NCBI C++ ToolKit
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unit_test_feature_table_reader.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/test_boost.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqloc/Seq_point.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Prot_ref.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/seqfeat/Gene_ref.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/misc/sequence_util_macros.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/readers/readfeat.hpp>
#include <objtools/readers/table_filter.hpp>
#include <objtools/readers/message_listener.hpp>
#include <objtools/readers/line_error.hpp>
+ Include dependency graph for unit_test_feature_table_reader.cpp:

Go to the source code of this file.

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Classes

struct  SRegulatoryFeatSubtypeCases
 

Typedefs

typedef list< ILineError::EProblem > TErrList
 
typedef list< CRef< CSeq_annot > > TAnnotRefList
 
typedef unique_ptr< TAnnotRefList > TAnnotRefListPtr
 

Functions

 USING_SCOPE (objects)
 
static bool s_IgnoreError (const ILineError &line_error)
 
static void s_ListLinesWithPattern (const CTempString &str, const CTempString &pattern, vector< size_t > &out_vecOfLinesThatMatch)
 
static size_t s_CountOccurrences (const CTempString &str, const CTempString &pattern)
 
static void s_CheckErrorsVersusExpected (ILineErrorListener *pMessageListener, TErrList expected_errors)
 
static CRef< CSeq_annot > s_ReadOneTableFromString (const char *str, const TErrList &expected_errors=TErrList(), CFeature_table_reader::TFlags additional_flags=0, ILineErrorListener *pMessageListener=nullptr, CSimpleTableFilter *p_tbl_filter=nullptr)
 
static TAnnotRefListPtr s_ReadMultipleTablesFromString (const char *str, const TErrList &expected_errors=TErrList(), CFeature_table_reader::TFlags additional_flags=0, ILineErrorListener *pMessageListener=nullptr)
 
static void CheckExpectedQuals (CConstRef< CSeq_feat > feat, const set< string > &expected_quals)
 
 NCBITEST_INIT_CMDLINE (descrs)
 
 BOOST_AUTO_TEST_CASE (Test_FeatureTableWithGeneAndCodingRegion)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_MultipleFeatureTables)
 Test reading multiple tables. More...
 
 BOOST_AUTO_TEST_CASE (Test_FlybaseFeatureTableWithMultiIntervalTranslExcept)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_NCTableWithtRNAs)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_NCTableWithtRNAsWithCodons)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_CPTableWithncRNAs)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_TableWithVariationsAndGoTerms)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_CapitalizedQualifiers)
 Test a simple table. More...
 
 BOOST_AUTO_TEST_CASE (Test_tRNAAnticodonQualifiers)
 
 BOOST_AUTO_TEST_CASE (Test_ForbidMixedStrandAnticodonQualifier)
 
 BOOST_AUTO_TEST_CASE (TestCDSInGenesCheck)
 
 BOOST_AUTO_TEST_CASE (TestCreateGenesFromCDSs)
 
 BOOST_AUTO_TEST_CASE (TestOffsetCommand)
 
 BOOST_AUTO_TEST_CASE (TestBetweenBaseIntervals)
 
 BOOST_AUTO_TEST_CASE (TestSpacesBeforeFeature)
 
 BOOST_AUTO_TEST_CASE (TestErrorIfRangeAfterQuals)
 
 BOOST_AUTO_TEST_CASE (TestIfHandlesWhenJunkAfterFeature)
 
 BOOST_AUTO_TEST_CASE (TestCaseInsensitivity)
 
 BOOST_AUTO_TEST_CASE (TestDiscouragedKeys)
 
 BOOST_AUTO_TEST_CASE (TestRegulatoryFeat)
 
 BOOST_AUTO_TEST_CASE (TestPeptideFeats)
 
 BOOST_AUTO_TEST_CASE (TestBadTranslTable)
 
 BOOST_AUTO_TEST_CASE (TestRiboswitch)
 
 BOOST_AUTO_TEST_CASE (TestSimpleTableFilter)
 
 BOOST_AUTO_TEST_CASE (TestRW1172)
 

