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.

Go to the SVN repository for this file.

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();                                                 \
}

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

)

Definition at line 797 of file ntscan_unit_test.cpp.

References eMBLookupTable, eMBWordTwoTemplates, eNa_strand_both, GetOffsetArraySize(), i, kWordSize, NULL, BlastMBLookupTable::template_length, and TRUE.

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().