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NCBI C++ ToolKit: src/objtools/edit/unit_test/unit_test_loc_edit.cpp File Reference

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  NCBITEST_INIT_TREE ()     NCBITEST_INIT_CMDLINE (arg_desc)     NCBITEST_AUTO_INIT ()   void  s_CheckLocationResults (const CSeq_loc &loc, bool partial5, bool partial3, TSeqPos start, TSeqPos stop)   void  s_CheckLocationPolicyResults (const CSeq_feat &cds, bool partial5, bool partial3, TSeqPos start, TSeqPos stop)     BOOST_AUTO_TEST_CASE (Test_SeqLocPrintUseBestID)     BOOST_AUTO_TEST_CASE (Test_ApplyPolicyToFeature)   void  s_CheckLocationAndStrandResults (const CSeq_loc &loc, bool partial5, bool partial3, TSeqPos start, TSeqPos stop, ENa_strand strand)     BOOST_AUTO_TEST_CASE (Test_ReverseComplementLocation)     BOOST_AUTO_TEST_CASE (Test_ReverseComplementFeature)   void  s_CheckInterval (const CSeq_interval &interval, TSeqPos from, TSeqPos to)   void  s_MakePackedInt (CSeq_loc &loc, const CSeq_id &id, vector< TSeqPos > from, vector< TSeqPos > to)   void  s_CheckPackedInt (const CPacked_seqint &pack, vector< TSeqPos > from, vector< TSeqPos > to)   void  s_MakeMixLoc (CSeq_loc &loc, const CSeq_id &id, vector< TSeqPos > from, vector< TSeqPos > to)   void  s_CheckMixLoc (const CSeq_loc &mix, vector< TSeqPos > from, vector< TSeqPos > to)     BOOST_AUTO_TEST_CASE (Test_AdjustForTrim)     BOOST_AUTO_TEST_CASE (Test_AdjustForInsert)     BOOST_AUTO_TEST_CASE (Test_SplitLocationForGap)     BOOST_AUTO_TEST_CASE (Test_SplitLocationForGap_GB8665Plus)     BOOST_AUTO_TEST_CASE (Test_SplitLocationForGapFirstInt_GB8665Minus)     BOOST_AUTO_TEST_CASE (Test_SplitLocationForGapLastInt_GB8665Minus)     BOOST_AUTO_TEST_CASE (Test_GetGeneForFeature)     BOOST_AUTO_TEST_CASE (Test_CorrectIntervalOrder)   void  Check5Policy (CSeq_feat &imp, CScope &scope, edit::CLocationEditPolicy::EPartialPolicy policy_choice, bool expect_set5, bool expect_clear5, bool extend=false)   void  Check3Policy (CSeq_feat &imp, CScope &scope, edit::CLocationEditPolicy::EPartialPolicy policy_choice, bool expect_set3, bool expect_clear3, bool extend=false)   void  SetSequenceStart (CBioseq &seq, bool good, bool is_minus)   void  SetSequenceEnd (CBioseq &seq, bool good, bool is_minus)   CRef< CSeq_entry >  MakeMultiSeqCDS (bool good_end, bool is_minus, bool already_partial)   void  TruncateTransSplicedCDSForExtension (CRef< CSeq_entry > entry, bool on_5, bool on_3)   void  Check5Policy (bool good_end, bool is_minus, bool already_partial)   void  Check5Extend (bool good_end, bool is_minus, bool already_partial)   void  Check3Extend (bool good_end, bool is_minus, bool already_partial)   void  Check3Policy (bool good_end, bool is_minus, bool already_partial)     BOOST_AUTO_TEST_CASE (Test_GB_7703)   void  CheckAdjustStart (TSeqPos start, TSeqPos expect_start, bool partial_start, CCdregion::EFrame frame, bool is_minus=false)   void  CheckAdjustStop (TSeqPos stop, TSeqPos expect_stop, bool partial_stop, bool is_minus=false)   static void  CheckAdjustStartAndStop (const CRange< TSeqPos > &range, const CRange< TSeqPos > &expected_range, bool partial_start, CCdregion::EFrame frame, bool partial_stop, bool is_minus=false)     BOOST_AUTO_TEST_CASE (Test_RW_566)   ◆ BOOST_AUTO_TEST_CASE() [1/14] BOOST_AUTO_TEST_CASE ( Test_AdjustForInsert  )

Definition at line 909 of file unit_test_loc_edit.cpp.

References CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), s_CheckInterval(), s_CheckMixLoc(), s_CheckPackedInt(), s_MakeMixLoc(), s_MakePackedInt(), SeqLocAdjustForInsert(), CSeq_loc::SetInt(), and CSeq_loc::SetPnt().

◆ BOOST_AUTO_TEST_CASE() [2/14] BOOST_AUTO_TEST_CASE ( Test_AdjustForTrim  )

Definition at line 618 of file unit_test_loc_edit.cpp.

References CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), s_CheckInterval(), s_CheckMixLoc(), s_CheckPackedInt(), s_MakeMixLoc(), s_MakePackedInt(), SeqLocAdjustForTrim(), CSeq_loc::SetInt(), and CSeq_loc::SetPnt().

◆ BOOST_AUTO_TEST_CASE() [3/14] BOOST_AUTO_TEST_CASE ( Test_ApplyPolicyToFeature  )

Definition at line 219 of file unit_test_loc_edit.cpp.

References ApplyPolicyToFeature(), BuildGoodNucProtSet(), CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, CSeq_entry::GetAnnot(), CSeqFeatData_Base::GetCdregion(), GetCDSFromGoodNucProtSet(), CSeq_annot_Handle::GetCompleteSeq_annot(), CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_annot_Base::C_Data::GetFtable(), kEmptyStr, s_CheckLocationPolicyResults(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), STANDARD_SETUP, and CSeqTranslator::Translate().

◆ BOOST_AUTO_TEST_CASE() [4/14] BOOST_AUTO_TEST_CASE ( Test_CorrectIntervalOrder  )

Definition at line 1391 of file unit_test_loc_edit.cpp.

References a, b, CorrectIntervalOrder(), eNa_strand_minus, eNa_strand_plus, CSerialObject::Equals(), f, CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), CSeq_id_Base::SetLocal(), CSeq_loc::SetMix(), CSeq_loc::SetPacked_pnt(), CSeq_loc::SetPnt(), CObject_id_Base::SetStr(), and CSeq_interval_Base::SetStrand().

◆ BOOST_AUTO_TEST_CASE() [5/14] BOOST_AUTO_TEST_CASE ( Test_GB_7703  ) ◆ BOOST_AUTO_TEST_CASE() [6/14] BOOST_AUTO_TEST_CASE ( Test_GetGeneForFeature  )

Definition at line 1338 of file unit_test_loc_edit.cpp.

References AddFeat(), AddGoodImpFeat(), CSeq_feat::AddSeqFeatXref(), BuildGoodSeq(), GetGeneForFeature(), CSeq_feat_Base::GetId(), CRef< C, Locker >::GetPointer(), MakeGeneForFeature(), NULL, CSeq_feat_Base::SetData(), CSeq_feat_Base::SetId(), and STANDARD_SETUP.

◆ BOOST_AUTO_TEST_CASE() [7/14] BOOST_AUTO_TEST_CASE ( Test_ReverseComplementFeature  )

Definition at line 501 of file unit_test_loc_edit.cpp.

References BuildGoodNucProtSet(), BuildGoodtRNA(), eExtreme_Biological, eNa_strand_minus, eNa_strand_plus, GetCDSFromGoodNucProtSet(), CCode_break_Base::GetLoc(), ReverseComplementFeature(), s_CheckLocationAndStrandResults(), CCode_break_Base::SetLoc(), and STANDARD_SETUP.

◆ BOOST_AUTO_TEST_CASE() [8/14] BOOST_AUTO_TEST_CASE ( Test_ReverseComplementLocation  )

Definition at line 428 of file unit_test_loc_edit.cpp.

References AddGoodImpFeat(), BuildGoodSeq(), eExtreme_Biological, eNa_strand_minus, eNa_strand_plus, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_loc_Base::GetPacked_pnt(), CPacked_seqpnt_Base::GetPoints(), CSeq_entry_Base::GetSeq(), CPacked_seqpnt_Base::GetStrand(), MakeMixLoc(), ReverseComplementFeature(), ReverseComplementLocation(), s_CheckLocationAndStrandResults(), CSeq_loc::SetPacked_pnt(), and STANDARD_SETUP.

◆ BOOST_AUTO_TEST_CASE() [9/14] BOOST_AUTO_TEST_CASE ( Test_RW_566  ) ◆ BOOST_AUTO_TEST_CASE() [10/14] BOOST_AUTO_TEST_CASE ( Test_SeqLocPrintUseBestID  )

Definition at line 168 of file unit_test_loc_edit.cpp.

