Definitions used throughout BLAST.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definitions for various programs supported by core BLAST.
EBlastProgramType
Defines the engine's notion of the different applications of the BLAST algorithm.
BlastQueryInfo * BlastQueryInfoDup(const BlastQueryInfo *query_info)
Duplicates the query information structure.
Int4 Blast_GetQueryIndexFromQueryOffset(Int4 query_offset, EBlastProgramType program, const BlastQueryInfo *query_info)
Return the query index (zero based), given the query offset in the initial HSP as the program.
BlastQueryInfo * BlastQueryInfoFree(BlastQueryInfo *query_info)
Deallocate memory for query information structure.
EMagicBlastSegmentInfo
Information about paired segments (for mapping short reads)
@ eFirstSegment
The first sequence of a pair with both sequences read and accepted.
@ fPartialFlag
The other segment is not present (did not pass quality filtering.
@ fFirstSegmentFlag
The first sequence of a pair.
@ fLastSegmentFlag
The last sequence of a pair.
@ eNoSegments
Sequence is not part of a pair.
Int4 Blast_GetQueryIndexFromContext(Int4 context, EBlastProgramType program)
Given a context from BLAST engine core, return the query index.
Int2 Blast_GetOneQueryStructs(BlastQueryInfo **one_query_info_ptr, BLAST_SequenceBlk **one_query_ptr, const BlastQueryInfo *query_info, BLAST_SequenceBlk *query, Int4 query_index)
Create auxiliary query structures with all data corresponding to a single query sequence within a con...
Int8 BlastQueryInfoGetEffSearchSpace(const BlastQueryInfo *qinfo, EBlastProgramType program, Int4 query_index)
Retrieve a query sequence's search space.
struct BlastQueryInfo BlastQueryInfo
The query related information.
Int4 BSearchContextInfo(Int4 n, const BlastQueryInfo *A)
Search BlastContextInfo structures for the specified offset.
Int4 * ContextOffsetsToOffsetArray(const BlastQueryInfo *info)
Copy the context query offsets to an allocated array of Int4.
void OffsetArrayToContextOffsets(BlastQueryInfo *info, Int4 *new_offsets, EBlastProgramType prog)
Copy the context query offsets from an array of Int4, allocating the context array if needed.
void BlastQueryInfoSetEffSearchSpace(BlastQueryInfo *qinfo, EBlastProgramType program, Int4 query_index, Int8 eff_searchsp)
Set a query sequence's search space.
Uint4 QueryInfo_GetSeqBufLen(const BlastQueryInfo *qinfo)
Get the number of bytes required for the concatenated sequence buffer, given a query info structure.
struct BlastContextInfo BlastContextInfo
The context related information.
Int4 BlastQueryInfoGetQueryLength(const BlastQueryInfo *qinfo, EBlastProgramType program, Int4 query_index)
Obtains the sequence length for a given query in the query, without taking into consideration any app...
BlastQueryInfo * BlastQueryInfoNew(EBlastProgramType program, int num_queries)
Allocate memory for query information structure.
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
int8_t Int1
1-byte (8-bit) signed integer
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Uint1 Boolean
bool replacment for C
Structure to hold a sequence.
The context related information.
Int4 query_length
Length of this query, strand or frame.
Boolean is_valid
Determine if this context is valid or not.
Int4 segment_flags
Flags describing segments for paired reads.
Int4 query_offset
Offset of this query, strand or frame in the concatenated super-query.
Int4 length_adjustment
Length adjustment for boundary conditions.
Int8 eff_searchsp
Effective search space for this context.
Int4 query_index
Index of query (same for all frames)
Int1 frame
Frame number (-1, -2, -3, 0, 1, 2, or 3)
The query related information.
Int4 first_context
Index of the first element of the context array.
BlastContextInfo * contexts
Information per context.
int num_queries
Number of query sequences.
Uint4 min_length
Length of the shortest among the concatenated queries.
struct SPHIQueryInfo * pattern_info
Counts of PHI BLAST pattern occurrences, used in PHI BLAST only.
Int4 last_context
Index of the last element of the context array.
Uint4 max_length
Length of the longest among the concatenated queries.
In PHI BLAST, structure containing information about all pattern occurrences in query.
static CS_CONTEXT * context
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