Variables

 USING_NCBI_SCOPE
 
static const char * sc_Table1
 
static const char * sc_Table2
 
static const char * sc_Table3
 
static const char * sc_Table4
 
static const char * sc_TableTrnaWithCodon
 
static const char * sc_Table5
 
static const char * sc_Table6
 
static const char * sc_Table7
 
static const char * sc_Table8
 
static const char * sc_Table9
 
static const char * sc_Table10
 
static const char * sc_Table11
 
static const char * sc_Table12
 
static const char * sc_Table13
 
static const char * sc_Table14
 
static const char * sc_Table15
 
static const char * sc_Table16
 
static const char * sc_Table17
 
const SRegulatoryFeatSubtypeCases subtype_cases []
 
static const char * sc_Table18
 
static const char * sc_Table19
 
static const char * sc_Table20
 
static const char * sc_Table21
 
static const char * sc_Table22
 

Typedef Documentation

◆ TAnnotRefList

typedef list< CRef<CSeq_annot> > TAnnotRefList

Definition at line 231 of file unit_test_feature_table_reader.cpp.

◆ TAnnotRefListPtr

typedef unique_ptr<TAnnotRefList> TAnnotRefListPtr

Definition at line 232 of file unit_test_feature_table_reader.cpp.

◆ TErrList

typedef list<ILineError::EProblem> TErrList

Definition at line 150 of file unit_test_feature_table_reader.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/25]

BOOST_AUTO_TEST_CASE ( Test_CapitalizedQualifiers  )

Test a simple table.

Definition at line 1387 of file unit_test_feature_table_reader.cpp.

References s_ReadOneTableFromString(), and sc_Table7.

◆ BOOST_AUTO_TEST_CASE() [2/25]

BOOST_AUTO_TEST_CASE ( Test_CPTableWithncRNAs  )

Test a simple table.

Definition at line 719 of file unit_test_feature_table_reader.cpp.

References CRNA_ref_Base::eType_ncRNA, ftable, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeqFeatData_Base::GetRna(), CSeqFeatData_Base::IsRna(), CSeq_feat_Base::IsSetData(), rna, s_ReadOneTableFromString(), and sc_Table5.

◆ BOOST_AUTO_TEST_CASE() [3/25]

BOOST_AUTO_TEST_CASE ( Test_FeatureTableWithGeneAndCodingRegion  )

Test a simple table.

Definition at line 343 of file unit_test_feature_table_reader.cpp.

References ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), s_ReadOneTableFromString(), and sc_Table1.

◆ BOOST_AUTO_TEST_CASE() [4/25]

BOOST_AUTO_TEST_CASE ( Test_FlybaseFeatureTableWithMultiIntervalTranslExcept  )

Test a simple table.

Definition at line 453 of file unit_test_feature_table_reader.cpp.

References CheckExpectedQuals(), ftable, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_feat_Base::GetQual(), CSeq_feat_Base::GetXref(), set< Key, Compare >::insert(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetData(), NCBITEST_CHECK, s_ReadOneTableFromString(), and sc_Table3.

◆ BOOST_AUTO_TEST_CASE() [5/25]

BOOST_AUTO_TEST_CASE ( Test_ForbidMixedStrandAnticodonQualifier  )

Definition at line 1467 of file unit_test_feature_table_reader.cpp.

References CheckExpectedQuals(), ILineError::eProblem_QualifierBadValue, CRNA_ref_Base::eType_tRNA, ftable, CSeq_annot_Base::GetData(), CRNA_ref_Base::GetExt(), CSeq_annot_Base::C_Data::GetFtable(), CRNA_ref_Base::C_Ext::GetTRNA(), CRNA_ref_Base::GetType(), CTrna_ext_Base::IsSetAa(), CTrna_ext_Base::IsSetAnticodon(), s_ReadOneTableFromString(), and sc_Table9.

◆ BOOST_AUTO_TEST_CASE() [6/25]

BOOST_AUTO_TEST_CASE ( Test_MultipleFeatureTables  )

Test reading multiple tables.