References AddGoodImpFeat(), AddProtFeat(), CScope::AddTopLevelSeqEntry(), BuildGoodNucProtSet(), eNa_strand_minus, CObjectManager::GetInstance(), GetProteinSequenceFromGoodNucProtSet(), CSeq_loc_Base::IsInt(), MakeMixLoc(), NCBITEST_CHECK_MESSAGE, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), SeqLocPrintUseBestID(), CTextseq_id_Base::SetAccession(), CBioseq_Base::SetAnnot(), CDbtag_Base::SetDb(), CSeq_id_Base::SetGenbank(), CSeq_id_Base::SetGeneral(), CSeq_point_Base::SetId(), CBioseq_Base::SetId(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CSeq_loc::SetPnt(), CSeq_point_Base::SetPoint(), CSeq_entry_Base::SetSeq(), CSeq_point_Base::SetStrand(), CDbtag_Base::SetTag(), and strtmp.

◆ BOOST_AUTO_TEST_CASE() [11/14] BOOST_AUTO_TEST_CASE ( Test_SplitLocationForGap  )

Definition at line 1037 of file unit_test_loc_edit.cpp.

References CSeq_loc_Base::e_not_set, eSplitLocOption_make_partial, eSplitLocOption_split_in_exon, eSplitLocOption_split_in_intron, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc_Base::Reset(), s_CheckInterval(), s_CheckMixLoc(), s_CheckPackedInt(), s_MakeMixLoc(), s_MakePackedInt(), CSeq_loc::SetInt(), CSeq_loc::SetPnt(), SplitLocationForGap(), and CSeq_loc_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [12/14] BOOST_AUTO_TEST_CASE ( Test_SplitLocationForGap_GB8665Plus  )

Definition at line 1199 of file unit_test_loc_edit.cpp.

References CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, eSplitLocOption_make_partial, eSplitLocOption_split_in_exon, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::Reset(), s_CheckInterval(), s_CheckMixLoc(), s_CheckPackedInt(), s_MakeMixLoc(), s_MakePackedInt(), SplitLocationForGap(), and CSeq_loc_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [13/14] BOOST_AUTO_TEST_CASE ( Test_SplitLocationForGapFirstInt_GB8665Minus  )

Definition at line 1243 of file unit_test_loc_edit.cpp.

References CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, eNa_strand_minus, eSplitLocOption_make_partial, eSplitLocOption_split_in_exon, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::Reset(), s_CheckInterval(), s_CheckMixLoc(), s_CheckPackedInt(), s_MakeMixLoc(), s_MakePackedInt(), CSeq_loc::SetStrand(), SplitLocationForGap(), and CSeq_loc_Base::Which().

◆ BOOST_AUTO_TEST_CASE() [14/14] BOOST_AUTO_TEST_CASE ( Test_SplitLocationForGapLastInt_GB8665Minus  )

Definition at line 1291 of file unit_test_loc_edit.cpp.

References CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_Packed_int, eNa_strand_minus, eSplitLocOption_make_partial, eSplitLocOption_split_in_exon, CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::Reset(), s_CheckInterval(), s_CheckMixLoc(), s_CheckPackedInt(), s_MakeMixLoc(), s_MakePackedInt(), CSeq_loc::SetStrand(), SplitLocationForGap(), and CSeq_loc_Base::Which().

◆ Check3Extend() void Check3Extend ( bool  good_end, bool  is_minus, bool  already_partial  ) ◆ Check3Policy() [1/2] void Check3Policy ( bool  good_end, bool  is_minus, bool  already_partial  )

Definition at line 1777 of file unit_test_loc_edit.cpp.

References AddMiscFeature(), BuildGoodEcoSet(), Check3Policy(), eExtreme_Biological, CCdregion_Base::eFrame_two, eNa_strand_minus, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::SetData(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), SetSequenceEnd(), CSeq_entry_Base::SetSet(), and STANDARD_SETUP.

◆ Check3Policy() [2/2] void Check3Policy ( CSeq_feat &  imp, CScope &  scope, edit::CLocationEditPolicy::EPartialPolicy  policy_choice, bool  expect_set3, bool  expect_clear3, bool  extend = false  ) ◆ Check5Extend() void Check5Extend ( bool  good_end, bool  is_minus, bool  already_partial  )

Definition at line 1719 of file unit_test_loc_edit.cpp.

