#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>

Include dependency graph for split_query.h:

This graph shows which files directly or indirectly include this file:

Classes
struct	SSplitQueryBlk
	Structure to keep track of which query sequences are allocated to each query chunk. More...

Typedefs
typedef struct SDynamicUint4Array	SQueriesPerChunk
	Forward declaration of dynamic array. More...

typedef struct SDynamicInt4Array	SContextsPerChunk
	Forward declaration of dynamic array. More...

typedef struct SDynamicUint4Array	SContextOffsetsPerChunk
	Forward declaration of dynamic array. More...

typedef struct SSeqRange	SQueryChunkBoundary
	Convenience typedef. More...

typedef struct SSplitQueryBlk	SSplitQueryBlk
	Structure to keep track of which query sequences are allocated to each query chunk. More...

Functions
SSplitQueryBlk *	SplitQueryBlkNew (Uint4 num_chunks, Boolean gapped_merge)
	Allocate a new split query chunk structure. More...

SSplitQueryBlk *	SplitQueryBlkFree (SSplitQueryBlk *squery_blk)
	Deallocate a split query chunk structure. More...

Boolean	SplitQueryBlk_AllowGap (SSplitQueryBlk *squery_blk)
	Determines whether HSPs on different diagnonals may be merged. More...

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. More...

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. More...

Int2	SplitQueryBlk_AddQueryToChunk (SSplitQueryBlk *squery_blk, Uint4 query_index, Uint4 chunk_num)
	Add a query index to a given chunk. More...

Int2	SplitQueryBlk_AddContextToChunk (SSplitQueryBlk *squery_blk, Int4 ctx_index, Uint4 chunk_num)
	Add a query context index to a given chunk. More...

Int2	SplitQueryBlk_AddContextOffsetToChunk (SSplitQueryBlk *squery_blk, Uint4 offset, Uint4 chunk_num)
	Add a context offset to a given chunk. More...

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. More...

Int2	SplitQueryBlk_GetQueryIndicesForChunk (const SSplitQueryBlk squery_blk, Uint4 chunk_num, Uint4 *query_indices)
	Retrieve an array of query indices for the requested chunk. More...

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. More...

Int2	SplitQueryBlk_GetContextOffsetsForChunk (const SSplitQueryBlk squery_blk, Uint4 chunk_num, Uint4 *context_offsets)
	Retrieve an array of context offsets for the requested chunk. More...

Int2	SplitQueryBlk_SetChunkOverlapSize (SSplitQueryBlk *squery_blk, size_t size)
	Sets the query chunk overlap size. More...

size_t	SplitQueryBlk_GetChunkOverlapSize (const SSplitQueryBlk *squery_blk)
	Returns the query chunk overlap size. More...

Variables
const Int4	kInvalidContext
	Value to represent an invalid context. More...

const Int2	kBadParameter
	Invalid parameter used in a function call. More...

const Int2	kOutOfMemory
	Failure due to out-of-memory condition. More...

Typedef Documentation

◆ SContextOffsetsPerChunk

typedef struct SDynamicUint4Array SContextOffsetsPerChunk

Forward declaration of dynamic array.

Definition at line 1 of file split_query.h.

◆ SContextsPerChunk

typedef struct SDynamicInt4Array SContextsPerChunk

Forward declaration of dynamic array.

Definition at line 1 of file split_query.h.

◆ SQueriesPerChunk

typedef struct SDynamicUint4Array SQueriesPerChunk

Forward declaration of dynamic array.

Definition at line 1 of file split_query.h.

◆ SQueryChunkBoundary

typedef struct SSeqRange SQueryChunkBoundary

Convenience typedef.

Definition at line 1 of file split_query.h.

◆ SSplitQueryBlk

typedef struct SSplitQueryBlk SSplitQueryBlk

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

Function Documentation

◆ SplitQueryBlk_AddContextOffsetToChunk()

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

Add a context offset to a given chunk.

