Search Toolkit Book for CBlastOptionsBuilder
Class to build CBlastOptionsHandle from blast4 ASN objects. More...
#include <algo/blast/api/blast_options_builder.hpp>
Collaboration diagram for CBlastOptionsBuilder:
Classes | |
| class | SOptional |
| Optional-value idiom. More... | |
Public Types | |
| typedef objects::CBlast4_parameters::Tdata | TValueList |
| List of name/value pairs. More... | |
| typedef list< CRef< objects::CBlast4_mask > > | TMaskList |
| List of Blast4 masks. More... | |
Public Member Functions | |
| CBlastOptionsBuilder (const string &program, const string &service, CBlastOptions::EAPILocality locality=CBlastOptions::eLocal, bool ignore_unsupported_options=false) | |
| Constructor. More... | |
| CRef< CBlastOptionsHandle > | GetSearchOptions (const objects::CBlast4_parameters *aopts, const objects::CBlast4_parameters *popts, const objects::CBlast4_parameters *fopts, string *task_name=NULL) |
| Build and return options as a CBlastOptionsHandle. More... | |
| bool | HaveEntrezQuery () |
| Check whether an Entrez query is specified. More... | |
| string | GetEntrezQuery () |
| Get the Entrez query. More... | |
| bool | HaveFirstDbSeq () |
| Check whether an OID range start point is specified. More... | |
| int | GetFirstDbSeq () |
| Get the OID range start point. More... | |
| bool | HaveFinalDbSeq () |
| Check whether an OID range end point is specified. More... | |
| int | GetFinalDbSeq () |
| Get the OID range end point. More... | |
| bool | HaveGiList () |
| Check whether a GI list is specified. More... | |
| list< TGi > | GetGiList () |
| Get the GI list. More... | |
| bool | HaveNegativeGiList () |
| Check whether a negative GI list is specified. More... | |
| list< TGi > | GetNegativeGiList () |
| Get the negative GI list. More... | |
| bool | HaveTaxidList () |
| list< TTaxId > | GetTaxidList () |
| Get the Tax list. More... | |
| bool | HaveNegativeTaxidList () |
| Check whether a negative tax id list is specified. More... | |
| list< TTaxId > | GetNegativeTaxidList () |
| Get the negative tax id list. More... | |
| bool | HasDbFilteringAlgorithmId () |
| Check whether a database filtering algorithm ID is specified. More... | |
| int | GetDbFilteringAlgorithmId () |
| Get the database filtering algorithm ID. More... | |
| bool | HasDbFilteringAlgorithmKey () |
| Check whether a database filtering algorithm key is specified. More... | |
| string | GetDbFilteringAlgorithmKey () |
| Get the database filtering algorithm key. More... | |
| bool | HasSubjectMaskingType () |
| Get Subject Maksing Type (soft/hard) More... | |
| ESubjectMaskingType | GetSubjectMaskingType () |
| bool | HaveQueryMasks () |
| Check whether query masks are specified. More... | |
| TMaskList | GetQueryMasks () |
| Get the query masks. More... | |
| TSeqRange | GetRestrictedQueryRange () |
| Return the range that was used to restrict the query sequence(s) (returns TSeqRange::GetEmpty() if not applicable) More... | |
| void | SetIgnoreUnsupportedOptions (bool ignore) |
| Set the 'ignore unsupported options' flag. More... | |
Static Public Member Functions | |
| static EProgram | ComputeProgram (const string &program, const string &service) |
| Compute the EProgram value to use for this search. More... | |
| static EProgram | AdjustProgram (const TValueList *L, EProgram program, const string &program_string) |
| Adjust the EProgram based on option values. More... | |
Private Member Functions | |
| void | x_ApplyInteractions (CBlastOptionsHandle &boh) |
| Apply values directly to BlastOptions object. More... | |
| void | x_ProcessOneOption (CBlastOptionsHandle &opts, objects::CBlast4_parameter &p) |
| Apply the value of one option to the CBlastOptionsHandle. More... | |
| void | x_ProcessOptions (CBlastOptionsHandle &opts, const TValueList *L) |
| Apply the value of all options to the CBlastOptionsHandle. More... | |
Private Attributes | |
| string | m_Program |
| Program value for blast4 protocol. More... | |
| string | m_Service |
| Service value for blast4 protocol. More... | |
| bool | m_PerformCulling |
| Whether to perform culling. More... | |
| int | m_HspRangeMax |
| How much culling to do. More... | |
| SOptional< string > | m_EntrezQuery |
| The entreq query to use (or none). More... | |
| SOptional< int > | m_FirstDbSeq |
| The first OID to process (or none). More... | |
| SOptional< int > | m_FinalDbSeq |
| The last OID to process (or none). More... | |
| SOptional< list< TGi > > | m_GiList |
| The GI list (or none). More... | |
| SOptional< list< TGi > > | m_NegativeGiList |
| The negative GI list (or none). More... | |
| SOptional< int > | m_DbFilteringAlgorithmId |
| The GI list (or none). More... | |
| SOptional< string > | m_DbFilteringAlgorithmKey |
| SOptional< ESubjectMaskingType > | m_SubjectMaskingType |
| SOptional< TMaskList > | m_QueryMasks |
| The query masking locations. More... | |
| bool | m_IgnoreQueryMasks |
| Indicated that query masks have already been collected. More... | |
| TSeqRange | m_QueryRange |
| The range to restrict the query sequence(s) More... | |
| CBlastOptions::EAPILocality | m_Locality |
| API Locality of resulting options. More... | |
| bool | m_IgnoreUnsupportedOptions |
| Should this class quietly ignore unsupported options. More... | |
| bool | m_ForceMbIndex |
| Should loading of the megablast BLAST DB index be required? More... | |
| string | m_MbIndexName |
| Which megablast BLAST DB index name to load. More... | |
| SOptional< list< TTaxId > > | m_TaxidList |
| The tax id list (or none). More... | |
| SOptional< list< TTaxId > > | m_NegativeTaxidList |
| The negative tax id list (or none). More... | |
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 57 of file blast_options_builder.hpp.
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