References eExtreme_Biological, CCdregion_Base::eFrame_not_set, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_feat_Base::GetLocation(), CBioseq_set_Base::GetSeq_set(), CSeq_entry_Base::GetSet(), CSeq_loc::GetStart(), MakeMultiSeqCDS(), CBioseq_set_Base::SetAnnot(), CSeq_entry_Base::SetSet(), STANDARD_SETUP, and TruncateTransSplicedCDSForExtension().

Referenced by BOOST_AUTO_TEST_CASE().

◆ Check5Policy() [1/2] void Check5Policy ( bool  good_end, bool  is_minus, bool  already_partial  ) ◆ Check5Policy() [2/2] void Check5Policy ( CSeq_feat &  imp, CScope &  scope, edit::CLocationEditPolicy::EPartialPolicy  policy_choice, bool  expect_set5, bool  expect_clear5, bool  extend = false  ) ◆ CheckAdjustStart()

Definition at line 1914 of file unit_test_loc_edit.cpp.

References AddMiscFeature(), BuildGoodDeltaSeq(), CSeqFeatData_Base::e_Cdregion, eExtreme_Biological, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, eNa_strand_minus, ExtendPartialFeatureEnds(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CCdregion_Base::GetFrame(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CMappedFeat::GetLocation(), CSeq_entry_Base::GetSeq(), CSeq_loc::GetStart(), IsExtendable(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.

Referenced by BOOST_AUTO_TEST_CASE().

◆ CheckAdjustStartAndStop()

Definition at line 1978 of file unit_test_loc_edit.cpp.

References AddMiscFeature(), BuildGoodDeltaSeq(), CSeqFeatData_Base::e_Cdregion, eExtreme_Biological, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, eNa_strand_minus, ExtendPartialFeatureEnds(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CCdregion_Base::GetFrame(), CRange_Base::GetFrom(), CMappedFeat::GetLocation(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CRange_Base::GetTo(), IsExtendable(), CCdregion_Base::IsSetFrame(), and STANDARD_SETUP.

Referenced by BOOST_AUTO_TEST_CASE().

◆ CheckAdjustStop()

Definition at line 1946 of file unit_test_loc_edit.cpp.

References AddMiscFeature(), BuildGoodDeltaSeq(), CSeqFeatData_Base::e_Cdregion, eExtreme_Biological, CCdregion_Base::eFrame_not_set, CCdregion_Base::eFrame_one, eNa_strand_minus, ExtendPartialFeatureEnds(), CSeqFeatData_Base::GetCdregion(), CSeq_feat_Handle::GetData(), CCdregion_Base::GetFrame(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CMappedFeat::GetLocation(), CSeq_entry_Base::GetSeq(), CSeq_loc::GetStop(), IsExtendable(), CCdregion_Base::IsSetFrame(), CSeq_feat_Base::SetData(), CSeq_feat_Base::SetLocation(), and STANDARD_SETUP.

Referenced by BOOST_AUTO_TEST_CASE().

◆ MakeMultiSeqCDS()

Definition at line 1590 of file unit_test_loc_edit.cpp.

References AddMiscFeature(), BuildGoodEcoSet(), eExtreme_Biological, eNa_strand_minus, CBioseq_Base::GetId(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_feat_Base::SetData(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), SetSequenceStart(), and CSeq_entry_Base::SetSet().

Referenced by Check3Extend(), Check5Extend(), and Check5Policy().

◆ NCBITEST_AUTO_INIT() ◆ NCBITEST_INIT_CMDLINE() ◆ NCBITEST_INIT_TREE() ◆ s_CheckInterval() ◆ s_CheckLocationAndStrandResults() ◆ s_CheckLocationPolicyResults() ◆ s_CheckLocationResults() ◆ s_CheckMixLoc() ◆ s_CheckPackedInt() ◆ s_MakeMixLoc() ◆ s_MakePackedInt() ◆ SetSequenceEnd() ◆ SetSequenceStart() ◆ TruncateTransSplicedCDSForExtension()

Definition at line 1628 of file unit_test_loc_edit.cpp.

References CCdregion_Base::eFrame_three, eNa_strand_minus, CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_loc::GetStrand(), CSeq_loc::IsSetStrand(), CBioseq_set_Base::SetAnnot(), CSeq_feat_Base::SetData(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by Check3Extend(), Check5Extend(), and Check5Policy().

◆ s_debugMode

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