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NCBI C++ ToolKit: include/objtools/unit_test_util/unit_test_util.hpp File Reference

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void  SetDbxref (objects::CBioSource &src, string db, objects::CObject_id::TId id)   void  SetDbxref (objects::CBioSource &src, string db, string id)   void  SetDbxref (CRef< objects::CSeq_entry > entry, string db, objects::CObject_id::TId id)   void  SetDbxref (CRef< objects::CSeq_entry > entry, string db, string id)   void  SetDbxref (CRef< objects::CSeq_feat > feat, string db, objects::CObject_id::TId id)   void  SetDbxref (CRef< objects::CSeq_feat > feat, string db, string id)   void  RemoveDbxref (objects::CBioSource &src, string db, objects::CObject_id::TId id)   void  RemoveDbxref (CRef< objects::CSeq_entry > entry, string db, objects::CObject_id::TId id)   void  RemoveDbxref (CRef< objects::CSeq_feat > feat, string db, objects::CObject_id::TId id)   void  SetSubSource (objects::CBioSource &src, objects::CSubSource::TSubtype subtype, string val)   void  SetSubSource (CRef< objects::CSeq_entry > entry, objects::CSubSource::TSubtype subtype, string val)   void  SetCompleteness (CRef< objects::CSeq_entry > entry, objects::CMolInfo::TCompleteness completeness)   void  SetTaxon (objects::CBioSource &src, size_t taxon)   void  SetTaxon (CRef< objects::CSeq_entry > entry, size_t taxon)   void  AddGoodSource (CRef< objects::CSeq_entry > entry)   void  AddFeatAnnotToSeqEntry (CRef< objects::CSeq_annot > annot, CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  AddProtFeat (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  AddGoodSourceFeature (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  MakeMiscFeature (CRef< objects::CSeq_id > id, size_t right_end=10, size_t left_end=0)   CRef< objects::CSeq_id >  IdFromEntry (CRef< objects::CSeq_entry > entry)   void  SetTaxname (CRef< objects::CSeq_entry > entry, string taxname)   void  SetSebaea_microphylla (CRef< objects::CSeq_entry > entry)   void  SetSynthetic_construct (CRef< objects::CSeq_entry > entry)   void  SetDrosophila_melanogaster (CRef< objects::CSeq_entry > entry)   void  SetCommon (CRef< objects::CSeq_entry > entry, string common)   void  SetLineage (CRef< objects::CSeq_entry > entry, string lineage)   void  SetDiv (CRef< objects::CSeq_entry > entry, string div)   void  SetOrigin (CRef< objects::CSeq_entry > entry, objects::CBioSource::TOrigin origin)   void  SetGcode (CRef< objects::CSeq_entry > entry, objects::COrgName::TGcode gcode)   void  SetMGcode (CRef< objects::CSeq_entry > entry, objects::COrgName::TGcode mgcode)   void  SetPGcode (CRef< objects::CSeq_entry > entry, objects::COrgName::TGcode pgcode)   void  ResetOrgname (CRef< objects::CSeq_entry > entry)   void  SetFocus (CRef< objects::CSeq_entry > entry)   void  ClearFocus (CRef< objects::CSeq_entry > entry)   void  SetGenome (CRef< objects::CSeq_entry > entry, objects::CBioSource::TGenome genome)   void  SetChromosome (objects::CBioSource &src, string chromosome)   void  SetChromosome (CRef< objects::CSeq_entry > entry, string chromosome)   void  SetTransgenic (objects::CBioSource &src, bool do_set)   void  SetTransgenic (CRef< objects::CSeq_entry > entry, bool do_set)   void  SetOrgMod (objects::CBioSource &src, objects::COrgMod::TSubtype subtype, string val)   void  SetOrgMod (CRef< objects::CSeq_entry > entry, objects::COrgMod::TSubtype subtype, string val)   CRef< objects::CSeqdesc >  BuildGoodPubSeqdesc ()   void  AddGoodPub (CRef< objects::CSeq_entry > entry)   CRef< objects::CAuthor >  BuildGoodAuthor ()   CRef< objects::CPub >  BuildGoodArticlePub ()   CRef< objects::CPub >  BuildGoodCitGenPub (CRef< objects::CAuthor > author, int serial_number)   CRef< objects::CPub >  BuildGoodCitSubPub ()   void  MakeSeqLong (objects::CBioseq &seq)   void  SetBiomol (CRef< objects::CSeq_entry > entry, objects::CMolInfo::TBiomol biomol)   void  SetTech (CRef< objects::CSeq_entry > entry, objects::CMolInfo::TTech tech)   CRef< objects::CSeq_entry >  MakeProteinForGoodNucProtSet (string id)   CRef< objects::CSeq_feat >  MakeCDSForGoodNucProtSet (const string &nuc_id, const string &prot_id)   void  AdjustProtFeatForNucProtSet (CRef< objects::CSeq_entry > entry)   void  SetNucProtSetProductName (CRef< objects::CSeq_entry > entry, string new_name)   CRef< objects::CSeq_entry >  GetNucleotideSequenceFromGoodNucProtSet (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_entry >  GetProteinSequenceFromGoodNucProtSet (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  GetProtFeatFromGoodNucProtSet (CRef< objects::CSeq_entry > entry)   void  RetranslateCdsForNucProtSet (CRef< objects::CSeq_entry > entry, objects::CScope &scope)   void  SetNucProtSetPartials (CRef< objects::CSeq_entry > entry, bool partial5, bool partial3)   void  SetProteinPartial (CRef< objects::CSeq_entry > pentry, bool partial5, bool partial3)   void  ChangeNucProtSetProteinId (CRef< objects::CSeq_entry > entry, CRef< objects::CSeq_id > id)   void  ChangeNucProtSetNucId (CRef< objects::CSeq_entry > entry, CRef< objects::CSeq_id > id)   void  MakeNucProtSet3Partial (CRef< objects::CSeq_entry > entry)   void  ChangeId (CRef< objects::CSeq_annot > annot, CRef< objects::CSeq_id > id)   void  ChangeProductId (CRef< objects::CSeq_annot > annot, CRef< objects::CSeq_id > id)   void  ChangeNucId (CRef< objects::CSeq_entry > np_set, CRef< objects::CSeq_id > id)   void  ChangeProtId (CRef< objects::CSeq_entry > np_set, CRef< objects::CSeq_id > id)   CRef< objects::CSeq_id >  BuildRefSeqId (void)   void  ChangeId (CRef< objects::CSeq_entry > entry, CRef< objects::CSeq_id > id)   void  ChangeId (CRef< objects::CSeq_annot > annot, string suffix)   void  ChangeId (CRef< objects::CSeq_entry > entry, string suffix)   CRef< objects::CSeq_entry >  BuildGenProdSetNucProtSet (CRef< objects::CSeq_id > nuc_id, CRef< objects::CSeq_id > prot_id)   CRef< objects::CSeq_feat >  MakemRNAForCDS (CRef< objects::CSeq_feat > feat)   CRef< objects::CSeq_entry >  BuildGoodGenProdSet ()   CRef< objects::CSeq_entry >  GetGenomicFromGenProdSet (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  GetmRNAFromGenProdSet (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_entry >  GetNucProtSetFromGenProdSet (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  GetCDSFromGenProdSet (CRef< objects::CSeq_entry > entry)   void  RevComp (objects::CBioseq &bioseq)   void  RevComp (objects::CSeq_loc &loc, size_t len)   void  RevComp (CRef< objects::CSeq_entry > entry)   void  RemoveDeltaSeqGaps (CRef< objects::CSeq_entry > entry)   void  AddToDeltaSeq (CRef< objects::CSeq_entry > entry, string seq)   CRef< objects::CSeq_entry >  BuildSegSetPart (string id_str)   CRef< objects::CSeq_entry >  BuildGoodSegSet (void)   CRef< objects::CSeq_entry >  BuildGoodEcoSet ()   CRef< objects::CSeq_entry >  BuildGoodEcoSetWithAlign (size_t front_insert=5)   CRef< objects::CSeq_align >  BuildGoodAlign ()   void  ReverseAlignmentStrand (objects::CDense_seg &denseg, size_t pos, size_t seq_len)   CRef< objects::CSeq_annot >  BuildGoodGraphAnnot (string id)   void  RemoveDescriptorType (CRef< objects::CSeq_entry > entry, objects::CSeqdesc::E_Choice desc_choice)   CRef< objects::CSeq_feat >  BuildtRNA (CRef< objects::CSeq_id > id)   CRef< objects::CSeq_feat >  BuildGoodtRNA (CRef< objects::CSeq_id > id)   CRef< objects::CSeq_loc >  MakeMixLoc (CRef< objects::CSeq_id > id)   CRef< objects::CSeq_feat >  MakeIntronForMixLoc (CRef< objects::CSeq_id > id)   void  SetSpliceForMixLoc (objects::CBioseq &seq)   CRef< objects::CSeq_feat >  MakeGeneForFeature (CRef< objects::CSeq_feat > feat)   CRef< objects::CSeq_feat >  AddGoodImpFeat (CRef< objects::CSeq_entry > entry, string key)   CRef< objects::CSeq_feat >  AddMiscFeature (CRef< objects::CSeq_entry > entry)   CRef< objects::CSeq_feat >  AddMiscFeature (CRef< objects::CSeq_entry > entry, size_t right_end)   CRef< objects::CSeq_annot >  AddFeat (CRef< objects::CSeq_feat > feat, CRef< objects::CSeq_entry > entry)   CRef< CSeq_feat >  BuildGoodFeat ()   CRef< objects::CSeq_entry >  BuildGoodNucProtSet (void)   CRef< objects::CSeq_entry >  BuildGoodSeq (void)   CRef< objects::CSeq_entry >  BuildGoodProtSeq (void)   CRef< objects::CSeq_entry >  BuildGoodDeltaSeq (void)   CRef< objects::CSeq_feat >  GetCDSFromGoodNucProtSet (CRef< objects::CSeq_entry > entry)   void  TraverseAndRunTestCases (ITestRunner *pTestRunner, CDir dirWithTestCases, const set< string > &setOfRequiredSuffixes, const set< string > &setOfOptionalSuffixes=set< string >(), const set< string > &setOfIgnoredSuffixes=set< string >(), TTraverseAndRunTestCasesFlags fFlags=0)   This is for running data-driven test cases below the given top-level test directory. More...
  ◆ TTraverseAndRunTestCasesFlags ◆ ETraverseAndRunTestCasesFlags

