unit_test_cds_fix.cpp File Reference

#include <ncbi_pch.hpp>
#include "unit_test_cds_fix.hpp"
#include <corelib/ncbi_system.hpp>
#include <corelib/test_boost.hpp>
#include <objects/biblio/Id_pat.hpp>
#include <objects/biblio/Title.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/User_object.hpp>
#include <objects/macro/Simple_replace.hpp>
#include <objects/macro/Replace_func.hpp>
#include <objects/macro/Replace_rule.hpp>
#include <objects/macro/Search_func.hpp>
#include <objects/macro/String_constraint.hpp>
#include <objects/macro/Suspect_rule.hpp>
#include <objects/macro/Word_substitution.hpp>
#include <objects/macro/Word_substitution_set.hpp>
#include <objects/medline/Medline_entry.hpp>
#include <objects/misc/sequence_macros.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/GIBB_mol.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/Ref_ext.hpp>
#include <objects/seq/Map_ext.hpp>
#include <objects/seq/Seg_ext.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objects/seq/Seq_descr.hpp>
#include <objects/seq/Seqdesc.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/seq/Pubdesc.hpp>
#include <objects/seq/Seq_hist.hpp>
#include <objects/seq/Seq_hist_rec.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqblock/GB_block.hpp>
#include <objects/seqblock/EMBL_block.hpp>
#include <objects/seqfeat/BioSource.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <objects/seqloc/Giimport_id.hpp>
#include <objects/seqloc/Patent_seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/seq_loc_util.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/bioseq_set_handle.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objtools/unit_test_util/unit_test_util.hpp>
#include <corelib/ncbiapp.hpp>
#include <objtools/edit/cds_fix.hpp>
#include <common/test_assert.h>

Include dependency graph for unit_test_cds_fix.cpp:

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Functions
	NCBITEST_INIT_TREE ()
	NCBITEST_INIT_CMDLINE (arg_desc)
	NCBITEST_AUTO_INIT ()
void	CheckTerminalExceptionResults (CSeq_feat &cds, CScope &scope, bool strict, bool extend, bool expected_rval, bool set_codebreak, bool set_comment, TSeqPos expected_endpoint)
void	OneTerminalTranslationExceptionTest (bool strict, bool extend, TSeqPos endpoint, const string &seq, bool expected_rval, bool set_codebreak, bool set_comment, TSeqPos expected_endpoint)
	BOOST_AUTO_TEST_CASE (Test_AddTerminalTranslationException)
	BOOST_AUTO_TEST_CASE (Test_FeaturePartialSynchronization)
	BOOST_AUTO_TEST_CASE (Test_MakemRNAforCDS)
	BOOST_AUTO_TEST_CASE (Test_MakemRNAforCDS_with_complex_UTR)
	BOOST_AUTO_TEST_CASE (Test_MakemRNAforCDS_with_exons)
	BOOST_AUTO_TEST_CASE (Test_GetmRNAforCDS)
	BOOST_AUTO_TEST_CASE (Test_GetGeneticCodeForBioseq)
	BOOST_AUTO_TEST_CASE (Test_TruncateCDSAtStop)
	BOOST_AUTO_TEST_CASE (Test_ExtendCDSToStopCodon)
	BOOST_AUTO_TEST_CASE (Test_MakemRNAAnnotOnly)
	BOOST_AUTO_TEST_CASE (Test_SimpleReplace)
	BOOST_AUTO_TEST_CASE (Test_ReplaceFunc)
	BOOST_AUTO_TEST_CASE (Test_SuspectRule)
	BOOST_AUTO_TEST_CASE (Test_FindMatchingFrame)
	BOOST_AUTO_TEST_CASE (Test_PromoteCDSToNucProtSet_And_DemoteCDSToNucSeq)
	BOOST_AUTO_TEST_CASE (Test_GetNewProtId)
	BOOST_AUTO_TEST_CASE (Test_GetNewProtIdFromExistingProt)

Variables
const string	sc_TestEntry
const string	sc_TestEntry2
const string	sc_TestEntry3 = "cds_fix_test_cases/GB-8277.asn"
const string	sc_mrna_loc
const string	sc_mrna1
const string	sc_mrna2
const string	sc_mrna3
static bool	s_debugMode = false

Function Documentation

BOOST_AUTO_TEST_CASE() [1/17]

BOOST_AUTO_TEST_CASE

(

Test_AddTerminalTranslationException

)

Definition at line 224 of file unit_test_cds_fix.cpp.

References OneTerminalTranslationExceptionTest().

