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NCBI C++ ToolKit: include/algo/blast/api/local_blast.hpp Source File

* user_data =

) {

m_PrelimSearch->SetInterruptCallback(fnptr, user_data);

GetNumExtensions();

class ::CBlastFilterTest;

Boolean(* TInterruptFnPtr)(SBlastProgress *progress_info)

Prototype for function pointer to determine whether the BLAST search should proceed or be interrupted...

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Defines interface for retrieving sequence identifiers.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

Runs the BLAST algorithm between 2 sequences.

Class to perform a BLAST search on local BLAST databases Note that PHI-BLAST can be run using this cl...

Class that supports setting the number of threads to use with a given algorithm.

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

CRef< IBlastSeqInfoSrc > m_SeqInfoSrc

User-specified IBlastSeqInfoSrc implementation (may be used for non-standard databases,...

CRef< SInternalData > m_InternalData

Internal core data structures which are used in the preliminary and traceback stages of the search.

CRef< CBlastPrelimSearch > m_PrelimSearch

Object which runs the preliminary stage of the search.

void SetBatchNumber(int batch_num)

CRef< CBlastOptions > m_Opts

Options to use.

TSearchMessages m_Messages

Warnings and error messages.

TInterruptFnPtr SetInterruptCallback(TInterruptFnPtr fnptr, void *user_data=NULL)

Set a function callback to be invoked by the CORE of BLAST to allow interrupting a BLAST search in pr...

TSearchMessages GetSearchMessages() const

Retrieve any error/warning messages that occurred during the search.

size_t SplitQuery_GetChunkSize(EProgram program)

Returns the optimal chunk size for a given task.

CRef< CBlastTracebackSearch > m_TbackSearch

Object which runs the traceback stage of the search.

std::string m_batch_num_str

CRef< CLocalDbAdapter > m_LocalDbAdapter

Local DB adaptor (if one was) passed to constructor.

CRef< IQueryFactory > m_QueryFactory

Query factory from which to obtain the query sequence data.

int32_t Int4

4-byte (32-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.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

void Run(void)

Enter the main loop.

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

Return statistics from the BLAST search.

Complete type definition of Blast Sequence Source ADT.

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

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