIDATOR ◆ EXCEPTION_PROBLEM_ERR #define EXCEPTION_PROBLEM_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "ExceptionProblem", "unclassified translation discrepancy is not a legal exception explanation"));Definition at line 12818 of file unit_test_validator.cpp.
◆ INTERNAL_STOP_ERR #define INTERNAL_STOP_ERR Value:"1 internal stops (and illegal start codon). Genetic code [0]"));
@ eDiag_Error
Error message.
Definition at line 12806 of file unit_test_validator.cpp.
◆ NO_PUB_ERR #define NO_PUB_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "NoPubFound", "No publications anywhere on this entire record."));Definition at line 12811 of file unit_test_validator.cpp.
◆ NO_SRC_ERR #define NO_SRC_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Error, "NoSourceDescriptor", "No source information included on this record."));Definition at line 12820 of file unit_test_validator.cpp.
◆ NO_STOP_ERR ◆ NO_SUB_ERR #define NO_SUB_ERR expected_errors.push_back(new CExpectedError("lcl|nuc", eDiag_Info, "MissingPubRequirement", "No submission citation anywhere on this entire record."));Definition at line 12816 of file unit_test_validator.cpp.
◆ PROT_LEN_ERR ◆ START_CODON_AND_INT_STOP_ERR #define START_CODON_AND_INT_STOP_ERR Value:"Illegal start codon (and 1 internal stops). Probably wrong genetic code [0]"));
Definition at line 12803 of file unit_test_validator.cpp.
◆ test_gene_syn #define test_gene_syn ( name ) Value:gene->SetData().SetGene().ResetSyn(); \
gene->SetData().SetGene().SetSyn().push_back(name); \
msg = "Uninformative gene synonym '"; \
msg.append(name); \
msg.append("'"); \
expected_errors[0]->SetErrMsg(
msg); \
eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors);
static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)
Definition at line 18344 of file unit_test_validator.cpp.
◆ test_undesired_protein_name #define test_undesired_protein_name ( name ) Value: prot->SetData().SetProt().ResetName(); \
prot->SetData().SetProt().SetName().push_back(name); \
msg = "Uninformative protein name '"; \
msg.append(name); \
msg.append("'"); \
expected_errors[0]->SetErrMsg(
msg); \
eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors);
Definition at line 18420 of file unit_test_validator.cpp.
◆ TESTPOPPHYMUTECO #define TESTPOPPHYMUTECO ( seh, entry ) Value:eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors); \
eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors); \
eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors); \
eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors); \
scope.RemoveTopLevelSeqEntry(seh);
\seh = scope.AddTopLevelSeqEntry(*entry); \
eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors);
@ eClass_pop_set
population study
@ eClass_phy_set
phylogenetic study
@ eClass_mut_set
set of mutations
@ eClass_eco_set
ecological sample study
@ eClass_small_genome_set
viral segments or mitochondrial minicircles
@ e_Title
a title for this sequence
void RemoveDescriptorType(CRef< objects::CSeq_entry > entry, objects::CSeqdesc::E_Choice desc_choice)
Definition at line 11203 of file unit_test_validator.cpp.
◆ TESTWGS #define TESTWGS ( seh, entry ) Value:eval = validator.Validate(seh, options); \
CheckErrors(*eval, expected_errors);
@ eClass_wgs_set
whole genome shotgun project
Definition at line 11223 of file unit_test_validator.cpp.
◆ THostStringsVector ◆ AddCdregionToSmallGenomeSet() void AddCdregionToSmallGenomeSet ( CRef< CSeq_entry > entry, size_t cdr1_num, size_t cdr2_num, size_t cdr_pos, size_t p_pos ) ◆ AddCDSAndProtForBigGoodNucProtSet() ◆ AddChromosomeNoLocation() [1/2] ◆ AddChromosomeNoLocation() [2/2]Definition at line 417 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), CSeq_id::AsFastaString(), CBioseq_set_Base::eClass_nuc_prot, eGetId_Best, CBioseq_set_Base::GetClass(), GetId(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_entry_Base::GetSeq(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
◆ AddDay() void AddDay ( CDate & add_date ) ◆ AddGenbankKeyword() ◆ AddGeneticCode() ◆ AddMonth() void AddMonth ( CDate & add_date ) ◆ AddOrgmod() ◆ AddOrgmodDescriptor() ◆ AddOrgmodFeat() ◆ AddRefGeneTrackingUserObject()Definition at line 1993 of file unit_test_validator.cpp.
References CUser_object::eObjectType_RefGeneTracking, CUser_object::eRefGeneTrackingStatus_INFERRED, CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::SetDescr(), CBioseq_set_Base::SetDescr(), CUser_object::SetObjectType(), CUser_object::SetRefGeneTrackingStatus(), CSeq_entry_Base::SetSeq(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetUser().
Referenced by BOOST_AUTO_TEST_CASE().
◆ AddSgmlError() ◆ AddStrainDescriptor() ◆ AddStrainDescriptorNew() ◆ AddStrsField() ◆ AddTpaAssemblyUserObject() ◆ AddYear() void AddYear ( CDate & add_date ) ◆ AdjustGap() ◆ BOOST_AUTO_TEST_CASE() [1/458] BOOST_AUTO_TEST_CASE ( Fix_Structured_Voucher ) ◆ BOOST_AUTO_TEST_CASE() [2/458] BOOST_AUTO_TEST_CASE ( Test_AllNs ) ◆ BOOST_AUTO_TEST_CASE() [3/458] BOOST_AUTO_TEST_CASE ( Test_AssemblyGapFeatureProblem ) ◆ BOOST_AUTO_TEST_CASE() [4/458] BOOST_AUTO_TEST_CASE ( Test_BadBioSourceFrequencyValue )Definition at line 6800 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, CSubSource_Base::eSubtype_frequency, SetLineage(), SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [5/458] BOOST_AUTO_TEST_CASE ( Test_BadDBLink )Definition at line 24482 of file unit_test_validator.cpp.
References AddStrsField(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, CUser_object::eObjectType_DBLink, CBioseq_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [6/458] BOOST_AUTO_TEST_CASE ( Test_BadHTGSeq )Definition at line 3908 of file unit_test_validator.cpp.
References AddGenbankKeyword(), BuildGoodDeltaSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, RemoveDeltaSeqGaps(), SetTech(), and STANDARD_SETUP_NAME.
◆ BOOST_AUTO_TEST_CASE() [7/458] BOOST_AUTO_TEST_CASE ( Test_BadKeywordUnverified )Definition at line 24422 of file unit_test_validator.cpp.
References AddGenbankKeyword(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CUser_object::eObjectType_Unverified, CMolInfo_Base::eTech_barcode, CBioseq_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSeq(), SetTech(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [8/458] BOOST_AUTO_TEST_CASE ( Test_BadLocation )Definition at line 22149 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodEcoSet(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Title, CBioseq_set_Base::eClass_small_genome_set, eDiag_Error, CBioSource_Base::eGenome_chloroplast, RemoveDescriptorType(), CBioseq_set_Base::SetClass(), CSeq_feat_Base::SetData(), SetGenome(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [9/458] BOOST_AUTO_TEST_CASE ( Test_BadPlastidName )Definition at line 6757 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioSource_Base::eGenome_unknown, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, SetGenome(), SetLineage(), SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [10/458] BOOST_AUTO_TEST_CASE ( Test_BadProteinMoltype )Definition at line 1295 of file unit_test_validator.cpp.
References BuildGoodProtSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CSeq_inst_Base::eStrand_ds, CSeq_inst_Base::eStrand_mixed, CSeq_inst_Base::eStrand_not_set, CSeq_inst_Base::eStrand_other, CSeq_inst_Base::eStrand_ss, CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [11/458] BOOST_AUTO_TEST_CASE ( Test_BADRRNAcomponentOverlapTRNA ) ◆ BOOST_AUTO_TEST_CASE() [12/458] BOOST_AUTO_TEST_CASE ( Test_BadTextInSourceQualifier )Definition at line 6540 of file unit_test_validator.cpp.
References AddGoodSourceFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_metagenomic, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_transgenic, SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [13/458] BOOST_AUTO_TEST_CASE ( Test_BadVariety ) ◆ BOOST_AUTO_TEST_CASE() [14/458] BOOST_AUTO_TEST_CASE ( Test_BINDoesNotMatch )Definition at line 24445 of file unit_test_validator.cpp.
References CSerialObject::Assign(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CUser_field_Base::SetData(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_field_Base::SetLabel(), CSeq_entry_Base::SetSeq(), SetTaxname(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [15/458] BOOST_AUTO_TEST_CASE ( Test_BIOS_1527 ) ◆ BOOST_AUTO_TEST_CASE() [16/458] BOOST_AUTO_TEST_CASE ( Test_BioSourceMissing )Definition at line 4529 of file unit_test_validator.cpp.
References AddGoodSource(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Source, eDiag_Fatal, eDiag_Warning, RemoveDescriptorType(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [17/458] BOOST_AUTO_TEST_CASE ( Test_BulkSpecificHostFix )Definition at line 22545 of file unit_test_validator.cpp.
References AddOrgmod(), AddOrgmodDescriptor(), AddOrgmodFeat(), CTaxValidationAndCleanup::AdjustOrgRefsWithSpecificHostReply(), CTaxValidationAndCleanup::AdjustOrgRefsWithTaxLookupReply(), CSerialObject::Assign(), BuildGoodSeq(), NStr::Equal(), variation::Equals(), COrgMod_Base::eSubtype_nat_host, CTaxValidationAndCleanup::GetDesc(), CTaxValidationAndCleanup::GetFeat(), COrgName_Base::GetMod(), COrg_ref_Base::GetOrgname(), CTaxValidationAndCleanup::GetSpecificHostLookupRequest(), CTaxValidationAndCleanup::GetTaxonomyLookupRequest(), CTaxValidationAndCleanup::Init(), n, CTaxValidationAndCleanup::NumDescs(), CTaxValidationAndCleanup::NumFeats(), om, CTaxon3::SendOrgRefList(), CSeq_feat_Base::SetData(), CBioSource_Base::SetOrg(), COrg_ref_Base::SetOrgname(), CSeqdesc_Base::SetSource(), COrg_ref_Base::SetTaxname(), TestBulkSpecificHostFixList(), and CTaxon3::yes.
◆ BOOST_AUTO_TEST_CASE() [18/458] BOOST_AUTO_TEST_CASE ( Test_BulkSpecificHostFixIncremental )Definition at line 22750 of file unit_test_validator.cpp.
References AddOrgmod(), AddOrgmodDescriptor(), AddOrgmodFeat(), CTaxValidationAndCleanup::AdjustOrgRefsForSpecificHosts(), BuildGoodSeq(), chunk_size, COrgMod_Base::eSubtype_nat_host, CTaxValidationAndCleanup::GetSpecificHostLookupRequest(), i, CTaxValidationAndCleanup::IncrementalSpecificHostMapUpdate(), CTaxValidationAndCleanup::Init(), CTaxValidationAndCleanup::IsSpecificHostMapUpdateComplete(), kEmptyStr, len, min(), CTaxon3::SendOrgRefList(), COrg_ref_Base::SetTaxname(), and CTaxon3::yes.
◆ BOOST_AUTO_TEST_CASE() [19/458] BOOST_AUTO_TEST_CASE ( Test_BulkStrainIncremental )Definition at line 22903 of file unit_test_validator.cpp.
References AddStrainDescriptor(), BuildGoodSeq(), chunk_size, env, CNcbiApplicationAPI::GetEnvironment(), CTaxValidationAndCleanup::GetStrainLookupRequest(), i, CTaxValidationAndCleanup::IncrementalStrainMapUpdate(), CTaxValidationAndCleanup::Init(), CNcbiApplication::Instance(), CTaxValidationAndCleanup::IsStrainMapUpdateComplete(), kEmptyStr, len, min(), CTaxon3::SendOrgRefList(), TAX_ID_CONST, TestOneStrain(), TestOneStrainNew(), NStr::ToLower(), CTaxon3::yes, and ZERO_TAX_ID.
◆ BOOST_AUTO_TEST_CASE() [20/458] BOOST_AUTO_TEST_CASE ( Test_CheckEnds )Definition at line 21230 of file unit_test_validator.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckBioseqEndsForNAndGap(), eBioseqEndIsType_All, eBioseqEndIsType_Last, eBioseqEndIsType_None, CObjectManager::GetInstance(), CSeq_entry_Handle::GetSeq(), CScope::RemoveTopLevelSeqEntry(), CBioseq_Base::SetInst(), and CSeq_entry_Base::SetSeq().
◆ BOOST_AUTO_TEST_CASE() [21/458] BOOST_AUTO_TEST_CASE ( Test_CollidingLocusTags )Definition at line 1153 of file unit_test_validator.cpp.
References CScope::AddTopLevelSeqEntry(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, CValidator::eVal_far_fetch_mrna_products, CValidator::eVal_indexer_version, CValidator::eVal_need_isojta, CValidator::eVal_use_entrez, CValidator::eVal_validate_id_set, CObjectManager::GetInstance(), MSerial_AsnText, sc_TestEntryCollidingLocusTags, and CValidator::Validate().
◆ BOOST_AUTO_TEST_CASE() [22/458] BOOST_AUTO_TEST_CASE ( Test_CompleteCircleProblem )Definition at line 3870 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Warning, CSeq_inst_Base::eTopology_circular, SetCompleteness(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [23/458] BOOST_AUTO_TEST_CASE ( Test_CompleteTitleProblem )Definition at line 3826 of file unit_test_validator.cpp.
References BuildGoodDeltaSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Warning, SetCompleteness(), CBioseq_Base::SetId(), SetLineage(), CSeq_entry_Base::SetSeq(), SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [24/458] BOOST_AUTO_TEST_CASE ( Test_DBLinkOnSet ) ◆ BOOST_AUTO_TEST_CASE() [25/458] BOOST_AUTO_TEST_CASE ( Test_DeltaComponentIsGi0 ) ◆ BOOST_AUTO_TEST_CASE() [26/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadAltitude ) ◆ BOOST_AUTO_TEST_CASE() [27/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadCollectionCode ) ◆ BOOST_AUTO_TEST_CASE() [28/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadCollectionDate ) ◆ BOOST_AUTO_TEST_CASE() [29/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadCountryCapitalization ) ◆ BOOST_AUTO_TEST_CASE() [30/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadInstitutionCode ) ◆ BOOST_AUTO_TEST_CASE() [31/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadKeyword )Definition at line 9117 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, CMolInfo_Base::eTech_barcode, CBioseq_Base::SetDescr(), CSeqdesc_Base::SetGenbank(), CGB_block_Base::SetKeywords(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [32/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadOrganelle )Definition at line 5406 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_macronuclear, CBioSource_Base::eGenome_nucleomorph, CBioSource_Base::eGenome_plastid, SetDrosophila_melanogaster(), SetGenome(), SetSebaea_microphylla(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [33/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadOrgMod )Definition at line 5536 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Warning, COrgMod_Base::eSubtype_common, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_type_material, COrgMod_Base::eSubtype_variety, SetCommon(), SetOrgMod(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [34/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadPCRPrimerName ) ◆ BOOST_AUTO_TEST_CASE() [35/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadPCRPrimerSequence )Definition at line 7524 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_rev_primer_seq, CPCRPrimerSeq::IsValid(), CBioseq_Base::SetDescr(), CPCRReaction_Base::SetForward(), CPCRPrimer_Base::SetName(), CPCRReaction_Base::SetReverse(), CPCRPrimer_Base::SetSeq(), CSeq_entry_Base::SetSeq(), SetSubSource(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [36/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadPunctuation ) ◆ BOOST_AUTO_TEST_CASE() [37/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadSpecificHost ) ◆ BOOST_AUTO_TEST_CASE() [38/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadStructuredCommentFormat )Definition at line 9267 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, NStr::Equal(), i, CUser_object_Base::ResetData(), CUser_field_Base::SetData(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_field_Base::SetLabel(), CSeq_entry_Base::SetSeq(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [39/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BadSubSource ) ◆ BOOST_AUTO_TEST_CASE() [40/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BioSourceDbTagConflict ) ◆ BOOST_AUTO_TEST_CASE() [41/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BioSourceInconsistency )Definition at line 6828 of file unit_test_validator.cpp.
References AddGoodSourceFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, eDiag_Error, eDiag_Warning, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_unknown, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, COrgMod_Base::eSubtype_breed, CSubSource_Base::eSubtype_cell_line, CSubSource_Base::eSubtype_cell_type, COrgMod_Base::eSubtype_cultivar, CSubSource_Base::eSubtype_dev_stage, CSubSource_Base::eSubtype_environmental_sample, COrgMod_Base::eSubtype_gb_synonym, CSubSource_Base::eSubtype_germline, COrgMod_Base::eSubtype_isolate, CSubSource_Base::eSubtype_isolation_source, CSubSource_Base::eSubtype_mating_type, COrgMod_Base::eSubtype_metagenome_source, CSubSource_Base::eSubtype_metagenomic, COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_rearranged, CSubSource_Base::eSubtype_sex, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_synonym, CSubSource_Base::eSubtype_tissue_type, CSubSource_Base::eSubtype_transgenic, f, SetBiomol(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), SetDiv(), SetFocus(), SetGenome(), CBioseq_Base::SetInst(), SetLineage(), SetOrgMod(), CSeq_entry_Base::SetSeq(), SetSubSource(), SetTaxname(), SetTaxon(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [42/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BioSourceNeedsChromosome )Definition at line 9517 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eCompleteness_complete, eDiag_Info, eDiag_Warning, CBioSource_Base::eGenome_chromosome, CSeq_inst_Base::eMol_rna, SetBiomol(), SetCompleteness(), SetGenome(), CBioseq_Base::SetInst(), SetLineage(), CSeq_entry_Base::SetSeq(), SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [43/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BioSourceNeedsFocus ) ◆ BOOST_AUTO_TEST_CASE() [44/458] BOOST_AUTO_TEST_CASE ( Test_Descr_BioSourceOnProtein ) ◆ BOOST_AUTO_TEST_CASE() [45/458] BOOST_AUTO_TEST_CASE ( Test_Descr_ChromosomeLocation ) ◆ BOOST_AUTO_TEST_CASE() [46/458] BOOST_AUTO_TEST_CASE ( Test_Descr_CollidingPublications )Definition at line 6222 of file unit_test_validator.cpp.
References BuildGoodAuthor(), BuildGoodPubSeqdesc(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, ENTREZ_ID_CONST, CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CBioseq_Base::SetDescr(), CPub_Base::SetMuid(), CPub_Base::SetPmid(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), CCit_art_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [47/458] BOOST_AUTO_TEST_CASE ( Test_Descr_DuplicatePCRPrimerSequence )Definition at line 7777 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_rev_primer_seq, r1, r2, s_ArePrimersUnique(), CPCRReactionSet_Base::Set(), CPCRPrimer_Base::SetName(), CPCRPrimer_Base::SetSeq(), SetSubSource(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [48/458] BOOST_AUTO_TEST_CASE ( Test_Descr_FakeStructuredComment ) ◆ BOOST_AUTO_TEST_CASE() [49/458] BOOST_AUTO_TEST_CASE ( Test_Descr_FastaBracketTitle )Definition at line 7353 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CDbtag_Base::SetDb(), CSeq_id_Base::SetGeneral(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), CDbtag_Base::SetTag(), SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [50/458] BOOST_AUTO_TEST_CASE ( Test_Descr_IdenticalInstitutionCode ) ◆ BOOST_AUTO_TEST_CASE() [51/458] BOOST_AUTO_TEST_CASE ( Test_Descr_InconsistentBiosources )Definition at line 5216 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Title, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_pop_set, eDiag_Error, eDiag_Warning, first(), RemoveDescriptorType(), CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetDescr(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetTaxname(), SetTaxon(), CSeqdesc_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [52/458] BOOST_AUTO_TEST_CASE ( Test_Descr_InconsistentProteinTitle ) ◆ BOOST_AUTO_TEST_CASE() [53/458] BOOST_AUTO_TEST_CASE ( Test_Descr_IncorrectlyFormattedVoucherID ) ◆ BOOST_AUTO_TEST_CASE() [54/458] BOOST_AUTO_TEST_CASE ( Test_Descr_InvalidForType )Definition at line 4549 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), AddTpaAssemblyUserObject(), BuildGoodProtSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Method, CSeqdesc_Base::e_Modif, CSeqdesc_Base::e_Mol_type, CSeqdesc_Base::e_Org, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_genomic_mRNA, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_ncRNA, CMolInfo_Base::eBiomol_other, CMolInfo_Base::eBiomol_other_genetic, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_rRNA, CMolInfo_Base::eBiomol_scRNA, CMolInfo_Base::eBiomol_snoRNA, CMolInfo_Base::eBiomol_snRNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_transcribed_RNA, CMolInfo_Base::eBiomol_tRNA, CMolInfo_Base::eBiomol_unknown, eDiag_Error, eDiag_Info, eDiag_Warning, eGIBB_method_other, eGIBB_mod_dna, eGIBB_mod_rna, eGIBB_mol_genomic, eGIBB_mol_genomic_mRNA, eGIBB_mol_mRNA, eGIBB_mol_other, eGIBB_mol_other_genetic, eGIBB_mol_peptide, eGIBB_mol_pre_mRNA, eGIBB_mol_rRNA, eGIBB_mol_scRNA, eGIBB_mol_snRNA, eGIBB_mol_tRNA, eGIBB_mol_unknown, CBioSource_Base::eOrigin_synthetic, CMolInfo_Base::eTech_barcode, CMolInfo_Base::eTech_both, CMolInfo_Base::eTech_composite_wgs_htgs, CMolInfo_Base::eTech_concept_trans, CMolInfo_Base::eTech_concept_trans_a, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_genemap, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_physmap, CMolInfo_Base::eTech_seq_pept, CMolInfo_Base::eTech_seq_pept_homol, CMolInfo_Base::eTech_seq_pept_overlap, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_wgs, RemoveDescriptorType(), CRef< C, Locker >::Reset(), SetBiomol(), CSeq_entry::SetDescr(), CBioseq_Base::SetDescr(), SetErrorsAccessions(), CBioseq_Base::SetId(), CSeqdesc_Base::SetMethod(), CSeqdesc_Base::SetModif(), CSeqdesc_Base::SetMol_type(), CSeqdesc_Base::SetOrg(), SetSebaea_microphylla(), CSeq_entry_Base::SetSeq(), SetSynthetic_construct(), COrg_ref_Base::SetTaxname(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [55/458] BOOST_AUTO_TEST_CASE ( Test_Descr_LatLonCountry ) ◆ BOOST_AUTO_TEST_CASE() [56/458] BOOST_AUTO_TEST_CASE ( Test_Descr_LatLonFormat ) ◆ BOOST_AUTO_TEST_CASE() [57/458] BOOST_AUTO_TEST_CASE ( Test_Descr_LatLonRange ) ◆ BOOST_AUTO_TEST_CASE() [58/458] BOOST_AUTO_TEST_CASE ( Test_Descr_LatLonState ) ◆ BOOST_AUTO_TEST_CASE() [59/458] BOOST_AUTO_TEST_CASE ( Test_Descr_LatLonValue ) ◆ BOOST_AUTO_TEST_CASE() [60/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MissingChromosome )Definition at line 9183 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_chloroplast, CBioSource_Base::eGenome_chromoplast, CBioSource_Base::eGenome_cyanelle, CBioSource_Base::eGenome_hydrogenosome, CBioSource_Base::eGenome_kinetoplast, CBioSource_Base::eGenome_leucoplast, CBioSource_Base::eGenome_mitochondrion, CBioSource_Base::eGenome_nucleomorph, CBioSource_Base::eGenome_proplastid, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_linkage_group, SetDiv(), SetGenome(), CBioseq_Base::SetId(), SetLineage(), CSeq_entry_Base::SetSeq(), SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [61/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MissingKeyword )Definition at line 437 of file unit_test_validator.cpp.
References CUser_object::AddField(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, CUser_object::eParse_String, CBioseq_Base::SetDescr(), CSeqdesc_Base::SetGenbank(), CGB_block_Base::SetKeywords(), CSeq_entry_Base::SetSeq(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [62/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MissingLineage )Definition at line 5292 of file unit_test_validator.cpp.
References BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, ResetOrgname(), CBioseq_Base::SetId(), SetLineage(), CSeq_entry_Base::SetSeq(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [63/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MissingText )Definition at line 7393 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CSeqdesc_Base::SetComment(), CBioseq_Base::SetDescr(), CSeqdesc_Base::SetName(), CSeqdesc_Base::SetRegion(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [64/458] BOOST_AUTO_TEST_CASE ( Test_Descr_ModifyPCRPrimer ) ◆ BOOST_AUTO_TEST_CASE() [65/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MolInfoConflictsWithBioSource ) ◆ BOOST_AUTO_TEST_CASE() [66/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MultipleBioSources ) ◆ BOOST_AUTO_TEST_CASE() [67/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MultipleChromosomes ) ◆ BOOST_AUTO_TEST_CASE() [68/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MultipleComments ) ◆ BOOST_AUTO_TEST_CASE() [69/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MultipleNames ) ◆ BOOST_AUTO_TEST_CASE() [70/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MultipleSourceQualifiers )Definition at line 8777 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource::NCBI_UseGeoLocNameForCountry(), SetSubSource(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [71/458] BOOST_AUTO_TEST_CASE ( Test_Descr_MultipleTitles ) ◆ BOOST_AUTO_TEST_CASE() [72/458] BOOST_AUTO_TEST_CASE ( Test_Descr_NoMolInfoFound ) ◆ BOOST_AUTO_TEST_CASE() [73/458] BOOST_AUTO_TEST_CASE ( Test_Descr_NoOrganismInTitle )Definition at line 9146 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), BuildGoodSeq(), ChangeProtId(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CTextseq_id_Base::SetAccession(), CBioseq_Base::SetId(), CSeq_id_Base::SetOther(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [74/458] BOOST_AUTO_TEST_CASE ( Test_Descr_NoOrgFound )Definition at line 5085 of file unit_test_validator.cpp.
References AddGoodSource(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Source, eDiag_Error, eDiag_Fatal, eDiag_Warning, RemoveDescriptorType(), CPatent_seq_id_Base::SetCit(), SetErrorsAccessions(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CBioseq_set_Base::SetSeq_set(), CPatent_seq_id_Base::SetSeqid(), CSeq_entry_Base::SetSet(), SetTaxname(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [75/458] BOOST_AUTO_TEST_CASE ( Test_Descr_NoPubFound )Definition at line 4999 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), AddGoodPub(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Pub, eDiag_Error, eDiag_Info, eDiag_Warning, CMolInfo_Base::eTech_wgs, MakeGps(), RemoveDescriptorType(), CTextseq_id_Base::SetAccession(), CSeq_id_Base::SetGpipe(), CSeq_id_Base::SetOther(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [76/458] BOOST_AUTO_TEST_CASE ( Test_Descr_NoTaxonID ) ◆ BOOST_AUTO_TEST_CASE() [77/458] BOOST_AUTO_TEST_CASE ( Test_Descr_ObsoleteSourceLocation ) ◆ BOOST_AUTO_TEST_CASE() [78/458] BOOST_AUTO_TEST_CASE ( Test_Descr_ObsoleteSourceQual ) ◆ BOOST_AUTO_TEST_CASE() [79/458] BOOST_AUTO_TEST_CASE ( Test_Descr_RefGeneTrackingIllegalStatus ) ◆ BOOST_AUTO_TEST_CASE() [80/458] BOOST_AUTO_TEST_CASE ( Test_Descr_RefGeneTrackingOnNonRefSeq )Definition at line 6440 of file unit_test_validator.cpp.
References AddRefGeneTrackingUserObject(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CBioseq_set_Base::eClass_genbank, eDiag_Error, CBioseq_set_Base::SetClass(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [81/458] BOOST_AUTO_TEST_CASE ( Test_Descr_RefGeneTrackingWithoutStatus )Definition at line 6143 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CUser_object::eObjectType_RefGeneTracking, CUser_field_Base::SetData(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CUser_field_Base::SetLabel(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [82/458] BOOST_AUTO_TEST_CASE ( Test_Descr_ReplacedCountryCode ) ◆ BOOST_AUTO_TEST_CASE() [83/458] BOOST_AUTO_TEST_CASE ( Test_Descr_SerialInComment ) ◆ BOOST_AUTO_TEST_CASE() [84/458] BOOST_AUTO_TEST_CASE ( Test_Descr_StructuredCommentPrefixOrSuffixMissing )Definition at line 9671 of file unit_test_validator.cpp.
References CUser_object::AddField(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, CUser_object::eParse_String, CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [85/458] BOOST_AUTO_TEST_CASE ( Test_Descr_StructuredSourceNote ) ◆ BOOST_AUTO_TEST_CASE() [86/458] BOOST_AUTO_TEST_CASE ( Test_Descr_TaxonomyLookupProblem ) ◆ BOOST_AUTO_TEST_CASE() [87/458] BOOST_AUTO_TEST_CASE ( Test_Descr_TitleHasPMID ) ◆ BOOST_AUTO_TEST_CASE() [88/458] BOOST_AUTO_TEST_CASE ( Test_Descr_TransgenicProblem ) ◆ BOOST_AUTO_TEST_CASE() [89/458] BOOST_AUTO_TEST_CASE ( Test_Descr_UnbalancedParentheses )Definition at line 8905 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CheckUnbalancedParenthesesOrgMod(), CheckUnbalancedParenthesesSubSource(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_environmental_sample, CSubSource_Base::eSubtype_germline, CSubSource_Base::eSubtype_haplogroup, COrgMod_Base::eSubtype_metagenome_source, CSubSource_Base::eSubtype_metagenomic, COrgMod_Base::eSubtype_old_lineage, COrgMod_Base::eSubtype_old_name, COrgMod_Base::eSubtype_other, CSubSource_Base::eSubtype_other, CSubSource_Base::eSubtype_rearranged, COrgMod_Base::eSubtype_strain, CSubSource_Base::eSubtype_transgenic, OrgModHasOtherRules(), SetOrgMod(), SetSebaea_microphylla(), SetTaxname(), STANDARD_SETUP, and SubSourceHasOtherRules().
◆ BOOST_AUTO_TEST_CASE() [90/458] BOOST_AUTO_TEST_CASE ( Test_Descr_Unknown ) ◆ BOOST_AUTO_TEST_CASE() [91/458] BOOST_AUTO_TEST_CASE ( Test_Descr_UnnecessaryBioSourceFocus ) ◆ BOOST_AUTO_TEST_CASE() [92/458] BOOST_AUTO_TEST_CASE ( Test_Descr_UnstructuredVoucher ) ◆ BOOST_AUTO_TEST_CASE() [93/458] BOOST_AUTO_TEST_CASE ( Test_Descr_UnwantedCompleteFlag )Definition at line 6170 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Warning, CBioSource_Base::eOrigin_artificial, CMolInfo_Base::eTech_htgs_3, SetCompleteness(), CBioseq_Base::SetId(), SetLineage(), SetOrigin(), CSeq_entry_Base::SetSeq(), SetTech(), SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [94/458] BOOST_AUTO_TEST_CASE ( Test_Descr_WrongVoucherType ) ◆ BOOST_AUTO_TEST_CASE() [95/458] BOOST_AUTO_TEST_CASE ( Test_DetectDateFormat ) ◆ BOOST_AUTO_TEST_CASE() [96/458] BOOST_AUTO_TEST_CASE ( TEST_DisableStrainForwarding ) ◆ BOOST_AUTO_TEST_CASE() [97/458] BOOST_AUTO_TEST_CASE ( Test_DSmRNA )Definition at line 4479 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, eDiag_Error, CSeq_inst_Base::eMol_rna, CSeq_inst_Base::eStrand_ds, CSeq_inst_Base::eStrand_mixed, CSeq_inst_Base::eStrand_not_set, CSeq_inst_Base::eStrand_other, CSeq_inst_Base::eStrand_ss, SetBiomol(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [98/458] BOOST_AUTO_TEST_CASE ( Test_Empty_Taxon_Reply ) ◆ BOOST_AUTO_TEST_CASE() [99/458] BOOST_AUTO_TEST_CASE ( Test_ExceptionRequiresLocusTag ) ◆ BOOST_AUTO_TEST_CASE() [100/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_CdTransFail )Definition at line 12776 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, eDiagFilter_All, GetCDSFromGoodNucProtSet(), HasNoStop(), SetDiagFilter(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [101/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_ExceptInconsistent )Definition at line 13243 of file unit_test_validator.cpp.
