Search Toolkit Book for CRemoteBlast
API for Remote Blast Requests. More...
#include <algo/blast/api/remote_blast.hpp>
Inheritance diagram for CRemoteBlast:
Collaboration diagram for CRemoteBlast:
Public Types | |
| enum | ESearchStatus { eStatus_Unknown , eStatus_Done , eStatus_Pending , eStatus_Failed } |
| Represents the status of previously submitted search/RID. More... | |
| enum | EDebugMode { eDebug = 0 , eSilent } |
| Debugging support can be turned on with eDebug or off with eSilent. More... | |
| typedef list< CRef< objects::CSeq_loc > > | TSeqLocList |
| Typedef for a list of Seq-locs. More... | |
| typedef list< CRef< objects::CBlast4_ka_block > > | TKarlinAltschulBlocks |
| Convenience typedef for a list of CRef<CBlast4_ka_block> More... | |
| typedef vector< CRef< objects::CSeq_interval > > | TSeqIntervalVector |
| Defines a std::vector of CRef<CSeq_interval> More... | |
| typedef vector< CRef< objects::CSeq_data > > | TSeqDataVector |
| Defines a std::vector of CRef<CSeq_data> More... | |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
Public Member Functions | |
| CRemoteBlast (const string &RID) | |
| Use the specified RID to get results for an existing search. More... | |
| CRemoteBlast (CNcbiIstream &f) | |
| Uses the file to populate results. More... | |
| CRemoteBlast (CBlastOptionsHandle *any_opts) | |
| Create a search using any kind of options handle. More... | |
| CRemoteBlast (CRef< IQueryFactory > queries, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &db) | |
| Create a sequence search and set options, queries, and database. More... | |
| CRemoteBlast (CRef< IQueryFactory > queries, CRef< CBlastOptionsHandle > opts_handle, CRef< IQueryFactory > subjects) | |
| Create a search and set options, queries, and subject sequences. More... | |
| CRemoteBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &db) | |
| Create a PSSM search and set options, queries, and database. More... | |
| ~CRemoteBlast () | |
| Destruct the search object. More... | |
| void | SetGIList (const list< TGi > &gi_list) |
| This restricts the subject database to this list of GIs (this is not supported yet on the server end). More... | |
| void | SetNegativeGIList (const list< TGi > &gi_list) |
| This excludes the provided GIs from the subject database (this is not supported yet on the server end). More... | |
| void | SetDbFilteringAlgorithmId (int algo_id, ESubjectMaskingType mask_type=eSoftSubjMasking) |
| Sets the filtering algorithm ID to be applied to the BLAST database (not supported by server yet) More... | |
| void | SetDbFilteringAlgorithmKey (string algo_key, ESubjectMaskingType mask_type=eSoftSubjMasking) |
| Sets the filtering algorithm key to be applied to the BLAST database (not supported by server yet) More... | |
| ESubjectMaskingType | GetSubjectMaskingType () const |
| void | SetDatabase (const string &x) |
| Set the name of the database to search against. More... | |
| void | SetSubjectSequences (CRef< IQueryFactory > subj) |
| Set a list of subject sequences to search against. More... | |
| void | SetSubjectSequences (const list< CRef< objects::CBioseq > > &subj) |
| Set a list of subject sequences to search against. More... | |
| void | SetEntrezQuery (const char *x) |
| Restrict search to sequences matching this Entrez query. More... | |
| void | SetQueries (CRef< objects::CBioseq_set > bioseqs) |
| Set the query as a Bioseq_set. More... | |
| void | SetQueries (CRef< objects::CBioseq_set > bioseqs, const TSeqLocInfoVector &masking_locations) |
| Set the query as a Bioseq_set along with the corresponding masking locations. More... | |
| void | SetQueryMasks (const TSeqLocInfoVector &masking_locations) |
| Set the masking locations for queries. More... | |
| void | SetQueries (TSeqLocList &seqlocs) |
| Set the query as a list of Seq_locs. More... | |
| void | SetQueries (TSeqLocList &seqlocs, const TSeqLocInfoVector &masking_locations) |
| Set the query as a list of Seq_locs. More... | |
| void | SetQueries (CRef< objects::CPssmWithParameters > pssm) |
| Set a PSSM query (as for PSI blast), which must include a bioseq set. More... | |
| CRef< CSearchResultSet > | GetResultSet () |
| Submit the search (if necessary) and return the results. More... | |
| bool | SubmitSync (void) |
| This submits the search (if necessary) and polls for results. More... | |
| bool | SubmitSync (int timeout) |
| This submits the search (if necessary) and polls for results. More... | |
| bool | Submit (void) |
| This submits the search (if necessary) and returns immediately. More... | |
| ESearchStatus | CheckStatus () |
| Returns the status of a previously submitted search/RID. More... | |
| bool | CheckDone (void) |
| Check whether the search has completed. More... | |
| string | GetErrors (void) |
