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

;

unique_ptr<SSeqLoc> ssl

BOOST_REQUIRE_EQUAL(0, status);

query_sequence.

- 2);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(query_blk->

[0] != 0);

BOOST_REQUIRE(query_blk->

[query_blk->

- 1] != 0);

subject_id(

);

unique_ptr<SSeqLoc> subject_ssl

BOOST_REQUIRE_EQUAL(0, status);

subj_sequence.

- 2);

BOOST_REQUIRE_EQUAL(0, status);

full_range.

= 0;

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(subject_blk !=

);

BOOST_REQUIRE(subject_blk->

[0] != 0);

BOOST_REQUIRE(subject_blk->

[subject_blk->

- 1] != 0);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(sbp !=

);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(offset_pairs !=

);

(offset_pairs);

query_length = query_blk->length;

subject_length = subject_blk->length;

BOOST_REQUIRE(scansub !=

);

scan_range[2] = subject_blk->length - lut->

;

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

BOOST_REQUIRE(offset_pairs[0].qs_offsets.s_off > s_off);

(

= 1;

< hits;

++)

BOOST_REQUIRE(offset_pairs[

].qs_offsets.q_off <

(

)(query_length-2));

BOOST_REQUIRE(offset_pairs[

].qs_offsets.s_off <

(

)(subject_length-2));

(offset_pairs[

].qs_offsets.s_off ==

offset_pairs[

-1].qs_offsets.s_off)

BOOST_REQUIRE(offset_pairs[

].qs_offsets.q_off >

offset_pairs[

-1].qs_offsets.q_off);

BOOST_REQUIRE(offset_pairs[

].qs_offsets.s_off >

offset_pairs[

-1].qs_offsets.s_off);

s_off = offset_pairs[hits-1].qs_offsets.s_off;

BOOST_REQUIRE((

)s_off < scan_range[1]);

hits, found_hits, expected_hits;

found_hits = expected_hits = 0;

BOOST_REQUIRE(scansub !=

);

scan_range[2] = subject_blk->length - lut->

;

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

expected_hits += hits;

scan_range[2] = subject_blk->length - lut->

;

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

BOOST_REQUIRE(hits <= new_max_size);

BOOST_REQUIRE_EQUAL(found_hits, expected_hits);

subject_length = subject_blk->length;

found_hits, expected_hits;

found_hits = expected_hits = 0;

BOOST_REQUIRE(scansub !=

);

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

kNumRanges = (

(ranges2scan)/

(*ranges2scan));

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

(

= 0;

< hits;

++) {

s_off = offset_pairs[

].qs_offsets.s_off;

hit_found =

;

(

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

( s_off >= (

)ranges2scan[j].left &&

s_off < (

)ranges2scan[j].right ) {

BOOST_REQUIRE( hit_found );

query_length = query_blk->length;

subject_length = subject_blk->length;

found_hits, expected_hits;

found_hits = expected_hits = 0;

BOOST_REQUIRE(scansub !=

);

scan_range[2] = subject_blk->length - lut->

;

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

(

= 0;

< hits;

++)

*qres = query_blk->sequence + offset_pairs[

].qs_offsets.q_off;

subject_blk->sequence + offset_pairs[

].qs_offsets.s_off;

score = sbp->matrix->data[qres[0]][sres[0]] +

sbp->matrix->data[qres[1]][sres[1]] +

sbp->matrix->data[qres[2]][sres[2]];

exact = (sres[0] == qres[0]) &&

(sres[1] == qres[1]) &&

(sres[2] == qres[2]);

(

= 0;

< (query_length - 2);

++)

*w = query_blk->sequence;

*s = subject_blk->sequence;

*p0 = sbp->matrix->data[w[

]];

*p1 = sbp->matrix->data[w[

+1]];

*p2 = sbp->matrix->data[w[

+2]];

(

j = 0; j < (subject_length - 2); j++)

score = p0[s[j]] + p1[s[j+1]] + p2[s[j+2]];

different = (w[

] ^ s[j]) |

(w[

+1] ^ s[j+1]) |

BOOST_REQUIRE_EQUAL(found_hits, expected_hits);

unique_ptr<SSeqLoc> ssl

BOOST_REQUIRE_EQUAL(0, status);

query_sequence.

- 2);

BOOST_REQUIRE_EQUAL(0, status);

subject_id(

);

unique_ptr<SSeqLoc> subject_ssl

BOOST_REQUIRE_EQUAL(0, status);

subj_sequence.

- 2);

BOOST_REQUIRE_EQUAL(0, status);

full_range.

