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◆ BOOST_AUTO_TEST_CASE() [1/66] BOOST_AUTO_TEST_CASE ( Test_Align2IdentSeq )Definition at line 4260 of file unit_test_sequpdate.cpp.
References CScope::AddTopLevelSeqEntry(), BuildScope(), CSeq_inst_Base::eMol_na, CBioseq_Base::GetId(), CRef< C, Locker >::GetObject(), CSeq_entry_Base::GetSeq(), MakeAsn(), CSeq_entry::Parentize(), ReadEntryFromFile(), CUpdateSeq_Input::s_Align2IdenticalSeq(), and CUpdateSeq_Input::s_FixCollidingIDs_Entry().
◆ BOOST_AUTO_TEST_CASE() [2/66] BOOST_AUTO_TEST_CASE ( Test_Extend3Sequence_DoNotIgnoreAlign )Definition at line 3182 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateExtend3, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend3, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [3/66] BOOST_AUTO_TEST_CASE ( Test_Extend3Sequence_DoNotIgnoreAlign_ImportAllFeatures_Var1 )Definition at line 3266 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateExtend3, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend3, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [4/66] BOOST_AUTO_TEST_CASE ( Test_Extend3Sequence_DonotIgnoreAlign_ImportAllFeatures_Var2 )Definition at line 3333 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, SUpdateSeqParams::eSeqUpdateExtend3, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [5/66] BOOST_AUTO_TEST_CASE ( Test_Extend3Sequence_IgnoreAlign )Definition at line 3037 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateExtend3, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CUpdateSeq_Input::GetOldBioseq(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend3, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [6/66] BOOST_AUTO_TEST_CASE ( Test_Extend3Sequence_IgnoreAlign_ImportAllFeatures )Definition at line 3113 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateExtend3, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend3, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [7/66] BOOST_AUTO_TEST_CASE ( Test_Extend3Sequence_NoAlign )Definition at line 3611 of file unit_test_sequpdate.cpp.
References cmd, eExtreme_Biological, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateExtend3, CSeqFeatData::eSubtype_rRNA, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CSequenceUpdater::IsOldSequenceOK(), CSequenceUpdater::IsUpdateSequenceRaw(), ReadFromFile(), rna, SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [8/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_DoNotIgnoreAlign )Definition at line 2745 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatRemoveOption, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend5, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [9/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_DonotIgnoreAlign_ImportAllFeatures_Var1 )Definition at line 2829 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend5, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [10/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_DonotIgnoreAlign_ImportAllFeatures_Var2 )Definition at line 2895 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend5_AlignWithGap, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [11/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_DonotIgnoreAlign_ImportAllFeatures_Var3 )Definition at line 2964 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [12/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_IgnoreAlign )Definition at line 2533 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CUpdateSeq_Input::GetOldBioseq(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend5, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [13/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_IgnoreAlign_ImportAllFeatures_Var1 )Definition at line 2611 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend5, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [14/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_IgnoreAlign_ImportAllFeatures_Var2 )Definition at line 2678 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Extend5_AlignWithGap, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [15/66] BOOST_AUTO_TEST_CASE ( Test_Extend5Sequence_NoAlign )Definition at line 3548 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateExtend5, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CSequenceUpdater::IsOldSequenceOK(), CSequenceUpdater::IsUpdateSequenceRaw(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [16/66] BOOST_AUTO_TEST_CASE ( Test_FixCollidingIDs ) ◆ BOOST_AUTO_TEST_CASE() [17/66] BOOST_AUTO_TEST_CASE ( Test_GoodAlignment_GB7819 ) ◆ BOOST_AUTO_TEST_CASE() [18/66] BOOST_AUTO_TEST_CASE ( Test_GoodAlignment_GB8669 ) ◆ BOOST_AUTO_TEST_CASE() [19/66] BOOST_AUTO_TEST_CASE ( Test_NoChange )Definition at line 204 of file unit_test_sequpdate.cpp.
References cmd, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Replace, SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [20/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_Delete_ImportAllFeatures )Definition at line 1124 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveAll, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_prot, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [21/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_DeleteAlignedFeatures )Definition at line 227 of file unit_test_sequpdate.cpp.
