CBlastOptionsFactory Class Reference

Search Toolkit Book for CBlastOptionsFactory

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

#include <algo/blast/api/blast_options_handle.hpp>

Public Types
enum	ETaskSets { eNuclNucl , eProtProt , eMapping , eAll }
	Sets of tasks for the command line BLAST binaries. More...
typedef CBlastOptions::EAPILocality	EAPILocality
	Convenience define. 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. More...
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. More...
static set< string >	GetTasks (ETaskSets choice=eAll)
	Retrieve the set of supported tasks. More...
static string	GetDocumentation (const string &task_name)
	Return the documentation for the provided task. More...

Private Member Functions
	CBlastOptionsFactory ()
	Private c-tor. More...

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.

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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