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

:

);

pair<TSeqPos, TSeqPos> sequence_range(0,

);

objects::CSeq_id seqid(seqid_string);

unique_ptr<blast::SSeqLoc> sl

blast::SBlastSequence seq =

->GetSequence(arg);

ordinal_id = *(

*

(oid));

->GetSequenceLength(ordinal_id);

->GetNumSeqs();

->GetMaxSeqLen();

->GetAvgSeqLen();

->GetTotLen();

->GetSeqSrcName();

->GetIsProt();

->ReleaseSequence(arg);

->IteratorNext(itr);

ncbi::NStr::IntToString(

(

));

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

#define BLAST_SEQSRC_ERROR

Error while retrieving sequence.

BlastSeqSrc * BlastSeqSrcNew(const BlastSeqSrcNewInfo *bssn_info)

Allocates memory for a BlastSeqSrc structure and then invokes the constructor function defined in its...

#define BLAST_SEQSRC_SUCCESS

Successful sequence retrieval.

#define BLAST_SEQSRC_EOF

No more sequences available.

Definitions needed for implementing the BlastSeqSrc interface and low level details of the implementa...

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetReleaseSequence(BlastSeqSrc *var, ReleaseSeqBlkFnPtr arg)

NCBI_XBLAST_EXPORT void * _BlastSeqSrcImpl_GetDataStructure(const BlastSeqSrc *var)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetSequence(BlastSeqSrc *var, GetSeqBlkFnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetTotLen(BlastSeqSrc *var, GetInt8FnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetSeqLen(BlastSeqSrc *var, GetInt4FnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetIsProt(BlastSeqSrc *var, GetBoolFnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetDataStructure(BlastSeqSrc *var, void *arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetAvgSeqLen(BlastSeqSrc *var, GetInt4FnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetIterNext(BlastSeqSrc *var, AdvanceIteratorFnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetInitErrorStr(BlastSeqSrc *var, char *arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetDeleteFnPtr(BlastSeqSrc *var, BlastSeqSrcDestructor arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetName(BlastSeqSrc *var, GetStrFnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetMaxSeqLen(BlastSeqSrc *var, GetInt4FnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetNumSeqs(BlastSeqSrc *var, GetInt4FnPtr arg)

Various auxiliary BLAST utility functions.

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 BlastSeqBlkNew(BLAST_SequenceBlk **retval)

Allocates a new sequence block structure.

Mock BlastSeqSrc implementation which fails randomly.

virtual ~CRandomlyFailMockBlastSeqSrc()

Int4 GetSequenceLength(Int4 oid)

static const char * kDefaultString

CRandomlyFailMockBlastSeqSrc()

Boolean m_IsProtein

Determine whether this mock BlastSeqSrc contains protein or nucleotide sequences.

Int4 IteratorNext(BlastSeqSrcIterator *itr)

static const Int4 kDefaultOid

static const char * kNullString

const char * GetSeqSrcName()

T x_SelectRandomlyBetween(T success_value, T failure_value)

Auxiliary function to randomly select a value among the two possible options passed in as arguments.

static const Int8 kDefaultInt8

void x_PopulateBLAST_SequenceBlk(BlastSeqSrcGetSeqArg *seq_arg)

Populate structure with some dummy data.

void ReleaseSequence(BlastSeqSrcGetSeqArg *seq_arg)

Int2 GetSequence(BlastSeqSrcGetSeqArg *seq_arg)

ncbi::CRandom * m_RandGen

The random number generator.

static const Int4 kDefaultInt4

static CTestObjMgr & Instance()

The NCBI C++ standard methods for dealing with std::string.

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.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

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 ASSERT

macro for assert.

BlastSeqSrc * MockBlastSeqSrcInit(EMockBlastSeqSrcMode mode)

Mock BlastSeqSrc initialization function.

static const char * s_MockBlastSeqSrcGetSeqSrcName(void *mock_handle, void *)

static Int2 s_MockBlastSeqSrcGetSequence(void *mock_handle, BlastSeqSrcGetSeqArg *arg)

static Int4 s_MockBlastSeqSrcItrNext(void *mock_handle, BlastSeqSrcIterator *itr)

BlastSeqSrc * s_MockBlastSeqSrcFree(BlastSeqSrc *seq_src)

static Int4 s_MockBlastSeqSrcGetMaxSeqLen(void *mock_handle, void *)

static Int4 s_MockBlastSeqSrcGetNumSeqs(void *mock_handle, void *)

static Int4 s_MockBlastSeqSrcGetSeqLen(void *mock_handle, void *oid)

static void s_MockBlastSeqSrcReleaseSequence(void *mock_handle, BlastSeqSrcGetSeqArg *arg)

static Int8 s_MockBlastSeqSrcGetTotLen(void *mock_handle, void *)

static Int4 s_MockBlastSeqSrcGetAvgSeqLen(void *mock_handle, void *)

static Boolean s_MockBlastSeqSrcGetIsProt(void *mock_handle, void *)

static BlastSeqSrc * s_MockBlastSeqSrcNew(BlastSeqSrc *retval, void *args)

Mock object which implements the BlastSeqSrc interface for testing purposes.

@ eMBSS_RandomlyFail

returns failure randomly on operations

@ eMBSS_AlwaysFail

returns failure on all operations

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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].

EBlastEncoding encoding

Encoding of sequence, i.e.

BLAST_SequenceBlk * seq

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

Complete type definition of Blast Sequence Source Iterator.

Complete type definition of the structure used to create a new BlastSeqSrc.

BlastSeqSrcConstructor constructor

User-defined function to initialize a BlastSeqSrc structure.

void * ctor_argument

Argument to the above function.

Complete type definition of Blast Sequence Source ADT.

Mock BlastSeqSrc implementation which always fails.

Abstract base class which defines a common interface for mock BlastSeqSrc objects to implement.

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