References cmd, count, SUpdateSeqParams::eFeatRemoveAligned, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_prot, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatRemoveOption, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [22/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_DeleteAllFeatures )Definition at line 288 of file unit_test_sequpdate.cpp.
References cmd, count, SUpdateSeqParams::eFeatRemoveAll, SUpdateSeqParams::eSeqUpdateNoChange, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatRemoveOption, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [23/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_DeleteNotAlignedFeatures )Definition at line 257 of file unit_test_sequpdate.cpp.
References cmd, count, SUpdateSeqParams::eFeatRemoveNotAligned, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatRemoveOption, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [24/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_ExceptDuplicates )Definition at line 1027 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllExceptDups, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [25/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_KeepId1 )Definition at line 900 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, SUpdateSeqParams::m_KeepProteinId, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [26/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_KeepId2 )Definition at line 963 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, SUpdateSeqParams::m_KeepProteinId, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [27/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_Merge )Definition at line 996 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllMergeDups, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [28/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_NewId1 )Definition at line 869 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [29/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_NewId2 )Definition at line 932 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [30/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportCDSFeatures_ReplaceDuplicates )Definition at line 1058 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllReplaceDups, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_cdregion, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [31/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportFeats_ShortSeq )Definition at line 1176 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_prot, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_ImportFeatures, ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [32/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportFeatures_MixedAlign1 )Definition at line 3649 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_tRNA, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [33/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportFeatures_MixedAlign2 )Definition at line 3712 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [34/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures1 )Definition at line 314 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_any, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [35/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures2 )Definition at line 369 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_tRNA, CTrna_ext_Base::GetAnticodon(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_loc::GetId(), CBioseq::GetLocalId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), CRNA_ref_Base::C_Ext::GetTRNA(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, CSeq_id::Match(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [36/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures_ExceptDupl )Definition at line 559 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllExceptDups, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_tRNA, CTrna_ext_Base::GetAnticodon(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_loc::GetId(), CBioseq::GetLocalId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), CRNA_ref_Base::C_Ext::GetTRNA(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, CSeq_id::Match(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [37/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures_IncludeDupl )Definition at line 456 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_tRNA, CTrna_ext_Base::GetAnticodon(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_loc::GetId(), CBioseq::GetLocalId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), CRNA_ref_Base::C_Ext::GetTRNA(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, CSeq_id::Match(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [38/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures_MergeDupl1 )Definition at line 747 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllMergeDups, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_tRNA, CTrna_ext_Base::GetAnticodon(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_loc::GetId(), CBioseq::GetLocalId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), CRNA_ref_Base::C_Ext::GetTRNA(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, CSeq_id::Match(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [39/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures_MergeDupl2 )Definition at line 838 of file unit_test_sequpdate.cpp.
References cmd, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllMergeDups, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_gene, CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), output, ReadEntryFromFile(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [40/66] BOOST_AUTO_TEST_CASE ( Test_NoChange_ImportNewFeatures_ReplaceDupl )Definition at line 657 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveNone, SUpdateSeqParams::eFeatUpdateAllReplaceDups, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_tRNA, CTrna_ext_Base::GetAnticodon(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_loc::GetId(), CBioseq::GetLocalId(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), CRNA_ref_Base::C_Ext::GetTRNA(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, CSeq_id::Match(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [41/66] BOOST_AUTO_TEST_CASE ( Test_PatchSequence )Definition at line 2325 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, SUpdateSeqParams::eSeqUpdatePatch, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [42/66] BOOST_AUTO_TEST_CASE ( Test_PatchSequence_ImportFeatures )Definition at line 2404 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, SUpdateSeqParams::eSeqUpdatePatch, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [43/66] BOOST_AUTO_TEST_CASE ( Test_PatchSequence_UpdateProteins01 )Definition at line 3405 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_inst_Base::eMol_na, eNa_strand_plus, SUpdateSeqParams::eProtUpdate, SUpdateSeqParams::eSeqUpdatePatch, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_prot, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetScope(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_UpdateProteins, ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [44/66] BOOST_AUTO_TEST_CASE ( Test_PatchSeqWithinSet_FeatsAtSeqEnd )Definition at line 1840 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_set_Base::eClass_nuc_prot, eExtreme_Biological, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdatePatch, CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_preRNA, CSeqFeatData::eSubtype_prot, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tRNA, CBioseq_Handle::GetBioseqLength(), CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CBioseq_set_Handle::IsSetClass(), MakeAsn(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [45/66] BOOST_AUTO_TEST_CASE ( Test_PatchSeqWithinSet_ImportFeatures )Definition at line 1981 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_set_Base::eClass_nuc_prot, eExtreme_Biological, SUpdateSeqParams::eFeatRemoveAll, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdatePatch, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tRNA, CBioseq_Handle::GetBioseqLength(), CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CBioseq_set_Handle::IsSetClass(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [46/66] BOOST_AUTO_TEST_CASE ( Test_Replace_DeltaSeqFarPointers )Definition at line 3925 of file unit_test_sequpdate.cpp.