= 0;

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(sbp !=

);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE_EQUAL(0, status);

BOOST_REQUIRE(offset_pairs !=

);

(offset_pairs);

query_length = query_blk->length;

subject_length = subject_blk->length;

BOOST_REQUIRE(scansub !=

);

scan_range[2] = subject_blk->length - lut->

;

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

BOOST_REQUIRE(offset_pairs[0].qs_offsets.s_off > s_off);

(

= 1;

< hits;

++)

BOOST_REQUIRE(offset_pairs[

].qs_offsets.q_off <

(

)(query_length-2));

BOOST_REQUIRE(offset_pairs[

].qs_offsets.s_off <

(

)(subject_length-2));

(offset_pairs[

].qs_offsets.s_off ==

offset_pairs[

-1].qs_offsets.s_off)

BOOST_REQUIRE(offset_pairs[

].qs_offsets.q_off >

offset_pairs[

-1].qs_offsets.q_off);

BOOST_REQUIRE(offset_pairs[

].qs_offsets.s_off >

offset_pairs[

-1].qs_offsets.s_off);

s_off = offset_pairs[hits-1].qs_offsets.s_off;

BOOST_REQUIRE((

)s_off < scan_range[1]);

query_length = query_blk->length;

subject_length = subject_blk->length;

BOOST_REQUIRE(scansub !=

);

scan_range[2] = subject_blk->length - lut->

;

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr, subject_blk, offset_pairs,

(lookup_wrap_ptr), scan_range);

BOOST_REQUIRE_EQUAL(found_hits, 2098);

subject_length = subject_blk->length;

found_hits, expected_hits;

found_hits = expected_hits = 0;

BOOST_REQUIRE(scansub !=

);

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

kNumRanges = (

(ranges2scan)/

(*ranges2scan));

(scan_range[1] < scan_range[2])

hits = scansub(lookup_wrap_ptr,

(

= 0;

< hits;

++) {

s_off = offset_pairs[

].qs_offsets.s_off;

hit_found =

;

(

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

( s_off >= (

)ranges2scan[j].left &&

s_off < (

)ranges2scan[j].right ) {

BOOST_REQUIRE( hit_found );

int compare_offsets(const void *x, const void *y)

BOOST_AUTO_TEST_CASE(ScanOffsetTest)

Declares the CBl2Seq (BLAST 2 Sequences) class.

Routines for creating protein BLAST lookup tables.

Routines for creating protein BLAST lookup tables.

void BlastChooseProteinScanSubject(LookupTableWrap *lookup_wrap)

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

Int4(* TAaScanSubjectFunction)(const LookupTableWrap *lookup_wrap, const BLAST_SequenceBlk *subject, BlastOffsetPair *offset_pairs, Int4 max_hits, Int4 *s_range)

Generic prototype for nucleotide subject scanning routines.

union BlastOffsetPair BlastOffsetPair

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

#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 ...

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.

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

#define BLAST_GAP_OPEN_PROT

Protein gap costs are the defaults for the BLOSUM62 scoring matrix.

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.

#define BLAST_GAP_EXTN_PROT

cost to extend a gap.

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.

#define BLAST_WORD_THRESHOLD_BLASTP

neighboring word score thresholds; a threshold of zero means that only query and subject words that m...

@ eAaLookupTable

standard protein (blastp) lookup table

@ eCompressedAaLookupTable

compressed alphabet (blastp) lookup table

BlastScoringOptions * BlastScoringOptionsFree(BlastScoringOptions *options)

Deallocate memory for BlastScoringOptions.

LookupTableOptions * LookupTableOptionsFree(LookupTableOptions *options)

Deallocates memory for LookupTableOptions*.

Utilities initialize/setup BLAST.

Int2 Blast_ScoreBlkMatrixInit(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, BlastScoreBlk *sbp, GET_MATRIX_PATH get_path)

Initializes the substitution matrix in the BlastScoreBlk according to the scoring options specified.

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

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

BlastScoreBlk * BlastScoreBlkNew(Uint1 alphabet, Int4 number_of_contexts)

Allocates and initializes BlastScoreBlk.

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 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!)

#define BLASTAA_SEQ_CODE

== Seq_code_ncbistdaa

TAutoUint1Ptr data

Sequence data.

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

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.

@ eBlastEncodingProtein

NCBIstdaa.

@ eNoSentinels

Do not use sentinel bytes.

element_type * release(void)

Release will release ownership of pointer to caller.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

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.

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.

The test fixture to use for all test cases in this file.

LookupTableWrap * lookup_wrap_ptr

BlastScoringOptions * score_options

BLAST_SequenceBlk * subject_blk

BlastOffsetPair * offset_pairs

BLAST_SequenceBlk * query_blk

LookupTableOptions * lookup_options

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).

The basic lookup table structure for blastp searches.

void * scansub_callback

function for scanning subject sequences

Int4 word_length

Length in letters of the full word match required to trigger extension.

The lookup table structure for protein searches using a compressed alphabet.

void * scansub_callback

function for scanning subject sequences

Int4 word_length

Length in letters of the full word match required to trigger extension.

Structure used for scoring calculations.

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.

BlastScoringOptions * score_options

LookupTableOptions * lookup_options

BLAST_SequenceBlk * subject_blk

CompressedAascanTestFixture()

~CompressedAascanTestFixture()

BLAST_SequenceBlk * query_blk

BlastOffsetPair * offset_pairs

LookupTableWrap * lookup_wrap_ptr

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

Wrapper structure for different types of BLAST lookup tables.

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.

Int4 left

left endpoint of range (zero based)

Int4 right

right endpoint of range (zero based)

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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