Flags that control TraverseAndRunTestCases, if needed.

Enumerator fTraverseAndRunTestCasesFlags_DoNOTIgnoreREADMEFiles 

Overrides default behavior (which is to disregard files whose prefix is "README")

Definition at line 242 of file unit_test_util.hpp.

◆ AddFeat() ◆ AddFeatAnnotToSeqEntry() void AddFeatAnnotToSeqEntry ( CRef< objects::CSeq_annot >  annot, CRef< objects::CSeq_entry >  entry  ) ◆ AddGoodImpFeat() ◆ AddGoodPub() ◆ AddGoodSource() ◆ AddGoodSourceFeature() ◆ AddMiscFeature() [1/2] CRef<objects::CSeq_feat> AddMiscFeature ( CRef< objects::CSeq_entry >  entry )

Referenced by AddOrgmodFeat(), AddProtFeat(), BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), Check3Policy(), CheckAdjustStart(), CheckAdjustStartAndStop(), CheckAdjustStop(), CheckRegulatoryFeatures(), CreateCds(), CreateTrna(), GetGoodSeqEntryWithFeatureIds(), MakeMultiSeqCDS(), MakeRegulatoryFeature(), MakeRegulatoryFeatureTest(), MakeRptRegion(), MakeTrnaWithAnticodon(), TestMultipleEquivBioSources(), TestNewAccessionAsInference(), TestOneMiscPartial(), TestOverlappingRNAFeatures(), TestUTRPair(), TryMiscWithNs(), TryOneCase(), TryOneCaseMixLoc(), and TryOneCDSCase().