Definition at line 384 of file unit_test_feature_table_reader.cpp.

References ftable, ITERATE, s_ReadMultipleTablesFromString(), and sc_Table2.

◆ BOOST_AUTO_TEST_CASE() [7/25]

BOOST_AUTO_TEST_CASE ( Test_NCTableWithtRNAs  )

Test a simple table.

Definition at line 631 of file unit_test_feature_table_reader.cpp.

References CheckExpectedQuals(), NStr::Equal(), CRNA_ref_Base::eType_rRNA, CRNA_ref_Base::eType_tRNA, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), set< Key, Compare >::insert(), NStr::IsBlank(), CGene_ref_Base::IsSetLocus(), ITERATE, prot, rna, s_ReadOneTableFromString(), sc_Table4, and tag.

◆ BOOST_AUTO_TEST_CASE() [8/25]

BOOST_AUTO_TEST_CASE ( Test_NCTableWithtRNAsWithCodons  )

Test a simple table.

Definition at line 688 of file unit_test_feature_table_reader.cpp.

References CRNA_ref_Base::eType_tRNA, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), ITERATE, rna, s_ReadOneTableFromString(), and sc_TableTrnaWithCodon.

◆ BOOST_AUTO_TEST_CASE() [9/25]

BOOST_AUTO_TEST_CASE ( Test_TableWithVariationsAndGoTerms  )

Test a simple table.

Definition at line 1334 of file unit_test_feature_table_reader.cpp.

References NStr::Equal(), ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), ITERATE, s_ReadOneTableFromString(), and sc_Table6.

◆ BOOST_AUTO_TEST_CASE() [10/25]

BOOST_AUTO_TEST_CASE ( Test_tRNAAnticodonQualifiers  )

Definition at line 1408 of file unit_test_feature_table_reader.cpp.

References CheckExpectedQuals(), CSerialObject::Equals(), CRNA_ref_Base::eType_tRNA, ftable, CTrna_ext_Base::GetAa(), CTrna_ext_Base::GetAnticodon(), CSeq_annot_Base::GetData(), CRNA_ref_Base::GetExt(), CSeq_annot_Base::C_Data::GetFtable(), CTrna_ext_Base::C_Aa::GetNcbieaa(), CRNA_ref_Base::C_Ext::GetTRNA(), CRNA_ref_Base::GetType(), ITERATE, MSerial_AsnText, s_ReadOneTableFromString(), and sc_Table8.

◆ BOOST_AUTO_TEST_CASE() [11/25]

BOOST_AUTO_TEST_CASE ( TestBadTranslTable  )

Definition at line 2085 of file unit_test_feature_table_reader.cpp.

References CheckExpectedQuals(), ILineError::eProblem_QualifierBadValue, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), s_ReadOneTableFromString(), and sc_Table19.

◆ BOOST_AUTO_TEST_CASE() [12/25]

BOOST_AUTO_TEST_CASE ( TestBetweenBaseIntervals  )

Definition at line 1805 of file unit_test_feature_table_reader.cpp.

References NStr::BoolToString(), CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, ILineError::eProblem_BadFeatureInterval, FIELD_IS_SET_AND_IS, ftable, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_point_Base::GetFuzz(), CSeqFeatData_Base::GetImp(), CImp_feat_Base::GetKey(), CInt_fuzz_Base::GetLim(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CSeq_loc::IsReverseStrand(), ITERATE_BOTH_BOOL_VALUES, NStr::Replace(), s_ReadOneTableFromString(), and sc_Table13.

◆ BOOST_AUTO_TEST_CASE() [13/25]

BOOST_AUTO_TEST_CASE ( TestCaseInsensitivity  )

Definition at line 1918 of file unit_test_feature_table_reader.cpp.

References CSeqFeatData::eSubtype_otherRNA, CSeqFeatData::eSubtype_rRNA, ftable, CSeq_annot_Base::GetData(), CRNA_ref_Base::GetExt(), CSeq_annot_Base::C_Data::GetFtable(), CRNA_ref_Base::C_Ext::GetName(), CSeqFeatData_Base::GetRna(), CSeqFeatData::GetSubtype(), s_ReadOneTableFromString(), and sc_Table16.

