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NCBI C++ ToolKit: include/algo/blast/core/split_query.h File Reference

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Forward declaration of dynamic array.

Definition at line 1 of file split_query.h.

Forward declaration of dynamic array.

Definition at line 1 of file split_query.h.

Forward declaration of dynamic array.

Definition at line 1 of file split_query.h.

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

Retrieve an array of context offsets for the requested chunk.

Each offset is the correction needed for the query range of HSPs found in the specified chunk

Parameters

squery_blk split query block structure [in] chunk_num number of chunk to retrieve query indices [in] context_offsets offsets for the contexts in the requested chunk, this will be allocated in this function and the last element in the array will be assigned the value UINT4_MAX. Caller is responsible for deallocating this.

Returns

0 on success or kOutOfMemory

Definition at line 293 of file split_query.c.

References SSplitQueryBlk::chunk_offset_map, SDynamicUint4Array::data, kBadParameter, kOutOfMemory, malloc(), NULL, SSplitQueryBlk::num_chunks, SDynamicUint4Array::num_used, and UINT4_MAX.

Referenced by BlastHSPStreamMerge(), and CSplitQueryBlk::GetContextOffsets().

Retrieve an array of query contexts for the requested chunk.

Parameters

squery_blk split query block structure [in] chunk_num number of chunk to retrieve query indices [in] query_contexts contexts for the chunk requested, this will be allocated in this function, caller is responsible for deallocating this. num_query_contexts size of the returned array in query_contexts

Returns

0 on success or kOutOfMemory

Definition at line 262 of file split_query.c.

References SSplitQueryBlk::chunk_ctx_map, SDynamicInt4Array::data, kBadParameter, kOutOfMemory, malloc(), NULL, SSplitQueryBlk::num_chunks, and SDynamicInt4Array::num_used.

Referenced by BlastHSPStreamMerge(), BOOST_AUTO_TEST_CASE(), and CSplitQueryBlk::GetQueryContexts().

Retrieve an array of query indices for the requested chunk.

Parameters

squery_blk split query block structure [in] chunk_num number of chunk to retrieve query indices [in] query_indices indices for the chunk requested, this will be allocated in this function and the last element in the array will be assigned the value UINT4_MAX. Caller is responsible for deallocating this.

Returns

0 on success or kOutOfMemory

Definition at line 235 of file split_query.c.

References SSplitQueryBlk::chunk_query_map, SDynamicUint4Array::data, kBadParameter, kOutOfMemory, malloc(), NULL, SSplitQueryBlk::num_chunks, SDynamicUint4Array::num_used, and UINT4_MAX.

Referenced by BlastHSPStreamMerge(), BOOST_AUTO_TEST_CASE(), and CSplitQueryBlk::GetQueryIndices().

Deallocate a split query chunk structure.

Parameters

squery_blk structure to deallocate [in]

Returns

NULL

Definition at line 116 of file split_query.c.

References SSplitQueryBlk::chunk_bounds, SSplitQueryBlk::chunk_ctx_map, SSplitQueryBlk::chunk_offset_map, SSplitQueryBlk::chunk_query_map, DynamicInt4ArrayFree(), DynamicUint4ArrayFree(), i, NULL, SSplitQueryBlk::num_chunks, and sfree.

Referenced by SplitQueryBlkNew(), and CSplitQueryBlk::~CSplitQueryBlk().

Allocate a new split query chunk structure.

Parameters

num_chunks number of chunks in which the query will be split [in]

Returns

newly allocated structure or NULL in case of memory allocation failure

Definition at line 42 of file split_query.c.

References calloc(), SSplitQueryBlk::chunk_bounds, SSplitQueryBlk::chunk_ctx_map, SSplitQueryBlk::chunk_offset_map, SSplitQueryBlk::chunk_query_map, DynamicInt4ArrayNew(), DynamicUint4ArrayNew(), SSplitQueryBlk::gapped_merge, i, NULL, SSplitQueryBlk::num_chunks, and SplitQueryBlkFree().

Referenced by CSplitQueryBlk::CSplitQueryBlk().

Invalid parameter used in a function call.

Definition at line 37 of file split_query.c.

Referenced by BOOST_AUTO_TEST_CASE(), SplitQueryBlk_AddContextOffsetToChunk(), SplitQueryBlk_AddContextToChunk(), SplitQueryBlk_AddQueryToChunk(), SplitQueryBlk_GetChunkBounds(), SplitQueryBlk_GetChunkOverlapSize(), SplitQueryBlk_GetContextOffsetsForChunk(), SplitQueryBlk_GetNumQueriesForChunk(), SplitQueryBlk_GetQueryContextsForChunk(), SplitQueryBlk_GetQueryIndicesForChunk(), SplitQueryBlk_SetChunkBounds(), and SplitQueryBlk_SetChunkOverlapSize().

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