References CScope::AddDataLoader(), CScope::AddTopLevelSeqEntry(), BuildScope(), cmd, CObjectManager::eDefault, SUpdateSeqParams::eFeatRemoveNone, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateNoChange, CSeqFeatData::eSubtype_gene, CScope::GetBioseqHandle(), CObjectManager::GetInstance(), CGBDataLoader::GetLoaderNameFromArgs(), CBioseq_Handle::GetTopLevelEntry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportType, SUpdateSeqParams::m_FeatRemoveOption, SUpdateSeqParams::m_ImportFeatures, NULL, ReadEntryFromFile(), CGBDataLoader::RegisterInObjectManager(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [47/66] BOOST_AUTO_TEST_CASE ( Test_Replace_DeltaSequence )Definition at line 3881 of file unit_test_sequpdate.cpp.
References cmd, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, CSeq_inst_Base::eRepr_raw, SUpdateSeqParams::eSeqUpdateReplace, CSeq_inst_Base::eStrand_ds, CSeq_inst_Base::eTopology_tandem, CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetInst(), CBioseq_Handle::GetInst_Mol(), CBioseq_Handle::GetInst_Repr(), CBioseq_Handle::GetInst_Strand(), CBioseq_Handle::GetInst_Topology(), CSeq_inst_Base::GetSeq_data(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), CSeq_data_Base::IsNcbi4na(), CSeq_inst_Base::IsSetExt(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [48/66] BOOST_AUTO_TEST_CASE ( Test_Replace_MixedAlign )Definition at line 3779 of file unit_test_sequpdate.cpp.
References cmd, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eMol_na, eNa_strand_plus, NStr::EqualNocase(), SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_misc_feature, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), MakeAsn(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [49/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceProteinSeqs1 )Definition at line 3972 of file unit_test_sequpdate.cpp.
References CCmdComposite::AddCommand(), CScope::AddTopLevelSeqEntry(), BuildScope(), cmd, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eMol_aa, map_checker< Container >::empty(), eNa_strand_plus, SUpdateSeqParams::eSeqUpdateReplace, CCmdComposite::Execute(), CUpdateMultipleSeq_Input::GetIdenticalUpdates(), CUpdateMultipleSeq_Input::GetNonIdenticalUpdates(), CSeqVector::GetSeqData(), CUpdateMultipleSeq_Input::GetSeqsWithoutUpdates(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), ok, CUpdateMultipleSeq_Input::PrepareMultipleSequenceInputsForUnitTest(), ReadEntryFromFile(), ReadFastaSeqsFromFile(), CUpdateMultipleSeq_Input::SetOldEntryAndScope(), CUpdateMultipleSeq_Input::SetUpdateEntry(), map_checker< Container >::size(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [50/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceProteinSeqs2 )Definition at line 4019 of file unit_test_sequpdate.cpp.