Parameters

squery_blk	split query block structure [in]
offset	the context offset to assign [in]
chunk_num	number of chunk to assign query index [in]

Returns: 0 on success or kOutOfMemory

Definition at line 222 of file split_query.c.

References SSplitQueryBlk::chunk_offset_map, DynamicUint4Array_Append(), kBadParameter, SSplitQueryBlk::num_chunks, and offset.

Referenced by CSplitQueryBlk::AddContextOffsetToChunk().

◆ SplitQueryBlk_AddContextToChunk()

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

Add a query context index to a given chunk.

Parameters

squery_blk	split query block structure [in]
ctx_index	query context index to assign [in]
chunk_num	number of chunk to assign query index [in]

Returns: 0 on success or kOutOfMemory

Definition at line 211 of file split_query.c.

References SSplitQueryBlk::chunk_ctx_map, DynamicInt4Array_Append(), kBadParameter, and SSplitQueryBlk::num_chunks.

Referenced by CSplitQueryBlk::AddContextToChunk(), and BOOST_AUTO_TEST_CASE().

◆ SplitQueryBlk_AddQueryToChunk()

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

Add a query index to a given chunk.

Parameters

squery_blk	split query block structure [in]
query_index	query index to assign [in]
chunk_num	number of chunk to assign query index [in]

Returns: 0 on success or kOutOfMemory

Definition at line 201 of file split_query.c.

References SSplitQueryBlk::chunk_query_map, DynamicUint4Array_Append(), kBadParameter, and SSplitQueryBlk::num_chunks.

Referenced by CSplitQueryBlk::AddQueryToChunk(), and BOOST_AUTO_TEST_CASE().

◆ SplitQueryBlk_AllowGap()

Boolean SplitQueryBlk_AllowGap ( SSplitQueryBlk * squery_blk )

Determines whether HSPs on different diagnonals may be merged.

Parameters

squery_blk split query block structure [in]

Returns: TRUE if possible, FALSE otherwise

Definition at line 154 of file split_query.c.

References FALSE, SSplitQueryBlk::gapped_merge, and TRUE.

Referenced by BlastHSPStreamMerge().

◆ SplitQueryBlk_GetChunkBounds()

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.

Parameters

squery_blk	split query block structure [in]
chunk_num	number of chunk to assign bounds [in]
starting_offset	starting offset of this chunk [in\|out]
ending_offset	ending offset of this chunk [in\|out]

Returns: 0 on success or kBadParameter if chunk_num is invalid

Definition at line 174 of file split_query.c.

References SSplitQueryBlk::chunk_bounds, kBadParameter, SSeqRange::left, SSplitQueryBlk::num_chunks, and SSeqRange::right.

Referenced by CSplitQueryBlk::GetChunkBounds().

◆ SplitQueryBlk_GetChunkOverlapSize()

size_t SplitQueryBlk_GetChunkOverlapSize ( const SSplitQueryBlk * squery_blk )

Returns the query chunk overlap size.

Parameters

squery_blk split query block structure [in]

Returns: chunk overlap size, 0 if value wasn't set or kBadParameter if squery_blk is NULL

Definition at line 332 of file split_query.c.

References SSplitQueryBlk::chunk_overlap_sz, and kBadParameter.

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

◆ SplitQueryBlk_GetContextOffsetsForChunk()

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

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().

◆ SplitQueryBlk_GetNumQueriesForChunk()

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.

Parameters

squery_blk	split query block structure [in]
chunk_num	number of chunk to retrieve query indices [in]
num_queries	the return value of this function [in\|out]

Returns: 0 on success or kBadParameter

Definition at line 189 of file split_query.c.

References SSplitQueryBlk::chunk_query_map, kBadParameter, SSplitQueryBlk::num_chunks, and SDynamicUint4Array::num_used.

Referenced by BOOST_AUTO_TEST_CASE(), and CSplitQueryBlk::GetNumQueriesForChunk().

◆ SplitQueryBlk_GetQueryContextsForChunk()

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.