| This returns a string containing any errors that were produced by the search. More... | |
| string | GetWarnings (void) |
| This returns any warnings encountered. More... | |
| const vector< string > & | GetWarningVector () |
| This returns any warnings encountered as a vector of strings. More... | |
| const vector< string > & | GetErrorVector () |
| This returns any errors encountered as a vector of strings. More... | |
| const string & | GetRID (void) |
| Gets the request id (RID) associated with the search. More... | |
| CRef< objects::CSeq_align_set > | GetAlignments (void) |
| Get the seqalign set from the results. More... | |
| TSeqAlignVector | GetSeqAlignSets () |
| Get the seqalign vector from the results. More... | |
| CRef< objects::CBlast4_phi_alignments > | GetPhiAlignments (void) |
| Get the results of a PHI-Align request, if PHI pattern was set. More... | |
| TKarlinAltschulBlocks | GetKABlocks (void) |
| Get the Karlin/Altschul parameter blocks produced by the search. More... | |
| TSeqLocInfoVector | GetMasks (void) |
| Get the queries' masked locations. More... | |
| list< string > | GetSearchStats (void) |
| Get the search statistics block as a list of strings. More... | |
| CRef< objects::CPssmWithParameters > | GetPSSM (void) |
| Get the PSSM produced by the search. More... | |
| void | SetVerbose (EDebugMode verb=eDebug) |
| Adjust the debugging level. More... | |
| bool | IsDbSearch () |
| Return values states whether GetDatabases or GetSubjectSequences call should be used. More... | |
| CRef< objects::CBlast4_database > | GetDatabases () |
| Get the database used by the search. More... | |
| list< CRef< objects::CBioseq > > | GetSubjectSequences () |
| Returns subject sequences if "bl2seq" mode used. More... | |
| CBlast4_subject::TSeq_loc_list | GetSubjectSeqLocs () |
| string | GetProgram () |
| Get the program used for this search. More... | |
| string | GetService () |
| Get the service used for this search. More... | |
| string | GetCreatedBy () |
| Get the created-by string associated with this search. More... | |
| CRef< objects::CBlast4_queries > | GetQueries () |
| Get the queries used for this search. More... | |
| CRef< CBlastOptionsHandle > | GetSearchOptions () |
| Get the search options used for this search. More... | |
| CRef< objects::CBlast4_request > | GetSearchStrategy () |
| Fetch the search strategy for this object without submitting the search. More... | |
| Int4 | GetDbFilteringAlgorithmId () const |
| Returns the filtering algorithm ID used in the database. More... | |
| string | GetDbFilteringAlgorithmKey () const |
| Returns the filtering algorithm key used in the database. More... | |
| string | GetTask () const |
| Returns the task used to create the remote search (if any) More... | |
| string | GetClientId () const |
| Retrieves the client ID used by this object to send requests. More... | |
| void | SetClientId (const string &client_id) |
| Sets the client ID used by this object to send requests. More... | |
| bool | LoadFromArchive () |
| Loads next chunk of archive from file. More... | |
| string | GetTitle (void) |
| Get the title assigned for this search. More... | |
| void | EnableDiskCacheUse () |
| Controls disk cache usage for results retrieval. More... | |
| void | DisableDiskCacheUse () |
| bool | IsDiskCacheActive (void) |
| bool | IsDiskCacheError (void) |
| disk cache error handling More... | |
| void | ClearDiskCacheError (void) |
| string | GetDiskCacheErrorMessahe (void) |
| CRef< objects::CBlast4_reply > | x_GetSearchStatsOnly (void) |
| CRef< objects::CBlast4_reply > | x_GetSearchResultsHTTP (void) |
| unsigned int | GetPsiNumberOfIterations (void) |
| bool | IsErrMsgArchive (void) |
| set< TTaxId > & | GetTaxidList () |
| set< TTaxId > & | GetNegativeTaxidList () |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Static Public Member Functions | |
| static objects::CBlast4_get_search_results_reply::TMasks | ConvertToRemoteMasks (const TSeqLocInfoVector &masking_locations, EBlastProgramType program, vector< string > *warnings=NULL) |
| Convert a TSeqLocInfoVector to a list< CRef<CBlast4_mask> > objects. More... | |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
Private Types | |
| enum | EState { eStart = 0 , eFailed , eWait , eDone } |
| Various states the search can be in. More... | |
| enum | EImmediacy { ePollAsync = 0 , ePollImmed } |
| Indicates whether to use async mode. More... | |
| enum | ENeedConfig { eNoConfig = 0x0 , eProgram = 0x1 , eService = 0x2 , eQueries = 0x4 , eSubject = 0x8 , eNeedAll = 0xF } |
| This class attempts to verify whether all necessary configuration is complete before attempting to submit the search. More... | |
| typedef list< CRef< objects::CBlast4_parameter > > | TValueList |
| Value list. More... | |