References CCmdComposite::AddCommand(), CScope::AddTopLevelSeqEntry(), BuildScope(), cmd, CSeqFeatData_Base::e_Prot, CBioseq_Handle::eCoding_Iupac, CSeq_inst_Base::eMol_aa, map_checker< Container >::empty(), eNa_strand_plus, CProt_ref_Base::eProcessed_signal_peptide, SUpdateSeqParams::eSeqUpdateReplace, CCmdComposite::Execute(), CBioseq_Handle::GetBioseqLength(), CUpdateMultipleSeq_Input::GetIdenticalUpdates(), CProt_ref_Base::GetName(), CUpdateMultipleSeq_Input::GetNonIdenticalUpdates(), CProt_ref_Base::GetProcessed(), CSeqVector::GetSeqData(), CUpdateMultipleSeq_Input::GetSeqsWithoutUpdates(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CProt_ref_Base::IsSetProcessed(), MakeAsn(), ok, CUpdateMultipleSeq_Input::PrepareMultipleSequenceInputsForUnitTest(), ReadEntryFromFile(), ReadFastaSeqsFromFile(), CUpdateMultipleSeq_Input::SetOldEntryAndScope(), CUpdateMultipleSeq_Input::SetUpdateEntry(), map_checker< Container >::size(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [51/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence )Definition at line 1232 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_Handle::eCoding_Iupac, eExtreme_Biological, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, eNa_strand_plus, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetInst_Mol(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [52/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_CitSub2 )Definition at line 2234 of file unit_test_sequpdate.cpp.
References cmd, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateReplace, CBioseq_Handle::GetBioseqLength(), CSequenceUpdater::GetCitSubMessage(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_AddCitSub, ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [53/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_FeatAtSeqEnd )Definition at line 1350 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [54/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_Import_ExceptDuplFeatures )Definition at line 2466 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatUpdateAllExceptDups, CSeq_inst_Base::eMol_na, NStr::EqualNocase(), SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [55/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_ImportFeatures )Definition at line 2080 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_ImportFeatures, ReadBioSeqs(), sc_MainSequence, sc_UpdSequence_Patch, SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [56/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_NoAlign )Definition at line 3485 of file unit_test_sequpdate.cpp.
References cmd, count, eExtreme_Biological, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_prot, CBioseq_Handle::GetBioseqLength(), CSeq_entry_Handle::GetCompleteSeq_entry(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CSequenceUpdater::IsOldSequenceOK(), CSequenceUpdater::IsUpdateSequenceRaw(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [57/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_ProteinId_5_Partial_CitSub1 )Definition at line 2144 of file unit_test_sequpdate.cpp.
References check, cmd, CurrentTime(), CSeqFeatData_Base::e_Cdregion, CSeqdesc_Base::e_Pub, eExtreme_Biological, CSeq_inst_Base::eMol_na, CDate::ePrecision_day, SUpdateSeqParams::eSeqUpdateReplace, FOR_EACH_PUB_ON_PUBDESC, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CCit_sub_Base::GetDate(), CCit_sub_Base::GetDescr(), CBioseq_Base::GetId(), CSeq_feat_Base::GetLocation(), CSeq_feat_Handle::GetOriginalSeq_feat(), CSeq_feat_Base::GetProduct(), CPubdesc_Base::GetPub(), CSeq_entry_Handle::GetScope(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), CUpdateSeq_Input::GetUpdateBioseq(), i, IsGeneralIdProtPresent(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CCit_sub_Base::IsSetDate(), CCit_sub_Base::IsSetDescr(), ITERATE, SUpdateSeqParams::m_AddCitSub, MakeAsn(), ReadFromFile(), CDate::SetToTime(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [58/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_UpdateProteins_DoNot_KeepProteinId )Definition at line 1778 of file unit_test_sequpdate.cpp.
References cmd, CBioseq_Handle::eCoding_Iupac, eExtreme_Positional, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, eNa_strand_plus, SUpdateSeqParams::eProtUpdate, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_prot, CSeq_descr_Base::Get(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CBioseq_Base::GetDescr(), CBioseq::GetFirstId(), CSeq_id::GetLabel(), CMappedFeat::GetLocation(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_KeepProteinId, SUpdateSeqParams::m_UpdateProteins, ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [59/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_UpdateProteins_KeepProteinId )Definition at line 1714 of file unit_test_sequpdate.cpp.
