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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/ntscan_unit_test.cpp Source File

;

[] = {1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1};

[] = {1,0,1,1,0,1,1,0,0,1,0,1,1,0,1,1,0,1};

[] = {1,0,0,1,0,1,1,0,0,1,0,1,1,0,0,1,0,1,1,0,1};

[] = {1,1,1,0,0,1,0,1,1,0,1,1,0,1,1,1};

[] = {1,1,1,0,1,0,0,1,0,1,1,0,0,1,0,1,1,1};

[] = {1,1,1,0,1,0,0,1,0,1,0,0,0,1,0,0,1,0,1,1,1};

[] = {1,1,1,1,1,0,1,1,0,1,1,0,1,1,0,1};

[] = {1,0,1,1,0,1,1,0,1,1,0,1,1,0,1,1,0,1};

[] = {1,0,0,1,0,1,1,0,1,1,0,1,1,0,0,1,0,1,1,0,1};

[] = {1,1,1,0,1,1,0,1,1,0,1,1,0,1,1,1};

[] = {1,1,1,0,1,0,1,1,0,0,1,0,1,1,0,1,1,1};

[] = {1,1,1,0,1,0,0,1,0,1,1,0,0,1,0,0,1,0,1,1,1};

lookup_segments =

;

lookup_wrap_ptr =

;

offset_pairs =

;

word_options =

;

hitsaving_options =

;

sprintf(

,

, query_gi);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(query_blk->

> 0);

BOOST_REQUIRE(query_blk !=

);

kStrandLength = (query_blk->

- 1)/2;

sprintf(

,

, subject_gi);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(subject_blk !=

);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(subject_blk->

> 0);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(query_blk !=

);

kScalingFactor = 1.0;

program_number, &sbp, kScalingFactor,

&blast_message,

);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(blast_message ==

);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(query_options ==

);

BOOST_REQUIRE(offset_pairs !=

);

BOOST_REQUIRE(lookup_options ==

);

BOOST_REQUIRE(score_options ==

);

SetUpLookupTable(mb_lookup, disco_type, disco_size, word_size);

(offset_pairs);

(hitsaving_options)

TearDownLookupTable();

lookup_wrap_ptr->

;

lookup_wrap_ptr->

;

BOOST_REQUIRE(callback !=

);

callback(lookup_wrap_ptr, subject_blk,

offset_pairs, max_hits, scan_range);

query_bases, subject_bases;

bases_per_lut_word;

last_s_off = 0;

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(subject_blk !=

);

BOOST_REQUIRE(lookup_wrap_ptr !=

);

BOOST_REQUIRE(offset_pairs !=

);

BOOST_REQUIRE(lookup_segments !=

);

subject_bases = subject_blk->

;

query_bases = query_blk->

;

scan_range[1] = subject_bases - bases_per_lut_word;

scan_range[1] = subject_bases - bases_per_lut_word;

(scan_range[0] <= scan_range[1])

hits = RunScanSubject(scan_range,

BOOST_REQUIRE(offset_pairs[0].qs_offsets.

> last_s_off);

(

= 1;

< hits;

++)

BOOST_REQUIRE(offset_pairs[

].qs_offsets.

<=

(

)(query_bases - bases_per_lut_word) &&

BOOST_REQUIRE(offset_pairs[

].qs_offsets.

<

(

)subject_bases);

(offset_pairs[

].qs_offsets.

==

BOOST_REQUIRE(offset_pairs[

].qs_offsets.

<

BOOST_REQUIRE(offset_pairs[

].qs_offsets.

>

BOOST_REQUIRE(offset_pairs[

].qs_offsets.

>

hits, found_hits, expected_hits;

found_hits = expected_hits = 0;

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(subject_blk !=

);

BOOST_REQUIRE(lookup_wrap_ptr !=

);

BOOST_REQUIRE(offset_pairs !=

);

BOOST_REQUIRE(lookup_segments !=

);

subject_bases = subject_blk->

;

(scan_range[0] <= scan_range[1])

hits = RunScanSubject(scan_range,

expected_hits += hits;

(scan_range[0] <= scan_range[1])

hits = RunScanSubject(scan_range,

BOOST_REQUIRE(hits <= new_max_size);

BOOST_REQUIRE_EQUAL(found_hits, expected_hits);

hits, found_hits, expected_hits;

bases_per_lut_word;

found_hits = expected_hits = 0;

