NCBI C++ ToolKit
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ntscan_unit_test.cpp File Reference
#include <ncbi_pch.hpp>
#include <corelib/test_boost.hpp>
#include <corelib/ncbitime.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/util/sequence.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <serial/serial.hpp>
#include <serial/iterator.hpp>
#include <serial/objostr.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include "blast_objmgr_priv.hpp"
#include <algo/blast/core/blast_setup.h>
#include <algo/blast/core/blast_encoding.h>
#include <algo/blast/core/blast_nalookup.h>
#include <algo/blast/core/blast_nascan.h>
#include <algo/blast/core/na_ungapped.h>
#include <algo/blast/core/blast_stat.h>
#include <algo/blast/core/lookup_util.h>
#include "test_objmgr.hpp"
+ Include dependency graph for ntscan_unit_test.cpp:

Go to the source code of this file.

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Classes

struct  TestFixture
 

Macros

#define TINY_GI   80982444
 
#define SM_GI   1945386
 
#define MED_GI   19572546
 
#define LG_GI   39919153
 
#define SUBJECT_GI   39103910
 
#define NULL_NUCL_SENTINEL   0xf
 
#define DECLARE_TEST(name, gi, d_size, d_type, wordsize)
 

Functions

 BOOST_AUTO_TEST_CASE (DiscontigTwoSubjects)
 
 BOOST_AUTO_TEST_CASE (TinyScanOffsetSize4)
 
 BOOST_AUTO_TEST_CASE (TinyScanOffsetSize5)
 
 BOOST_AUTO_TEST_CASE (TinyScanOffsetSize6)
 
 BOOST_AUTO_TEST_CASE (TinyScanOffsetSize7)
 
 BOOST_AUTO_TEST_CASE (SmallScanOffsetSize6)
 
 BOOST_AUTO_TEST_CASE (SmallScanOffsetSize7)
 
 BOOST_AUTO_TEST_CASE (SmallScanOffsetSize8)
 
 BOOST_AUTO_TEST_CASE (SmallScanOffsetSize9)
 
 BOOST_AUTO_TEST_CASE (SmallScanOffsetSize10)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize9)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize10)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize13)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize14)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize15)
 
 BOOST_AUTO_TEST_CASE (MediumScanOffsetSize20)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize13)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize15)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize20)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize25)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize28)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize33)
 
 BOOST_AUTO_TEST_CASE (LargeScanOffsetSize37)
 
 BOOST_AUTO_TEST_CASE (Disco_Coding_16_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_Coding_18_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_Coding_21_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_Optimal_16_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_Optimal_18_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_Optimal_21_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_2Templ_16_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_2Templ_18_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_2Templ_21_ScanOffsetSize11)
 
 BOOST_AUTO_TEST_CASE (Disco_Coding_16_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_Coding_18_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_Coding_21_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_Optimal_16_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_Optimal_18_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_Optimal_21_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_2Templ_16_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_2Templ_18_ScanOffsetSize12)
 
 BOOST_AUTO_TEST_CASE (Disco_2Templ_21_ScanOffsetSize12)
 

Variables

static Uint1 template_11_16 [] = {1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1}
 
static Uint1 template_11_18 [] = {1,0,1,1,0,1,1,0,0,1,0,1,1,0,1,1,0,1}
 
static Uint1 template_11_21 [] = {1,0,0,1,0,1,1,0,0,1,0,1,1,0,0,1,0,1,1,0,1}
 
static Uint1 template_11_16_opt [] = {1,1,1,0,0,1,0,1,1,0,1,1,0,1,1,1}
 
static Uint1 template_11_18_opt [] = {1,1,1,0,1,0,0,1,0,1,1,0,0,1,0,1,1,1}
 
static Uint1 template_11_21_opt [] = {1,1,1,0,1,0,0,1,0,1,0,0,0,1,0,0,1,0,1,1,1}
 
static Uint1 template_12_16 [] = {1,1,1,1,1,0,1,1,0,1,1,0,1,1,0,1}
 
static Uint1 template_12_18 [] = {1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1}
 