References cmd, CBioseq_Handle::eCoding_Iupac, eExtreme_Positional, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, eNa_strand_plus, SUpdateSeqParams::eProtUpdate, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_prot, CSeq_descr_Base::Get(), CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CBioseq_Base::GetDescr(), CBioseq::GetFirstId(), CSeq_id::GetLabel(), CMappedFeat::GetLocation(), CSeqVector::GetSeqData(), CBioseq_Handle::GetSeqVector(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), SUpdateSeqParams::m_KeepProteinId, SUpdateSeqParams::m_UpdateProteins, ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [60/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_WithoutAlign )Definition at line 2265 of file unit_test_sequpdate.cpp.
References CCmdComposite::AddCommand(), CScope::AddTopLevelSeqEntry(), BuildScope(), cmd, eExtreme_Positional, CSeq_inst_Base::eMol_na, map_checker< Container >::empty(), SUpdateSeqParams::eSeqUpdateReplace, CCmdComposite::Execute(), CUpdateMultipleSeq_Input::GetIdenticalUpdates(), CMappedFeat::GetLocation(), CUpdateMultipleSeq_Input::GetNonIdenticalUpdates(), CUpdateMultipleSeq_Input::GetSeqsWithoutUpdates(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), ok, CUpdateMultipleSeq_Input::PrepareMultipleSequenceInputsForUnitTest(), ReadEntryFromFile(), CUpdateMultipleSeq_Input::SetOldEntryAndScope(), CUpdateMultipleSeq_Input::SetUpdateEntry(), map_checker< Container >::size(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [61/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSequence_WithoutFeats )Definition at line 1304 of file unit_test_sequpdate.cpp.
References check, cmd, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateReplace, CBioseq_Handle::GetBioseqLength(), CBioseq_Handle::GetCompleteBioseq(), CBioseq_Base::GetId(), CSeq_entry_Handle::GetTopLevelEntry(), i, IsGeneralIdProtPresent(), ITERATE, MakeAsn(), ReadFromFile(), SetupForUpdate(), and CSequenceUpdater::Update().
◆ BOOST_AUTO_TEST_CASE() [62/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSeqWithinSet_FeatsAtSeqEnd1_AddCitSub )Definition at line 1404 of file unit_test_sequpdate.cpp.
References cmd, count, CurrentTime(), CBioseq_set_Base::eClass_nuc_prot, eExtreme_Biological, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, CDate::ePrecision_day, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_preRNA, CSeqFeatData::eSubtype_prot, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tRNA, FOR_EACH_PUB_ON_PUBDESC, FOR_EACH_SEQDESC_ON_BIOSEQ, CBioseq_Handle::GetBioseqLength(), CBioseq_set_Handle::GetClass(), CBioseq_Handle::GetCompleteBioseq(), CSeq_entry_Handle::GetCompleteSeq_entry(), CCit_sub_Base::GetDate(), CCit_sub_Base::GetDescr(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CBioseq_set_Handle::IsSetClass(), CCit_sub_Base::IsSetDate(), CCit_sub_Base::IsSetDescr(), SUpdateSeqParams::m_AddCitSub, SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), ReadFromFile(), CDate::SetToTime(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [63/66] BOOST_AUTO_TEST_CASE ( Test_ReplaceSeqWithinSet_FeatsAtSeqEnd2 )Definition at line 1566 of file unit_test_sequpdate.cpp.
References cmd, count, CBioseq_set_Base::eClass_nuc_prot, eExtreme_Biological, SUpdateSeqParams::eFeatUpdateAll, CSeq_inst_Base::eMol_na, SUpdateSeqParams::eSeqUpdateReplace, CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_preRNA, CSeqFeatData::eSubtype_prot, CSeqFeatData::eSubtype_region, CSeqFeatData::eSubtype_rRNA, CSeqFeatData::eSubtype_tRNA, CBioseq_Handle::GetBioseqLength(), CBioseq_set_Handle::GetClass(), CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_set_Handle::GetParentEntry(), CBioseq_Handle::GetSeq_entry_Handle(), CSeq_entry_Handle::GetTopLevelEntry(), IsGeneralIdProtPresent(), CBioseq_set_Handle::IsSetClass(), SUpdateSeqParams::m_FeatImportOption, SUpdateSeqParams::m_ImportFeatures, MakeAsn(), ReadFromFile(), SetupForUpdate(), CSequenceUpdater::Update(), and VISIT_ALL_SEQFEATS_WITHIN_SEQENTRY.