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().

◆ SplitQueryBlk_GetQueryIndicesForChunk()

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

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().

◆ SplitQueryBlk_SetChunkBounds()

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.

Parameters

squery_blk	split query block structure [in]
chunk_num	number of chunk to assign bounds [in]
starting_offset	starting offset of this chunk [in]
ending_offset	ending offset of this chunk [in]

Returns: 0 on success or kBadParameter if chunk_num is invalid

Definition at line 160 of file split_query.c.

References SSplitQueryBlk::chunk_bounds, kBadParameter, SSeqRange::left, SSplitQueryBlk::num_chunks, and SSeqRange::right.

Referenced by CSplitQueryBlk::SetChunkBounds().

◆ SplitQueryBlk_SetChunkOverlapSize()

Int2 SplitQueryBlk_SetChunkOverlapSize	(	SSplitQueryBlk *	squery_blk,
		size_t	size
	)

Sets the query chunk overlap size.

Parameters

squery_blk	split query block structure [in]
size	size of the chunk overlap size [in]

Returns: 0 on success or kBadParameter is squery_blk is NULL

Definition at line 322 of file split_query.c.

References SSplitQueryBlk::chunk_overlap_sz, kBadParameter, and ncbi::grid::netcache::search::fields::size.

Referenced by CSplitQueryBlk::SetChunkOverlapSize().

◆ SplitQueryBlkFree()

SSplitQueryBlk* SplitQueryBlkFree ( SSplitQueryBlk * squery_blk )

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().

◆ SplitQueryBlkNew()

SSplitQueryBlk* SplitQueryBlkNew	(	Uint4	num_chunks,
		Boolean	gapped_merge
	)

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().

Variable Documentation

◆ kBadParameter

const Int2 kBadParameter

extern

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().

◆ kInvalidContext

const Int4 kInvalidContext

extern

Value to represent an invalid context.

Definition at line 39 of file split_query.c.

Referenced by CContextTranslator::GetContextInChunk(), CContextTranslator::GetStartingChunk(), s_GetAbsoluteContextLength(), CQuerySplitter::x_ComputeContextOffsets_NonTranslatedQueries(), CQuerySplitter::x_ComputeContextOffsets_TranslatedQueries(), CQuerySplitter::x_ComputeQueryContextsForChunks(), and CSplitQueryTestFixture::x_TestCContextTranslator().

◆ kOutOfMemory

const Int2 kOutOfMemory

extern

Failure due to out-of-memory condition.

Definition at line 38 of file split_query.c.

Referenced by s_LOG_Handler(), SplitQueryBlk_GetContextOffsetsForChunk(), SplitQueryBlk_GetQueryContextsForChunk(), and SplitQueryBlk_GetQueryIndicesForChunk().

Classes

Typedefs

Functions

Variables

Typedef Documentation

◆ SContextOffsetsPerChunk

◆ SContextsPerChunk

◆ SQueriesPerChunk

◆ SQueryChunkBoundary

◆ SSplitQueryBlk

Function Documentation

◆ SplitQueryBlk_AddContextOffsetToChunk()

◆ SplitQueryBlk_AddContextToChunk()

◆ SplitQueryBlk_AddQueryToChunk()

◆ SplitQueryBlk_AllowGap()

◆ SplitQueryBlk_GetChunkBounds()

◆ SplitQueryBlk_GetChunkOverlapSize()

◆ SplitQueryBlk_GetContextOffsetsForChunk()

◆ SplitQueryBlk_GetNumQueriesForChunk()

◆ SplitQueryBlk_GetQueryContextsForChunk()

◆ SplitQueryBlk_GetQueryIndicesForChunk()

◆ SplitQueryBlk_SetChunkBounds()

◆ SplitQueryBlk_SetChunkOverlapSize()

◆ SplitQueryBlkFree()

◆ SplitQueryBlkNew()

Variable Documentation

◆ kBadParameter

◆ kInvalidContext

◆ kOutOfMemory