BOOST_AUTO_TEST_CASE() [2/17]

BOOST_AUTO_TEST_CASE

(

Test_ExtendCDSToStopCodon

)

Definition at line 537 of file unit_test_cds_fix.cpp.

References AddMiscFeature(), BuildGoodSeq(), eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, ExtendCDSToStopCodon(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStop(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.

BOOST_AUTO_TEST_CASE() [3/17]

BOOST_AUTO_TEST_CASE

(

Test_FeaturePartialSynchronization

)

Definition at line 269 of file unit_test_cds_fix.cpp.

References AdjustFeaturePartialFlagForLocation(), AdjustForCDSPartials(), AdjustProteinFeaturePartialsToMatchCDS(), AdjustProteinMolInfoToMatchCDS(), BuildGoodNucProtSet(), CMolInfo_Base::eCompleteness_complete, CMolInfo_Base::eCompleteness_no_left, CMolInfo_Base::eCompleteness_unknown, eExtreme_Biological, GetCDSFromGoodNucProtSet(), CMolInfo_Base::GetCompleteness(), CSeq_feat_Base::GetLocation(), CSeqdesc_Base::GetMolinfo(), GetProteinSequenceFromGoodNucProtSet(), GetProtFeatFromGoodNucProtSet(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::IsSetPartial(), NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CBioseq_Base::SetDescr(), CSeqdesc_Base::SetMolinfo(), CSeq_entry_Base::SetSeq(), and STANDARD_SETUP.

BOOST_AUTO_TEST_CASE() [4/17]

BOOST_AUTO_TEST_CASE

(

Test_FindMatchingFrame

)

Definition at line 840 of file unit_test_cds_fix.cpp.

References CScope::AddTopLevelSeqEntry(), CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CObjectManager::GetInstance(), MSerial_AsnText, sc_TestEntry, CBioseq_set_Base::SetAnnot(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and CSeq_entry_Base::SetSet().

BOOST_AUTO_TEST_CASE() [5/17]

BOOST_AUTO_TEST_CASE

(

Test_GetGeneticCodeForBioseq

)

Definition at line 469 of file unit_test_cds_fix.cpp.

References BuildGoodSeq(), CBioSource_Base::eGenome_apicoplast, CBioSource_Base::eGenome_mitochondrion, CSeq_inst_Base::eMol_na, GetGeneticCodeForBioseq(), SetGcode(), SetGenome(), SetMGcode(), SetPGcode(), and STANDARD_SETUP.

BOOST_AUTO_TEST_CASE() [6/17]

BOOST_AUTO_TEST_CASE

(

Test_GetmRNAforCDS

)

Definition at line 448 of file unit_test_cds_fix.cpp.

References AddFeat(), CSeq_entry_EditHandle::AttachAnnot(), BuildGoodNucProtSet(), CConstRef< C, Locker >::Empty(), GetCDSFromGoodNucProtSet(), CSeq_entry_Handle::GetEditHandle(), GetmRNAforCDS(), GetNucleotideSequenceFromGoodNucProtSet(), MakemRNAForCDS(), CSeq_feat_Base::SetData(), and STANDARD_SETUP.

BOOST_AUTO_TEST_CASE() [7/17]

BOOST_AUTO_TEST_CASE

(

Test_GetNewProtId

)

Definition at line 925 of file unit_test_cds_fix.cpp.

References CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), ChangeId(), CObjectManager::GetInstance(), GetNewProtId(), CSeq_entry_Handle::GetSeq(), nuc, offset, CDbtag_Base::SetDb(), CSeq_id_Base::SetGeneral(), and CDbtag_Base::SetTag().

BOOST_AUTO_TEST_CASE() [8/17]

BOOST_AUTO_TEST_CASE

(

Test_GetNewProtIdFromExistingProt

)

Definition at line 955 of file unit_test_cds_fix.cpp.

References CScope::AddTopLevelSeqEntry(), BuildGoodNucProtSet(), ChangeId(), CObjectManager::GetInstance(), GetNewProtIdFromExistingProt(), GetProteinSequenceFromGoodNucProtSet(), CSeq_entry_Handle::GetSeq(), offset, prot, CScope::RemoveTopLevelSeqEntry(), CSeq_id_Base::SetLocal(), and CObject_id_Base::SetStr().

BOOST_AUTO_TEST_CASE() [9/17]

BOOST_AUTO_TEST_CASE

(

Test_MakemRNAAnnotOnly

)

Definition at line 574 of file unit_test_cds_fix.cpp.