◆ BOOST_AUTO_TEST_CASE() [64/66] BOOST_AUTO_TEST_CASE ( Test_s_ExtendOneEndOfSequence )Definition at line 4108 of file unit_test_sequpdate.cpp.
References CScope::AddTopLevelSeqEntry(), BuildGoodSeq(), CSeqConvert::Convert(), CSeqUtil::e_Iupacna, CSeqUtil::e_Ncbi2na, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_rna, SUpdateSeqParams::eSeqUpdateExtend3, SUpdateSeqParams::eSeqUpdateExtend5, CAliasBase< TPrim >::Get(), CObjectManager::GetInstance(), CSeq_inst_Base::GetLength(), CSeq_inst_Base::GetMol(), CSeq_data_Base::GetNcbi2na(), CSeq_inst_Base::GetSeq_data(), CSequenceUpdater::s_ExtendOneEndOfSequence(), CBioseq_Base::SetInst(), and CSeq_entry_Base::SetSeq().
◆ BOOST_AUTO_TEST_CASE() [65/66] BOOST_AUTO_TEST_CASE ( Test_s_OffsetFeature )Definition at line 4150 of file unit_test_sequpdate.cpp.
References CSeq_id_Base::e_Local, eNa_strand_minus, CRNA_ref_Base::eType_tRNA, CTrna_ext_Base::GetAnticodon(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CSeq_feat_Base::GetLocation(), CSeqFeatData_Base::GetRna(), CRNA_ref_Base::C_Ext::GetTRNA(), MakeAsn(), MakeMiscFeature(), CSequenceUpdater::s_GetValidExtension(), CSequenceUpdater::s_OffsetFeature(), CTrna_ext_Base::SetAnticodon(), CSeq_feat_Base::SetData(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), and CRNA_ref_Base::C_Ext::SetTRNA().
◆ BOOST_AUTO_TEST_CASE() [66/66] BOOST_AUTO_TEST_CASE ( Test_SameSequence ) ◆ BuildScope() ◆ MakeAsn() ◆ NCBITEST_AUTO_FINI() ◆ NCBITEST_AUTO_INIT() ◆ ReadBioSeqs() ◆ ReadEntry() ◆ ReadEntryFromFile() ◆ ReadFastaSeqsFromFile()Definition at line 96 of file unit_test_sequpdate.cpp.
References Error(), CFastaReader::fAddMods, CFastaReader::fHyphensIgnoreAndWarn, flags, CFastaReader::fNoSplit, CFastaReader::fUniqueIDs, in(), kMax_Int, LOG_POST, CFastaReader::ReadSet(), and CException::ReportAll().
Referenced by BOOST_AUTO_TEST_CASE().
◆ ReadFromFile() ◆ SetupForUpdate() ◆ USING_SCOPE() ◆ sc_MainSequence const char * sc_MainSequence ◆ sc_UpdSequence_Extend3 const char * sc_UpdSequence_Extend3 ◆ sc_UpdSequence_Extend5 const char * sc_UpdSequence_Extend5 ◆ sc_UpdSequence_Extend5_AlignWithGap const char * sc_UpdSequence_Extend5_AlignWithGap ◆ sc_UpdSequence_Patch const char * sc_UpdSequence_Patch ◆ sc_UpdSequence_Replace const char * sc_UpdSequence_Replace Initial value:= "\
Seq-entry ::= seq { \
id { \
local str \"Seq_02\" } , \
inst { \
repr raw , \
mol dna , \
length 1360 , \
seq-data iupacna \"\
GAGGCACGGGGAGCTTGCTCCCTGGTGGCGAGCGGCGGACGGGTGAGTAATGTAGGAA\
TCTGCCCGGTAGTGGGGGATAACGTGGGGAAACCCACGCTAATACCGCATACGTCCTACGGGAGAAAGCG\
GAGGATCTTCGGACTTCGCGCTATCGGATGAGCCTATGTCGGATTAGCTAGTTGGTAAGGTAACGGCTTA\
CCAAGGCGACGATCCGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACT\
CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTTGATCCAGCCATGCCGCGTGTGT\
GAAGAAGGCTTTCGGGTTGTAAAGCACTTTCAGCGAGGAAGAAAGCCTGGTGGTTAATACCCATCAGGAA\
GGACATCACTCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGC\
GTTAATCGGAATTACTGGGCGTAAAGCGCGCGTAGGTGGCTTGGCACGCCGGTTGTGAAAGCCCCGGGCT\
CAACCTGGGAACGGCATCCGGAACGGCCAGGCTAGAGTGCAGGAGAGGAAGGTAGAATTCCCGGTGTAGC\
GGTGAAATGCGTAGAGATCGGGAGGAATACCAGTGGCGAAGGCGGCCTTCTGGCCTGACACTGACACTGA\
GGTGCGAAAGCGTGGGTAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTAG\
CCGTTGGGACCTTTAAGGACTTAGTGGCGCAGTTAACGCGATAAGTCGACCGCCTGGGGGAGTACGGCCG\
CAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCA\
ACGCGAAGAACCTTACCTACCCTTGACATCCTGCGAATTTGGTAGAGATACCTTAGTGCCTTCGGGAGCG\
CAGTGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGTAACGAGCG\
CAACCCTTTGTCCTTATTTGCCAGCACGTAATGGTGGGAACTCTAAGGAGACTGCCGGTGACAAACCGGA\
GGAAGGTGGGGACGACGTCGGCCCTTACGGGTAGGGCTACACACGTGCTACAATGGCCGG\
TACAAAGGGTTGCGAGACCGCGAGGTGGAGCGAATCCCAGAAAGCCGGCCTCAGTCCGGATCGGAGTCTG\
CAACTCGACTCCGTGAAGTCGGAAAGTAATCGTGAATCAGAATGTCACGGTGAATACGTTCCCGG\
GCCTTGTACACACCGCCCGTCACACCATGGGAGTGGACTGCACCAGAAGTGGTTAGC\" } \
}"
Definition at line 4510 of file unit_test_sequpdate.cpp.
Referenced by BOOST_AUTO_TEST_CASE().
◆ sc_UpdSequence_Same const char * sc_UpdSequence_Same Initial value:= "\
Seq-entry ::= seq { \
id { \
local str \"Seq_01\" } , \
inst { \
repr raw , \
mol dna , \
length 985 , \
seq-data iupacna \"\
TGCAGTCGAGCGGCAGCACGGGGAGCTTGCTCCCTGGTGGCGAGCGGCGGACGGGTGAGTAATGTAGGAA\
TCTGCCCGGTAGTGGGGGATAACGTGGGGAAACCCACGCTAATACCGCATACGTCCTACGGGAGAAAGCG\
GAGGATCTTCGGACTTCGCGCTATCGGATGAGCCTATGTCGGATTAGCTAGTTGGTAAGGTAACGGCTTA\
CCAAGGCGACGATCCGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACT\
CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGAAAGCCTTGATCCAGCCATGCCGCGTGTGT\
GAAGAAGGCTTTCGGGTTGTAAAGCACTTTCAGCGAGGAAGAAAGCCTGGTGGTTAAAGCACCGGCTAAC\
TCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGCGCG\
TAGGTGGCTTGGCACGCCGGTTGTGAAAGCCCCGGGCTCAACCTGGGAACGGCATCCGGAACGGCCAGGC\
TAGAGTGCAGGAGAGGAAGGTAGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAATACCA\
GTGGCGAAGGCGGCCTTCTGGCCTGACACTGACACTGAGGTGCGAAAGCGTGGGTAGCAAACAGGATTAG\
ATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTAGCCGTTGGGACCTTTAAGGACTTAGTGGCGCAG\
TTAACGCGATAAGTCGACCGCCTGGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGC\
CCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACCCTTGACATCCT\
GCGAATTTGGTAGAGATACCTTAGTGCCTTCGGGAGCGCAGTGACAGGTGCTGCATGGCTGTCGTCAGCT\
CGCGC\" } \
}"
Definition at line 4484 of file unit_test_sequpdate.cpp.
Referenced by BOOST_AUTO_TEST_CASE().
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