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NCBI C++ ToolKit: src/algo/blast/api/effsearchspace_calc.cpp Source File

: m_OptsMemento(opts_memento), m_FilterString(0), m_FilterOpts(0)

m_OptsMemento->m_QueryOpts->filter_string = m_FilterString;

m_OptsMemento->m_QueryOpts->filtering_options = m_FilterOpts;

: m_QueryFactory(query_factory), m_Program(options.GetProgramType())

delete_sbp =

;

unique_ptr<CBlastOptionsMemento> opts_memento

db_num_bases, db_num_seqs,

(delete_sbp ==

)

);

((

)query_index < m_QueryInfo->num_queries);

((

)ctx_index <= m_QueryInfo->last_context);

Classes that capture the state of the BLAST options (or subsets of options) and restore them later (u...

SBlastFilterOptions * SBlastFilterOptionsFree(SBlastFilterOptions *filter_options)

Frees SBlastFilterOptions and all subservient structures.

@ eEmpty

no filtering at all.

Int2 SBlastFilterOptionsNew(SBlastFilterOptions **filter_options, EFilterOptions type)

Allocates memory for SBlastFilterOptions and.

Int2 BlastEffectiveLengthsParametersNew(const BlastEffectiveLengthsOptions *options, Int8 db_length, Int4 num_seqs, BlastEffectiveLengthsParameters **parameters)

Allocate memory for BlastEffectiveLengthsParameters.

Int8 BlastQueryInfoGetEffSearchSpace(const BlastQueryInfo *qinfo, EBlastProgramType program, Int4 query_index)

Retrieve a query sequence's search space.

Utilities initialize/setup BLAST.

Int2 BLAST_CalcEffLengths(EBlastProgramType program_number, const BlastScoringOptions *scoring_options, const BlastEffectiveLengthsParameters *eff_len_params, const BlastScoreBlk *sbp, BlastQueryInfo *query_info, Blast_Message **blast_message)

Function to calculate effective query length and db length as well as effective search space.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Wrapper class for BlastEffectiveLengthsParameters .

Defines BLAST error codes (user errors included)

Class that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLA...

Encapsulates ALL the BLAST algorithm's options.

Memento class to save, null out, and restore the filtering options of the CBlastOptionsMemento object...

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

Declares auxiliary class to calculate the effective search space.

CBlastOptionsMemento * m_OptsMemento

snapshopt of BLAST options

const CBlastOptionsMemento * CreateSnapshot() const

Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs...

CRef< IQueryFactory > m_QueryFactory

source of query sequence(s)

EBlastProgramType m_Program

BLAST program.

~CFilteringMemento()

Destructor.

Int8 GetEffSearchSpaceForContext(size_t ctx_index) const

Retrieve the effective search space calculated for a given query context.

SBlastFilterOptions * m_FilterOpts

original filtering options specified in m_OptsMemento

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

static BlastScoreBlk * CreateScoreBlock(const CBlastOptionsMemento *opts_memento, CRef< ILocalQueryData > query_data, BlastSeqLoc **lookup_segments, TSearchMessages &search_messages, TSeqLocInfoVector *masked_query_regions=NULL, const CBlastRPSInfo *rps_info=NULL)

Initializes the BlastScoreBlk.

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

BlastQueryInfo * GetQueryInfo() const

Retrieve the BlastQueryInfo structure that stores the effective search spaces for all queries.

CFilteringMemento(CBlastOptionsMemento *opts_memento)

Parametrized constructor.

BlastQueryInfo * m_QueryInfo

struct to store eff. search spaces

CEffectiveSearchSpaceCalculator(CRef< IQueryFactory > query_factory, const CBlastOptions &options, Int4 db_num_seqs, Int8 db_num_bases, BlastScoreBlk *sbp=NULL)

Constructor.

QuerySetUpOptions * m_QueryOpts

char * m_FilterString

original filtering string specified in m_OptsMemento

Int8 GetEffSearchSpace(size_t query_index=0) const

Retrieve the effective search space calculated for a given query.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

Int8 eff_searchsp

Effective search space for this context.

The query related information.

BlastContextInfo * contexts

Information per context.

Structure used for scoring calculations.

char * filter_string

DEPRECATED, filtering options above.

SBlastFilterOptions * filtering_options

structured options for all filtering offered from algo/blast/core for BLAST.

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