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

;

lookup_segments=

;

lookup_options=

;

lookup_wrap_ptr=

;

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(query_blk->

[0] != kNullByte);

BOOST_REQUIRE(query_blk->

[query_blk->

- 1] != kNullByte);

sequence[

+1] = 0;

(

=0;

<

-1;

++) sequence[

-

+2+

] = sequence[

];

lookup_segments=

;

(

=0;

<

+2;

++) sequence[

] = 0;

lookup_segments=

;

(hasNeighbor)? 11: -1,

GetSeqBlk(

);

BOOST_REQUIRE_EQUAL(0,

->threshold);

BOOST_REQUIRE_EQUAL(0,

->neighbor_matches);

num_hits_found = 0,

;

(

=0;

<

->backbone_size;

++) {

BOOST_REQUIRE_EQUAL(230, num_hits_found);

(

=0;

<

->backbone_size;

++) {

BOOST_REQUIRE_EQUAL( num_used, 0 );

BOOST_REQUIRE_EQUAL( num_used, 1 );

FillLookupTable(

);

( (score >= 11) || ( (u==x) && (v==y) && (w==z) ) )

index = (u << 10) | (v << 5) | (w);

BOOST_REQUIRE_EQUAL(

, num_used);

BOOST_REQUIRE_EQUAL(num_used,

-2);

BOOST_REQUIRE_EQUAL(num_used,

-2);

sequence[

+1] = 0;

(

=0;

<

-1;

++)

sequence[

-

+2+

] = sequence[

];

(

=0;

<

;

++)

pssm_sbp->posMatrix[

][j] = sbp->

[j][sequence[

+1]];

lookup_segments_debruijn,

index = (

<< 10) | (j << 5) | (k);

lookup_segments=

;

lookup_options=

;

lookup_wrap_ptr=

;

BOOST_REQUIRE(query_blk !=

);

BOOST_REQUIRE(query_blk->

[0] != kNullByte);

BOOST_REQUIRE(query_blk->

[query_blk->

- 1] != kNullByte);

GetSeqBlk(

);

BOOST_REQUIRE_EQUAL(

->threshold, 2100);

BOOST_REQUIRE_EQUAL(

->word_length, 6);

BOOST_REQUIRE_EQUAL(

->compressed_alphabet_size, 15);

backbone_cell =

->backbone + 6189626;

BOOST_REQUIRE_EQUAL(backbone_cell->

, 2);

index[8] ={6189626,3308318, 6298163, 9877654, 4975326, 3450036, 6447263, 500762};

num_used[8] ={2, 1, 1, 0, 1, 2, 2, 0};

(

=0;

< 8;

++) {

backbone_cell =

->backbone + index[

];

BOOST_REQUIRE_EQUAL(backbone_cell->

, num_used[

]);

GetSeqBlk(

);

BOOST_REQUIRE_EQUAL(

->threshold, 2100);

BOOST_REQUIRE_EQUAL(

->word_length, 6);

BOOST_REQUIRE_EQUAL(

->compressed_alphabet_size, 15);

index[8] ={9958159, 8870278 , 44768, 3870741, 1960395 , 6981008 , 5035027, 166507 };

num_used[8] ={9, 8, 7, 5, 3, 2, 1 , 0};

(

=0;

< 8;

++) {

backbone_cell =

->backbone + index[

];

BOOST_REQUIRE_EQUAL(backbone_cell->

, num_used[

]);

BOOST_AUTO_TEST_CASE(BackboneIntegrityTest)

Declares the CBl2Seq (BLAST 2 Sequences) class.

Routines for creating protein BLAST lookup tables.

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.

@ 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.

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

Stores the sequence in the sequence block structure.

Int2 BlastSetUp_SeqBlkNew(const Uint1 *buffer, Int4 length, BLAST_SequenceBlk **seq_blk, Boolean buffer_allocated)

Allocates memory for *sequence_blk and then populates it.

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()

static int lookup(const char *name, const struct lookup_int *table)

TSeqPos length

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

#define BLASTAA_SIZE

Size of aminoacid alphabet.

#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.

Uint1 GetSentinelByte(EBlastEncoding encoding) THROWS((CBlastException))

Convenience function to centralize the knowledge of which sentinel bytes we use for supported encodin...

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

uint16_t Uint2

2-byte (16-bit) unsigned integer

Utility functions for lookup table generation.

Int4 iexp(Int4 x, Int4 n)

Integer exponentiation using right to left binary algorithm.

void debruijn(Int4 n, Int4 k, Uint1 *output, Uint1 *alphabet)

generates a de Bruijn sequence containing all substrings of length n over an alphabet of size k.

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.

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

Defines: CTimeFormat - storage class for time format.

structure defining one cell of the compacted lookup table

structure defining one cell of the small (i.e., use short) lookup table

A general lookup table for the test.

BlastSeqLoc * lookup_segments

LookupTableWrap * lookup_wrap_ptr

void GetSeqBlk(string gid)

LookupTableOptions * lookup_options

BLAST_SequenceBlk * query_blk

void FillLookupTable(bool hasNeighbor=false)

BlastAaLookupTable * lookup

Structure to hold a sequence.

Uint1 * sequence_start

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

Int4 length

Length of sequence.

Uint1 * sequence

Sequence used for search (could be translation).

The basic lookup table structure for blastp searches.

void * thick_backbone

may point to BackboneCell, SmallboneCell, or TinyboneCell.

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

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.

BlastSeqLoc * lookup_segments

CompressedAalookupTestFixture()

BlastCompressedAaLookupTable * lookup

BLAST_SequenceBlk * query_blk

LookupTableOptions * lookup_options

LookupTableWrap * lookup_wrap_ptr

~CompressedAalookupTestFixture()

void GetSeqBlk(const string &id)

structure for hashtable of indexed query offsets

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

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?

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 ...

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

voidp calloc(uInt items, uInt size)

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