◆ AddMiscFeature() [2/2] CRef<objects::CSeq_feat> AddMiscFeature ( CRef< objects::CSeq_entry >  entry, size_t  right_end  ) ◆ AddProtFeat() ◆ AddToDeltaSeq() ◆ AdjustProtFeatForNucProtSet() ◆ BuildGenProdSetNucProtSet() ◆ BuildGoodAlign() CRef<objects::CSeq_align> BuildGoodAlign ( ) ◆ BuildGoodArticlePub() CRef<objects::CPub> BuildGoodArticlePub ( ) ◆ BuildGoodAuthor() CRef<objects::CAuthor> BuildGoodAuthor ( ) ◆ BuildGoodCitGenPub() ◆ BuildGoodCitSubPub() CRef<objects::CPub> BuildGoodCitSubPub ( ) ◆ BuildGoodDeltaSeq() CRef<objects::CSeq_entry> BuildGoodDeltaSeq ( void  )

Definition at line 1643 of file unit_test_util.cpp.

References BuildGoodSeq(), CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_delta, CBioseq_Base::SetInst(), and CSeq_entry_Base::SetSeq().

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CheckAdjustStart(), CheckAdjustStartAndStop(), CheckAdjustStop(), MakeTrnaWithAnticodon(), TestDeltaTechAllowed(), TestDeltaTechNotAllowed(), TestStartGapSeg(), TryOneCase(), and TryOneCaseMixLoc().

◆ BuildGoodEcoSet() CRef<objects::CSeq_entry> BuildGoodEcoSet ( )

Definition at line 1768 of file unit_test_util.cpp.

References BuildGoodSeq(), ChangeId(), CBioseq_set_Base::eClass_eco_set, CBioseq_set_Base::SetClass(), CBioseq_set_Base::SetDescr(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeqdesc_Base::SetTitle().

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGoodEcoSetWithAlign(), Check3Policy(), MakeMultiSeqCDS(), and TestCollidingAccessionFixes().

◆ BuildGoodEcoSetWithAlign() CRef<objects::CSeq_entry> BuildGoodEcoSetWithAlign ( size_t  front_insert = 5 )

Definition at line 1790 of file unit_test_util.cpp.

References BuildGoodEcoSet(), CSeq_align_Base::eType_global, CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), i, offset, orig, CBioseq_set_Base::SetAnnot(), CSeq_annot_Base::SetData(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CSeq_align_Base::SetType().

Referenced by BOOST_AUTO_TEST_CASE(), CreateBioseqsAndAlign(), and GetGoodSeqEntryWithFeatureIds().

◆ BuildGoodFeat() ◆ BuildGoodGenProdSet() CRef<objects::CSeq_entry> BuildGoodGenProdSet ( )

Definition at line 1505 of file unit_test_util.cpp.

References AddFeat(), CSerialObject::Assign(), BuildGenProdSetNucProtSet(), 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(), and BOOST_FIXTURE_TEST_CASE().

◆ BuildGoodGraphAnnot() CRef<objects::CSeq_annot> BuildGoodGraphAnnot ( string  id ) ◆ BuildGoodNucProtSet() CRef<objects::CSeq_entry> BuildGoodNucProtSet ( void  )

Definition at line 1136 of file unit_test_util.cpp.

References AddFeat(), AddGoodPub(), AddGoodSource(), CMolInfo_Base::eBiomol_genomic, CBioseq_set_Base::eClass_nuc_prot, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_raw, MakeCDSForGoodNucProtSet(), MakeProteinForGoodNucProtSet(), 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(), BOOST_FIXTURE_TEST_CASE(), BuildGenProdSetBigNucProtSet(), BuildGenProdSetNucProtSet(), BuildGoodSpliceNucProtSet(), BuildSmallGenomeSet(), MakeRegulatoryFeatureTest(), OneTerminalTranslationExceptionTest(), s_BuildBadEcNumberEntry(), TestBadProtId(), TestGoodNucId(), TestGoodProtId(), TestMatPeptideListing(), TestNewAccessionOnNucProt(), TestTrimForFrame(), and TryOneCDSCase().