References CScope::AddDefaults(), CScope::AddSeq_annot(), eExtreme_Biological, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, CRNA_ref_Base::eType_mRNA, CSeq_feat_Base::GetData(), CSeq_feat_Handle::GetFeatSubtype(), CObjectManager::GetInstance(), CSeq_feat_Base::GetLocation(), CMappedFeat::GetOriginalFeature(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeqFeatData::GetSubtype(), MakemRNAforCDS(), CScope::RemoveSeq_annot(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

BOOST_AUTO_TEST_CASE() [10/17]

BOOST_AUTO_TEST_CASE

(

Test_MakemRNAforCDS

)

Definition at line 323 of file unit_test_cds_fix.cpp.

References AddFeat(), AddGoodImpFeat(), BuildGoodNucProtSet(), Compare(), eContained, eExtreme_Biological, eSame, fCompareOverlapping, GetCDSFromGoodNucProtSet(), CSeq_feat_Base::GetLocation(), GetNucleotideSequenceFromGoodNucProtSet(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), MakemRNAforCDS(), CSeq_feat_Base::ResetComment(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.

BOOST_AUTO_TEST_CASE() [11/17]

BOOST_AUTO_TEST_CASE

(

Test_MakemRNAforCDS_with_complex_UTR

)

Definition at line 382 of file unit_test_cds_fix.cpp.

References CScope::AddTopLevelSeqEntry(), Compare(), eSame, fCompareOverlapping, CObjectManager::GetInstance(), CSeq_feat_Base::GetLocation(), MakemRNAforCDS(), MSerial_AsnText, sc_mrna_loc, sc_TestEntry2, CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

BOOST_AUTO_TEST_CASE() [12/17]

BOOST_AUTO_TEST_CASE

(

Test_MakemRNAforCDS_with_exons

)

Definition at line 403 of file unit_test_cds_fix.cpp.

References CScope::AddTopLevelSeqEntry(), CSerialObject::Equals(), CObjectManager::GetInstance(), MakemRNAforCDS(), MSerial_AsnText, sc_mrna1, sc_mrna2, sc_mrna3, sc_TestEntry3, CBioseq_set_Base::SetAnnot(), and CSeq_entry_Base::SetSet().

BOOST_AUTO_TEST_CASE() [13/17]

BOOST_AUTO_TEST_CASE

(

Test_PromoteCDSToNucProtSet_And_DemoteCDSToNucSeq

)

Definition at line 871 of file unit_test_cds_fix.cpp.

References AddMiscFeature(), CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), ChangeId(), DemoteCDSToNucSeq(), CBioseq_set_Base::eClass_nuc_prot, CSeq_feat_Handle::GetAnnot(), CScope::GetBioseqHandle(), CObjectManager::GetInstance(), CSeq_annot_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CScope::GetSeq_featHandle(), nuc, PromoteCDSToNucProtSet(), CScope::RemoveTopLevelSeqEntry(), CBioseq_set_Base::SetClass(), CSeq_id_Base::SetLocal(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and CObject_id_Base::SetStr().

BOOST_AUTO_TEST_CASE() [14/17]

BOOST_AUTO_TEST_CASE

(

Test_ReplaceFunc

)

Definition at line 667 of file unit_test_cds_fix.cpp.

References CReplace_func::ApplyToString(), NULL, CReplace_func_Base::SetHaem_replace(), CSimple_replace_Base::SetReplace(), CReplace_func_Base::SetSimple_replace(), CSimple_replace_Base::SetWeasel_to_putative(), and test().

BOOST_AUTO_TEST_CASE() [15/17]

BOOST_AUTO_TEST_CASE

(

Test_SimpleReplace

)

Definition at line 649 of file unit_test_cds_fix.cpp.

References NULL, and test().

BOOST_AUTO_TEST_CASE() [16/17]

BOOST_AUTO_TEST_CASE

(

Test_SuspectRule

)

Definition at line 696 of file unit_test_cds_fix.cpp.

References CSuspect_rule::ApplyToString(), eString_location_ends, eString_location_equals, eString_location_starts, CRef< C, Locker >::GetObject(), CRef< C, Locker >::Reset(), CSuspect_rule_Base::SetFind(), CSuspect_rule_Base::SetReplace(), and test().

BOOST_AUTO_TEST_CASE() [17/17]

BOOST_AUTO_TEST_CASE

(

Test_TruncateCDSAtStop

)

Definition at line 500 of file unit_test_cds_fix.cpp.

References AddMiscFeature(), BuildGoodSeq(), eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::GetLocation(), CSeq_entry_Base::GetSeq(), CSeq_loc::GetStop(), CSeq_loc::IsPartialStop(), CSeq_feat_Base::SetData(), CBioseq_Base::SetInst(), CSeq_feat_Base::SetLocation(), CSeq_entry_Base::SetSeq(), STANDARD_SETUP, and TruncateCDSAtStop().