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(subject_blk !=

);

BOOST_REQUIRE(lookup_wrap_ptr !=

);

BOOST_REQUIRE(offset_pairs !=

);

BOOST_REQUIRE(lookup_segments !=

);

subject_bases = subject_blk->

;

scan_range[1] = subject_bases - bases_per_lut_word;

scan_range[1] = subject_bases - bases_per_lut_word;

(scan_range[0] <= scan_range[1])

hits = RunScanSubject(scan_range,

(

= 0;

< hits;

++)

query_word = 0;

query_word2 = 0;

subject_word = 0;

subject_word2 = 0;

s_index, s_byte;

template_size = 0;

(j = 0; j < template_size; j++, s_index++) {

(disco_template[j] == 1) {

query_word = (query_word << 2) | q[j];

s_byte = subject_blk->

[ s_index /

subject_word = (subject_word << 2) |

(j = 0; j < template_size; j++, s_index++) {

(disco_template2[j] == 1) {

query_word2 = (query_word2 << 2) | q[j];

s_byte = subject_blk->

[ s_index /

subject_word2 = (subject_word2 << 2) |

(j = 0; j < bases_per_lut_word; j++, s_index++) {

query_word = (query_word << 2) | q[j];

s_byte = subject_blk->

[ s_index /

subject_word = (subject_word << 2) |

BOOST_REQUIRE(query_word == subject_word ||

query_word2 == subject_word2);

BOOST_REQUIRE_EQUAL(query_word, subject_word);

subject_bases = subject_blk->

;

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(subject_blk !=

);

BOOST_REQUIRE(lookup_wrap_ptr !=

);

BOOST_REQUIRE(offset_pairs !=

);

BOOST_REQUIRE(lookup_segments !=

);

ranges2scan[] = { {0, 501}, {700, 1001} , {subject_bases, subject_bases}};

kNumRanges = (

(ranges2scan)/

(*ranges2scan));

sbp, query_info, subject_bases,

BOOST_REQUIRE_EQUAL(0, retval);

hit_params, lookup_wrap_ptr,

sbp, query_info, subject_bases,

BOOST_REQUIRE_EQUAL(0, retval);

BOOST_REQUIRE_EQUAL(0, retval);

word_params, ewp, offset_pairs,

init_hitlist, &ungapped_stats);

BOOST_REQUIRE_EQUAL(0, retval);

(

= 0;

< init_hitlist->

;

++) {

hit_found =

;

(

j = 0; j < kNumRanges; j++) {

( s_off >= (

)ranges2scan[j].left &&

s_off < (

)ranges2scan[j].right ) {

BOOST_REQUIRE( hit_found );

BOOST_REQUIRE(hit_params ==

);

BOOST_REQUIRE(word_params ==

);

BOOST_REQUIRE(ewp ==

);

BOOST_REQUIRE(init_hitlist ==

);

kTemplateSize = 21;

SetUpSubject(313959);

subject_bases = subject_blk->length;

(scan_range[0] <= scan_range[1])

hits = RunScanSubject(scan_range,

SetUpSubject(271065);

subject_bases = subject_blk->length;

(scan_range[0] <= scan_range[1])

hits = RunScanSubject(scan_range,

(

= 0;

< hits;

++) {

BOOST_REQUIRE(offset_pairs[

].qs_offsets.s_off <

(

)subject_bases);

Declares the CBl2Seq (BLAST 2 Sequences) class.

union BlastOffsetPair BlastOffsetPair

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...

#define COMPRESSION_RATIO

Compression ratio of nucleotide bases (4 bases in 1 byte)

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

BlastInitHitList * BLAST_InitHitListNew(void)

Allocate memory for the BlastInitHitList structure.

Blast_ExtendWord * BlastExtendWordFree(Blast_ExtendWord *ewp)

Deallocate memory for the word extension structure.

BlastInitHitList * BLAST_InitHitListFree(BlastInitHitList *init_hitlist)

Free memory for the BlastInitList structure.

Int2 BlastExtendWordNew(Uint4 query_length, const BlastInitialWordParameters *word_params, Blast_ExtendWord **ewp_ptr)

Initializes the word extension structure.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

BlastSeqLoc * BlastSeqLocNew(BlastSeqLoc **head, Int4 from, Int4 to)

Create and initialize a new sequence interval.

Blast_Message * Blast_MessageFree(Blast_Message *blast_msg)

Deallocates message memory.