static Uint1 template_12_21 [] = {1,0,0,1,0,1,1,0,1,1,0,1,1,0,0,1,0,1,1,0,1}
 
static Uint1 template_12_16_opt [] = {1,1,1,0,1,1,0,1,1,0,1,1,0,1,1,1}
 
static Uint1 template_12_18_opt [] = {1,1,1,0,1,0,1,1,0,0,1,0,1,1,0,1,1,1}
 
static Uint1 template_12_21_opt [] = {1,1,1,0,1,0,0,1,0,1,1,0,0,1,0,0,1,0,1,1,1}
 

Macro Definition Documentation

◆ DECLARE_TEST

#define DECLARE_TEST (   name,
  gi,
  d_size,
  d_type,
  wordsize 
)
Value:
BOOST_AUTO_TEST_CASE( name##ScanOffsetSize##wordsize ) { \
SetUpQuerySubjectAndLUT(TRUE, gi, (EDiscWordType)d_type, d_size, wordsize);\
ScanOffsetTestCore((EDiscWordType)d_type); \
ScanCheckHitsCore((EDiscWordType)d_type); \
ScanMaxHitsTestCore(); \
SkipMaskedRangesCore(); \
}
EDiscWordType
General types of discontiguous word templates.
BOOST_AUTO_TEST_CASE(DiscontigTwoSubjects)
@ TRUE
Definition: testodbc.c:27

Definition at line 846 of file ntscan_unit_test.cpp.

◆ LG_GI

#define LG_GI   39919153

Definition at line 87 of file ntscan_unit_test.cpp.

◆ MED_GI

#define MED_GI   19572546

Definition at line 86 of file ntscan_unit_test.cpp.

◆ NULL_NUCL_SENTINEL

#define NULL_NUCL_SENTINEL   0xf

Definition at line 90 of file ntscan_unit_test.cpp.

◆ SM_GI

#define SM_GI   1945386

Definition at line 85 of file ntscan_unit_test.cpp.

◆ SUBJECT_GI

#define SUBJECT_GI   39103910

Definition at line 88 of file ntscan_unit_test.cpp.

◆ TINY_GI

#define TINY_GI   80982444

Definition at line 84 of file ntscan_unit_test.cpp.

Function Documentation

◆ BOOST_AUTO_TEST_CASE() [1/45]

BOOST_AUTO_TEST_CASE ( Disco_2Templ_16_ScanOffsetSize11  )

Definition at line 892 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [2/45]

BOOST_AUTO_TEST_CASE ( Disco_2Templ_16_ScanOffsetSize12  )

Definition at line 903 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [3/45]

BOOST_AUTO_TEST_CASE ( Disco_2Templ_18_ScanOffsetSize11  )

Definition at line 893 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [4/45]

BOOST_AUTO_TEST_CASE ( Disco_2Templ_18_ScanOffsetSize12  )

Definition at line 904 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [5/45]

BOOST_AUTO_TEST_CASE ( Disco_2Templ_21_ScanOffsetSize11  )

Definition at line 894 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [6/45]

BOOST_AUTO_TEST_CASE ( Disco_2Templ_21_ScanOffsetSize12  )

Definition at line 905 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [7/45]

BOOST_AUTO_TEST_CASE ( Disco_Coding_16_ScanOffsetSize11  )

Definition at line 885 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [8/45]

BOOST_AUTO_TEST_CASE ( Disco_Coding_16_ScanOffsetSize12  )

Definition at line 896 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [9/45]

BOOST_AUTO_TEST_CASE ( Disco_Coding_18_ScanOffsetSize11  )

Definition at line 886 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [10/45]

BOOST_AUTO_TEST_CASE ( Disco_Coding_18_ScanOffsetSize12  )

Definition at line 897 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [11/45]

BOOST_AUTO_TEST_CASE ( Disco_Coding_21_ScanOffsetSize11  )

Definition at line 887 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [12/45]

BOOST_AUTO_TEST_CASE ( Disco_Coding_21_ScanOffsetSize12  )

Definition at line 898 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [13/45]

BOOST_AUTO_TEST_CASE ( Disco_Optimal_16_ScanOffsetSize11  )

Definition at line 888 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [14/45]

BOOST_AUTO_TEST_CASE ( Disco_Optimal_16_ScanOffsetSize12  )

Definition at line 899 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [15/45]

BOOST_AUTO_TEST_CASE ( Disco_Optimal_18_ScanOffsetSize11  )

Definition at line 889 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [16/45]

BOOST_AUTO_TEST_CASE ( Disco_Optimal_18_ScanOffsetSize12  )

Definition at line 900 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [17/45]

BOOST_AUTO_TEST_CASE ( Disco_Optimal_21_ScanOffsetSize11  )

Definition at line 890 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [18/45]

BOOST_AUTO_TEST_CASE ( Disco_Optimal_21_ScanOffsetSize12  )

Definition at line 901 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [19/45]

BOOST_AUTO_TEST_CASE ( DiscontigTwoSubjects  )

