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

m_MinLength(1), m_AvgLength(0), m_QuerySource(0), m_NumSeqs(0)

);

m_MinLength(1), m_AvgLength(0), m_QuerySource(0), m_NumSeqs(static_cast<

>(subj_seqs.

()))

vector<Int2> strand_v;

strand_v.push_back((

) (*iter).seqloc->GetStrand());

sl->

(*((*iter).seqloc));

mask_sl->

(*((*iter).mask));

sseq_loc(*sl, *((*iter).scope), *mask_sl);

temp_slv.push_back(sseq_loc);

sseq_loc(*sl, *((*iter).scope));

temp_slv.push_back(sseq_loc);

(vector<Int2>, s_iter, strand_v)

std::out_of_range(

);

(*seq_info)->GetMaxLength();

(*seq_info)->GetMinLength();

((*seq_info)->GetAvgLength() == 0) {

num_seqs((*seq_info)->GetNumSeqs());

total_length(0);

(

index = 0; index < num_seqs; ++index)

total_length += (

) (*seq_info)->GetSeqBlk(index)->length;

(*seq_info)->SetAvgLength((

) (total_length / num_seqs));

(*seq_info)->GetAvgLength();

(*seq_info)->GetNumSeqs();

(

) (*seq_info)->GetIsProtein();

((*seq_info)->GetNumSeqs() == 0 || !args)

{ seq_blk = (*seq_info)->GetSeqBlk(args->

); }

(

std::out_of_range&) {

index = *((

*) args);

(*seq_info)->GetSeqBlk(index)->length;

(itr->

>= (*seq_info)->GetNumSeqs())

}

(

ncbi::CException& e) {

}

(

std::exception& e) {

(

));

(query_factory.

() && subj_seqs.empty()) {

);

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

Declares the BLAST exception class.

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

Boolean Blast_SubjectIsProtein(EBlastProgramType p)

Returns true if the subject is protein.

EBlastProgramType

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

Boolean Blast_SubjectIsTranslated(EBlastProgramType p)

Returns true if the subject is translated.

#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_SetResetChunkIterator(BlastSeqSrc *var, ResetChunkIteratorFnPtr arg)

NCBI_XBLAST_EXPORT void * _BlastSeqSrcImpl_GetDataStructure(const BlastSeqSrc *var)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetTotLenStats(BlastSeqSrc *var, GetInt8FnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetSequence(BlastSeqSrc *var, GetSeqBlkFnPtr arg)

NCBI_XBLAST_EXPORT void _BlastSeqSrcImpl_SetGetNumSeqsStats(BlastSeqSrc *var, GetInt4FnPtr 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_SetCopyFnPtr(BlastSeqSrc *var, BlastSeqSrcCopier 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_SetGetMinSeqLen(BlastSeqSrc *var, GetInt4FnPtr 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)

BLAST_SequenceBlk * BlastSequenceBlkFree(BLAST_SequenceBlk *seq_blk)

Deallocate memory for a sequence block.

void BlastSequenceBlkCopy(BLAST_SequenceBlk **copy, BLAST_SequenceBlk *src)

Copies contents of the source sequence block without copying sequence buffers; sets all "field_alloca...

Defines BLAST error codes (user errors included)

Implements the IBlastQuerySource interface using a CBioseq_set as data source.

Contains information about all sequences in a set.

TSeqLocVector subj_seqs

The subject sequences.

Uint4 GetAvgLength()

Returns average length.

void SetupSubjects(TSeqLocVector &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Sets up internal subject data structure for the BLAST search.

unsigned int m_MaxLength

Length of the longest sequence in this set.

BLAST_SequenceBlk * GetSeqBlk(Uint4 index)

Returns sequence block structure for one of the sequences.

EBlastProgramType program

BLAST program.

SQueryFactorySrcNewArgs(CRef< IQueryFactory > qf, const TSeqLocVector &subj_seqs, EBlastProgramType p)

Constructor.

CQueryFactoryInfo(CRef< IQueryFactory > qf, EBlastProgramType program)

Constructor from a vector of sequence location/scope pairs and a BLAST program type.

void SetupSubjects_OMF(IBlastQuerySource &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Object manager free version of SetupSubjects.

BlastSeqSrc * QueryFactoryBlastSeqSrcInit(CRef< IQueryFactory > query_factory, EBlastProgramType program)

Initialize the sequence source structure from a query factory.

static Int4 s_QueryFactoryGetSeqLen(void *multiseq_handle, void *args)

Retrieve length of a given sequence.

unsigned int m_AvgLength

Average length of sequences in this set.

bool m_IsProt

Are these sequences protein or nucleotide?