Routines for creating nucleotide BLAST lookup tables.

EDiscWordType

General types of discontiguous word templates.

@ eDiscTemplate_12_18_Optimal

@ eDiscTemplate_11_18_Optimal

@ eDiscTemplate_12_16_Optimal

@ eDiscTemplate_12_16_Coding

@ eDiscTemplate_11_21_Coding

@ eDiscTemplate_11_18_Coding

@ eDiscTemplate_12_21_Coding

@ eDiscTemplate_11_16_Optimal

@ eDiscTemplate_11_21_Optimal

@ eDiscTemplate_12_21_Optimal

@ eDiscTemplate_12_18_Coding

@ eDiscTemplate_11_16_Coding

Routines for scanning nucleotide BLAST lookup tables.

Int4(* TNaScanSubjectFunction)(const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 max_hits, Int4 *scan_range)

Generic prototype for nucleotide subject scanning routines.

void BlastChooseNucleotideScanSubject(LookupTableWrap *lookup_wrap)

Choose the most appropriate function to scan through nucleotide subject sequences.

Definitions which are dependant on the NCBI C++ Object Manager.

BlastHitSavingOptions * BlastHitSavingOptionsFree(BlastHitSavingOptions *options)

Deallocate memory for BlastHitSavingOptions.

Int2 BlastQuerySetUpOptionsNew(QuerySetUpOptions **options)

Allocate memory for QuerySetUpOptions and fill with default values.

#define BLAST_GAP_OPEN_NUCL

default gap open penalty (blastn)

Int2 BLAST_FillScoringOptions(BlastScoringOptions *options, EBlastProgramType program, Boolean greedy_extension, Int4 penalty, Int4 reward, const char *matrix, Int4 gap_open, Int4 gap_extend)

Fill non-default values in the BlastScoringOptions structure.

BlastInitialWordOptions * BlastInitialWordOptionsFree(BlastInitialWordOptions *options)

Deallocate memory for BlastInitialWordOptions.

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

Int2 BLAST_FillLookupTableOptions(LookupTableOptions *options, EBlastProgramType program, Boolean is_megablast, double threshold, Int4 word_size)

Allocate memory for lookup table options and fill with default values.

Int2 LookupTableOptionsNew(EBlastProgramType program, LookupTableOptions **options)

Allocate memory for lookup table options and fill with default values.

BlastExtensionOptions * BlastExtensionOptionsFree(BlastExtensionOptions *options)

Deallocate memory for BlastExtensionOptions.

Int2 BlastHitSavingOptionsNew(EBlastProgramType program, BlastHitSavingOptions **options, Boolean gapped_calculation)

Allocate memory for BlastHitSavingOptions.

#define BLAST_GAP_EXTN_NUCL

default gap open penalty (blastn)

Int2 BlastInitialWordOptionsNew(EBlastProgramType program, BlastInitialWordOptions **options)

Allocate memory for BlastInitialWordOptions and fill with default values.

@ eSmallNaLookupTable

lookup table for blastn with small query

@ eMBLookupTable

megablast lookup table (includes both contiguous and discontiguous megablast)

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

LookupTableOptions * LookupTableOptionsFree(LookupTableOptions *options)

Deallocates memory for LookupTableOptions*.

QuerySetUpOptions * BlastQuerySetUpOptionsFree(QuerySetUpOptions *options)

Deallocate memory for QuerySetUpOptions.

Int2 BlastExtensionOptionsNew(EBlastProgramType program, BlastExtensionOptions **options, Boolean gapped)

Allocate memory for BlastExtensionOptions and fill with default values.

BlastHitSavingParameters * BlastHitSavingParametersFree(BlastHitSavingParameters *parameters)

Deallocate memory for BlastHitSavingOptions*.

BlastInitialWordParameters * BlastInitialWordParametersFree(BlastInitialWordParameters *parameters)

Deallocate memory for BlastInitialWordParameters.

Int2 BlastInitialWordParametersNew(EBlastProgramType program_number, const BlastInitialWordOptions *word_options, const BlastHitSavingParameters *hit_params, const LookupTableWrap *lookup_wrap, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Uint4 subject_length, BlastInitialWordParameters **parameters)

Allocate memory for BlastInitialWordParameters and set x_dropoff.