◆ BuildGoodProtSeq() CRef<objects::CSeq_entry> BuildGoodProtSeq ( void  ) ◆ BuildGoodPubSeqdesc() CRef<objects::CSeqdesc> BuildGoodPubSeqdesc ( ) ◆ BuildGoodSegSet() CRef<objects::CSeq_entry> BuildGoodSegSet ( void  )

Definition at line 1707 of file unit_test_util.cpp.

References AddGoodPub(), BuildSegSetPart(), CMolInfo_Base::eBiomol_genomic, CBioseq_set_Base::eClass_parts, CBioseq_set_Base::eClass_segset, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_seg, CSubSource_Base::eSubtype_chromosome, SetBiomol(), CBioseq_set_Base::SetClass(), CDbtag_Base::SetDb(), CSeq_entry::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSubSource_Base::SetName(), CBioSource_Base::SetOrg(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), CSeqdesc_Base::SetSource(), CSubSource_Base::SetSubtype(), CBioSource_Base::SetSubtype(), CDbtag_Base::SetTag(), and CSeq_loc::SetWhole().

◆ BuildGoodSeq() CRef<objects::CSeq_entry> BuildGoodSeq ( void  )

Definition at line 127 of file unit_test_util.cpp.

References AddGoodPub(), AddGoodSource(), CMolInfo_Base::eBiomol_genomic, CSeq_inst_Base::eMol_dna, CSeq_inst_Base::eRepr_raw, CMolInfo_Base::SetBiomol(), CBioseq_Base::SetDescr(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeqdesc_Base::SetMolinfo(), and CSeq_entry_Base::SetSeq().

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildAlignmentWithInternalGap(), BuildGapFuzz100DeltaSeq(), BuildGenProdSetWithBigProduct(), BuildGoodDeltaSeq(), BuildGoodEcoSet(), BuildGoodGenProdSet(), BuildGoodProtSeq(), CheckGeneOntologyTermDuplicate(), CheckGeneOntologyTermNotDuplicate(), CheckInfluenzaDefline(), CheckLocalId(), CheckOneSpecificHost(), CheckRegulatoryFeatures(), CheckUnbalancedParenthesesOrgMod(), CheckUnbalancedParenthesesSubSource(), MakeEntryForDeltaConversion(), s_ArePrimersUnique(), TestBulkSpecificHostFixList(), TestConsultRequired(), TestMultipleEquivBioSources(), TestNewAccessionAsInference(), TestNewAccessionOnNuc(), TestOneGeneralSeqId(), TestOneLatLonCountry(), TestOneLongGeneral(), TestOneOrganelleSequenceDefline(), TestOneOtherAcc(), TestOnePlasmid(), TestOneReplicon(), TestOneStrain(), TestOneStrainNew(), TestOverlappingRNAFeatures(), TestSpecificHostNoError(), TestUTRPair(), and TryMiscWithNs().

◆ BuildGoodtRNA() ◆ BuildRefSeqId() CRef<objects::CSeq_id> BuildRefSeqId ( void  ) ◆ BuildSegSetPart() CRef<objects::CSeq_entry> BuildSegSetPart ( string  id_str ) ◆ BuildtRNA() ◆ ChangeId() [1/4] ◆ ChangeId() [2/4] void ChangeId ( CRef< objects::CSeq_annot >  annot, string  suffix  ) ◆ ChangeId() [3/4] void ChangeId ( CRef< objects::CSeq_entry >  entry, CRef< objects::CSeq_id >  id  ) ◆ ChangeId() [4/4] void ChangeId ( CRef< objects::CSeq_entry >  entry, string  suffix  ) ◆ ChangeNucId() ◆ ChangeNucProtSetNucId() ◆ ChangeNucProtSetProteinId() ◆ ChangeProductId() void ChangeProductId ( CRef< objects::CSeq_annot >  annot, CRef< objects::CSeq_id >  id  ) ◆ ChangeProtId() ◆ ClearFocus() ◆ GetCDSFromGenProdSet() ◆ GetCDSFromGoodNucProtSet() CRef<objects::CSeq_feat> GetCDSFromGoodNucProtSet ( CRef< objects::CSeq_entry >  entry )

Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), BuildGenProdSetBigNucProtSet(), BuildGenProdSetWithBigProduct(), BuildGoodSpliceNucProtSet(), BuildSmallGenomeSet(), ChangeGoodNucProtSetIdToGenbankName(), OneTerminalTranslationExceptionTest(), TestMatPeptideListing(), TestTrimForFrame(), and TryOneCDSCase().