◆ BOOST_AUTO_TEST_CASE() [14/25]

BOOST_AUTO_TEST_CASE ( TestCDSInGenesCheck  )

Definition at line 1525 of file unit_test_feature_table_reader.cpp.

References ILineError::eProblem_FeatMustBeInXrefdGene, CFeature_table_reader::fCDSsMustBeInTheirGenes, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), ITERATE_0_IDX, ILineError::Line(), ILineError::OtherLines(), s_CountOccurrences(), s_ListLinesWithPattern(), s_ReadOneTableFromString(), and sc_Table10.

◆ BOOST_AUTO_TEST_CASE() [15/25]

BOOST_AUTO_TEST_CASE ( TestCreateGenesFromCDSs  )

Definition at line 1586 of file unit_test_feature_table_reader.cpp.

References CTempString::begin(), set< Key, Compare >::begin(), NStr::BoolToString(), CTempString::empty(), CTempString::end(), set< Key, Compare >::end(), ILineError::eProblem_FeatMustBeInXrefdGene, NStr::eTrunc_Begin, CFeature_table_reader::fCDSsMustBeInTheirGenes, CFeature_table_reader::fCreateGenesFromCDSs, FIELD_IS_SET_AND_IS, CTempString::find_first_of(), ftable, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeqFeatData_Base::GetGene(), CSeq_feat::GetGeneXref(), CGene_ref_Base::GetLocus(), set< Key, Compare >::insert(), isspace(), ITERATE, ITERATE_0_IDX, ITERATE_BOTH_BOOL_VALUES, kEmptyStr, CTempString::length(), ILineError::Line(), NCBITEST_CHECK, NPOS, ILineError::OtherLines(), ILineError::Problem(), RAW_FIELD_IS_EMPTY_OR_UNSET, s_CountOccurrences(), s_ReadOneTableFromString(), sc_Table11, set< Key, Compare >::size(), ct::sort(), NStr::SplitByPattern(), NStr::StartsWith(), CTempString::substr(), and NStr::TruncateSpacesInPlace().

◆ BOOST_AUTO_TEST_CASE() [16/25]

BOOST_AUTO_TEST_CASE ( TestDiscouragedKeys  )

Definition at line 1962 of file unit_test_feature_table_reader.cpp.

References ILineError::eProblem_DiscouragedFeatureName, ILineError::eProblem_DiscouragedQualifierName, CFeature_table_reader::fReportDiscouragedKey, s_ReadOneTableFromString(), and sc_Table17.

◆ BOOST_AUTO_TEST_CASE() [17/25]

BOOST_AUTO_TEST_CASE ( TestErrorIfRangeAfterQuals  )

Definition at line 1885 of file unit_test_feature_table_reader.cpp.

References ILineError::eProblem_NoFeatureProvidedOnIntervals, s_ReadOneTableFromString(), and sc_Table14.

◆ BOOST_AUTO_TEST_CASE() [18/25]

BOOST_AUTO_TEST_CASE ( TestIfHandlesWhenJunkAfterFeature  )

Definition at line 1902 of file unit_test_feature_table_reader.cpp.

References s_ReadOneTableFromString(), and sc_Table15.

◆ BOOST_AUTO_TEST_CASE() [19/25]

BOOST_AUTO_TEST_CASE ( TestOffsetCommand  )

Definition at line 1740 of file unit_test_feature_table_reader.cpp.

References ArraySize(), copy(), eExtreme_Biological, ILineError::eProblem_UnrecognizedSquareBracketCommand, FIELD_IS_SET_AND_IS, CSeq_loc::GetStart(), CSeq_loc::GetStop(), ITERATE, ITERATE_0_IDX, s_ReadMultipleTablesFromString(), and sc_Table12.