◆ BOOST_AUTO_TEST_CASE() [20/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize11  )

Definition at line 875 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [21/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize12  )

Definition at line 876 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [22/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize13  )

Definition at line 877 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [23/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize15  )

Definition at line 878 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [24/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize20  )

Definition at line 879 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [25/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize25  )

Definition at line 880 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [26/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize28  )

Definition at line 881 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [27/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize33  )

Definition at line 882 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [28/45]

BOOST_AUTO_TEST_CASE ( LargeScanOffsetSize37  )

Definition at line 883 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [29/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize10  )

Definition at line 867 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [30/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize11  )

Definition at line 868 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [31/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize12  )

Definition at line 869 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [32/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize13  )

Definition at line 870 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [33/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize14  )

Definition at line 871 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [34/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize15  )

Definition at line 872 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [35/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize20  )

Definition at line 873 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [36/45]

BOOST_AUTO_TEST_CASE ( MediumScanOffsetSize9  )

Definition at line 866 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [37/45]

BOOST_AUTO_TEST_CASE ( SmallScanOffsetSize10  )

Definition at line 864 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [38/45]

BOOST_AUTO_TEST_CASE ( SmallScanOffsetSize6  )

Definition at line 860 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [39/45]

BOOST_AUTO_TEST_CASE ( SmallScanOffsetSize7  )

Definition at line 861 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [40/45]

BOOST_AUTO_TEST_CASE ( SmallScanOffsetSize8  )

Definition at line 862 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [41/45]

BOOST_AUTO_TEST_CASE ( SmallScanOffsetSize9  )

Definition at line 863 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [42/45]

BOOST_AUTO_TEST_CASE ( TinyScanOffsetSize4  )

Definition at line 855 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [43/45]

BOOST_AUTO_TEST_CASE ( TinyScanOffsetSize5  )

Definition at line 856 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [44/45]

BOOST_AUTO_TEST_CASE ( TinyScanOffsetSize6  )

Definition at line 857 of file ntscan_unit_test.cpp.

◆ BOOST_AUTO_TEST_CASE() [45/45]

BOOST_AUTO_TEST_CASE ( TinyScanOffsetSize7  )

Definition at line 858 of file ntscan_unit_test.cpp.

Variable Documentation

◆ template_11_16

Uint1 template_11_16[] = {1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1}
static

Definition at line 70 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_11_16_opt

Uint1 template_11_16_opt[] = {1,1,1,0,0,1,0,1,1,0,1,1,0,1,1,1}
static

Definition at line 73 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_11_18

Uint1 template_11_18[] = {1,0,1,1,0,1,1,0,0,1,0,1,1,0,1,1,0,1}
static

Definition at line 71 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_11_18_opt

Uint1 template_11_18_opt[] = {1,1,1,0,1,0,0,1,0,1,1,0,0,1,0,1,1,1}
static

Definition at line 74 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_11_21

Uint1 template_11_21[] = {1,0,0,1,0,1,1,0,0,1,0,1,1,0,0,1,0,1,1,0,1}
static

Definition at line 72 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_11_21_opt

Uint1 template_11_21_opt[] = {1,1,1,0,1,0,0,1,0,1,0,0,0,1,0,0,1,0,1,1,1}
static

Definition at line 75 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_12_16

Uint1 template_12_16[] = {1,1,1,1,1,0,1,1,0,1,1,0,1,1,0,1}
static

Definition at line 77 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_12_16_opt

Uint1 template_12_16_opt[] = {1,1,1,0,1,1,0,1,1,0,1,1,0,1,1,1}
static

Definition at line 80 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_12_18

Uint1 template_12_18[] = {1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1}
static

Definition at line 78 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_12_18_opt

Uint1 template_12_18_opt[] = {1,1,1,0,1,0,1,1,0,0,1,0,1,1,0,1,1,1}
static

Definition at line 81 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_12_21

Uint1 template_12_21[] = {1,0,0,1,0,1,1,0,1,1,0,1,1,0,0,1,0,1,1,0,1}
static

Definition at line 79 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

◆ template_12_21_opt

Uint1 template_12_21_opt[] = {1,1,1,0,1,0,0,1,0,1,1,0,0,1,0,0,1,0,1,1,1}
static

Definition at line 82 of file ntscan_unit_test.cpp.

Referenced by TestFixture::ScanCheckHitsCore().

Modified on Sun Mar 03 03:09:53 2024 by modify_doxy.py rev. 669887