CBlastOptionsFactory Class Reference
[BLAST (Basic Local Alignment Search Tool)]

Search Toolkit Book for CBlastOptionsFactory

#include <blast_options_handle.hpp>

List of all members.

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Detailed Description

Creates BlastOptionsHandle objects with default values for the programs/tasks requested.

This factory is provided as a convenience to create CBlastOptionsHandles which are configured with default values for a given program/task and will NOT be modified before passing them to objects which will execute the BLAST algorithm. If you need to set options for the specific task at hand, please instantiate the appropriate CBlastOptionsHandle subclass.

See also:

C++ BLAST Options Cookbook

Example:

 ...
 CRef<CBlastOptionsHandle> opts(CBlastOptionsFactory::Create(eBlastn));
 CBl2Seq blaster(query, subject, *opts);
 TSeqAlignVector results = blaster.Run();
 ...
 opts.Reset(CBlastOptionsFactory::Create(eMegablast));
 blaster.SetOptionsHandle() = *opts;
 results = blaster.Run();
 ...
 opts.Reset(CBlastOptionsFactory::Create(eDiscMegablast));
 blaster.SetOptionsHandle() = *opts;
 results = blaster.Run();
 ...

Definition at line 80 of file blast_options_handle.hpp.

Public Types
typedef CBlastOptions::EAPILocality	EAPILocality
	Convenience define.
enum	ETaskSets { eNuclNucl, eProtProt, eAll }
	Sets of tasks for the command line BLAST binaries. More...
Static Public Member Functions
static CBlastOptionsHandle *	Create (EProgram program, EAPILocality locality=CBlastOptions::eLocal)
	Creates an options handle object configured with default options for the requested program, throws an exception if an unsupported program is requested.
static CBlastOptionsHandle *	CreateTask (string task, EAPILocality locality=CBlastOptions::eLocal)
	Creates an options handle object configured with default options for the requested task, throws an exception if an unsupported task is requested.
static set< string >	GetTasks (ETaskSets choice=eAll)
	Retrieve the set of supported tasks.
static string	GetDocumentation (const string &task_name)
	Return the documentation for the provided task.
Private Member Functions
	CBlastOptionsFactory ()
	Private c-tor.

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Member Typedef Documentation

typedef CBlastOptions::EAPILocality CBlastOptionsFactory::EAPILocality

Convenience define. See also: CBlastOptions class Definition at line 85 of file blast_options_handle.hpp.

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Member Enumeration Documentation

enum CBlastOptionsFactory::ETaskSets

Sets of tasks for the command line BLAST binaries. Enumerator: eNuclNucl  Nucleotide-nucleotide tasks. eProtProt  Protein-protein tasks. eAll  Retrieve all available tasks. Definition at line 111 of file blast_options_handle.hpp.

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Constructor & Destructor Documentation

CBlastOptionsFactory::CBlastOptionsFactory (   )  [private]

Private c-tor.

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The documentation for this class was generated from the following files:

• include/algo/blast/api/blast_options_handle.hpp
• src/algo/blast/api/blast_options_handle.cpp

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