◆ BOOST_AUTO_TEST_CASE() [20/25]

BOOST_AUTO_TEST_CASE ( TestPeptideFeats  )

Definition at line 2057 of file unit_test_feature_table_reader.cpp.

References CProt_ref_Base::eProcessed_mature, CProt_ref_Base::eProcessed_propeptide, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CProt_ref_Base::GetProcessed(), CSeqFeatData_Base::GetProt(), s_ReadOneTableFromString(), and sc_Table18.

◆ BOOST_AUTO_TEST_CASE() [21/25]

BOOST_AUTO_TEST_CASE ( TestRegulatoryFeat  )

Definition at line 1990 of file unit_test_feature_table_reader.cpp.

References ArraySize(), NStr::BoolToString(), ILineError::eProblem_DiscouragedFeatureName, ILineError::eProblem_QualifierBadValue, CSeqFeatData::eSubtype_10_signal, CFeature_table_reader::fReportDiscouragedKey, CSeqFeatData::GetRegulatoryClass(), SRegulatoryFeatSubtypeCases::is_regulatory, ITERATE_0_IDX, ITERATE_BOTH_BOOL_VALUES, s_ReadOneTableFromString(), SRegulatoryFeatSubtypeCases::subtype, subtype_cases, and CSeqFeatData::SubtypeValueToName().

◆ BOOST_AUTO_TEST_CASE() [22/25]

BOOST_AUTO_TEST_CASE ( TestRiboswitch  )

Definition at line 2110 of file unit_test_feature_table_reader.cpp.

References s_ReadOneTableFromString(), and sc_Table20.

◆ BOOST_AUTO_TEST_CASE() [23/25]

BOOST_AUTO_TEST_CASE ( TestRW1172  )

Definition at line 2156 of file unit_test_feature_table_reader.cpp.

References ILineError::eProblem_BadFeatureInterval, ILineError::eProblem_FeatureBadStartAndOrStop, ILineError::eProblem_QualifierWithoutFeature, s_ReadOneTableFromString(), and sc_Table22.

◆ BOOST_AUTO_TEST_CASE() [24/25]

BOOST_AUTO_TEST_CASE ( TestSimpleTableFilter  )

Definition at line 2127 of file unit_test_feature_table_reader.cpp.

References ITableFilter::eAction_Disallowed, ITableFilter::eAction_Okay, ILineError::eProblem_FeatureNameNotAllowed, ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), s_ReadOneTableFromString(), sc_Table21, and CSimpleTableFilter::SetActionForFeat().

◆ BOOST_AUTO_TEST_CASE() [25/25]

BOOST_AUTO_TEST_CASE ( TestSpacesBeforeFeature  )

Definition at line 1858 of file unit_test_feature_table_reader.cpp.

References ftable, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), ITERATE_0_IDX, s_ReadOneTableFromString(), and string.

◆ CheckExpectedQuals()

static void CheckExpectedQuals ( CConstRef< CSeq_feat >  feat,
const set< string > &  expected_quals 
)
static

Definition at line 283 of file unit_test_feature_table_reader.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::end(), CSeq_feat_Base::GetQual(), set< Key, Compare >::insert(), and ITERATE.

Referenced by BOOST_AUTO_TEST_CASE().

◆ NCBITEST_INIT_CMDLINE()

NCBITEST_INIT_CMDLINE ( descrs  )

Definition at line 316 of file unit_test_feature_table_reader.cpp.

◆ s_CheckErrorsVersusExpected()

static void s_CheckErrorsVersusExpected ( ILineErrorListener *  pMessageListener,
TErrList  expected_errors 
)
static

Definition at line 153 of file unit_test_feature_table_reader.cpp.

References ILineErrorListener::Count(), ILineErrorListener::GetError(), i, ILineError::Message(), ILineError::ProblemStr(), and s_IgnoreError().

Referenced by s_ReadMultipleTablesFromString(), and s_ReadOneTableFromString().

◆ s_CountOccurrences()

static size_t s_CountOccurrences ( const CTempString &  str,
const CTempString &  pattern 
)
static

Definition at line 140 of file unit_test_feature_table_reader.cpp.