Int2 BlastHitSavingParametersNew(EBlastProgramType program_number, const BlastHitSavingOptions *options, const BlastScoreBlk *sbp, const BlastQueryInfo *query_info, Int4 avg_subject_length, Int4 compositionBasedStats, BlastHitSavingParameters **parameters)

Allocate memory and initialize the BlastHitSavingParameters structure.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

BlastQueryInfo * BlastQueryInfoFree(BlastQueryInfo *query_info)

Deallocate memory for query information structure.

BlastQueryInfo * BlastQueryInfoNew(EBlastProgramType program, int num_queries)

Allocate memory for query information structure.

Utilities initialize/setup BLAST.

Int2 BlastSetup_ScoreBlkInit(BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, const BlastScoringOptions *scoring_options, EBlastProgramType program_number, BlastScoreBlk **sbpp, double scale_factor, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

Initializes the score block structure.

Definitions and prototypes used by blast_stat.c to calculate BLAST statistics.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

BLAST_SequenceBlk * BlastSequenceBlkFree(BLAST_SequenceBlk *seq_blk)

Deallocate memory for a sequence block.

Int2 BlastSeqBlkSetSeqRanges(BLAST_SequenceBlk *seq_blk, SSeqRange *seq_ranges, Uint4 num_seq_ranges, Boolean copy_seq_ranges, ESubjectMaskingType mask_type)

Sets the seq_range and related fields appropriately in the BLAST_SequenceBlk structure.

Int2 BlastSeqBlkSetSequence(BLAST_SequenceBlk *seq_blk, const Uint1 *sequence, Int4 seqlen)

Stores the sequence in the sequence block structure.

Int2 BlastSeqBlkSetCompressedSequence(BLAST_SequenceBlk *seq_blk, const Uint1 *sequence)

Stores the compressed nucleotide sequence in the sequence block structure for the subject sequence wh...

Int2 BlastSeqBlkNew(BLAST_SequenceBlk **retval)

Allocates a new sequence block structure.

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

static CTestObjMgr & Instance()

TSeqPos length

Length of the buffer above (not necessarily sequence length!)

TAutoUint1Ptr data

Sequence data.

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

@ eBlastEncodingNucleotide

Special encoding for preliminary stage of BLAST: permutation of NCBI4na.

@ eBlastEncodingNcbi2na

NCBI2na.

@ eNoSentinels

Do not use sentinel bytes.

@ eSentinels

Use sentinel bytes.

element_type * release(void)

Release will release ownership of pointer to caller.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

ENa_strand

strand of nucleic acid

@ eNa_strand_both

in forward orientation

if(yy_accept[yy_current_state])

Utility functions for lookup table generation.

Int4 GetOffsetArraySize(LookupTableWrap *lookup)

Determine the size of the offsets arrays to be filled by the ScanSubject function.

LookupTableWrap * LookupTableWrapFree(LookupTableWrap *lookup)

Deallocate memory for the lookup table.

Int2 LookupTableWrapInit(BLAST_SequenceBlk *query, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, BlastSeqLoc *lookup_segments, BlastScoreBlk *sbp, LookupTableWrap **lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message **error_msg, BlastSeqSrc *seqsrc)

Create the lookup table for all query words.

Nucleotide ungapped extension code.

void BlastChooseNaExtend(LookupTableWrap *lookup_wrap)

Choose the best routine to use for creating ungapped alignments.

Int2 BlastNaWordFinder(BLAST_SequenceBlk *subject, BLAST_SequenceBlk *query, BlastQueryInfo *query_info, LookupTableWrap *lookup_wrap, Int4 **matrix, const BlastInitialWordParameters *word_params, Blast_ExtendWord *ewp, BlastOffsetPair *offset_pairs, Int4 max_hits, BlastInitHitList *init_hitlist, BlastUngappedStats *ungapped_stats)

Find all words for a given subject sequence and perform ungapped extensions, assuming ordinary blastn...

Magic spell ;-) needed for some weird compilers... very empiric.

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

#define MAX(a, b)

returns larger of a and b.

Defines: CTimeFormat - storage class for time format.

static const char * kWordSize

static Uint1 template_12_16[]

static Uint1 template_12_16_opt[]

static Uint1 template_11_21_opt[]

#define NULL_NUCL_SENTINEL

static Uint1 template_11_18_opt[]

static Uint1 template_11_18[]

static Uint1 template_11_16[]

#define DECLARE_TEST(name, gi, d_size, d_type, wordsize)

static Uint1 template_12_18[]

static Uint1 template_11_21[]

static Uint1 template_12_21[]

static Uint1 template_12_21_opt[]

BOOST_AUTO_TEST_CASE(DiscontigTwoSubjects)

static Uint1 template_12_18_opt[]

static Uint1 template_11_16_opt[]

Structure to hold a sequence.