References CSeq_feat::AddQualifier(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::ResetExcept_text(), CSeq_feat_Base::ResetQual(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [102/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_GenCodeMismatch )Definition at line 13306 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_unknown, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), SetGcode(), SetGenome(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [103/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_GeneRefHasNoData ) ◆ BOOST_AUTO_TEST_CASE() [104/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_InternalStop )Definition at line 12928 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eErr_SEQ_FEAT_InternalStop, format, GetCDSFromGoodNucProtSet(), HasBadStartCodon(), HasInternalStop(), HasNoStop(), HasStopInProtein(), MakeGeneForFeature(), CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [105/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_InvalidForType )Definition at line 11581 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), BuildGoodSeq(), ChangeErrorAcc(), ChangeId(), ChangeProtId(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, eDiag_Error, eDiag_Info, eDiag_Warning, CSeq_inst_Base::eMol_rna, CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_preprotein, CProt_ref_Base::eProcessed_signal_peptide, CProt_ref_Base::eProcessed_transit_peptide, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_mRNA, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), ncbi::grid::netcache::search::fields::key, prot, CBioseq_Base::ResetAnnot(), rna, CTextseq_id_Base::SetAccession(), SetBiomol(), CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeq_id_Base::SetOther(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CObject_id_Base::SetStr(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [106/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_InvalidType ) ◆ BOOST_AUTO_TEST_CASE() [107/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_MisMatchAA ) ◆ BOOST_AUTO_TEST_CASE() [108/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_MissingQualOnImpFeat ) ◆ BOOST_AUTO_TEST_CASE() [109/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_MixedStrand )Definition at line 12665 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, eNa_strand_minus, eNa_strand_plus, MakeMixLoc(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [110/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_NoProtein ) ◆ BOOST_AUTO_TEST_CASE() [111/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_NoProtRefFound )Definition at line 13175 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CBioseq_Base::ResetAnnot(), CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [112/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_NoStop ) ◆ BOOST_AUTO_TEST_CASE() [113/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_OrfCdsHasProduct ) ◆ BOOST_AUTO_TEST_CASE() [114/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_PartialProblem )Definition at line 11921 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), AddProtFeat(), BuildGoodNucProtSet(), BuildGoodSeq(), BuildGoodSpliceNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::eCompleteness_partial, CMolInfo_Base::eCompleteness_unknown, eDiag_Critical, eDiag_Error, eDiag_Info, eDiag_Warning, eExtreme_Biological, CSeq_inst_Base::eMol_rna, first(), GetCDSFromGoodNucProtSet(), last(), MakeMixLoc(), CRef< C, Locker >::Reset(), CBioseq_Base::ResetAnnot(), CBioseq_set_Base::ResetAnnot(), CTextseq_id_Base::SetAccession(), CBioseq_Base::SetAnnot(), SetBiomol(), SetCompleteness(), CSeq_feat_Base::SetData(), SetDiv(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetNull(), CSeq_id_Base::SetOther(), CSeq_feat_Base::SetPartial(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [115/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_ProtRefHasNoData ) ◆ BOOST_AUTO_TEST_CASE() [116/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_Range )Definition at line 12526 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, eDiagFilter_All, CCdregion_Base::eFrame_three, CRNA_ref_Base::eType_tRNA, GetCDSFromGoodNucProtSet(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_entry_Base::GetSeq(), kInvalidSeqPos, RetranslateCdsForNucProtSet(), CSeq_feat_Base::SetData(), SetDiagFilter(), CBioseq_Base::SetId(), CCode_break_Base::SetLoc(), CSeq_feat_Base::SetLocation(), SetNucProtSetPartials(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [117/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_RNAtype0 ) ◆ BOOST_AUTO_TEST_CASE() [118/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_SeqLocOrder )Definition at line 12737 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, MakeMixLoc(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [119/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_StartCodon )Definition at line 12824 of file unit_test_validator.cpp.
References AddFeat(), CSerialObject::Assign(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, EXCEPTION_PROBLEM_ERR, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), HasBadStartCodon(), HasInternalStop(), HasNoStop(), INTERNAL_STOP_ERR, NO_PUB_ERR, NO_SRC_ERR, NO_STOP_ERR, NO_SUB_ERR, nuc, PROT_LEN_ERR, CSeq_feat_Base::ResetExcept_text(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), STANDARD_SETUP, and START_CODON_AND_INT_STOP_ERR.
◆ BOOST_AUTO_TEST_CASE() [120/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_TransLen )Definition at line 13047 of file unit_test_validator.cpp.
References CSeq_feat::AddQualifier(), AdjustProtFeatForNucProtSet(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [121/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_TranslExcept )Definition at line 13138 of file unit_test_validator.cpp.
References CSeq_feat::AddQualifier(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [122/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_UnknownImpFeatKey ) ◆ BOOST_AUTO_TEST_CASE() [123/458] BOOST_AUTO_TEST_CASE ( Test_FEAT_UnknownImpFeatQual ) ◆ BOOST_AUTO_TEST_CASE() [124/458] BOOST_AUTO_TEST_CASE ( Test_FixFormatDate ) ◆ BOOST_AUTO_TEST_CASE() [125/458] BOOST_AUTO_TEST_CASE ( Test_FixLatLonCountry ) ◆ BOOST_AUTO_TEST_CASE() [126/458] BOOST_AUTO_TEST_CASE ( Test_FixLatLonFormat ) ◆ BOOST_AUTO_TEST_CASE() [127/458] BOOST_AUTO_TEST_CASE ( Test_FixSpecificHost ) ◆ BOOST_AUTO_TEST_CASE() [128/458] BOOST_AUTO_TEST_CASE ( Test_FormatBadSpecificHostAlternateName ) ◆ BOOST_AUTO_TEST_CASE() [129/458] BOOST_AUTO_TEST_CASE ( Test_GapInProtein_and_BadProteinStart ) ◆ BOOST_AUTO_TEST_CASE() [130/458] BOOST_AUTO_TEST_CASE ( Test_GB_3714 ) ◆ BOOST_AUTO_TEST_CASE() [131/458] BOOST_AUTO_TEST_CASE ( Test_GB_6395 ) ◆ BOOST_AUTO_TEST_CASE() [132/458] BOOST_AUTO_TEST_CASE ( Test_GB_7601 ) ◆ BOOST_AUTO_TEST_CASE() [133/458] BOOST_AUTO_TEST_CASE ( Test_Geneious )Definition at line 24732 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, eNa_strand_minus, CValidator::eVal_far_fetch_cds_products, MakeGeneious(), MakeMixLoc(), CSeq_submit_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [134/458] BOOST_AUTO_TEST_CASE ( Test_Generic_AuthorListHasEtAl )Definition at line 9743 of file unit_test_validator.cpp.
References BuildGoodAuthor(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioseq_Base::SetAnnot(), CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CCit_book_Base::SetAuthors(), CCit_gen_Base::SetAuthors(), CCit_sub_Base::SetAuthors(), CCit_proc_Base::SetBook(), CPub_Base::SetBook(), CCit_let_Base::SetCit(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), CCit_gen_Base::SetDate(), CCit_sub_Base::SetDate(), CSeq_entry::SetDescr(), CPub_Base::SetGen(), CSeq_feat_Base::SetLocation(), CPub_Base::SetMan(), CAuthor_Base::SetName(), CPub_Base::SetProc(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), CPub_Base::SetSub(), CCit_gen_Base::SetTitle(), CCit_art_Base::SetTitle(), CCit_book_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [135/458] BOOST_AUTO_TEST_CASE ( Test_Generic_BadDate )Definition at line 10330 of file unit_test_validator.cpp.
References CSerialObject::Assign(), BuildGoodArticlePub(), BuildGoodAuthor(), BuildGoodCitSubPub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, gen, MakeBadSeasonDate(), CPub_Base::SetArticle(), CSeqdesc_Base::SetCreate_date(), CCit_sub_Base::SetDate(), CSeq_entry::SetDescr(), CBioseq_Base::SetDescr(), CCit_art_Base::SetFrom(), CSeq_entry_Base::SetSeq(), CPub_Base::SetSub(), CSeqdesc_Base::SetUpdate_date(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [136/458] BOOST_AUTO_TEST_CASE ( Test_Generic_BadPageNumbering )Definition at line 10249 of file unit_test_validator.cpp.
References BuildGoodArticlePub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CPub_Base::SetArticle(), CSeq_entry::SetDescr(), CCit_art_Base::SetFrom(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [137/458] BOOST_AUTO_TEST_CASE ( Test_Generic_CollidingSerialNumbers )Definition at line 10442 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodCitGenPub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSeq_feat_Base::SetData(), CSeq_entry::SetDescr(), CSeq_feat_Base::SetLocation(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [138/458] BOOST_AUTO_TEST_CASE ( Test_Generic_EmbeddedScript )Definition at line 10470 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodAuthor(), BuildGoodCitGenPub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, COrgMod_Base::eSubtype_acronym, CSubSource_Base::eSubtype_cell_line, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::ResetTitle(), CSeq_feat_Base::SetComment(), CSeq_entry::SetDescr(), CPub_Base::SetGen(), SetLineage(), CAuthor_Base::SetName(), SetOrgMod(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), SetSubSource(), CCit_gen_Base::SetTitle(), CSeq_feat_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [139/458] BOOST_AUTO_TEST_CASE ( Test_Generic_MedlineEntryPub ) ◆ BOOST_AUTO_TEST_CASE() [140/458] BOOST_AUTO_TEST_CASE ( Test_Generic_MissingPubRequirement )Definition at line 9951 of file unit_test_validator.cpp.
References BuildGoodAuthor(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, CImprint_Base::ePrepub_in_press, ePubStatus_aheadofprint, ePubStatus_epublish, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_unknown, CCit_gen_Base::ResetDate(), CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CCit_gen_Base::SetAuthors(), CCit_sub_Base::SetAuthors(), CCit_gen_Base::SetCit(), CSeq_submit_Base::SetData(), CCit_gen_Base::SetDate(), CCit_sub_Base::SetDate(), CSeq_entry::SetDescr(), CCit_art_Base::SetFrom(), CPub_Base::SetGen(), CBioseq_Base::SetId(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), CSeq_submit_Base::SetSub(), CPub_Base::SetSub(), SetTech(), CCit_art_Base::SetTitle(), STANDARD_SETUP, and NStr::StartsWith().
◆ BOOST_AUTO_TEST_CASE() [141/458] BOOST_AUTO_TEST_CASE ( Test_Generic_NonAsciiAsn )Definition at line 9691 of file unit_test_validator.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), BuildGoodNucProtSet(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Fatal, CValidator::eVal_far_fetch_mrna_products, CValidator::eVal_indexer_version, CValidator::eVal_need_isojta, CValidator::eVal_non_ascii, CValidator::eVal_use_entrez, CValidator::eVal_validate_id_set, CObjectManager::GetInstance(), CScope::RemoveTopLevelSeqEntry(), and CValidator::Validate().
◆ BOOST_AUTO_TEST_CASE() [142/458] BOOST_AUTO_TEST_CASE ( Test_Generic_PublicationInconsistency )Definition at line 10532 of file unit_test_validator.cpp.
References BuildGoodArticlePub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CImprint_Base::ePrepub_in_press, ePubStatus_aheadofprint, ePubStatus_epublish, CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CBioseq_Base::SetDescr(), CCit_art_Base::SetFrom(), CAuthor_Base::SetName(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [143/458] BOOST_AUTO_TEST_CASE ( Test_Generic_SgmlPresentInText )Definition at line 10604 of file unit_test_validator.cpp.
References AddMiscFeature(), AddSgmlError(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, COrgMod_Base::eSubtype_acronym, CSubSource_Base::eSubtype_cell_line, CRNA_ref_Base::eType_mRNA, CRNA_ref_Base::eType_rRNA, RemoveDbxref(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), SetDbxref(), SetOrgMod(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), SetSebaea_microphylla(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetSubSource(), SetTaxname(), CGb_qual_Base::SetVal(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [144/458] BOOST_AUTO_TEST_CASE ( Test_Generic_StructuredCitGenCit )Definition at line 10412 of file unit_test_validator.cpp.
References BuildGoodAuthor(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CCit_gen_Base::SetAuthors(), CCit_gen_Base::SetCit(), CCit_gen_Base::SetDate(), CSeq_entry::SetDescr(), CPub_Base::SetGen(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CCit_gen_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [145/458] BOOST_AUTO_TEST_CASE ( Test_Generic_UnexpectedPubStatusComment )Definition at line 10859 of file unit_test_validator.cpp.
References BuildGoodArticlePub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CImprint_Base::ePrepub_in_press, ePubStatus_aheadofprint, ePubStatus_epublish, ePubStatus_ppublish, CPub_Base::SetArticle(), CPubdesc_Base::SetComment(), CBioseq_Base::SetDescr(), CCit_art_Base::SetFrom(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [146/458] BOOST_AUTO_TEST_CASE ( Test_Generic_UnnecessaryPubEquiv ) ◆ BOOST_AUTO_TEST_CASE() [147/458] BOOST_AUTO_TEST_CASE ( Test_GiWithoutAccession ) ◆ BOOST_AUTO_TEST_CASE() [148/458] BOOST_AUTO_TEST_CASE ( Test_GP_9919 )Definition at line 21715 of file unit_test_validator.cpp.
References CValidErrorFormat::AddSuppression(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, eErr_SEQ_FEAT_ExceptionProblem, eErr_SEQ_FEAT_InternalStop, eErr_SEQ_INST_StopInProtein, CUser_object::eObjectType_ValidationSuppression, GetCDSFromGoodNucProtSet(), HasInternalStop(), HasStopInProtein(), CBioseq_set_Base::SetDescr(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [149/458] BOOST_AUTO_TEST_CASE ( Test_HighNContentPercent_and_HighNContentStretch )Definition at line 4329 of file unit_test_validator.cpp.
References BuildGoodDeltaSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, eDiag_Info, eDiag_Warning, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CMolInfo_Base::eTech_tsa, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), SetBiomol(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [150/458] BOOST_AUTO_TEST_CASE ( Test_HistAssemblyMissing ) ◆ BOOST_AUTO_TEST_CASE() [151/458] BOOST_AUTO_TEST_CASE ( Test_HistoryGiCollision ) ◆ BOOST_AUTO_TEST_CASE() [152/458] BOOST_AUTO_TEST_CASE ( Test_HIVMolType )Definition at line 6687 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, eDiag_Info, eDiag_Warning, CSeq_inst_Base::eMol_rna, COrgMod_Base::eSubtype_pathovar, SetBiomol(), CBioseq_Base::SetInst(), SetLineage(), SetOrgMod(), CSeq_entry_Base::SetSeq(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [153/458] BOOST_AUTO_TEST_CASE ( Test_InconsistentPseudogeneValue )Definition at line 23653 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_mRNA, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::ResetQual(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetQual(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [154/458] BOOST_AUTO_TEST_CASE ( Test_InconsistentVirusMoltype )Definition at line 7132 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_other, CMolInfo_Base::eBiomol_other_genetic, eDiag_Error, eDiag_Warning, CSeq_inst_Base::eMol_rna, CBioSource_Base::eOrigin_artificial, CBioSource_Base::eOrigin_mut, CBioSource_Base::eOrigin_synthetic, CBioSource_Base::eOrigin_unknown, RevComp(), SetBiomol(), CSeq_feat_Base::SetComment(), SetDiv(), CBioseq_Base::SetInst(), SetLineage(), SetOrigin(), SetSebaea_microphylla(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetSynthetic_construct(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [155/458] BOOST_AUTO_TEST_CASE ( Test_InternalGapsInSeqRaw ) ◆ BOOST_AUTO_TEST_CASE() [156/458] BOOST_AUTO_TEST_CASE ( Test_InternalNsAdjacentToGap ) ◆ BOOST_AUTO_TEST_CASE() [157/458] BOOST_AUTO_TEST_CASE ( Test_InternalNsInSeqLit )Definition at line 3561 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), AddToDeltaSeq(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CMolInfo_Base::eTech_composite_wgs_htgs, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [158/458] BOOST_AUTO_TEST_CASE ( Test_InternalNsInSeqRaw )Definition at line 4122 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, CMolInfo_Base::eTech_wgs, CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [159/458] BOOST_AUTO_TEST_CASE ( Test_InvalidAlleleDuplicates )Definition at line 23850 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_rRNA, MakeGeneForFeature(), rna, CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [160/458] BOOST_AUTO_TEST_CASE ( Test_InvalidCodonStart ) ◆ BOOST_AUTO_TEST_CASE() [161/458] BOOST_AUTO_TEST_CASE ( Test_InvalidCompareBadAccession ) ◆ BOOST_AUTO_TEST_CASE() [162/458] BOOST_AUTO_TEST_CASE ( Test_InvalidCompareMissingVersion ) ◆ BOOST_AUTO_TEST_CASE() [163/458] BOOST_AUTO_TEST_CASE ( Test_InvalidCompareRefSeqAccession ) ◆ BOOST_AUTO_TEST_CASE() [164/458] BOOST_AUTO_TEST_CASE ( Test_InvalidOperonMatchesGene ) ◆ BOOST_AUTO_TEST_CASE() [165/458] BOOST_AUTO_TEST_CASE ( Test_InvalidProductOnGene ) ◆ BOOST_AUTO_TEST_CASE() [166/458] BOOST_AUTO_TEST_CASE ( Test_InvalidPseudoQualifier ) ◆ BOOST_AUTO_TEST_CASE() [167/458] BOOST_AUTO_TEST_CASE ( Test_InvalidReplace )Definition at line 24076 of file unit_test_validator.cpp.