References NStr::SplitByPattern(), and str().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_IgnoreError()

static bool s_IgnoreError ( const ILineError &  line_error)
static

Definition at line 116 of file unit_test_feature_table_reader.cpp.

References eDiag_Info, and ILineError::Severity().

Referenced by s_CheckErrorsVersusExpected().

◆ s_ListLinesWithPattern()

static void s_ListLinesWithPattern ( const CTempString &  str,
const CTempString &  pattern,
vector< size_t > &  out_vecOfLinesThatMatch 
)
static

Definition at line 124 of file unit_test_feature_table_reader.cpp.

References NStr::Find(), ITERATE_0_IDX, NPOS, NStr::Split(), and str().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_ReadMultipleTablesFromString()

static TAnnotRefListPtr s_ReadMultipleTablesFromString ( const char *  str,
const TErrList &  expected_errors = TErrList(),
CFeature_table_reader::TFlags  additional_flags = 0,
ILineErrorListener *  pMessageListener = nullptr 
)
static

Definition at line 243 of file unit_test_feature_table_reader.cpp.

References ITableFilter::eAction_Disallowed, ITableFilter::eAction_Okay, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_annot::IsFtable(), ILineReader::New(), CFeature_table_reader::ReadSequinFeatureTable(), s_CheckErrorsVersusExpected(), CSimpleTableFilter::SetActionForFeat(), and str().

Referenced by BOOST_AUTO_TEST_CASE().

◆ s_ReadOneTableFromString()

static CRef< CSeq_annot > s_ReadOneTableFromString ( const char *  str,
const TErrList &  expected_errors = TErrList(),
CFeature_table_reader::TFlags  additional_flags = 0,
ILineErrorListener *  pMessageListener = nullptr,
CSimpleTableFilter *  p_tbl_filter = nullptr 
)
static

Definition at line 187 of file unit_test_feature_table_reader.cpp.

References ITableFilter::eAction_Disallowed, ITableFilter::eAction_Okay, CSeq_annot::IsFtable(), MSerial_AsnText, ILineReader::New(), CFeature_table_reader::ReadSequinFeatureTable(), s_CheckErrorsVersusExpected(), CSimpleTableFilter::SetActionForFeat(), and str().

Referenced by BOOST_AUTO_TEST_CASE().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ sc_Table1

const char* sc_Table1
static
Initial value:
= "\
>Feature lcl|seq_1\n\
1\t336\tgene\n\
\t\t\tgene\ta\n\
\t\t\tgene_desc\tb\n\
1\t336\tCDS\n\
\t\t\tproduct c\n\
\t\t\tprot_desc\td\n\
\t\t\tprotein_id\tlcl|seq_1_1\n\
\t\t\tnote\te\n\
"

Definition at line 103 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table10

const char* sc_Table10
static

Definition at line 1493 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table11

const char* sc_Table11
static
Initial value:
= "\
>Feature lcl|seq1\n\
1\t100\tgene\n\
\t\t\tgene\tSOME_GENE\n\
20\t70\tCDS\n\
\t\t\tnote\tokay\n\
150\t200\tCDS\n\
\t\t\tnote\tokay\n\
30\t80\tCDS\n\
\t\t\tgene\tSOME_GENE\n\
\t\t\tnote\tokay\n\
75\t400\tCDS\n\
\t\t\tgene\tSOME_GENE\n\
\t\t\tnote\terror_if_checking_bounds\n\
40\t90\tCDS\n\
\t\t\tgene\tCREATED_GENE_1\n\
\t\t\tnote\tokay\n\
80\t300\tCDS\n\
\t\t\tgene\tCREATED_GENE_2\n\
\t\t\tnote\tokay\n\
200\t250\tCDS\n\
\t\t\tgene\tCREATED_GENE_2\n\
\t\t\tnote\tokay\n\
50\t300\tCDS\n\
\t\t\tgene\tCREATED_GENE_2\n\
\t\t\tnote\terror_if_checking_bounds\n\
"