Uint1 * sequence_start

Start of sequence, usually one byte before sequence as that byte is a NULL sentinel byte.

Uint4 num_seq_ranges

Number of elements in seq_ranges.

Int4 length

Length of sequence.

Uint1 * sequence

Sequence used for search (could be translation).

Int4 query_length

Length of this query, strand or frame.

Boolean is_valid

Determine if this context is valid or not.

Int4 query_offset

Offset of this query, strand or frame in the concatenated super-query.

Options used for gapped extension These include: a.

Options used when evaluating and saving hits These include: a.

Parameter block that contains a pointer to BlastHitSavingOptions and the values derived from it.

Structure to hold the initial HSP information.

BlastOffsetPair offsets

Offsets in query and subject, or, in PHI BLAST, start and end of pattern in subject.

Structure to hold all initial HSPs for a given subject sequence.

Int4 total

Total number of hits currently saved.

BlastInitHSP * init_hsp_array

Array of offset pairs, possibly with scores.

Options needed for initial word finding and processing.

Parameter block that contains a pointer to BlastInitialWordOptions and the values derived from it.

The lookup table structure used for Mega BLAST.

Int4 lut_word_length

number of letters in a lookup table word

void * scansub_callback

function for scanning subject sequences

EDiscTemplateType template_type

Type of the discontiguous word template.

Int4 longest_chain

Largest number of query positions for a given word.

Boolean discontiguous

Are discontiguous words used?

Int4 template_length

Length of the discontiguous word template.

The query related information.

BlastContextInfo * contexts

Information per context.

Structure used for scoring calculations.

SBlastScoreMatrix * matrix

scoring matrix data

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Used to hold a set of positions, mostly used for filtering.

Lookup table structure for blastn searches with small queries.

void * scansub_callback

function for scanning subject sequences

Int4 longest_chain

length of the longest chain on the backbone

Int4 lut_word_length

Length in bases of a word indexed by the lookup table.

Structure containing hit counts from the ungapped stage of a BLAST search.

Structure for keeping initial word extension information.

Structure to hold the a message from the core of the BLAST engine.

Options needed to construct a lookup table Also needed: query sequence and query length.

Int4 mb_template_type

Type of a discontiguous word template.

Int4 mb_template_length

Length of the discontiguous words.

Wrapper structure for different types of BLAST lookup tables.

void * lut

Pointer to the actual lookup table structure.

ELookupTableType lut_type

What kind of a lookup table it is?

Options required for setting up the query sequence.

int ** data

actual scoring matrix data, stored in row-major form

Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array ...

A structure containing two integers, used e.g.

void SkipMaskedRangesCore(void)

BlastQueryInfo * query_info

BlastHitSavingOptions * hitsaving_options

BlastInitialWordOptions * word_options

BlastSeqLoc * lookup_segments

void ScanOffsetTestCore(EDiscWordType disco_type)

LookupTableWrap * lookup_wrap_ptr

BLAST_SequenceBlk * query_blk

void SetUpLookupTable(Boolean mb_lookup, EDiscWordType disco_type, Int4 disco_size, Int4 word_size)

void SetUpQuerySubjectAndLUT(Boolean mb_lookup, Int4 gi, EDiscWordType disco_type, Int4 disco_size, Int4 word_size)

void SetUpSubject(Uint4 subject_gi)

void ScanMaxHitsTestCore(void)

BlastOffsetPair * offset_pairs

void ScanCheckHitsCore(EDiscWordType disco_type)

BLAST_SequenceBlk * subject_blk

void SetUpQuery(Uint4 query_gi, ENa_strand strand)

Int4 RunScanSubject(Int4 *scan_range, Int4 max_hits)

void TearDownLookupTable()

EBlastProgramType program_number

BlastExtensionOptions * ext_options

Utility stuff for more convenient using of Boost.Test library.

This symbol enables the verbose option in makeblastdb and other BLAST+ search command line applicatio...

Uint4 q_off

Query offset.

Uint4 s_off

Subject offset.

struct BlastOffsetPair::@6 qs_offsets

Query/subject offset pair.

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