include/algo/blast/api/blast_dbindex.hpp File Reference

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Detailed Description

Declarations for indexed blast databases.

Definition in file blast_dbindex.hpp.

#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_seqsrc_impl.h>
#include <algo/blast/core/lookup_wrap.h>
#include <algo/blast/core/blast_filter.h>
#include <algo/blast/api/blast_types.hpp>

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Classes
class	CIndexedDbException
	Index wrapper exceptions. More...
Typedefs
typedef void(*	DbIndexPreSearchFnType )(BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Type of a callback that is called to invoke index based search.
typedef void(*	DbIndexSetQueryInfoFnType )(BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)
	Type of a callback to set the query information in the index structure.
typedef void(*	DbIndexRunSearchFnType )(BlastSeqSrc *seq_src, BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)
	Type of a callback to run the indexed seed search.
typedef void(*	DbIndexSetNumThreadsFnType )(BlastSeqSrc *seq_src, size_t n_threads)
	Type of a callback to set the number of threads for indexed seed search.
Functions
BlastSeqSrc *	DbIndexSeqSrcInit (const string &indexname, BlastSeqSrc *db)
	Wrap a BlastSeqSrc object db by another object that provides index based seed searching.
BlastSeqSrc *	CloneSeqSrcInit (BlastSeqSrc *src)
	Creates a clone of a BlastSeqSrc structure.
void	CloneSeqSrc (BlastSeqSrc *dst, BlastSeqSrc *src)
	Copies the contents of src to dst.
int	MinIndexWordSize ()
	Get minimal word size accepted by indexing library.
DbIndexPreSearchFnType	GetDbIndexPreSearchFn ()
	Return the appropriate pre-search callback.
DbIndexSetQueryInfoFnType	GetDbIndexSetQueryInfoFn ()
	Return the appropriate callback to set query information in the index.
DbIndexRunSearchFnType	GetDbIndexRunSearchFn ()
	Return the appropriate callback to run indexed seed search.
DbIndexSetNumThreadsFnType	GetDbIndexSetNumThreadsFn ()
	Return the appropriate callback to set the number of threads for indexed seed search.

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Typedef Documentation

typedef void(* DbIndexPreSearchFnType)(BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, BLAST_SequenceBlk *queries, BlastSeqLoc *locs, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Type of a callback that is called to invoke index based search. Parameters: seq_src  Indexed database source object. lt_wrap  Wrapper for CIndexedDb. queries  Queries descriptor. locs  Unmasked intervals of queries. lut_options  Lookup table parameters, like target word size. word_options  Contains window size of two-hits based search. Definition at line 87 of file blast_dbindex.hpp.

typedef void(* DbIndexRunSearchFnType)(BlastSeqSrc *seq_src, BLAST_SequenceBlk *queries, LookupTableOptions *lut_options, BlastInitialWordOptions *word_options)

Type of a callback to run the indexed seed search. Parameters: seq_src  sequence source (index) queries  query information structure lut_options  lookup table parameters word_options  word options Definition at line 143 of file blast_dbindex.hpp.

typedef void(* DbIndexSetNumThreadsFnType)(BlastSeqSrc *seq_src, size_t n_threads)

Type of a callback to set the number of threads for indexed seed search. Parameters: seq_src  sequence source (index) n_threads  number of threads Definition at line 157 of file blast_dbindex.hpp.

typedef void(* DbIndexSetQueryInfoFnType)(BlastSeqSrc *seq_src, LookupTableWrap *lt_wrap, CRef< CBlastSeqLocWrap > locs_wrap)

Type of a callback to set the query information in the index structure. Parameters: seq_src  sequence source (index) lt_wrap  lookup table wrapper object locs_wrap  lookup (unmasked) segments Definition at line 127 of file blast_dbindex.hpp.

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