Definition at line 1558 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table12

const char* sc_Table12
static
Initial value:
= "\
>Feature lcl|Seq1\n\
1\t20\tgene\n\
\t\t\tgene g0\n\
[offset=7]\n\
1\t20\tgene\n\
31\t41\n\
\t\t\tgene g1\n\
>Feature lcl|Seq2\n\
1\t20\tgene\n\
\t\t\tgene g2\n\
30\t40\tgene\n\
\t\t\tgene g3\n\
[offset=0]\n\
40\t50\tgene\n\
\t\t\tgene g4\n\
[offset=-30]\n\
40\t50\tgene\n\
\t\t\tgene g5\n\
[offset=abc]\n\
55\t45\tgene\n\
\t\t\tgene g6\n\
[nonsense=foo]\n\
55\t65\tgene\n\
\t\t\tgene g7\n\
"

Definition at line 1713 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table13

const char* sc_Table13
static
Initial value:
= "\
>Feature lcl|Seq1\n\
1\t20\tgene\n\
\t\t\tgene g0\n\
17^\tEND\tvariation\n\
\t\t\treplace\tCCT\n\
22^\t21\tvariation\n\
\t\t\treplace\tTAA\n\
"

Definition at line 1795 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table14

const char* sc_Table14
static
Initial value:
= "\
>Feature lcl|Seq1\n\
1\t1008\tCDS\n\
\t\t\tgene THE_GENE_NAME\n\
50\t200\n\
\t\t\tproduct THE_GENE_PRODUCT\n\
\n\
"

Definition at line 1876 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table15

const char* sc_Table15
static
Initial value:
= "\
>Features_blah_blah lcl|Seq1\n\
1\t1008\tCDS\n\
\t\t\tgene THE_GENE_NAME\n\
\n\
"

Definition at line 1895 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table16

const char* sc_Table16
static
Initial value:
= "\
>Feature lcl|seq1\n\
<1\t32\trRNA\n\
\t\tProduct\t18S ribosomal RNA\n\
33\t170\tmisc_RNA\n\
\t\tProduct\tinternal transcribed spacer 1\n\
\n\
"

Definition at line 1909 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table17

const char* sc_Table17
static
Initial value:
= "\
>Feature lcl|seq1\n\
<1\t32\tsnoRNA\n\
\t\t\tnote\tHello, this is a note.\n\
33\t170\tmobile_element\n\
\t\ttransposon\tSomeTransposon\n\
\n\
"

Definition at line 1952 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table18

const char* sc_Table18
static
Initial value:
= "\
>Feature lcl|seq1\n\
10\t60\tmat_peptide\n\
\t\t\tnote\tyo\n\
100\t170\tpropeptide\n\
\t\t\tnote\thello\n\
"

Definition at line 2049 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table19

const char* sc_Table19
static
Initial value:
= "\
>Feature lcl|seq1\n\
1\t1578\tCDS\n\
\t\t\tproduct\tcytochrome c oxidase subunit I\n\
\t\t\ttransl_table\t1111\n\
"

Definition at line 2077 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table2

const char* sc_Table2
static
Initial value:
= "\
>Feature lcl|seq_1\n\
1\t336\tgene\n\
\t\t\tgene\ta\n\
\t\t\tgene_desc\tb\n\
1\t336\tCDS\n\
\t\t\tproduct c\n\
\t\t\tprot_desc\td\n\
\t\t\tprotein_id\tlcl|seq_1_1\n\
\t\t\tnote\te\n\
>Feature lcl|seq_2\n\
1\t336\tgene\n\
\t\t\tgene\ta\n\
\t\t\tgene_desc\tb\n\
1\t336\tCDS\n\
\t\t\tproduct c\n\
\t\t\tprot_desc\td\n\
\t\t\tprotein_id\tlcl|seq_2_1\n\
\t\t\tnote\te\n\
"

Definition at line 359 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table20

const char* sc_Table20
static
Initial value:
= "\
>Feature gb|KY807921|\n\
3200\t3201\tregulatory \n\
\t\t\tnote\tcobalamin riboswitch \n\
\t\t\tbound_moiety\tcobalamin \n\
\t\t\tregulatory_class\triboswitch\n\
"

