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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/mockseqsrc2_unit_test.cpp Source File

36 #define BLAST_SECONDARY_SOURCE 1 44 using namespace

blast;

62  for

(

int i

= 0;

i

< 10;

i

++) {

70  for

(

int i

= 0;

i

< 10;

i

++) {

78  for

(

int i

= 0;

i

< 10;

i

++) {

86  for

(

int i

= 0;

i

< 10;

i

++) {

94  for

(

int i

= 0;

i

< 10;

i

++) {

97

BOOST_REQUIRE(

true

);

100  string

actual(

str

);

101

BOOST_REQUIRE_EQUAL(

expected

, actual);

108

BOOST_REQUIRE(rv ==

TRUE

|| rv ==

FALSE

);

112

BOOST_REQUIRE(rv == rv2);

118

memset((

void

*) &seq_arg, 0,

sizeof

(seq_arg));

121  bool

successful_return =

false

;

122  for

(

int i

= 0;

i

< 100;

i

++) {

127

successful_return =

true

;

132  if

(successful_return) {

133

BOOST_REQUIRE(seq_arg.

seq

);

147

memset((

void

*) &seq_arg, 0,

sizeof

(seq_arg));

150  for

(

int i

= 0;

i

< 10;

i

++) {

161

memset((

void

*) &seq_arg, 0,

sizeof

(seq_arg));

164  for

(

int i

= 0;

i

< 10;

i

++) {

193

BOOST_REQUIRE(rv ==

NULL

);

201

memset((

void

*) &seq_arg, 0,

sizeof

(seq_arg));

206

BOOST_REQUIRE(

true

);

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

#define BLAST_SEQSRC_ERROR

Error while retrieving sequence.

Int4 BlastSeqSrcIteratorNext(const BlastSeqSrc *seq_src, BlastSeqSrcIterator *itr)

Increments the BlastSeqSrcIterator.

Int4 BlastSeqSrcGetSeqLen(const BlastSeqSrc *seq_src, void *oid)

Retrieve sequence length (number of residues/bases)

Boolean BlastSeqSrcGetIsProt(const BlastSeqSrc *seq_src)

Find if the Blast Sequence Source contains protein or nucleotide sequences.

#define BLAST_SEQSRC_SUCCESS

Successful sequence retrieval.

void BlastSeqSrcReleaseSequence(const BlastSeqSrc *seq_src, BlastSeqSrcGetSeqArg *getseq_arg)

Deallocate individual sequence.

BlastSeqSrcIterator * BlastSeqSrcIteratorNew(void)

Allocate and initialize an iterator over a BlastSeqSrc with a default chunk size for MT-safe iteratio...

Int4 BlastSeqSrcGetAvgSeqLen(const BlastSeqSrc *seq_src)

Get the average length of all sequences in the sequence source.

char * BlastSeqSrcGetInitError(const BlastSeqSrc *seq_src)

Function to retrieve NULL terminated string containing the description of an initialization error or ...

Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc *seq_src)

Get the number of sequences contained in the sequence source.

Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc *seq_src)

Get the total length of all sequences in the sequence source.

Int4 BlastSeqSrcGetMaxSeqLen(const BlastSeqSrc *seq_src)

Get the length of the longest sequence in the sequence source.

const char * BlastSeqSrcGetName(const BlastSeqSrc *seq_src)

Get the Blast Sequence source name (e.g.

Int2 BlastSeqSrcGetSequence(const BlastSeqSrc *seq_src, BlastSeqSrcGetSeqArg *getseq_arg)

Retrieve an individual sequence.

#define BLAST_SEQSRC_EOF

No more sequences available.

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

Wrapper class for BlastSeqSrcIterator .

Wrapper class for BlastSeqSrc .

static const char * kDefaultString

static const Int4 kDefaultOid

static const Int8 kDefaultInt8

static const Int4 kDefaultInt4

static const char * expected[]

static const char * str(char *buf, int n)

void Reset(BlastSeqSrc *p=NULL)

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

BOOST_AUTO_TEST_CASE(TestNumberOfSeqs)

Uint1 Boolean

bool replacment for C

#define TRUE

bool replacment for C indicating true.

#define FALSE

bool replacment for C indicating false.

BlastSeqSrc * MockBlastSeqSrcInit(EMockBlastSeqSrcMode mode)

Mock BlastSeqSrc initialization function.

Mock object which implements the BlastSeqSrc interface for testing purposes.

@ eMBSS_RandomlyFail

returns failure randomly on operations

Int4 length

Length of sequence.

Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature,...

Int4 oid

Oid in BLAST database, index in an array of sequences, etc [in].

BLAST_SequenceBlk * seq

Sequence to return, if NULL, it should allocated by GetSeqBlkFnPtr (using BlastSeqBlkNew or BlastSetU...

Initializes m_SeqSrc with a BlastSeqSrc that fails randomly.

~RandomlyFailingMockSeqSrcTestFixture()

RandomlyFailingMockSeqSrcTestFixture()

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

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