References AddMiscFeature(), CSeq_feat::AddQualifier(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, GetProteinSequenceFromGoodNucProtSet(), prot, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetQual(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [168/458] BOOST_AUTO_TEST_CASE ( Test_InvalidRptUnitRange ) ◆ BOOST_AUTO_TEST_CASE() [169/458] BOOST_AUTO_TEST_CASE ( Test_InvalidRptUnitSeqCharacters ) ◆ BOOST_AUTO_TEST_CASE() [170/458] BOOST_AUTO_TEST_CASE ( Test_InvalidSexQualifier ) ◆ BOOST_AUTO_TEST_CASE() [171/458] BOOST_AUTO_TEST_CASE ( Test_InvalidVariationReplace ) ◆ BOOST_AUTO_TEST_CASE() [172/458] BOOST_AUTO_TEST_CASE ( Test_IsDateInPast )Definition at line 23536 of file unit_test_validator.cpp.
References CTime::eCurrent, CDate::ePrecision_day, CDate_std_Base::GetDay(), CDate_std_Base::GetMonth(), CDate_Base::GetStd(), CDate_std_Base::GetYear(), IsDateInPast(), CRef< C, Locker >::Reset(), CDate_std_Base::ResetDay(), CDate_std_Base::ResetMonth(), CDate_std_Base::SetDay(), CDate_std_Base::SetMonth(), CDate_Base::SetStd(), and CDate_std_Base::SetYear().
◆ BOOST_AUTO_TEST_CASE() [173/458] BOOST_AUTO_TEST_CASE ( Test_IsLikelyTaxname ) ◆ BOOST_AUTO_TEST_CASE() [174/458] BOOST_AUTO_TEST_CASE ( Test_IsLocationInFrame )Definition at line 21984 of file unit_test_validator.cpp.
References CScope::AddTopLevelSeqEntry(), CSeq_id::Assign(), CSeq_loc::Assign(), BuildGoodNucProtSet(), eExtreme_Biological, eLocationInFrame_BadStart, eLocationInFrame_BadStartAndStop, eLocationInFrame_BadStop, eLocationInFrame_InFrame, eLocationInFrame_NotIn, GetCDSFromGoodNucProtSet(), CSeq_interval_Base::GetFrom(), CSeq_interval_Base::GetId(), CObjectManager::GetInstance(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CScope::GetSeq_featHandle(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_interval_Base::GetTo(), IsLocationInFrame(), MakeMixLoc(), CSeq_loc::SetInt(), and CSeq_feat_Base::SetLocation().
◆ BOOST_AUTO_TEST_CASE() [175/458] BOOST_AUTO_TEST_CASE ( Test_LeadingX ) ◆ BOOST_AUTO_TEST_CASE() [176/458] BOOST_AUTO_TEST_CASE ( Test_MismatchedAllele )Definition at line 23825 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_rRNA, MakeGeneForFeature(), rna, CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [177/458] BOOST_AUTO_TEST_CASE ( Test_MissingGaps )Definition at line 3770 of file unit_test_validator.cpp.
References AddRefGeneTrackingUserObject(), BuildGoodDeltaSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, RemoveDeltaSeqGaps(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [178/458] BOOST_AUTO_TEST_CASE ( Test_MissingPlasmid )Definition at line 6719 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CBioSource_Base::eGenome_plasmid, CSubSource_Base::eSubtype_plasmid_name, SetGenome(), SetLineage(), SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [179/458] BOOST_AUTO_TEST_CASE ( Test_MobileElementInvalidQualifier ) ◆ BOOST_AUTO_TEST_CASE() [180/458] BOOST_AUTO_TEST_CASE ( Test_NewFixCountry ) ◆ BOOST_AUTO_TEST_CASE() [181/458] BOOST_AUTO_TEST_CASE ( Test_NoCDSbetweenUTRs ) ◆ BOOST_AUTO_TEST_CASE() [182/458] BOOST_AUTO_TEST_CASE ( Test_OrgModAutofix ) ◆ BOOST_AUTO_TEST_CASE() [183/458] BOOST_AUTO_TEST_CASE ( Test_OrgModMissingValue )Definition at line 6477 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, COrgMod_Base::eSubtype_biovar, COrgMod_Base::eSubtype_forma, COrgMod_Base::eSubtype_forma_specialis, COrgMod_Base::eSubtype_pathovar, COrgMod_Base::eSubtype_sub_species, COrgMod_Base::eSubtype_variety, SetLineage(), SetOrgMod(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [184/458] BOOST_AUTO_TEST_CASE ( Test_PKG_BioseqSetClassNotSet ) ◆ BOOST_AUTO_TEST_CASE() [185/458] BOOST_AUTO_TEST_CASE ( Test_PKG_ConSetProblem ) ◆ BOOST_AUTO_TEST_CASE() [186/458] BOOST_AUTO_TEST_CASE ( Test_PKG_EmptySet )Definition at line 11005 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CBioseq_set_Base::eClass_equiv, CBioseq_set_Base::eClass_genbank, CBioseq_set_Base::eClass_gi, CBioseq_set_Base::eClass_gibb, CBioseq_set_Base::eClass_pdb_entry, CBioseq_set_Base::eClass_pir, CBioseq_set_Base::eClass_pub_set, CBioseq_set_Base::eClass_swissprot, eDiag_Warning, CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [187/458] BOOST_AUTO_TEST_CASE ( Test_PKG_GenomicProductPackagingProblem )Definition at line 11070 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodGenProdSet(), BuildGoodNucProtSet(), ChangeId(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, eDiag_Critical, eDiag_Error, eDiag_Warning, CSeq_inst_Base::eMol_rna, CRNA_ref_Base::eType_mRNA, nuc, CBioseq_set_Base::ResetAnnot(), CSeq_feat_Base::ResetProduct(), CBioseq_Base::SetAnnot(), SetBiomol(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [188/458] BOOST_AUTO_TEST_CASE ( Test_PKG_GPSnonGPSPackaging )Definition at line 11367 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildGoodGenProdSet(), CLEAR_ERRORS, CBioseq_set_Base::eClass_genbank, eDiag_Error, eDiag_Warning, CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), STANDARD_SETUP, TESTPOPPHYMUTECO, and TESTWGS.
◆ BOOST_AUTO_TEST_CASE() [189/458] BOOST_AUTO_TEST_CASE ( Test_PKG_GraphPackagingProblem ) ◆ BOOST_AUTO_TEST_CASE() [190/458] BOOST_AUTO_TEST_CASE ( Test_PKG_ImproperlyNestedSets ) ◆ BOOST_AUTO_TEST_CASE() [191/458] BOOST_AUTO_TEST_CASE ( Test_PKG_InconsistentMolInfoBiomols )Definition at line 11229 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), CLEAR_ERRORS, CSeqdesc_Base::e_Title, CMolInfo_Base::eBiomol_cRNA, eDiag_Error, eDiag_Warning, RemoveDescriptorType(), SetBiomol(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), STANDARD_SETUP, TESTPOPPHYMUTECO, and TESTWGS.
◆ BOOST_AUTO_TEST_CASE() [192/458] BOOST_AUTO_TEST_CASE ( Test_PKG_INSDRefSeqPackaging ) ◆ BOOST_AUTO_TEST_CASE() [193/458] BOOST_AUTO_TEST_CASE ( Test_PKG_InternalGenBankSet )Definition at line 11276 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), CLEAR_ERRORS, CSeqdesc_Base::e_Title, CBioseq_set_Base::eClass_genbank, eDiag_Warning, RemoveDescriptorType(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), STANDARD_SETUP, TESTPOPPHYMUTECO, and TESTWGS.
◆ BOOST_AUTO_TEST_CASE() [194/458] BOOST_AUTO_TEST_CASE ( Test_PKG_MisplacedMolInfo )Definition at line 11522 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CMolInfo_Base::eTech_wgs, CBioseq_set_Base::SetDescr(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSet(), CMolInfo_Base::SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [195/458] BOOST_AUTO_TEST_CASE ( Test_PKG_NoBioseqFound ) ◆ BOOST_AUTO_TEST_CASE() [196/458] BOOST_AUTO_TEST_CASE ( Test_PKG_NoCdRegionPtr )Definition at line 10904 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), BuildGoodProtSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CSeqdesc_Base::IsPub(), CBioseq_Base::IsSetDescr(), CSeqdesc_Base::IsSource(), ListOrphanProteins(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [197/458] BOOST_AUTO_TEST_CASE ( Test_PKG_NucProtNotSegSet ) ◆ BOOST_AUTO_TEST_CASE() [198/458] BOOST_AUTO_TEST_CASE ( Test_PKG_NucProtProblem )Definition at line 10931 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeqdesc_Base::IsPub(), CBioseq_Base::IsSetDescr(), CSeqdesc_Base::IsSource(), CBioseq_set_Base::SetAnnot(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [199/458] BOOST_AUTO_TEST_CASE ( Test_PKG_OrphanedProtein )Definition at line 11451 of file unit_test_validator.cpp.
References BuildGoodProtSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, ListOrphanProteins(), CBioseq_Base::SetAnnot(), CPatent_seq_id_Base::SetCit(), CSeq_id_Base::SetGibbmt(), CSeq_id_Base::SetGibbsq(), CBioseq_Base::SetId(), CSeq_id_Base::SetPatent(), CSeq_entry_Base::SetSeq(), CPatent_seq_id_Base::SetSeqid(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [200/458] BOOST_AUTO_TEST_CASE ( Test_PKG_RefSeqPopSet )Definition at line 11407 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), CheckErrors(), CLEAR_ERRORS, CBioseq_set_Base::eClass_pop_set, eDiag_Critical, eDiag_Error, eDiag_Warning, CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [201/458] BOOST_AUTO_TEST_CASE ( Test_PKG_SegSetProblem ) ◆ BOOST_AUTO_TEST_CASE() [202/458] BOOST_AUTO_TEST_CASE ( Test_ProteinsHaveGeneralID )Definition at line 4295 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), BuildGoodProtSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, GetCDSFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), prot, s_AddGeneralAndLocal(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [203/458] BOOST_AUTO_TEST_CASE ( Test_RegulatoryClassOtherNeedsNote ) ◆ BOOST_AUTO_TEST_CASE() [204/458] BOOST_AUTO_TEST_CASE ( Test_RemoveLineageSourceNotes ) ◆ BOOST_AUTO_TEST_CASE() [205/458] BOOST_AUTO_TEST_CASE ( Test_RmCultureNotes ) ◆ BOOST_AUTO_TEST_CASE() [206/458] BOOST_AUTO_TEST_CASE ( Test_rRNADoesNotHaveProduct ) ◆ BOOST_AUTO_TEST_CASE() [207/458] BOOST_AUTO_TEST_CASE ( Test_RW_1063 )Definition at line 25244 of file unit_test_validator.cpp.
References BuildGoodSeq(), BuildRefSeqId(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, COrgMod_Base::eSubtype_serotype, COrgMod_Base::eSubtype_serovar, CBioseq_Base::SetId(), SetOrgMod(), CSeq_entry_Base::SetSeq(), SetTaxname(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [208/458] BOOST_AUTO_TEST_CASE ( Test_RW_1064 ) ◆ BOOST_AUTO_TEST_CASE() [209/458] BOOST_AUTO_TEST_CASE ( Test_SelfReferentialSequence ) ◆ BOOST_AUTO_TEST_CASE() [210/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_ANNOT_AnnotIDs ) ◆ BOOST_AUTO_TEST_CASE() [211/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_ANNOT_AnnotLOCs ) ◆ BOOST_AUTO_TEST_CASE() [212/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_DESCR_MissingPersonalCollectionName ) ◆ BOOST_AUTO_TEST_CASE() [213/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_AbuttingIntervals )Definition at line 14896 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, MakeMixLoc(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [214/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_AltStartCodonException )Definition at line 15800 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [215/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadAnticodonAA ) ◆ BOOST_AUTO_TEST_CASE() [216/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadAnticodonCodon ) ◆ BOOST_AUTO_TEST_CASE() [217/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadAnticodonStrand )Definition at line 18314 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eNa_strand_minus, CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [218/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadAuthorSuffix )Definition at line 18240 of file unit_test_validator.cpp.
References BuildGoodArticlePub(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CSeq_entry::SetDescr(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [219/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadCDScomment ) ◆ BOOST_AUTO_TEST_CASE() [220/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadCharInAuthorLastName )Definition at line 18923 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CSeq_entry::SetDescr(), CAuthor_Base::SetName(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CCit_art_Base::SetTitle(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [221/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadCharInAuthorName )Definition at line 16209 of file unit_test_validator.cpp.
References BuildGoodArticlePub(), BuildGoodAuthor(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CPub_Base::SetArticle(), CCit_art_Base::SetAuthors(), CBioseq_Base::SetDescr(), CAuthor_Base::SetName(), CPubdesc_Base::SetPub(), CSeqdesc_Base::SetPub(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [222/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadConflictFlag ) ◆ BOOST_AUTO_TEST_CASE() [223/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadEcNumberValue )Definition at line 914 of file unit_test_validator.cpp.
References AddMiscFeature(), CSeq_feat::AddQualifier(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), prot, s_BuildBadEcNumberEntry(), CSeq_feat_Base::SetData(), SetErrorsAccessions(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [224/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadFullLengthFeature )Definition at line 16391 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, ENTREZ_ID_CONST, CValidator::eVal_seqsubmit_parent, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CPub_Base::SetPmid(), SetTransgenic(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [225/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadGeneOntologyFormat ) ◆ BOOST_AUTO_TEST_CASE() [226/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadInternalCharacter )Definition at line 18747 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_rRNA, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, prot, CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [227/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadProductSeqId ) ◆ BOOST_AUTO_TEST_CASE() [228/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadProteinName ) ◆ BOOST_AUTO_TEST_CASE() [229/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadRRNAcomponentOrder )Definition at line 18641 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioSource_Base::eGenome_chloroplast, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_rRNA, r1, r2, r3, RevComp(), SetGenome(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [230/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadTrailingCharacter )Definition at line 18805 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_rRNA, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, prot, CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [231/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadTrailingHyphen )Definition at line 18842 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_rRNA, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, prot, CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [232/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadTrnaAA )Definition at line 15368 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), BuildGoodtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [233/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BadTrnaCodon ) ◆ BOOST_AUTO_TEST_CASE() [234/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_BothStrands )Definition at line 14114 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, eNa_strand_both, eNa_strand_both_rev, CRNA_ref_Base::eType_mRNA, MakeGeneForFeature(), MakeMixLoc(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [235/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSgeneRange )Definition at line 14437 of file unit_test_validator.cpp.
