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

Search Toolkit Book for CBlastOptionsBuilder

#include <blast_options_builder.hpp>

Collaboration diagram for CBlastOptionsBuilder:

[legend]List of all members.

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Detailed Description

Class to build CBlastOptionsHandle from blast4 ASN objects.

This class takes a program, service, and lists of name/value inputs in the form of the blast4 ASN objects, and builds a CBlastOptionsHandle object. Some fields expressed in blast4's returned data are not part of the CBlastOptionsHandle; these are returned via seperate getters.

Definition at line 54 of file blast_options_builder.hpp.

Public Types
typedef objects::CBlast4_parameters::Tdata	TValueList
	List of name/value pairs.
typedef list< CRef< objects::CBlast4_mask > >	TMaskList
	List of Blast4 masks.
Public Member Functions
	CBlastOptionsBuilder (const string &program, const string &service, CBlastOptions::EAPILocality locality=CBlastOptions::eLocal)
	Constructor.
CRef< CBlastOptionsHandle >	GetSearchOptions (const objects::CBlast4_parameters *aopts, const objects::CBlast4_parameters *popts, string *task_name=NULL)
	Build and return options as a CBlastOptionsHandle.
bool	HaveEntrezQuery ()
	Check whether an Entrez query is specified.
string	GetEntrezQuery ()
	Get the Entrez query.
bool	HaveFirstDbSeq ()
	Check whether an OID range start point is specified.
int	GetFirstDbSeq ()
	Get the OID range start point.
bool	HaveFinalDbSeq ()
	Check whether an OID range end point is specified.
int	GetFinalDbSeq ()
	Get the OID range end point.
bool	HaveGiList ()
	Check whether a GI list is specified.
list< int >	GetGiList ()
	Get the GI list.
bool	HaveNegativeGiList ()
	Check whether a negative GI list is specified.
list< int >	GetNegativeGiList ()
	Get the negative GI list.
bool	HaveDbFilteringAlgorithmIds ()
	Check whether a GI list is specified.
list< int >	GetDbFilteringAlgorithmIds ()
	Get the GI list.
bool	HaveQueryMasks ()
	Check whether query masks are specified.
TMaskList	GetQueryMasks ()
	Get the query masks.
TSeqRange	GetRestrictedQueryRange ()
	Return the range that was used to restrict the query sequence(s) (returns TSeqRange::GetEmpty() if not applicable).
Static Public Member Functions
static EProgram	ComputeProgram (const string &program, const string &service)
	Compute the EProgram value to use for this search.
static EProgram	AdjustProgram (const TValueList *L, EProgram program, const string &program_string)
	Adjust the EProgram based on option values.
Private Member Functions
void	x_ApplyInteractions (CBlastOptionsHandle &boh)
	Apply values directly to BlastOptions object.
void	x_ProcessOneOption (CBlastOptionsHandle &opts, objects::CBlast4_parameter &p)
	Apply the value of one option to the CBlastOptionsHandle.
void	x_ProcessOptions (CBlastOptionsHandle &opts, const TValueList *L)
	Apply the value of all options to the CBlastOptionsHandle.
Private Attributes
string	m_Program
	Program value for blast4 protocol.
string	m_Service
	Service value for blast4 protocol.
bool	m_PerformCulling
	Whether to perform culling.
int	m_HspRangeMax
	How much culling to do.
SOptional< string >	m_EntrezQuery
	The entreq query to use (or none).
SOptional< int >	m_FirstDbSeq
	The first OID to process (or none).
SOptional< int >	m_FinalDbSeq
	The last OID to process (or none).
SOptional< list< int > >	m_GiList
	The GI list (or none).
SOptional< list< int > >	m_NegativeGiList
	The negative GI list (or none).
SOptional< list< int > >	m_DbFilteringAlgorithmIds
	The GI list (or none).
SOptional< TMaskList >	m_QueryMasks
	The query masking locations.
bool	m_IgnoreQueryMasks
	Indicated that query masks have already been collected.
TSeqRange	m_QueryRange
	The range to restrict the query sequence(s).
CBlastOptions::EAPILocality	m_Locality
	API Locality of resulting options.
Classes
class	SOptional
	Optional-value idiom. More...

