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BlastSeqSrcGetSeqArg Struct Reference

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Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface. More...

#include <algo/blast/core/blast_seqsrc.h>

+ Collaboration diagram for BlastSeqSrcGetSeqArg:

Public Attributes

Int4 oid
 Oid in BLAST database, index in an array of sequences, etc [in]. More...
 
EBlastEncoding encoding
 Encoding of sequence, i.e. More...
 
Boolean reset_ranges
 This option allows the BLAST engine to communicate with the BlastSeqSrc that the offset ranges for a given OID should be reset and the entire sequence data should be fetched. More...
 
Boolean check_oid_exclusion
 Check whether an OID is excluded due to overlapping filtering. More...
 
BLAST_SequenceBlkseq
 Sequence to return, if NULL, it should allocated by GetSeqBlkFnPtr (using BlastSeqBlkNew or BlastSetUp_SeqBlkNew), else its contents are freed (using BlastSequenceBlkClean) and the structure is reused [out]. More...
 
BlastSeqSrcSetRangesArgranges
 

Detailed Description

Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature, associated with index-based implementations of the BlastSeqSrc interface.

Index-based implementations include BLAST databases or an array/vector of sequences.

Definition at line 257 of file blast_seqsrc.h.

Member Data Documentation

◆ check_oid_exclusion

Boolean BlastSeqSrcGetSeqArg::check_oid_exclusion

Check whether an OID is excluded due to overlapping filtering.

The disease is rare, and the test for it is somewhat expensive, so it is deferred to the traceback stage. TRUE to enable this test. [in]

Definition at line 279 of file blast_seqsrc.h.

Referenced by BLAST_ComputeTraceback_MT(), Blast_HSPListReevaluateUngapped(), BOOST_AUTO_TEST_CASE(), s_MatchingSequenceInitialize(), and s_SeqDbGetSequence().

◆ encoding

EBlastEncoding BlastSeqSrcGetSeqArg::encoding

◆ oid

Int4 BlastSeqSrcGetSeqArg::oid

◆ ranges

BlastSeqSrcSetRangesArg* BlastSeqSrcGetSeqArg::ranges

◆ reset_ranges

Boolean BlastSeqSrcGetSeqArg::reset_ranges

This option allows the BLAST engine to communicate with the BlastSeqSrc that the offset ranges for a given OID should be reset and the entire sequence data should be fetched.

The motivation for this option is to exploit CSeqDB's performance feature that allows to retrieve only pre-selected portions of the sequence data for the traceback stage. BlastSeqSrc implementations that do not have this feature can safely ignore this field. By default, this should be set to FALSE. [in]

Definition at line 273 of file blast_seqsrc.h.

Referenced by BLAST_ComputeTraceback_MT(), BOOST_AUTO_TEST_CASE(), and s_SeqDbGetSequence().

◆ seq

BLAST_SequenceBlk* BlastSeqSrcGetSeqArg::seq

The documentation for this struct was generated from the following file:
Modified on Fri Feb 23 11:43:30 2024 by modify_doxy.py rev. 669887