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

(chunk_num),

runtime_error(

);

vector<size_t> retval;

(chunk_num),

runtime_error(

);

(

= 0; query_indices[

] !=

;

++) {

retval.push_back(query_indices[

]);

(query_indices);

num_contexts = 0;

(chunk_num),

runtime_error(

);

(

= 0;

< num_contexts;

++) {

retval.push_back(query_contexts[

]);

(query_contexts);

vector<size_t> retval;

(chunk_num),

runtime_error(

);

(

= 0; context_offsets[

] !=

;

++) {

retval.push_back(context_offsets[

]);

(context_offsets);

pair<size_t, size_t> chunk_bounds(0, 0);

&chunk_bounds.second);

runtime_error(

);

retval.

(

(chunk_bounds.first),

(chunk_bounds.second));

(chunk_num),

runtime_error(

);

(chunk_num));

runtime_error(

);

context_index,

(chunk_num));

runtime_error(

);

context_offset,

(chunk_num));

runtime_error(

runtime_error(

(

<<

);

<< endl <<

<< kNumChunks << endl;

(

chunk_num = 0; chunk_num < kNumChunks; chunk_num++) {

<<

<< chunk_num <<

(

chunk_num = 0; chunk_num < kNumChunks; chunk_num++) {

<<

<< chunk_num <<

(

chunk_num = 0; chunk_num < kNumChunks; chunk_num++) {

<<

<< chunk_num <<

Definitions used throughout BLAST.

#define sfree(x)

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

Declares the BLAST exception class.

Defines system exceptions occurred while running BLAST.

Wrapper class around SSplitQueryBlk structure.

std::ofstream out("events_result.xml")

main entry point for tests

SSplitQueryBlk * m_SplitQueryBlk

The structure this object manages.

void AddQueryToChunk(size_t chunk_num, Int4 query_index)

Adds a query index to a given chunk.

TChunkRange GetChunkBounds(size_t chunk_num) const

Get the boundaries of a chunk in the concatenated query.

SSplitQueryBlk * GetCStruct() const

Returns the C structure managed by objects of this class.

~CSplitQueryBlk()

Destructor.

size_t GetNumQueriesForChunk(size_t chunk_num) const

Get the number of queries in a given chunk.

size_t GetNumChunks() const

Retrieve the number of chunks.

void SetChunkOverlapSize(size_t size)

Sets the size (# of bases/residues) of overlap between query chunks.

void SetChunkBounds(size_t chunk_num, const TChunkRange &chunk_range)

Set the boundaries of a chunk in the concatenated query.

void AddContextToChunk(size_t chunk_num, Int4 context_index)

Adds a query context to a given chunk.

ostream & operator<<(ostream &out, const CSplitQueryBlk &rhs)

void AddContextOffsetToChunk(size_t chunk_num, Int4 context_offset)

Adds a context offset (correction) to a given chunk.

size_t GetChunkOverlapSize() const

Gets the size (# of bases/residues) of overlap between query chunks.

vector< size_t > GetQueryIndices(size_t chunk_num) const

Get the indices of the queries contained in a given chunk.

vector< int > GetQueryContexts(size_t chunk_num) const

Get the contexts of the queries contained in a given chunk.

string s_PrintVector(const vector< T > &data2print)

Auxiliary function to print a vector.

vector< size_t > GetContextOffsets(size_t chunk_num) const

Get the context offsets (corrections) of the queries contained in a given chunk.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

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

position_type GetToOpen(void) const

position_type GetFrom(void) const

TThisType & SetOpen(position_type from, position_type toOpen)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

#define UINT4_MAX

largest number represented by unsigned int.

Int2 SplitQueryBlk_GetChunkBounds(const SSplitQueryBlk *squery_blk, Uint4 chunk_num, size_t *starting_offset, size_t *ending_offset)

Get the query chunk's bounds with respect to the full sized concatenated query.

Int2 SplitQueryBlk_GetQueryIndicesForChunk(const SSplitQueryBlk *squery_blk, Uint4 chunk_num, Uint4 **query_indices)

Retrieve an array of query indices for the requested chunk.

Int2 SplitQueryBlk_GetContextOffsetsForChunk(const SSplitQueryBlk *squery_blk, Uint4 chunk_num, Uint4 **context_offsets)

Retrieve an array of context offsets for the requested chunk.

Int2 SplitQueryBlk_GetQueryContextsForChunk(const SSplitQueryBlk *squery_blk, Uint4 chunk_num, Int4 **query_contexts, Uint4 *num_query_contexts)

Retrieve an array of query contexts for the requested chunk.

Int2 SplitQueryBlk_AddQueryToChunk(SSplitQueryBlk *squery_blk, Uint4 query_index, Uint4 chunk_num)

Add a query index to a given chunk.

SSplitQueryBlk * SplitQueryBlkNew(Uint4 num_chunks, Boolean gapped_merge)

Allocate a new split query chunk structure.

Int2 SplitQueryBlk_SetChunkOverlapSize(SSplitQueryBlk *squery_blk, size_t size)

Sets the query chunk overlap size.

Int2 SplitQueryBlk_SetChunkBounds(SSplitQueryBlk *squery_blk, Uint4 chunk_num, Uint4 starting_offset, Uint4 ending_offset)

Set the query chunk's bounds with respect to the full sized concatenated query.

Int2 SplitQueryBlk_GetNumQueriesForChunk(const SSplitQueryBlk *squery_blk, Uint4 chunk_num, size_t *num_queries)

Retrieve the number of queries that correspond to chunk number chunk_num.

Int2 SplitQueryBlk_AddContextOffsetToChunk(SSplitQueryBlk *squery_blk, Uint4 offset, Uint4 chunk_num)

Add a context offset to a given chunk.

Int2 SplitQueryBlk_AddContextToChunk(SSplitQueryBlk *squery_blk, Int4 ctx_index, Uint4 chunk_num)

Add a query context index to a given chunk.

size_t SplitQueryBlk_GetChunkOverlapSize(const SSplitQueryBlk *squery_blk)

Returns the query chunk overlap size.

SSplitQueryBlk * SplitQueryBlkFree(SSplitQueryBlk *squery_blk)

Deallocate a split query chunk structure.

Auxiliary functions and classes to assist in query splitting.

Definition of C++ wrapper for SSplitQueryBlk.

Structure to keep track of which query sequences are allocated to each query chunk.

Uint4 num_chunks

Total number of chunks.

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