References AddFeat(), CSeq_loc::Assign(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), nuc, prot, CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CSeq_feat_Base::SetId(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CSeq_feat_Base::SetXref(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [236/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDShasTooManyXs ) ◆ BOOST_AUTO_TEST_CASE() [237/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSmRNAmismatch )Definition at line 15953 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [238/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSmRNArange )Definition at line 14210 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_mRNA, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetLocation(), MakeMixLoc(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetSpliceForMixLoc(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [239/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSmRNAXrefLocationProblem )Definition at line 19267 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_interval_Base::GetTo(), MakemRNAForCDS(), nuc, CSeq_feat_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetXref(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [240/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSproductPackagingProblem ) ◆ BOOST_AUTO_TEST_CASE() [241/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSwithMultipleMRNAs )Definition at line 16264 of file unit_test_validator.cpp.
References AddFeat(), BuildGenProdSetNucProtSet(), BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Info, eDiag_Warning, GetCDSFromGenProdSet(), GetGenomicFromGenProdSet(), MakemRNAForCDS(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetProduct(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CObject_id_Base::SetStr(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [242/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CDSwithNoMRNA )Definition at line 16558 of file unit_test_validator.cpp.
References AddFeat(), BuildBigGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), i, MakeGeneForFeature(), MakemRNAForCDS(), nuc, CBioseq_set_Base::SetAnnot(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [243/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CodonQualifierUsed ) ◆ BOOST_AUTO_TEST_CASE() [244/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CollidingFeatureIDs ) ◆ BOOST_AUTO_TEST_CASE() [245/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_CollidingGeneNames ) ◆ BOOST_AUTO_TEST_CASE() [246/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ConflictFlagSet )Definition at line 15732 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), prot, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [247/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_DuplicateFeat )Definition at line 13846 of file unit_test_validator.cpp.
References AddMiscFeature(), CSerialObject::Assign(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, eExtreme_Biological, CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetComment(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), SetDrosophila_melanogaster(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CSeq_feat_Base::SetPseudo(), SetSebaea_microphylla(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [248/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_DuplicateGeneConflictingLocusTag ) ◆ BOOST_AUTO_TEST_CASE() [249/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_DuplicateGeneOntologyTerm ) ◆ BOOST_AUTO_TEST_CASE() [250/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_DuplicateInterval )Definition at line 14700 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, MakeMixLoc(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [251/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_DuplicateTranslExcept ) ◆ BOOST_AUTO_TEST_CASE() [252/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_EcNumberProblem )Definition at line 17503 of file unit_test_validator.cpp.
References AddMiscFeature(), CSeq_feat::AddQualifier(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), nuc, prot, CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [253/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ErroneousException )Definition at line 17439 of file unit_test_validator.cpp.
References BuildGenProdSetWithBigProduct(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGenProdSet(), GetGenomicFromGenProdSet(), GetmRNAFromGenProdSet(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [254/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ExceptionProblem )Definition at line 15471 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CRNA_ref_Base::eType_rRNA, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [255/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ExtraProteinFeature ) ◆ BOOST_AUTO_TEST_CASE() [256/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FarLocation )Definition at line 13828 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, MakeMixLoc(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [257/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatContentDup )Definition at line 15017 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), CSeq_feat::AddQualifier(), CSeq_feat::AddSeqFeatXref(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_mRNA, GetCDSFromGoodNucProtSet(), GetDuplicateFeaturesForRemoval(), CSeq_feat_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CSeq_interval_Base::GetTo(), MakeCDSForGoodNucProtSet(), MakeProteinForGoodNucProtSet(), CSeq_feat_Base::ResetProduct(), CSeq_feat_Base::SetData(), SetDbxref(), CSeq_feat_Base::SetId(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), set< Key, Compare >::size(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [258/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatureBeginsOrEndsInGap )Definition at line 18464 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CInt_fuzz_Base::eLim_unk, eNa_strand_minus, CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [259/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatureCitationProblem ) ◆ BOOST_AUTO_TEST_CASE() [260/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatureCrossesGap )Definition at line 18189 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, CInt_fuzz_Base::eLim_unk, CRNA_ref_Base::eType_mRNA, CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [261/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatureInsideGap )Definition at line 18144 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, CSeq_inst_Base::eMol_dna, CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [262/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatureLocationIsGi0 ) ◆ BOOST_AUTO_TEST_CASE() [263/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FeatureSeqIDCaseDifference ) ◆ BOOST_AUTO_TEST_CASE() [264/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_FocusOnBioSourceFeature ) ◆ BOOST_AUTO_TEST_CASE() [265/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GapFeatureProblem )Definition at line 17337 of file unit_test_validator.cpp.
References AddMiscFeature(), CSeq_feat::AddQualifier(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [266/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GeneOntologyTermMissingGOID ) ◆ BOOST_AUTO_TEST_CASE() [267/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GenesInconsistent )Definition at line 15832 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetGenomicFromGenProdSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [268/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GeneXrefNeeded )Definition at line 18978 of file unit_test_validator.cpp.
References AddCDSAndProtForBigGoodNucProtSet(), AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSeq_interval_Base::GetFrom(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_interval_Base::GetTo(), MakeGeneForFeature(), nuc, CBioseq_set_Base::SetAnnot(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [269/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GeneXrefStrandProblem )Definition at line 19227 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, eNa_strand_minus, MakeGeneForFeature(), RevComp(), CSeq_feat_Base::SetData(), CSeq_feat::SetGeneXref(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [270/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GeneXrefWithoutGene ) ◆ BOOST_AUTO_TEST_CASE() [271/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_GeneXrefWithoutLocus )Definition at line 17630 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CSeq_interval_Base::GetTo(), MakeGeneForFeature(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetXref(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [272/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_HypotheticalProteinMismatch ) ◆ BOOST_AUTO_TEST_CASE() [273/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_IdenticalGeneSymbolAndSynonym )Definition at line 19298 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioseq_Base::GetId(), CBioseq::GetLength(), CSeq_entry_Base::GetSeq(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [274/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_IllegalDbXref )Definition at line 13567 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, NStr::Equal(), MakeWrongCap(), RemoveDbxref(), SetDbxref(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [275/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ImpCDShasTranslation ) ◆ BOOST_AUTO_TEST_CASE() [276/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ImpCDSnotPseudo ) ◆ BOOST_AUTO_TEST_CASE() [277/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ImpFeatBadLoc ) ◆ BOOST_AUTO_TEST_CASE() [278/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ImproperBondLocation ) ◆ BOOST_AUTO_TEST_CASE() [279/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_InconsistentGeneOntologyTermAndId ) ◆ BOOST_AUTO_TEST_CASE() [280/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_InvalidFuzz )Definition at line 21468 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CSeq_interval_Base::SetFuzz_from(), CSeq_interval_Base::SetFuzz_to(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [281/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_InvalidInferenceValue ) ◆ BOOST_AUTO_TEST_CASE() [282/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_InvalidMatchingReplace ) ◆ BOOST_AUTO_TEST_CASE() [283/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_InvalidQualifierValue ) ◆ BOOST_AUTO_TEST_CASE() [284/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ITSdoesNotAbutRRNA )Definition at line 17256 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_miscRNA, CRNA_ref_Base::eType_rRNA, CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CSeq_interval_Base::GetTo(), RevComp(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [285/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_LocusTagProblem ) ◆ BOOST_AUTO_TEST_CASE() [286/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_LocusTagProductMismatch )Definition at line 16048 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), BuildRefSeqId(), ChangeNucProtSetNucId(), ChangeNucProtSetProteinId(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CValidator::eVal_locus_tag_general_match, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, prot, CSeq_feat_Base::SetData(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [287/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MinusStrandProtein ) ◆ BOOST_AUTO_TEST_CASE() [288/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MissingCDSproduct )Definition at line 15289 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CBioseq_set_Base::eClass_genbank, eDiag_Error, eDiag_Warning, eExtreme_Biological, CCdregion_Base::eFrame_three, HasBadStartCodon(), HasNoStop(), nuc, CSeq_feat_Base::ResetExcept(), CSeq_feat_Base::ResetExcept_text(), CSeq_feat_Base::ResetProduct(), CSeq_feat_Base::ResetPseudo(), CBioseq_set_Base::SetClass(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CSeq_feat_Base::SetProduct(), CSeq_feat_Base::SetPseudo(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [289/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MissingGeneLocusTag )Definition at line 18696 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [290/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MissingGeneXref )Definition at line 16103 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), CSeq_interval_Base::GetTo(), MakeGeneForFeature(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [291/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MissingTrnaAA ) ◆ BOOST_AUTO_TEST_CASE() [292/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_mRNAgeneRange ) ◆ BOOST_AUTO_TEST_CASE() [293/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultiIntervalGene )Definition at line 14997 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, MakeMixLoc(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [294/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultipleCDSproducts )Definition at line 14354 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [295/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultipleEquivBioSources ) ◆ BOOST_AUTO_TEST_CASE() [296/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultipleEquivPublications ) ◆ BOOST_AUTO_TEST_CASE() [297/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultipleGeneOverlap )Definition at line 18879 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [298/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultipleMRNAproducts )Definition at line 14536 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, CRNA_ref_Base::eType_mRNA, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetProduct(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [299/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_MultipleProtRefs )Definition at line 18722 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), GetProteinSequenceFromGoodNucProtSet(), CSeq_entry_Base::GetSeq(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [300/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_NeedsNote ) ◆ BOOST_AUTO_TEST_CASE() [301/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_NestedSeqLocMix )Definition at line 16150 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetMix(), CSeq_feat_Base::SetProduct(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [302/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_NoNameForProtein ) ◆ BOOST_AUTO_TEST_CASE() [303/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_NotSpliceConsensusAcceptor )Definition at line 17933 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Fatal, eDiag_Info, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeIntronForMixLoc(), MakeMixLoc(), nuc, RevComp(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [304/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_NotSpliceConsensusDonor )Definition at line 17844 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Fatal, eDiag_Info, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeIntronForMixLoc(), MakeMixLoc(), nuc, RevComp(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [305/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_OldLocusTagMismtach ) ◆ BOOST_AUTO_TEST_CASE() [306/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_OnlyGeneXrefs ) ◆ BOOST_AUTO_TEST_CASE() [307/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_OverlappingPeptideFeat )Definition at line 14283 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), BuildGoodProtSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_signal_peptide, CProt_ref_Base::eProcessed_transit_peptide, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [308/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PartialProblem )Definition at line 19329 of file unit_test_validator.cpp.
References AdjustProtFeatForNucProtSet(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_no_right, eDiag_Error, eDiag_Warning, eExtreme_Biological, GetCDSFromGoodNucProtSet(), nuc, prot, SetCompleteness(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [309/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PeptideFeatOutOfFrame ) ◆ BOOST_AUTO_TEST_CASE() [310/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PolyAsignalNotRange ) ◆ BOOST_AUTO_TEST_CASE() [311/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PolyAsiteNotPoint ) ◆ BOOST_AUTO_TEST_CASE() [312/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PolyATail )Definition at line 16231 of file unit_test_validator.cpp.
References BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), CBioseq_Base::SetAnnot(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [313/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ProteinNameEndsInBracket ) ◆ BOOST_AUTO_TEST_CASE() [314/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ProteinNameHasPMID ) ◆ BOOST_AUTO_TEST_CASE() [315/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PseudoCdsHasProduct )Definition at line 13519 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, CSeq_feat_Base::SetPseudo(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [316/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PseudoCDSmRNArange )Definition at line 18947 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, MakeMixLoc(), MakemRNAForCDS(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [317/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PseudoCdsViaGeneHasProduct )Definition at line 16082 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, CSeq_feat_Base::SetPseudo(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [318/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_PseudoRnaHasProduct )Definition at line 18550 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_rRNA, MakeGeneForFeature(), rna, CSeq_feat_Base::SetPseudo(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [319/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_RareSpliceConsensusDonor )Definition at line 18032 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeIntronForMixLoc(), MakeMixLoc(), nuc, RevComp(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [320/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_RareSpliceConsensusDonor_VR_65 )Definition at line 18063 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeIntronForMixLoc(), MakeMixLoc(), nuc, RevComp(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [321/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_RedundantFields )Definition at line 16440 of file unit_test_validator.cpp.
References AddFeat(), CSeq_feat::AddQualifier(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), nuc, prot, CSeq_feat_Base::ResetComment(), CSeq_feat_Base::ResetQual(), CSeq_feat_Base::SetComment(), CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [322/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ReplicatedGeneSequence ) ◆ BOOST_AUTO_TEST_CASE() [323/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_RnaProductMismatch )Definition at line 15204 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_rRNA, CMolInfo_Base::eBiomol_tRNA, CBioseq_set_Base::eClass_gen_prod_set, eDiag_Error, eDiag_Warning, CSeq_inst_Base::eMol_rna, CRNA_ref_Base::eType_mRNA, CRNA_ref_Base::eType_rRNA, CRNA_ref_Base::eType_tRNA, nuc, SetBiomol(), CBioseq_set_Base::SetClass(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [324/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_RptUnitRangeProblem ) ◆ BOOST_AUTO_TEST_CASE() [325/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_RubiscoProblem ) ◆ BOOST_AUTO_TEST_CASE() [326/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SelfReferentialProduct )Definition at line 17229 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, eExtreme_Biological, CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [327/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SeqDataLenWrong )Definition at line 15561 of file unit_test_validator.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CSeqportUtil::Convert(), CSeq_data_Base::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, eDiag_Critical, eDiag_Error, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_ref, CSeq_inst_Base::eRepr_seg, CValidator::eVal_far_fetch_mrna_products, CValidator::eVal_indexer_version, CValidator::eVal_need_isojta, CValidator::eVal_use_entrez, CValidator::eVal_validate_id_set, CObjectManager::GetInstance(), CGBDataLoader::RegisterInObjectManager(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_entry_Base::SetSeq(), and CValidator::Validate().
◆ BOOST_AUTO_TEST_CASE() [328/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SeqFeatXrefFeatureMissing ) ◆ BOOST_AUTO_TEST_CASE() [329/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SeqFeatXrefNotReciprocal )Definition at line 18095 of file unit_test_validator.cpp.
References AddFeat(), CSeq_feat::AddSeqFeatXref(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetId(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, CSeq_feat_Base::SetId(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [330/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SeqFeatXrefProblem )Definition at line 16789 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CreateReciprocalLinks(), eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_interval_Base::GetTo(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, CSeq_feat_Base::ResetXref(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetXref(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [331/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SerialInComment ) ◆ BOOST_AUTO_TEST_CASE() [332/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ShortExon )Definition at line 20668 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, NStr::EndsWith(), GetCDSFromGoodNucProtSet(), offset, prot, CBioseq_Base::SetAnnot(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), STANDARD_SETUP, and CSeqTranslator::Translate().
◆ BOOST_AUTO_TEST_CASE() [333/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_ShortIntron )Definition at line 19403 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, HasBadStartCodon(), HasNoStop(), CSeq_feat_Base::ResetPseudo(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [334/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_SuspiciousFrame )Definition at line 17707 of file unit_test_validator.cpp.
References AdjustProtFeatForNucProtSet(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_no_left, eDiag_Error, eDiag_Warning, eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, GetCDSFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), prot, SetCompleteness(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), STANDARD_SETUP, tmp, and CSeqTranslator::Translate().
◆ BOOST_AUTO_TEST_CASE() [335/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TerminalXDiscrepancy )Definition at line 17760 of file unit_test_validator.cpp.
References AdjustProtFeatForNucProtSet(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_no_right, eDiag_Error, eDiag_Warning, eExtreme_Biological, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), nuc, prot, SetCompleteness(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [336/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TooManyInferenceAccessions )Definition at line 19602 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, CValidator::eVal_inference_accns, i, NStr::IntToString(), CGb_qual_Base::SetQual(), CSeq_feat_Base::SetQual(), CGb_qual_Base::SetVal(), STANDARD_SETUP, and val.
◆ BOOST_AUTO_TEST_CASE() [337/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TranscriptLen )Definition at line 14607 of file unit_test_validator.cpp.
References BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [338/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TranscriptMismatches )Definition at line 14649 of file unit_test_validator.cpp.
References BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, GetNucleotideSequenceFromGoodNucProtSet(), GetNucProtSetFromGenProdSet(), CBioseq_Base::SetAnnot(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [339/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TranslExceptAndRnaEditing )Definition at line 15885 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, DoesFeatureHaveUnnecessaryException(), eDiag_Warning, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CCode_break_Base::SetLoc(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [340/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TranslExceptPhase )Definition at line 13997 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CheckStrings(), CLEAR_ERRORS, eDiag_Critical, eDiag_Warning, NStr::Equal(), CValidator::eVal_collect_locus_tags, expected, format, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, CSeq_feat_Base::SetData(), CCode_break_Base::SetLoc(), NStr::Split(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [341/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_TrnaCodonWrong ) ◆ BOOST_AUTO_TEST_CASE() [342/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UndesiredGeneSynonym )Definition at line 18355 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, msg(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), STANDARD_SETUP, and test_gene_syn.
◆ BOOST_AUTO_TEST_CASE() [343/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UndesiredProteinName ) ◆ BOOST_AUTO_TEST_CASE() [344/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UnnecessaryCitPubEquiv ) ◆ BOOST_AUTO_TEST_CASE() [345/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UnnecessaryException )Definition at line 15986 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodGenProdSet(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, DoesFeatureHaveUnnecessaryException(), eDiag_Warning, CValidator::eVal_val_exons, GetCDSFromGenProdSet(), GetCDSFromGoodNucProtSet(), GetmRNAFromGenProdSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeMixLoc(), MakemRNAForCDS(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), SetSpliceForMixLoc(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [346/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UnnecessaryGeneXref )Definition at line 13960 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, eExtreme_Biological, CSeq_feat_Base::SetData(), CSeq_feat::SetGeneXref(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [347/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UnnecessaryTranslExcept ) ◆ BOOST_AUTO_TEST_CASE() [348/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UnqualifiedException )Definition at line 19024 of file unit_test_validator.cpp.
References BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGenProdSet(), GetGenomicFromGenProdSet(), GetmRNAFromGenProdSet(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [349/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UTRdoesNotAbutCDS )Definition at line 15415 of file unit_test_validator.cpp.
References AddMiscFeature(), AdjustProtFeatForNucProtSet(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, eNa_strand_minus, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), RevComp(), CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [350/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_UTRdoesNotExtendToEnd )Definition at line 17657 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_mRNA, eDiag_Warning, CSeq_inst_Base::eMol_rna, GetCDSFromGoodNucProtSet(), CSeq_loc_Base::GetInt(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_interval_Base::GetTo(), nuc, SetBiomol(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [351/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_VectorContamination ) ◆ BOOST_AUTO_TEST_CASE() [352/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_VR_803 )Definition at line 18603 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodSeq(), ChangeId(), CheckErrors(), CLEAR_ERRORS, CRNA_ref_Base::eType_rRNA, MakeGeneForFeature(), rna, CSeq_feat_Base::SetPseudo(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [353/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_WholeLocation )Definition at line 17465 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CRNA_ref_Base::eType_mRNA, CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPseudo(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [354/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_FEAT_WrongQualOnCDS ) ◆ BOOST_AUTO_TEST_CASE() [355/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphACGTScore ) ◆ BOOST_AUTO_TEST_CASE() [356/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphACGTScoreMany )Definition at line 20415 of file unit_test_validator.cpp.
References BuildGoodByteGraph(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSeq_graph_Base::GetNumval(), i, CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_graph_Base::SetGraph(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [357/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphBioseqId )Definition at line 20391 of file unit_test_validator.cpp.
References BuildGoodByteGraph(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Warning, CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_graph_Base::SetLoc(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [358/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphByteLen ) ◆ BOOST_AUTO_TEST_CASE() [359/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphGapScore ) ◆ BOOST_AUTO_TEST_CASE() [360/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphLocInvalid_1 ) ◆ BOOST_AUTO_TEST_CASE() [361/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphLocInvalid_2 )Definition at line 20535 of file unit_test_validator.cpp.
References BuildGoodByteGraph(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, CSeq_graph_Base::ResetLoc(), CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [362/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphMax )Definition at line 20100 of file unit_test_validator.cpp.
References BuildGoodByteGraph(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_graph_Base::SetGraph(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [363/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphMin ) ◆ BOOST_AUTO_TEST_CASE() [364/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphNScore ) ◆ BOOST_AUTO_TEST_CASE() [365/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphNScoreMany )Definition at line 20442 of file unit_test_validator.cpp.
References BuildGoodByteGraph(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CBioseq_Base::ResetAnnot(), CByte_graph_Base::ResetValues(), CBioseq_Base::SetAnnot(), CByte_graph_Base::SetAxis(), CSeq_annot_Base::SetData(), CSeq_graph_Base::SetGraph(), CBioseq_Base::SetInst(), CSeq_literal_Base::SetLength(), CByte_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CSeq_entry_Base::SetSeq(), CSeq_literal_Base::SetSeq_data(), CByte_graph_Base::SetValues(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [366/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphOutOfOrder ) ◆ BOOST_AUTO_TEST_CASE() [367/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphOverlap ) ◆ BOOST_AUTO_TEST_CASE() [368/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphSeqLitLen ) ◆ BOOST_AUTO_TEST_CASE() [369/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_GRAPH_GraphStartPhase ) ◆ BOOST_AUTO_TEST_CASE() [370/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_BadDeltaSeq )Definition at line 2161 of file unit_test_validator.cpp.
References BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eTech_barcode, CMolInfo_Base::eTech_composite_wgs_htgs, CMolInfo_Base::eTech_derived, CMolInfo_Base::eTech_htc, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_standard, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, i, CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), STANDARD_SETUP, TestDeltaTechAllowed(), TestDeltaTechNotAllowed(), and TestStartGapSeg().
◆ BOOST_AUTO_TEST_CASE() [371/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_BadSecondaryAccn ) ◆ BOOST_AUTO_TEST_CASE() [372/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_CircularProtein )Definition at line 1256 of file unit_test_validator.cpp.
References BuildGoodProtSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Error, CSeq_inst_Base::eTopology_circular, CSeq_inst_Base::eTopology_linear, CSeq_inst_Base::eTopology_not_set, CSeq_inst_Base::eTopology_other, CSeq_inst_Base::eTopology_tandem, SetCompleteness(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [373/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_ConflictingBiomolTech )Definition at line 2580 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, eDiag_Error, eDiag_Info, eDiag_Warning, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eMol_rna, CMolInfo_Base::eTech_barcode, CMolInfo_Base::eTech_composite_wgs_htgs, CMolInfo_Base::eTech_est, CMolInfo_Base::eTech_htgs_0, CMolInfo_Base::eTech_htgs_1, CMolInfo_Base::eTech_htgs_2, CMolInfo_Base::eTech_htgs_3, CMolInfo_Base::eTech_sts, CMolInfo_Base::eTech_survey, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, i, IsProteinTech(), SetBiomol(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [374/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_ConflictingIdsOnBioseq )Definition at line 2396 of file unit_test_validator.cpp.
References BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, GI_CONST, CTextseq_id_Base::SetAccession(), CPatent_seq_id_Base::SetCit(), CDbtag_Base::SetDb(), CGiimport_id_Base::SetDb(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_id_Base::SetGi(), CSeq_id_Base::SetGibbmt(), CSeq_id_Base::SetGibbsq(), CSeq_id_Base::SetGiim(), CSeq_id_Base::SetGpipe(), CGiimport_id_Base::SetId(), CBioseq_Base::SetId(), CSeq_id_Base::SetLocal(), CPDB_seq_id_Base::SetMol(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPatent(), CSeq_id_Base::SetPdb(), CSeq_entry_Base::SetSeq(), CPatent_seq_id_Base::SetSeqid(), CObject_id_Base::SetStr(), CDbtag_Base::SetTag(), CTextseq_id_Base::SetVersion(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [375/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_DuplicateSegmentReferences )Definition at line 2684 of file unit_test_validator.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CSeq_inst_Base::eRepr_seg, CValidator::eVal_far_fetch_mrna_products, CValidator::eVal_indexer_version, CValidator::eVal_need_isojta, CValidator::eVal_use_entrez, CValidator::eVal_validate_id_set, CObjectManager::GetInstance(), CGBDataLoader::RegisterInObjectManager(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_entry_Base::SetSeq(), CSeq_loc::SetWhole(), and CValidator::Validate().
◆ BOOST_AUTO_TEST_CASE() [376/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_ExtNotAllowed )Definition at line 987 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, CSeq_inst_Base::eRepr_consen, CSeq_inst_Base::eRepr_const, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_map, CSeq_inst_Base::eRepr_not_set, CSeq_inst_Base::eRepr_other, CSeq_inst_Base::eRepr_raw, CSeq_inst_Base::eRepr_ref, CSeq_inst_Base::eRepr_virtual, CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [377/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_FuzzyLen ) ◆ BOOST_AUTO_TEST_CASE() [378/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_InvalidAlphabet )Definition at line 1392 of file unit_test_validator.cpp.
References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), BuildGoodProtSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, CValidator::eVal_far_fetch_mrna_products, CValidator::eVal_indexer_version, CValidator::eVal_need_isojta, CValidator::eVal_use_entrez, CValidator::eVal_validate_id_set, CObjectManager::GetInstance(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and CValidator::Validate().
◆ BOOST_AUTO_TEST_CASE() [379/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_InvalidResidue )Definition at line 1464 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodProtSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_peptide, eDiag_Critical, eDiag_Fatal, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_rna, CSeq_inst_Base::eRepr_delta, CSeq_feat_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [380/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_LongGeneralSeqId ) ◆ BOOST_AUTO_TEST_CASE() [381/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_MolNotSet ) ◆ BOOST_AUTO_TEST_CASE() [382/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_MolNuclAcid ) ◆ BOOST_AUTO_TEST_CASE() [383/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_PartialInconsistent )Definition at line 1754 of file unit_test_validator.cpp.
References BuildGoodProtSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::eCompleteness_partial, CMolInfo_Base::eCompleteness_unknown, eDiag_Error, eExtreme_Biological, CSeq_inst_Base::eRepr_seg, SetCompleteness(), CBioseq_Base::SetInst(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [384/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_ReprInvalid ) ◆ BOOST_AUTO_TEST_CASE() [385/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_SeqGapBadLinkage )Definition at line 2253 of file unit_test_validator.cpp.
References AdjustGap(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, CSeq_inst_Base::eMol_dna, CLinkage_evidence_Base::eType_align_genus, CSeq_gap_Base::eType_fragment, CSeq_gap_Base::eType_short_arm, CSeq_gap_Base::eType_unknown, CLinkage_evidence_Base::eType_unspecified, CSeq_gap_Base::ResetLinkage(), CSeq_gap_Base::ResetType(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [386/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_SeqIdNameHasSpace ) ◆ BOOST_AUTO_TEST_CASE() [387/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_ShortSeq )Definition at line 1885 of file unit_test_validator.cpp.
References BuildGoodProtSeq(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_ends, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, CMolInfo_Base::eCompleteness_other, CMolInfo_Base::eCompleteness_partial, CMolInfo_Base::eCompleteness_unknown, eDiag_Warning, CBioseq_Base::SetAnnot(), SetCompleteness(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [388/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_StopInProtein )Definition at line 1695 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), HasBadStartCodon(), HasInternalStop(), HasStopInProtein(), nuc, CSeq_feat_Base::ResetExcept(), CSeq_feat_Base::ResetExcept_text(), CSeq_feat_Base::SetExcept(), CSeq_feat_Base::SetExcept_text(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [389/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_TrailingX )Definition at line 2740 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_no_right, eDiag_Info, eDiag_Warning, eExtreme_Biological, GetCDSFromGoodNucProtSet(), nuc, prot, SetCompleteness(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetPartial(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [390/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_INST_ZeroGiNumber ) ◆ BOOST_AUTO_TEST_CASE() [391/458] BOOST_AUTO_TEST_CASE ( Test_SEQ_RW_1753 ) ◆ BOOST_AUTO_TEST_CASE() [392/458] BOOST_AUTO_TEST_CASE ( Test_SeqLitDataLength0 ) ◆ BOOST_AUTO_TEST_CASE() [393/458] BOOST_AUTO_TEST_CASE ( Test_SeqLitGapLength0 )Definition at line 3617 of file unit_test_validator.cpp.
References BuildGoodDeltaSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_unk, CRef< C, Locker >::Reset(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [394/458] BOOST_AUTO_TEST_CASE ( Test_SexQualifiers ) ◆ BOOST_AUTO_TEST_CASE() [395/458] BOOST_AUTO_TEST_CASE ( Test_SingleStrandViruses )Definition at line 7297 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_cRNA, eDiag_Warning, CSeq_inst_Base::eMol_rna, CBioSource_Base::eOrigin_artificial, CBioSource_Base::eOrigin_mut, CBioSource_Base::eOrigin_synthetic, SetBiomol(), SetDiv(), SetLineage(), SetOrigin(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), SetSynthetic_construct(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [396/458] BOOST_AUTO_TEST_CASE ( Test_SQD_1309 )Definition at line 21396 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_transcribed_RNA, eDiag_Warning, CSeq_inst_Base::eMol_rna, CMolInfo_Base::eTech_tsa, GetNucleotideSequenceFromGoodNucProtSet(), RevComp(), SetBiomol(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [397/458] BOOST_AUTO_TEST_CASE ( Test_SQD_1470 ) ◆ BOOST_AUTO_TEST_CASE() [398/458] BOOST_AUTO_TEST_CASE ( Test_SQD_1532 ) ◆ BOOST_AUTO_TEST_CASE() [399/458] BOOST_AUTO_TEST_CASE ( Test_SQD_2036 )Definition at line 21864 of file unit_test_validator.cpp.
References BuildGoodSeq(), CSubSource::CheckCellLine(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CSubSource_Base::eSubtype_cell_line, msg(), SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [400/458] BOOST_AUTO_TEST_CASE ( Test_SQD_292 )Definition at line 21329 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GI_CONST, nuc, CSeqdesc_Base::SetCreate_date(), CDate_std_Base::SetDay(), CBioseq_set_Base::SetDescr(), CSeq_id_Base::SetGi(), CDate_std_Base::SetMonth(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CDate_Base::SetStd(), CSeqdesc_Base::SetUpdate_date(), CDate_std_Base::SetYear(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [401/458] BOOST_AUTO_TEST_CASE ( Test_SQD_313 ) ◆ BOOST_AUTO_TEST_CASE() [402/458] BOOST_AUTO_TEST_CASE ( Test_SQD_4354 ) ◆ BOOST_AUTO_TEST_CASE() [403/458] BOOST_AUTO_TEST_CASE ( Test_SQD_4560 ) ◆ BOOST_AUTO_TEST_CASE() [404/458] BOOST_AUTO_TEST_CASE ( Test_SubSourceAutofix ) ◆ BOOST_AUTO_TEST_CASE() [405/458] BOOST_AUTO_TEST_CASE ( Test_TerminalGap )Definition at line 4007 of file unit_test_validator.cpp.
References BuildGoodDeltaSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Warning, CSeq_inst_Base::eTopology_circular, SetCompleteness(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [406/458] BOOST_AUTO_TEST_CASE ( Test_TerminalNs )Definition at line 3425 of file unit_test_validator.cpp.
References BuildGoodDeltaSeq(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Error, eDiag_Info, eDiag_Warning, CSeq_inst_Base::eTopology_circular, SetCompleteness(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [407/458] BOOST_AUTO_TEST_CASE ( TEST_TitleNotAppropriateForSet ) ◆ BOOST_AUTO_TEST_CASE() [408/458] BOOST_AUTO_TEST_CASE ( Test_TM_145 ) ◆ BOOST_AUTO_TEST_CASE() [409/458] BOOST_AUTO_TEST_CASE ( Test_TripletEncodesStopCodon )Definition at line 23421 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), CCDSTranslationProblems::GetNonsenseIntrons(), GetNucleotideSequenceFromGoodNucProtSet(), nuc, CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [410/458] BOOST_AUTO_TEST_CASE ( Test_tRNA_Mixed_Loc )Definition at line 12641 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), BuildtRNA(), CheckErrors(), CLEAR_ERRORS, eNa_strand_plus, MakeMixLoc(), CSeq_feat_Base::SetData(), CBioseq_Base::SetId(), CSeq_loc::SetMix(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [411/458] BOOST_AUTO_TEST_CASE ( Test_UnknownLengthGapNot100 ) ◆ BOOST_AUTO_TEST_CASE() [412/458] BOOST_AUTO_TEST_CASE ( Test_UnparsedtRNAAnticodon ) ◆ BOOST_AUTO_TEST_CASE() [413/458] BOOST_AUTO_TEST_CASE ( Test_UnparsedtRNAProduct ) ◆ BOOST_AUTO_TEST_CASE() [414/458] BOOST_AUTO_TEST_CASE ( Test_USAStateCleanup ) ◆ BOOST_AUTO_TEST_CASE() [415/458] BOOST_AUTO_TEST_CASE ( Test_ValidError_Format )Definition at line 635 of file unit_test_validator.cpp.
References AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), CheckStrings(), CValidErrItem::ConvertErrCode(), eErr_SEQ_FEAT_NotSpliceConsensusDonor, eSubmitterFormatErrorGroup_ConsensusSplice, COrgMod_Base::eSubtype_bio_material, CSubSource_Base::eSubtype_country, COrgMod_Base::eSubtype_culture_collection, CSubSource_Base::eSubtype_lat_lon, COrgMod_Base::eSubtype_specimen_voucher, expected, format, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), MakeGeneForFeature(), MakeIntronForMixLoc(), MakeMixLoc(), CSubSource::NCBI_UseGeoLocNameForCountry(), nuc, prot, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), SetOrgMod(), SetSubSource(), NStr::Split(), STANDARD_SETUP, and val.
◆ BOOST_AUTO_TEST_CASE() [416/458] BOOST_AUTO_TEST_CASE ( Test_ValidError_Format1 )Definition at line 812 of file unit_test_validator.cpp.
References CValidErrorFormat::GetFeatureIdLabel(), CSeq_feat_Base::ResetId(), CSeq_feat_Base::SetData(), CDbtag_Base::SetDb(), CFeat_id_Base::SetGeneral(), CSeq_feat_Base::SetId(), CSeq_feat_Base::SetIds(), CFeat_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CObject_id_Base::SetStr(), CDbtag_Base::SetTag(), and ToAsn1().
◆ BOOST_AUTO_TEST_CASE() [417/458] BOOST_AUTO_TEST_CASE ( Test_Validity_SpecificHost ) ◆ BOOST_AUTO_TEST_CASE() [418/458] BOOST_AUTO_TEST_CASE ( Test_VR_146 )Definition at line 21896 of file unit_test_validator.cpp.
References AddGoodPub(), BuildGoodNucProtSet(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CSeqdesc_Base::e_Pub, CBioseq_set_Base::eClass_phy_set, eDiag_Error, eDiag_Info, CValidator::eVal_genome_submission, RemoveDescriptorType(), CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [419/458] BOOST_AUTO_TEST_CASE ( TEST_VR_15 )Definition at line 23028 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, CSeq_inst_Base::eTopology_circular, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [420/458] BOOST_AUTO_TEST_CASE ( Test_VR_166 ) ◆ BOOST_AUTO_TEST_CASE() [421/458] BOOST_AUTO_TEST_CASE ( Test_VR_173 ) ◆ BOOST_AUTO_TEST_CASE() [422/458] BOOST_AUTO_TEST_CASE ( Test_VR_28 ) ◆ BOOST_AUTO_TEST_CASE() [423/458] BOOST_AUTO_TEST_CASE ( Test_VR_35 ) ◆ BOOST_AUTO_TEST_CASE() [424/458] BOOST_AUTO_TEST_CASE ( TEST_VR_477 ) ◆ BOOST_AUTO_TEST_CASE() [425/458] BOOST_AUTO_TEST_CASE ( Test_VR_478 )Definition at line 22360 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CBioseq_Base::GetId(), CSeq_entry_Base::GetSeq(), CSeq_feat_Base::SetData(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetQual(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [426/458] BOOST_AUTO_TEST_CASE ( Test_VR_601 ) ◆ BOOST_AUTO_TEST_CASE() [427/458] BOOST_AUTO_TEST_CASE ( Test_VR_612 ) ◆ BOOST_AUTO_TEST_CASE() [428/458] BOOST_AUTO_TEST_CASE ( Test_VR_616 ) ◆ BOOST_AUTO_TEST_CASE() [429/458] BOOST_AUTO_TEST_CASE ( Test_VR_630 ) ◆ BOOST_AUTO_TEST_CASE() [430/458] BOOST_AUTO_TEST_CASE ( Test_VR_660 ) ◆ BOOST_AUTO_TEST_CASE() [431/458] BOOST_AUTO_TEST_CASE ( Test_VR_664 )Definition at line 22311 of file unit_test_validator.cpp.
References CSerialObject::Assign(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, eDiag_Warning, CUser_field_Base::SetData(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CUser_field_Base::SetLabel(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [432/458] BOOST_AUTO_TEST_CASE ( Test_VR_709 )Definition at line 9486 of file unit_test_validator.cpp.
References CSerialObject::Assign(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Info, MkField(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [433/458] BOOST_AUTO_TEST_CASE ( Test_VR_711 )Definition at line 21937 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CValidator::eVal_genome_submission, CSeq_feat_Base::ResetComment(), CTextseq_id_Base::SetAccession(), CSeq_feat_Base::SetData(), CSeq_id_Base::SetEmbl(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), CTextseq_id_Base::SetVersion(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [434/458] BOOST_AUTO_TEST_CASE ( Test_VR_728 )Definition at line 23302 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, CDbtag_Base::SetDb(), CSeq_id_Base::SetGeneral(), CBioseq_Base::SetId(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CObject_id_Base::SetStr(), CDbtag_Base::SetTag(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [435/458] BOOST_AUTO_TEST_CASE ( Test_VR_733 ) ◆ BOOST_AUTO_TEST_CASE() [436/458] BOOST_AUTO_TEST_CASE ( Test_VR_742 ) ◆ BOOST_AUTO_TEST_CASE() [437/458] BOOST_AUTO_TEST_CASE ( Test_VR_746 )Definition at line 18784 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakeGeneForFeature(), nuc, CSeq_feat_Base::SetData(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [438/458] BOOST_AUTO_TEST_CASE ( Test_VR_748 ) ◆ BOOST_AUTO_TEST_CASE() [439/458] BOOST_AUTO_TEST_CASE ( Test_VR_751 ) ◆ BOOST_AUTO_TEST_CASE() [440/458] BOOST_AUTO_TEST_CASE ( Test_VR_763 ) ◆ BOOST_AUTO_TEST_CASE() [441/458] BOOST_AUTO_TEST_CASE ( Test_VR_78 )Definition at line 22199 of file unit_test_validator.cpp.
References AddFeat(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), MakeGeneForFeature(), MakemRNAForCDS(), nuc, prot, CSeq_feat_Base::SetData(), SetNucProtSetPartials(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [442/458] BOOST_AUTO_TEST_CASE ( Test_VR_787 )Definition at line 22689 of file unit_test_validator.cpp.
References CTaxValidationAndCleanup::AdjustOrgRefsWithTaxLookupReply(), CSerialObject::Assign(), COrgMod_Base::eSubtype_isolate, COrgMod_Base::eSubtype_nat_host, COrgMod_Base::eSubtype_strain, COrgMod_Base::eSubtype_sub_species, COrg_ref_Base::GetTaxname(), COrg_ref_Base::Reset(), CTaxon3::SendOrgRefList(), CDbtag_Base::SetDb(), COrg_ref_Base::SetDb(), COrg_ref_Base::SetOrgname(), CDbtag_Base::SetTag(), COrg_ref_Base::SetTaxname(), and CTaxon3::yes.
◆ BOOST_AUTO_TEST_CASE() [443/458] BOOST_AUTO_TEST_CASE ( Test_VR_793 )Definition at line 24912 of file unit_test_validator.cpp.
References eDiag_Error, eDiag_Info, eDiag_Warning, CSubSource_Base::eSubtype_chromosome, CSubSource_Base::eSubtype_endogenous_virus_name, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_linkage_group, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_segment, CSubSource_Base::eSubtype_transposon_name, TestAlwaysBadReplicon(), TestAlwaysGoodReplicon(), TestOneReplicon(), TestRepliconForbiddenWords(), and TestRepliconTaxname().
◆ BOOST_AUTO_TEST_CASE() [444/458] BOOST_AUTO_TEST_CASE ( Test_VR_796 )Definition at line 24262 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eCompleteness_complete, eDiag_Critical, eDiag_Error, CBioSource_Base::eGenome_mitochondrion, CSeq_inst_Base::eTopology_circular, SetCompleteness(), SetGenome(), CBioseq_Base::SetInst(), SetLineage(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [445/458] BOOST_AUTO_TEST_CASE ( Test_VR_812 ) ◆ BOOST_AUTO_TEST_CASE() [446/458] BOOST_AUTO_TEST_CASE ( Test_VR_814 ) ◆ BOOST_AUTO_TEST_CASE() [447/458] BOOST_AUTO_TEST_CASE ( Test_VR_819 ) ◆ BOOST_AUTO_TEST_CASE() [448/458] BOOST_AUTO_TEST_CASE ( Test_VR_824 ) ◆ BOOST_AUTO_TEST_CASE() [449/458] BOOST_AUTO_TEST_CASE ( Test_VR_828 )Definition at line 11843 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, CUser_object::eObjectType_StructuredComment, GetProteinSequenceFromGoodNucProtSet(), MakeStructuredCommentField(), prot, CSeq_feat_Base::SetData(), CUser_object_Base::SetData(), CBioseq_set_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSet(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [450/458] BOOST_AUTO_TEST_CASE ( Test_VR_829 )Definition at line 11866 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CUser_object::eObjectType_StructuredComment, GetProteinSequenceFromGoodNucProtSet(), MakeStructuredCommentField(), prot, CSeq_feat_Base::SetData(), CUser_object_Base::SetData(), CBioseq_set_Base::SetDescr(), CUser_object::SetObjectType(), CSeq_entry_Base::SetSet(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [451/458] BOOST_AUTO_TEST_CASE ( Test_VR_840 ) ◆ BOOST_AUTO_TEST_CASE() [452/458] BOOST_AUTO_TEST_CASE ( Test_VR_852 ) ◆ BOOST_AUTO_TEST_CASE() [453/458] ◆ BOOST_AUTO_TEST_CASE() [454/458] BOOST_AUTO_TEST_CASE ( Test_VR_875 )Definition at line 25214 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_environmental_sample, COrgMod_Base::eSubtype_isolate, CSubSource_Base::eSubtype_isolation_source, COrgMod_Base::eSubtype_metagenome_source, CSubSource_Base::eSubtype_metagenomic, COrgMod_Base::eSubtype_nat_host, CValidator::eVal_genome_submission, SetOrgMod(), SetSubSource(), SetTaxname(), SetTaxon(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [455/458] BOOST_AUTO_TEST_CASE ( VR_758 )Definition at line 23467 of file unit_test_validator.cpp.
References AddFeat(), AddGoodPub(), AddGoodSource(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eCompleteness_complete, eDiag_Error, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_delta, CMolInfo_Base::SetBiomol(), CMolInfo_Base::SetCompleteness(), CSeq_feat_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSeq(), CObject_id_Base::SetStr(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [456/458] BOOST_AUTO_TEST_CASE ( VR_762 ) ◆ BOOST_AUTO_TEST_CASE() [457/458] BOOST_AUTO_TEST_CASE ( VR_778 )Definition at line 23602 of file unit_test_validator.cpp.
References AddDay(), AddMonth(), AddYear(), CSerialObject::Assign(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, NULL, CCit_sub_Base::SetDate(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), CPub_Base::SetSub(), and STANDARD_SETUP.
◆ BOOST_AUTO_TEST_CASE() [458/458] BOOST_AUTO_TEST_CASE ( VR_V48 ) ◆ BOOST_FIXTURE_TEST_CASE() [1/28]Definition at line 5626 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodSeq(), ChangeErrorAcc(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CMolInfo_Base::eBiomol_genomic_mRNA, CMolInfo_Base::eBiomol_mRNA, CMolInfo_Base::eBiomol_ncRNA, CMolInfo_Base::eBiomol_pre_RNA, CMolInfo_Base::eBiomol_rRNA, CMolInfo_Base::eBiomol_scRNA, CMolInfo_Base::eBiomol_snoRNA, CMolInfo_Base::eBiomol_snRNA, CMolInfo_Base::eBiomol_tmRNA, CMolInfo_Base::eBiomol_transcribed_RNA, CMolInfo_Base::eBiomol_tRNA, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_no_right, eDiag_Error, eDiag_Warning, eGIBB_mod_complete, eGIBB_mod_cyanelle, eGIBB_mod_dna, eGIBB_mod_mitochondrial, eGIBB_mod_no_left, eGIBB_mod_no_right, eGIBB_mod_partial, eGIBB_mod_rna, eGIBB_mol_genomic, eGIBB_mol_pre_mRNA, CSeq_inst_Base::eMol_rna, CMolInfo_Base::eTech_fli_cdna, CMolInfo_Base::eTech_genemap, CMolInfo_Base::eTech_unknown, CMolInfo_Base::eTech_wgs, SetBiomol(), CMolInfo_Base::SetBiomol(), SetCompleteness(), CMolInfo_Base::SetCompleteness(), CSeqdesc_Base::SetCreate_date(), CBioseq_Base::SetDescr(), CSeqdesc_Base::SetEmbl(), CSeqdesc_Base::SetGenbank(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CGB_block_Base::SetKeywords(), CSeqdesc_Base::SetModif(), CSeqdesc_Base::SetMol_type(), CSeqdesc_Base::SetMolinfo(), CDate_std_Base::SetMonth(), CBioSource_Base::SetOrg(), CSeqdesc_Base::SetPdb(), CSeqdesc_Base::SetPir(), CSeqdesc_Base::SetPrf(), CSeq_entry_Base::SetSeq(), CSeqdesc_Base::SetSource(), CSeqdesc_Base::SetSp(), CDate_Base::SetStd(), SetTaxon(), SetTech(), CMolInfo_Base::SetTech(), CSeqdesc_Base::SetUpdate_date(), CDate_std_Base::SetYear(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [2/28] BOOST_FIXTURE_TEST_CASE ( Test_InconsistentBioSources_ConLocation , CGenBankFixture ) ◆ BOOST_FIXTURE_TEST_CASE() [3/28]Definition at line 3294 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, GI_CONST, CTextseq_id_Base::SetAccession(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGi(), CBioseq_Base::SetId(), CSeq_id_Base::SetOther(), CSeq_id_Base::SetPir(), CSeq_id_Base::SetPrf(), CSeq_entry_Base::SetSeq(), CSeq_id_Base::SetSwissprot(), CSeq_id_Base::SetTpd(), CSeq_id_Base::SetTpe(), CSeq_id_Base::SetTpg(), CTextseq_id_Base::SetVersion(), STANDARD_SETUP, and TestOneOtherAcc().
◆ BOOST_FIXTURE_TEST_CASE() [4/28] ◆ BOOST_FIXTURE_TEST_CASE() [5/28]Definition at line 19887 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [6/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_ALIGN_AlignDimSeqIdNotMatch , CGenBankFixture )Definition at line 19764 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiagFilter_All, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), SetDiagFilter(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [7/28]Definition at line 19942 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_annot_Base::SetDesc(), CSeq_entry_Base::SetSet(), CUser_object_Base::SetType(), CAnnotdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [8/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_ALIGN_DensegLenStart , CGenBankFixture )Definition at line 19690 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CSeq_align_Base::eType_global, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, FOR_EACH_SEQENTRY_ON_SEQSET, CSeq_entry_Base::GetSet(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), CSeq_align_Base::SetType(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [9/28]Definition at line 19790 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, RevComp(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetSegs(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [10/28]Definition at line 19832 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CSeq_align_Base::ResetSegs(), CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [11/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_ALIGN_PercentIdentity , CGenBankFixture )Definition at line 19968 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [12/28]Definition at line 19855 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [13/28]Definition at line 19914 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [14/28]Definition at line 19664 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [15/28]Definition at line 19732 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetSegs(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [16/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_ALIGN_UnexpectedAlignmentType , CGenBankFixture )Definition at line 20023 of file unit_test_validator.cpp.
References BuildGoodEcoSet(), BuildSetDendiagAlign(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CValidator::eVal_remote_fetch, CValidator::eVal_val_align, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [17/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_FEAT_FeatureProductInconsistency , CGenBankFixture )Definition at line 16601 of file unit_test_validator.cpp.