Uint4 m_NumSeqs

Number of sequences.

static void s_QueryFactoryReleaseSequence(void *, BlastSeqSrcGetSeqArg *args)

Deallocates the uncompressed sequence buffer if necessary.

static Int4 s_QueryFactoryGetNumSeqs(void *multiseq_handle, void *)

Retrieves the number of sequences in the BlastSeqSrc.

static Boolean s_QueryFactoryGetIsProt(void *multiseq_handle, void *)

Answers whether this object is for protein or nucleotide sequences.

static BlastSeqSrc * s_QueryFactoryBlastSeqSrcInit(CRef< IQueryFactory > query_factory, const TSeqLocVector &subj_seqs, EBlastProgramType program)

static const char * s_QueryFactoryGetName(void *, void *)

Always returns NcbiEmptyCStr.

~CQueryFactoryInfo()

Destructor.

static Int8 s_QueryFactoryGetTotLen(void *, void *)

Returns 0 as total length, indicating that this is NOT a database!

CRef< IBlastQuerySource > m_QuerySource

local query data obtained from the query factory

unsigned int m_MinLength

Length of the longest sequence in this set.

static Int8 s_QueryFactoryGetTotLenStats(void *, void *)

Returns 0 as total statistic length, as this implementation does not use alias files.

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

Multi-sequence source constructor.

static void s_QueryFactoryResetChunkIter(void *)

Resets the internal bookmark iterator (N/A in this case)

static Int2 s_QueryFactoryGetSequence(void *multiseq_handle, BlastSeqSrcGetSeqArg *args)

Retrieves the sequence for a given index, in a given encoding.

static Int4 s_QueryFactoryGetMinLength(void *multiseq_handle, void *)

Retrieves the length of the longest sequence in the BlastSeqSrc.

virtual CRef< objects::CBioseq_set > GetBioseqSet()=0

Accessor for the CBioseq_set.

static BlastSeqSrc * s_QueryFactorySrcFree(BlastSeqSrc *seq_src)

Multi sequence source destructor: frees its internal data structure.

static BlastSeqSrc * s_QueryFactorySrcCopy(BlastSeqSrc *seq_src)

Multi-sequence sequence source copier: creates a new reference to the CQueryFactoryInfo object and co...

CRef< IRemoteQueryData > MakeRemoteQueryData()

Creates and caches an IRemoteQueryData.

Uint4 GetMaxLength()

Setter and getter functions for the private fields.

static Int2 s_QueryFactoryGetNextChunk(void *multiseq_handle, BlastSeqSrcIterator *itr)

Mirrors the database iteration interface.

static Int4 s_QueryFactoryGetNumSeqsStats(void *, void *)

Returns zero as this implementation does not use an alias file.

vector< BLAST_SequenceBlk * > m_SeqBlkVector

Vector of sequence blocks.

Uint4 GetNumSeqs()

Returns number of sequences.

virtual TSeqPos Size() const =0

Return the number of elements in the sequence container.

static Int4 s_QueryFactoryIteratorNext(void *multiseq_handle, BlastSeqSrcIterator *itr)

Gets the next sequence index, given a BlastSeqSrc pointer.

void SetAvgLength(Uint4 val)

Sets average length.

CRef< IQueryFactory > query_factory

The query factory.

Uint4 GetMinLength()

Returns minimal length of a set of sequences.

static Int4 s_QueryFactoryGetMaxLength(void *multiseq_handle, void *)

The following functions interact with the C API, and have to be declared extern "C".

bool GetIsProtein()

Answers whether sequences in this object are protein or nucleotide.

static Int4 s_QueryFactoryGetAvgLength(void *multiseq_handle, void *)

Retrieves the average length of the sequence in the BlastSeqSrc.

@ eBlastEncodingNcbi4na

NCBI4na.

@ eBlastEncodingNucleotide

Special encoding for preliminary stage of BLAST: permutation of NCBI4na.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

@ eNa_strand_both

in forward orientation

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

Uint1 Boolean

bool replacment for C

#define FALSE

bool replacment for C indicating false.

#define UINT4_MAX

largest number represented by unsigned int.

Implementation of the BlastSeqSrc interface for a query factory.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

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 oid

The ordinal id of the current sequence.

BlastMaskLoc * lcase_mask

Locations to be masked from operations on this sequence: lookup table for query; scanning for subject...

Boolean lcase_mask_allocated

TRUE if memory has been allocated for lcase_mask.

Uint1 * sequence

Sequence used for search (could be translation).

Boolean sequence_start_allocated

TRUE if memory has been allocated for sequence_start.

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.

unsigned int current_pos

Keep track of this iterator's current position, implementations use UINT4_MAX to indicate this is uni...

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.

Encapsulates the arguments needed to initialize multi-sequence source.

Structure to represent a single sequence to be fed to BLAST.

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