◆ GetGenomicFromGenProdSet() ◆ GetmRNAFromGenProdSet() ◆ GetNucleotideSequenceFromGoodNucProtSet() ◆ GetNucProtSetFromGenProdSet() ◆ GetProteinSequenceFromGoodNucProtSet() ◆ GetProtFeatFromGoodNucProtSet() ◆ IdFromEntry() ◆ MakeCDSForGoodNucProtSet() ◆ MakeGeneForFeature() ◆ MakeIntronForMixLoc() ◆ MakeMiscFeature() ◆ MakeMixLoc() ◆ MakemRNAForCDS() ◆ MakeNucProtSet3Partial() ◆ MakeProteinForGoodNucProtSet() CRef<objects::CSeq_entry> MakeProteinForGoodNucProtSet ( string  id )

Definition at line 1092 of file unit_test_util.cpp.

References AddFeat(), CMolInfo_Base::eBiomol_peptide, CMolInfo_Base::eCompleteness_complete, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eRepr_raw, 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(), and CObject_id_Base::SetStr().

Referenced by AddCdregionToSmallGenomeSet(), AddCDSAndProtForBigGoodNucProtSet(), BOOST_AUTO_TEST_CASE(), and BuildGoodNucProtSet().

◆ MakeSeqLong() void MakeSeqLong ( objects::CBioseq &  seq ) ◆ RemoveDbxref() [1/3] void RemoveDbxref ( CRef< objects::CSeq_entry >  entry, string  db, objects::CObject_id::TId  id  ) ◆ RemoveDbxref() [2/3] void RemoveDbxref ( CRef< objects::CSeq_feat >  feat, string  db, objects::CObject_id::TId  id  ) ◆ RemoveDbxref() [3/3] ◆ RemoveDeltaSeqGaps() ◆ RemoveDescriptorType() void RemoveDescriptorType ( CRef< objects::CSeq_entry >  entry, objects::CSeqdesc::E_Choice  desc_choice  )

Referenced by BOOST_AUTO_TEST_CASE().

◆ ResetOrgname() ◆ RetranslateCdsForNucProtSet() ◆ RevComp() [1/3] void RevComp ( CRef< objects::CSeq_entry >  entry ) ◆ RevComp() [2/3] ◆ RevComp() [3/3] void RevComp ( objects::CSeq_loc &  loc, size_t  len  ) ◆ ReverseAlignmentStrand() void ReverseAlignmentStrand ( objects::CDense_seg &  denseg, size_t  pos, size_t  seq_len  ) ◆ SetBiomol() ◆ SetChromosome() [1/2] void SetChromosome ( CRef< objects::CSeq_entry >  entry, string  chromosome  ) ◆ SetChromosome() [2/2] ◆ SetCommon() ◆ SetCompleteness() ◆ SetDbxref() [1/6] void SetDbxref ( CRef< objects::CSeq_entry >  entry, string  db, objects::CObject_id::TId  id  ) ◆ SetDbxref() [2/6] ◆ SetDbxref() [3/6] void SetDbxref ( CRef< objects::CSeq_feat >  feat, string  db, objects::CObject_id::TId  id  ) ◆ SetDbxref() [4/6] ◆ SetDbxref() [5/6] ◆ SetDbxref() [6/6] void SetDbxref ( objects::CBioSource &  src, string  db, string  id  ) ◆ SetDiv() ◆ SetDrosophila_melanogaster() ◆ SetFocus() void SetFocus ( CRef< objects::CSeq_entry >  entry )

Referenced by BOOST_AUTO_TEST_CASE(), CDataMiningPanel::OnContextMenu(), CProjectTreePanel::OnContextMenu(), CDockPanel::OnContextMenu(), CGlWidgetPane::OnEnterWindow(), CWorkbenchFrame::OnIdle(), CSeqGraphicPane::OnLeftDown(), CPhyloTreePane::OnLeftDown(), CDockPanel::OnMenuButtonClick(), CGlWidgetPane::OnMouseDown(), CMapControl::OnMouseDown(), CTextItemPanel::OnMouseEvent(), ProgressMeter::ProgressMeter(), PtbConfigDialog(), and CAlnMultiPane::x_OnRowMouseEvent().