References AddCDSAndProtForBigGoodNucProtSet(), AddFeat(), AddMiscFeature(), BuildGoodNucProtSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), MakemRNAForCDS(), nuc, CBioseq_set_Base::SetAnnot(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [18/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_FEAT_MissingMRNAproduct , CGenBankFixture )Definition at line 14869 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodGenProdSet(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CRNA_ref_Base::eType_mRNA, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetProduct(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [19/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_GRAPH_GraphDiffNumber , CGenBankFixture ) ◆ BOOST_FIXTURE_TEST_CASE() [20/28] BOOST_FIXTURE_TEST_CASE ( Test_SEQ_GRAPH_GraphSeqLocLen , CGenBankFixture )Definition at line 20200 of file unit_test_validator.cpp.
References BuildGoodByteGraph(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CBioseq_Base::SetAnnot(), CSeq_annot_Base::SetData(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [21/28]Definition at line 2847 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), BuildGoodSeq(), ChangeErrorAcc(), ChangeNucId(), ChangeProtId(), CheckErrors(), CLEAR_ERRORS, eDiag_Critical, eDiag_Error, eDiag_Warning, GetCDSFromGoodNucProtSet(), CBioseq_Base::ResetId(), CTextseq_id_Base::SetAccession(), CBioseq_Base::SetAnnot(), CDbtag_Base::SetDb(), CSeq_id_Base::SetDdbj(), CSeq_id_Base::SetEmbl(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CBioseq_Base::SetId(), CSeq_id_Base::SetLocal(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CObject_id_Base::SetStr(), CDbtag_Base::SetTag(), CTextseq_id_Base::SetVersion(), STANDARD_SETUP, TestBadProtId(), TestGoodNucId(), and TestGoodProtId().
◆ BOOST_FIXTURE_TEST_CASE() [22/28] ◆ BOOST_FIXTURE_TEST_CASE() [23/28]Definition at line 3689 of file unit_test_validator.cpp.
References AddTpaAssemblyUserObject(), BuildGoodAlign(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, CBioseq_set_Base::eClass_genbank, eDiag_Error, eDiag_Warning, GI_CONST, CBioseq_set_Base::SetClass(), CSeq_id_Base::SetGi(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [24/28] BOOST_FIXTURE_TEST_CASE ( Test_UnexpectedIdentifierChange , CGenBankFixture ) ◆ BOOST_FIXTURE_TEST_CASE() [25/28]Definition at line 23111 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CMolInfo_Base::eTech_wgs, f, CUser_field_Base::SetData(), CUser_object_Base::SetData(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CUser_field_Base::SetLabel(), CSeq_entry_Base::SetSeq(), SetTech(), CUser_object_Base::SetType(), CSeqdesc_Base::SetUser(), and STANDARD_SETUP.
◆ BOOST_FIXTURE_TEST_CASE() [26/28] ◆ BOOST_FIXTURE_TEST_CASE() [27/28] ◆ BOOST_FIXTURE_TEST_CASE() [28/28] ◆ BuildBigGoodNucProtSet()Definition at line 16518 of file unit_test_validator.cpp.
References AddCDSAndProtForBigGoodNucProtSet(), AddGoodPub(), AddGoodSource(), CMolInfo_Base::eBiomol_genomic, CBioseq_set_Base::eClass_nuc_prot, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_raw, CBioseq_Base::GetInst(), GetLength(), i, NStr::IntToString(), offset, CMolInfo_Base::SetBiomol(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSeq(), and CSeq_entry_Base::SetSet().
Referenced by BOOST_AUTO_TEST_CASE().
◆ BuildGapFuzz100DeltaSeq() ◆ BuildGenProdSetBigNucProtSet()Definition at line 17385 of file unit_test_validator.cpp.
References AdjustProtFeatForNucProtSet(), BuildGoodNucProtSet(), ChangeNucProtSetNucId(), ChangeNucProtSetProteinId(), CMolInfo_Base::eBiomol_mRNA, CSeq_inst_Base::eMol_rna, GetCDSFromGoodNucProtSet(), GetNucleotideSequenceFromGoodNucProtSet(), GetProteinSequenceFromGoodNucProtSet(), nuc, prot, SetBiomol(), and CSeq_feat_Base::SetLocation().
Referenced by BuildGenProdSetWithBigProduct().
◆ BuildGenProdSetWithBigProduct()Definition at line 17410 of file unit_test_validator.cpp.
References AddFeat(), CSerialObject::Assign(), BuildGenProdSetBigNucProtSet(), BuildGoodSeq(), CBioseq_set_Base::eClass_gen_prod_set, GetCDSFromGoodNucProtSet(), MakemRNAForCDS(), CBioseq_set_Base::SetClass(), CBioseq_Base::SetInst(), CSeq_id_Base::SetLocal(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CObject_id_Base::SetStr().
Referenced by BOOST_AUTO_TEST_CASE().
◆ BuildGoodByteGraph()Definition at line 20048 of file unit_test_validator.cpp.
References CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_entry_Base::GetSeq(), kInvalidSeqPos, len, offset, CSeq_graph_Base::SetGraph(), CSeq_graph_Base::SetLoc(), CSeq_graph_Base::SetNumval(), and CSeq_graph_Base::SetTitle().
Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().
◆ BuildGoodSpliceNucProtSet()Definition at line 11891 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), GetCDSFromGoodNucProtSet(), MakeMixLoc(), prot, CBioseq_Base::SetAnnot(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().
Referenced by BOOST_AUTO_TEST_CASE().
◆ BuildSetAlign() ◆ BuildSetDendiagAlign() ◆ BuildSmallGenomeSet()Definition at line 24315 of file unit_test_validator.cpp.
References AddGeneticCode(), BuildGoodNucProtSet(), ChangeNucProtSetNucId(), ChangeNucProtSetProteinId(), CBioseq_set_Base::eClass_small_genome_set, CBioSource_Base::eGenome_chloroplast, GetCDSFromGoodNucProtSet(), i, MakeSmallGenomeSetNucId(), NStr::NumericToString(), CBioseq_set_Base::SetClass(), SetGenome(), CSeq_id_Base::SetLocal(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CObject_id_Base::SetStr().
Referenced by BOOST_AUTO_TEST_CASE().
◆ ChangeErrorAcc() ◆ ChangeGoodNucProtSetIdToGenbankName() ◆ CheckErrors()Definition at line 224 of file unit_test_validator.cpp.
References i, CExpectedError::PrintSeenError(), s_debugMode, and WriteErrors().
Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CheckGeneOntologyTermDuplicate(), CheckGeneOntologyTermNotDuplicate(), CheckLocalId(), CheckMiscPartialErrors(), CheckUnbalancedParenthesesOrgMod(), CheckUnbalancedParenthesesSubSource(), s_TestOneWrongQual(), TestBadProtId(), TestConsultRequired(), TestDeltaTechAllowed(), TestDeltaTechNotAllowed(), TestGoodNucId(), TestGoodProtId(), TestMultipleEquivBioSources(), TestNewAccessionAsInference(), TestNewAccessionOnNuc(), TestNewAccessionOnNucProt(), TestNewAccessionOnStandaloneProt(), TestOneGeneralSeqId(), TestOneLatLonCountry(), TestOneLongGeneral(), TestOneOtherAcc(), TestOnePlasmid(), TestOneReplicon(), TestOneStrain(), TestOneStrainNew(), TestOverlappingRNAFeatures(), TestSpecificHostNoError(), TestStartGapSeg(), and TestUTRPair().
◆ CheckGeneOntologyTermDuplicate() ◆ CheckGeneOntologyTermNotDuplicate() void CheckGeneOntologyTermNotDuplicate ( CRef< CSeq_feat > feat ) ◆ CheckHost() ◆ CheckLocalId() ◆ CheckMiscPartialErrors() ◆ CheckOneSpecificHost() ◆ CheckStrings() ◆ CheckUnbalancedParenthesesOrgMod() ◆ CheckUnbalancedParenthesesSubSource() ◆ CreateReciprocalLinks() ◆ IsProteinTech() ◆ MakeBadSeasonDate() ◆ MakeGeneious() ◆ MakeGeneOntologyFeat() ◆ MakeGoTerm() ◆ MakeGps() ◆ MakeLeft() ◆ MakeRight() ◆ MakeSmallGenomeSetNucId() ◆ MakeStructuredCommentField() ◆ MakeWrongCap() ◆ MkField() ◆ NCBITEST_AUTO_INIT() ◆ NCBITEST_INIT_CMDLINE() ◆ NCBITEST_INIT_TREE() ◆ OrgModHasOtherRules() ◆ s_AddGeneralAndLocal() void s_AddGeneralAndLocal ( CBioseq & seq ) ◆ s_ArePrimersUnique() ◆ s_BuildBadEcNumberEntry() ◆ s_CreateReplyWithMessage() ◆ s_USAStateTest() ◆ SetErrorsAccessions() ◆ SetFeatureLocationBond() ◆ SetRefGeneTrackingStatus() ◆ SetTitle()Definition at line 2024 of file unit_test_validator.cpp.
References NStr::IsBlank(), CSeq_entry::IsSetDescr(), CSeq_entry::SetDescr(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), and CSeqdesc_Base::SetTitle().
Referenced by BOOST_AUTO_TEST_CASE(), CEditingBtnsPanel::CEditingBtnsPanel(), CFeedbackWizard::Create(), CwxExportVectorImageDlg::Create(), CwxExportAlnmultiImgDlg::Create(), CEditSequence::CreateControls(), CSaveImagesSetupDlg::CSaveImagesSetupDlg(), CSeqdescTitleEdit::CSeqdescTitleEdit(), CwxSeqMarkerSetDlg::SetDlgTitle(), CAECRFrame::SetInitParameters(), CBLAST_DB_Dialog::SetToolName(), CGuiWidgetDlg::SetWidgetTitle(), SequenceViewerWindow::SetWindowTitle(), StructureWindow::SetWindowTitle(), UpdateViewerWindow::SetWindowTitle(), COpenViewDlg::x_SetCurrentPanel(), CRunToolDlg::x_SetCurrentPanel(), and COpenDlg::x_UpdateTitle().
◆ SetUpMiscForPartialTest() ◆ ShowOrgRef() [1/2] ◆ ShowOrgRef() [2/2]Definition at line 5509 of file unit_test_validator.cpp.
References CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_set_Base::GetDescr(), CSeq_entry_Base::GetSeq(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_entry_Base::IsSeq(), CSeq_entry_Base::IsSet(), CBioseq_Base::IsSetDescr(), CBioseq_set_Base::IsSetDescr(), CBioseq_set_Base::IsSetSeq_set(), and ShowOrgRef().
◆ SubSourceHasOtherRules()Definition at line 8825 of file unit_test_validator.cpp.
References CSubSource_Base::eSubtype_collection_date, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_frequency, CSubSource_Base::eSubtype_fwd_primer_name, CSubSource_Base::eSubtype_fwd_primer_seq, CSubSource_Base::eSubtype_insertion_seq_name, CSubSource_Base::eSubtype_lat_lon, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_plastid_name, CSubSource_Base::eSubtype_rev_primer_name, CSubSource_Base::eSubtype_rev_primer_seq, CSubSource_Base::eSubtype_sex, and CSubSource_Base::eSubtype_transposon_name.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestAlwaysBadReplicon() ◆ TestAlwaysGoodReplicon() ◆ TestBadProtId()Definition at line 2773 of file unit_test_validator.cpp.
References BuildGoodNucProtSet(), ChangeNucId(), ChangeProtId(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CTextseq_id_Base::SetAccession(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), and STANDARD_SETUP.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ TestBulkSpecificHostFixList()Definition at line 22486 of file unit_test_validator.cpp.
References AddOrgmodDescriptor(), AddOrgmodFeat(), CTaxValidationAndCleanup::AdjustOrgRefsWithSpecificHostReply(), CSerialObject::Assign(), BuildGoodSeq(), NStr::Equal(), COrgMod_Base::eSubtype_nat_host, CTaxValidationAndCleanup::GetSpecificHostLookupRequest(), CTaxValidationAndCleanup::Init(), om, CTaxon3::SendOrgRefList(), COrg_ref_Base::SetOrgname(), COrg_ref_Base::SetTaxname(), and CTaxon3::yes.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestConsultRequired() ◆ TestDeltaTechAllowed()Definition at line 2070 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, CMolInfo_Base::eTech_barcode, CMolInfo_Base::eTech_tsa, CMolInfo_Base::eTech_wgs, SetTech(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestDeltaTechNotAllowed() ◆ TestGoodNucId()Definition at line 2821 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodNucProtSet(), ChangeNucId(), ChangeProtId(), CheckErrors(), CLEAR_ERRORS, CMolInfo_Base::eTech_wgs, CTextseq_id_Base::SetAccession(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetLocal(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CObject_id_Base::SetStr(), SetTech(), and STANDARD_SETUP.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ TestGoodProtId() ◆ TestMultipleEquivBioSources()Definition at line 16316 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, CValidator::eVal_seqsubmit_parent, expected, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), SetTransgenic(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestNewAccessionAsInference() void TestNewAccessionAsInference ( const string & acc ) ◆ TestNewAccessionOnNuc()Definition at line 25089 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, CMolInfo_Base::eTech_wgs, CTextseq_id_Base::SetAccession(), CSeq_id_Base::SetGenbank(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestNewAccessionOnNucProt() ◆ TestNewAccessionOnStandaloneProt() void TestNewAccessionOnStandaloneProt ( const string & accession, bool is_nuc_acc, bool is_wgs ) ◆ TestOneGeneralSeqId() ◆ TestOneLatLonCountry()Definition at line 558 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CheckStrings(), CLEAR_ERRORS, eDiag_Info, CSubSource_Base::eSubtype_country, CSubSource_Base::eSubtype_lat_lon, CValidator::eVal_latlon_check_state, expected, format, CSubSource::NCBI_UseGeoLocNameForCountry(), SetSubSource(), NStr::Split(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestOneLongGeneral() void TestOneLongGeneral ( bool emb, bool err ) ◆ TestOneMiscPartial() ◆ TestOneOtherAcc()Definition at line 3261 of file unit_test_validator.cpp.
References CSeq_id::AsFastaString(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Info, eDiag_Warning, GI_CONST, CSeq_id_Base::SetGi(), CBioseq_Base::SetId(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
Referenced by BOOST_FIXTURE_TEST_CASE().
◆ TestOnePlasmid() ◆ TestOneReplicon()Definition at line 24789 of file unit_test_validator.cpp.
References BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CBioSource_Base::eGenome_plasmid, CSubSource_Base::eSubtype_plasmid_name, CSubSource_Base::eSubtype_segment, NStr::IsBlank(), msg(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), STANDARD_SETUP, and val.
Referenced by BOOST_AUTO_TEST_CASE(), TestAlwaysBadReplicon(), TestAlwaysGoodReplicon(), TestRepliconForbiddenWords(), and TestRepliconTaxname().
◆ TestOneStrain() ◆ TestOneStrainNew()Definition at line 22869 of file unit_test_validator.cpp.
References AddStrainDescriptorNew(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, NStr::IntToString(), CSeqdesc_Base::IsSource(), CBioseq_Base::SetDescr(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestOverlappingRNAFeatures() ◆ TestRepliconForbiddenWords() ◆ TestRepliconTaxname() ◆ TestSpecificHostNoError() ◆ TestStartGapSeg()Definition at line 2117 of file unit_test_validator.cpp.
References AddChromosomeNoLocation(), BuildGoodDeltaSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Error, eDiag_Warning, CSeq_inst_Base::eMol_dna, CMolInfo_Base::eTech_wgs, CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), SetTech(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ TestUTRPair() void TestUTRPair ( bool add_gene, bool is_minus )Definition at line 24589 of file unit_test_validator.cpp.
References AddMiscFeature(), BuildGoodSeq(), CheckErrors(), CLEAR_ERRORS, eDiag_Warning, eNa_strand_minus, CBioseq::GetLength(), CSeq_entry_Base::GetSeq(), MakeLeft(), MakeRight(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.
Referenced by BOOST_AUTO_TEST_CASE().
◆ ToAsn1() ◆ USING_SCOPE() ◆ WriteErrors() ◆ s_debugMode ◆ sc_TestEntryCollidingLocusTags ◆ USING_NCBI_SCOPERetroSearch is an open source project built by @garambo | Open a GitHub Issue
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