CheckTerminalExceptionResults()

void CheckTerminalExceptionResults	(	CSeq_feat &	cds,
		CScope &	scope,
		bool	strict,
		bool	extend,
		bool	expected_rval,
		bool	set_codebreak,
		bool	set_comment,
		TSeqPos	expected_endpoint
	)

Definition at line 167 of file unit_test_cds_fix.cpp.

References eExtreme_Biological, CSeqFeatData_Base::GetCdregion(), CCdregion_Base::GetCode_break(), CSeq_feat_Base::GetComment(), CSeq_feat_Base::GetData(), CSeq_feat_Base::GetLocation(), CSeq_loc::GetStop(), CCdregion_Base::IsSetCode_break(), CSeq_feat_Base::IsSetComment(), and SetTranslExcept().

Referenced by OneTerminalTranslationExceptionTest().

NCBITEST_AUTO_INIT()

NCBITEST_AUTO_INIT

(

)

Definition at line 156 of file unit_test_cds_fix.cpp.

References CNcbiApplicationAPI::GetArgs(), CNcbiApplication::Instance(), and s_debugMode.

NCBITEST_INIT_CMDLINE()

NCBITEST_INIT_CMDLINE

(

arg_desc

)

Definition at line 147 of file unit_test_cds_fix.cpp.

NCBITEST_INIT_TREE()

NCBITEST_INIT_TREE

(

)

Definition at line 139 of file unit_test_cds_fix.cpp.

References CNcbiApplication::Instance().

OneTerminalTranslationExceptionTest()

void OneTerminalTranslationExceptionTest	(	bool	strict,
		bool	extend,
		TSeqPos	endpoint,
		const string &	seq,
		bool	expected_rval,
		bool	set_codebreak,
		bool	set_comment,
		TSeqPos	expected_endpoint
	)

Definition at line 190 of file unit_test_cds_fix.cpp.

References BuildGoodNucProtSet(), CheckTerminalExceptionResults(), GetCDSFromGoodNucProtSet(), CBioseq::GetLength(), CCdregion_Base::ResetCode_break(), RevComp(), CBioseq_Base::SetInst(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.

Referenced by BOOST_AUTO_TEST_CASE().

Variable Documentation

s_debugMode

bool s_debugMode = false

static

Definition at line 145 of file unit_test_cds_fix.cpp.

Referenced by NCBITEST_AUTO_INIT().

sc_mrna1

const string sc_mrna1

Initial value:

= "Seq-feat ::= {\
  data rna {\
    type mRNA,\
    ext name \"F-box protein\"\
  },\
  partial TRUE,\
  location int {\
    from 0,\
    to 1012,\
    strand plus,\
    id local str \"S7_haplotype\",\
    fuzz-from lim lt\
  }\
}"

Definition at line 1697 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

sc_mrna2

const string sc_mrna2

Initial value:

= "Seq-feat ::= {\
  data rna {\
    type mRNA,\
    ext name \"S haplotype-specific F-box7\"\
  },\
  partial FALSE,\
  location mix {\
    int {\
      from 13002,\
      to 13124,\
      strand minus,\
      id genbank {\
        accession \"MH029536\"\
      }\
    },\
    int {\
      from 11708,\
      to 12916,\
      strand minus,\
      id genbank {\
        accession \"MH029536\"\
      }\
    }\
  }\
}"

Definition at line 1712 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

sc_mrna3

const string sc_mrna3

Initial value:

= "Seq-feat ::= {\
  data rna {\
    type mRNA,\
    ext name \"ribonuclease\"\
  },\
  partial FALSE,\
  location mix {\
    int {\
      from 7628,\
      to 7756,\
      strand plus,\
      id local str \"S7_haplotype\"\
    },\
    int {\
      from 8032,\
      to 8219,\
      strand plus,\
      id local str \"S7_haplotype\"\
    },\
    int {\
      from 9745,\
      to 10179,\
      strand plus,\
      id local str \"S7_haplotype\"\
    }\
  }\
}"

Definition at line 1738 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

sc_mrna_loc

const string sc_mrna_loc

Definition at line 1627 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

sc_TestEntry

const string sc_TestEntry

Definition at line 985 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

sc_TestEntry2

const string sc_TestEntry2

Definition at line 1089 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

sc_TestEntry3

const string sc_TestEntry3 = "cds_fix_test_cases/GB-8277.asn"

Definition at line 133 of file unit_test_cds_fix.cpp.

Referenced by BOOST_AUTO_TEST_CASE().