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Member Typedef Documentation

typedef list< CRef<objects::CBlast4_mask> > CBlastOptionsBuilder::TMaskList

List of Blast4 masks. Definition at line 60 of file blast_options_builder.hpp.

typedef objects::CBlast4_parameters::Tdata CBlastOptionsBuilder::TValueList

List of name/value pairs. Definition at line 57 of file blast_options_builder.hpp.

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Member Function Documentation

TSeqRange CBlastOptionsBuilder::GetRestrictedQueryRange (   )  [inline]

Return the range that was used to restrict the query sequence(s) (returns TSeqRange::GetEmpty() if not applicable). Definition at line 133 of file blast_options_builder.hpp.

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Member Data Documentation

SOptional< list<int> > CBlastOptionsBuilder::m_DbFilteringAlgorithmIds [private]

The GI list (or none). Definition at line 276 of file blast_options_builder.hpp. Referenced by GetDbFilteringAlgorithmIds(), and HaveDbFilteringAlgorithmIds().

SOptional<string> CBlastOptionsBuilder::m_EntrezQuery [private]

The entreq query to use (or none). Definition at line 261 of file blast_options_builder.hpp. Referenced by GetEntrezQuery(), and HaveEntrezQuery().

SOptional<int> CBlastOptionsBuilder::m_FinalDbSeq [private]

The last OID to process (or none). Definition at line 267 of file blast_options_builder.hpp. Referenced by GetFinalDbSeq(), and HaveFinalDbSeq().

SOptional<int> CBlastOptionsBuilder::m_FirstDbSeq [private]

The first OID to process (or none). Definition at line 264 of file blast_options_builder.hpp. Referenced by GetFirstDbSeq(), and HaveFirstDbSeq().

SOptional< list<int> > CBlastOptionsBuilder::m_GiList [private]

The GI list (or none). Definition at line 270 of file blast_options_builder.hpp. Referenced by GetGiList(), and HaveGiList().

int CBlastOptionsBuilder::m_HspRangeMax [private]

How much culling to do. Definition at line 258 of file blast_options_builder.hpp. Referenced by x_ApplyInteractions().

bool CBlastOptionsBuilder::m_IgnoreQueryMasks [private]

Indicated that query masks have already been collected. Definition at line 282 of file blast_options_builder.hpp. Referenced by GetSearchOptions().

CBlastOptions::EAPILocality CBlastOptionsBuilder::m_Locality [private]

API Locality of resulting options. Definition at line 288 of file blast_options_builder.hpp. Referenced by GetSearchOptions().

SOptional< list<int> > CBlastOptionsBuilder::m_NegativeGiList [private]

The negative GI list (or none). Definition at line 273 of file blast_options_builder.hpp. Referenced by GetNegativeGiList(), and HaveNegativeGiList().

bool CBlastOptionsBuilder::m_PerformCulling [private]

Whether to perform culling. Definition at line 255 of file blast_options_builder.hpp. Referenced by x_ApplyInteractions().

string CBlastOptionsBuilder::m_Program [private]

Program value for blast4 protocol. Definition at line 249 of file blast_options_builder.hpp. Referenced by GetSearchOptions().

SOptional< TMaskList > CBlastOptionsBuilder::m_QueryMasks [private]

The query masking locations. Definition at line 279 of file blast_options_builder.hpp. Referenced by GetQueryMasks(), GetSearchOptions(), and HaveQueryMasks().

TSeqRange CBlastOptionsBuilder::m_QueryRange [private]

The range to restrict the query sequence(s). Definition at line 285 of file blast_options_builder.hpp.

string CBlastOptionsBuilder::m_Service [private]

Service value for blast4 protocol. Definition at line 252 of file blast_options_builder.hpp. Referenced by GetSearchOptions().

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

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

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