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

;

BOOST_REQUIRE(status == 0);

BOOST_REQUIRE(status == 0);

BOOST_REQUIRE(status == 0);

BOOST_REQUIRE(query_blk.

() !=

);

BOOST_REQUIRE(query_blk->

[0] != kNullByte);

BOOST_REQUIRE(query_blk->

[query_blk->

- 1] != kNullByte);

runtime_error(errors->

);

Int2 BlastScoringOptionsNew(EBlastProgramType program, BlastScoringOptions **options)

Allocate memory for BlastScoringOptions and fill with default values.

EBlastProgramType

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

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.

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.

Wrapper class for BLAST_SequenceBlk .

Wrapper class for BlastQueryInfo .

Wrapper class for BlastScoringOptions .

BLAST_SequenceBlk * Get() const

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...

@ eBlastEncodingProtein

NCBIstdaa.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

static const int kScaleFactor

BlastQueryInfo * CreateProtQueryInfo(unsigned int query_size)

Creates and initializes a BlastQueryInfo structure for a single protein sequence.

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

#define FALSE

bool replacment for C indicating false.

BlastScoreBlk * InitializeBlastScoreBlk(const unsigned char *query, Uint4 query_size)

Utilities to develop and debug unit tests that deal with PSSM computation.

Uint1 * sequence_start

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

Boolean sequence_allocated

TRUE if memory has been allocated for sequence.

Int4 length

Length of sequence.

Uint1 * sequence

Sequence used for search (could be translation).

Boolean sequence_start_allocated

TRUE if memory has been allocated for sequence_start.

Structure used for scoring calculations.

Blast_KarlinBlk * kbp_ideal

Ideal values (for query with average database composition).

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

char * message

User message to be saved.

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

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