◆ SetGcode() ◆ SetGenome() ◆ SetLineage() ◆ SetMGcode() ◆ SetNucProtSetPartials() ◆ SetNucProtSetProductName() ◆ SetOrgMod() [1/2] void SetOrgMod ( CRef< objects::CSeq_entry >  entry, objects::COrgMod::TSubtype  subtype, string  val  ) ◆ SetOrgMod() [2/2] ◆ SetOrigin() ◆ SetPGcode() ◆ SetProteinPartial() void SetProteinPartial ( CRef< objects::CSeq_entry >  pentry, bool  partial5, bool  partial3  ) ◆ SetSebaea_microphylla() ◆ SetSpliceForMixLoc() ◆ SetSubSource() [1/2] void SetSubSource ( CRef< objects::CSeq_entry >  entry, objects::CSubSource::TSubtype  subtype, string  val  ) ◆ SetSubSource() [2/2] ◆ SetSynthetic_construct() ◆ SetTaxname() ◆ SetTaxon() [1/2] void SetTaxon ( CRef< objects::CSeq_entry >  entry, size_t  taxon  ) ◆ SetTaxon() [2/2] ◆ SetTech() ◆ SetTransgenic() [1/2] void SetTransgenic ( CRef< objects::CSeq_entry >  entry, bool  do_set  ) ◆ SetTransgenic() [2/2] ◆ TraverseAndRunTestCases()

This is for running data-driven test cases below the given top-level test directory.

In a given directory, each file is checked for its prefix and suffix, where the prefix is the part before the first '.' and the suffix is the part after. (e.g. "foo.input.asn" has prefix "foo" and suffix "input.asn"). Files with the same prefix are assumed to belong to the same test.

There can be more than one test case in a test-case descendent dir and test-cases is even permitted to have zero subdirectories and have all the files be at the top level (though this could get messy if you have many test cases)

Any errors are handled through ITestRunner::OnError except for a NULL ITestRunner which, by necessity, is handled by throwing an exception.

Parameters
pTestRunner This class's "RunTest" func is called for each test. dirWithTestCases This is the directory holding the test cases. Sub-directories of this are also checked for test-cases, although hidden subdirectories and files (that is, those starting with a period, such as ".svn") are skipped. setOfRequiredSuffixes Each test must have exactly one file with the given suffix. If any test is missing any required suffix, this function will halt before running any tests. At least one required suffix must be specified. setOfOptionalSuffixes These are the suffixes permitted but not required for each test. setOfIgnoredSuffixes This is the set of suffixes that are just ignored and not passed to the pTestRunner. If a file is found whose suffix is not in one of the "setOf[FOO]Suffixes" parameters, then an error will occur, except that files with prefix "README" are also ignored. fFlags This controls the behavior of the function (usually not needed).

Definition at line 2037 of file unit_test_util.cpp.

References map_checker< Container >::begin(), set< Key, Compare >::begin(), CDirEntry::CreateAbsolutePath(), map_checker< Container >::end(), set< Key, Compare >::end(), ERASE_ITERATE, CDir::Exists(), fFF_File, fFF_Recursive, NStr::Find(), set< Key, Compare >::find(), FindFilesInDir(), fTraverseAndRunTestCasesFlags_DoNOTIgnoreREADMEFiles, CDirEntry::GetPath(), CDirEntry::GetPathSeparator(), CDirEntry::IsDir(), ITERATE, NCBI_USER_THROW_FMT, NPOS, ITestRunner::OnError(), ITestRunner::RunTest(), set< Key, Compare >::size(), NStr::SplitInTwo(), NStr::StartsWith(), string, and transform().

Referenced by BOOST_AUTO_TEST_CASE().

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