Definition at line 2102 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table21

const char* sc_Table21
static
Initial value:
= "\
>Feature lcl|seq1\n\
<1\t32\trRNA\n\
\t\tProduct\t18S ribosomal RNA\n\
33\t170\tmisc_RNA\n\
\t\tProduct\tinternal transcribed spacer 1\n\
"

Definition at line 2119 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table22

const char* sc_Table22
static
Initial value:
= "\
>Feature MN517919\n\
>3137\t2563\tgene\n\
\t\tgene\trrn23\n\
\t\tstandard_name\trrn23 gene\n\
"

Definition at line 2149 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table3

const char* sc_Table3
static

Definition at line 403 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table4

const char* sc_Table4
static

Definition at line 482 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table5

const char* sc_Table5
static
Initial value:
= "\
>Feature gb|CP003382.1|\n\
1982606\t1982707\tgene\n\
\t\t\tlocus_tag\tDeipe_1981\n\
\t\t\tnote\tIMG reference gene:2509592968\n\
1982606\t1982707\tncRNA\n\
\t\t\tncRNA_class\tSRP_RNA\n\
\t\t\tproduct\tBacterial signal recognition particle RNA\n\
"

Definition at line 705 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table6

const char* sc_Table6
static

Definition at line 738 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table7

const char* sc_Table7
static
Initial value:
= "\
>Feature gb|CP003382.1|\n\
1982606\t1982707\tgene\n\
\t\t\tlocus_tag\tDeipe_1981\n\
\t\t\tnote\tIMG reference gene:2509592968\n\
1982606\t1982707\tncRNA\n\
\t\t\tncRNA_class\tSRP_RNA\n\
\t\t\tproduct\tBacterial signal recognition particle RNA\n\
\t\t\tEC_number\t1.2.3.4\n\
\t\t\tPCR_conditions\tabc\n\
1\t20\tmisc_feature\n\
\t\t\tSTS\tabc\n\
"

Definition at line 1369 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table8

const char* sc_Table8
static
Initial value:
= "\
>Feature lcl|seq1\n\
1\t10\ttRNA\n\
20\t30\n\
\t\t\tanticodon\t(pos:21..23,aa:His)\n\
101\t110\ttRNA\n\
120\t130\n\
\t\t\tanticodon\t(pos:complement(121..123),aa:Pro)\n\
201\t210\ttRNA\n\
220\t230\n\
\t\t\tanticodon\t(pos:join(210,220..221),aa:Ala)\n\
301\t310\ttRNA\n\
320\t330\n\
\t\t\tanticodon\t(pos:complement(join(310,320..321)),aa:Cys)\n\
"

Definition at line 1392 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_Table9

const char* sc_Table9
static
Initial value:
= "\
>Feature lcl|seq1\n\
1\t10\ttRNA\n\
20\t30\n\
\t\t\tanticodon\t(pos:join(10..10,complement(20..21)),aa:Pro)\n\
"

Definition at line 1460 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ sc_TableTrnaWithCodon

const char* sc_TableTrnaWithCodon
static
Initial value:
= "\
>Feature ref|NC_019571.1|\n\
1\t10\ttRNA\n\
\t\t\tproduct\ttRNA-Asn-GTT\n\
12\t20\ttRNA\n\
\t\t\tproduct\ttRNA-Met (ATT)\n\
"

Definition at line 677 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ subtype_cases

const SRegulatoryFeatSubtypeCases subtype_cases[]
Initial value:
= {
{ CSeqFeatData::eSubtype_regulatory, true },
{ CSeqFeatData::eSubtype_10_signal, false },
{ CSeqFeatData::eSubtype_CAAT_signal, false },
}

Definition at line 1981 of file unit_test_feature_table_reader.cpp.

Referenced by BOOST_AUTO_TEST_CASE().

◆ USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 68 of file unit_test_feature_table_reader.cpp.

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