| typedef objects::CBlast4_get_search_results_reply | TGSRR |
| An alias for the most commonly used part of the Blast4 search results. More... | |
Private Member Functions | |
| bool | x_HasRetrievedSubjects () const |
| CRef< objects::CBlast4_request_body > | x_GetBlast4SearchRequestBody () |
| Retrieve the request body for a search submission. More... | |
| void | x_SetDatabase (const string &x) |
| Sets a subset (only m_Dbs) of what the public SetDatabase sets. More... | |
| void | x_SetSubjectSequences (const list< CRef< objects::CBioseq > > &subj) |
| Set a list of subject sequences to search against (only m_SubjectSequences) More... | |
| TGSRR::TMasks | x_GetMasks (void) |
| Get the query masks from the results. More... | |
| int | x_DefaultTimeout (void) |
| The default timeout is 3.5 hours. More... | |
| void | x_Init (CNcbiIstream &f) |
| Uses the file to populate results. More... | |
| void | x_Init (CBlastOptionsHandle *algo_opts, const string &program, const string &service) |
| Called by new search constructors: initialize a new search. More... | |
| void | x_Init (CBlastOptionsHandle *algo_opts) |
| Called by new search constructors: initialize a new search. More... | |
| void | x_Init (const string &RID) |
| Called by RID constructor: set up monitoring of existing search. More... | |
| void | x_Init (CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &db) |
| Initialize a search with a database and options handle. More... | |
| void | x_InitQueries (CRef< IQueryFactory > queries) |
| Initialize queries based on a query factory. More... | |
| void | x_InitDiskCache (void) |
| Initialize disk caching. More... | |
| void | x_SetAlgoOpts (void) |
| Configure new search from options handle passed to constructor. More... | |
| void | x_SetOneParam (objects::CBlast4Field &field, const int *value) |
| Set an integer parameter (not used yet). More... | |
| void | x_SetOneParam (objects::CBlast4Field &field, const list< int > *value) |
| Set a list of integers. More... | |
| void | x_SetOneParam (objects::CBlast4Field &field, const list< Int8 > *value) |
| Set a list of 8 byte integers. More... | |
| void | x_SetOneParam (objects::CBlast4Field &field, const char **value) |
| Set a string parameter. More... | |
| void | x_SetOneParam (objects::CBlast4Field &field, CRef< objects::CBlast4_mask > mask) |
| Set a masking location for query. More... | |
| EState | x_GetState (void) |
| Determine what state the search is in. More... | |
| bool | x_IsUnknownRID (void) |
| Determine if this is an unknown RID. More... | |
| TGSRR * | x_GetGSRR (void) |
| Poll until done, return the CBlast4_get_search_results_reply. More... | |
| CRef< objects::CBlast4_reply > | x_SendRequest (CRef< objects::CBlast4_request_body > body) |
| Send a Blast4 request and get a reply. More... | |
| CRef< objects::CBlast4_reply > | x_GetSearchResults (void) |
| Try to get the search results. More... | |
| void | x_CheckConfig (void) |
| Verify that search object contains mandatory fields. More... | |
| void | x_SubmitSearch (void) |
| Submit the search and process results (of submit action). More... | |
| void | x_CheckResults (void) |
| Try to get and process results. More... | |
| void | x_CheckResultsDC (void) |
| Try to get and process results using disk cache. More... | |
| void | x_SearchErrors (CRef< objects::CBlast4_reply > reply) |
| Iterate over error list, splitting into errors and warnings. More... | |
| void | x_PollUntilDone (EImmediacy poll_immed, int seconds) |
| Poll until results are found, error occurs, or timeout expires. More... | |
| void | x_GetRequestInfo () |
| Fetch the request info (wait for completion if necessary). More... | |
| void | x_GetRequestInfoFromRID () |
| Fetch the requested info from splitd. More... | |
| void | x_GetRequestInfoFromFile () |
| Fetch the requested info from an archive file. More... | |
| void | x_ExtractQueryIds (CSearchResultSet::TQueryIdVector &query_ids) |
| Extract the query IDs from the CBlast4_queries for a given search. More... | |
| void | x_SetMaskingLocationsForQueries (const TSeqLocInfoVector &masking_locations) |
| Set the masking locations AFTER the queries have been set in the m_QSR field. More... | |
| void | x_ExtractUserSpecifiedMasks (CRef< IQueryFactory > query_factory, TSeqLocInfoVector &masks) |
| Extract the user specified masking locations from the query factory. More... | |
| void | x_QueryMaskingLocationsToNetwork () |
| Converts the provided query masking locations (if any) to the network representation following the BLAST 4 ASN.1 spec. More... | |
| void | x_ProcessOneOption (CBlastOptionsHandle &opts, const string &nm, const objects::CBlast4_value &v, struct SInteractingOptions &io) |
| Add an algorithm or program option to the provided handle. More... | |
| void | x_ProcessOptions (CBlastOptionsHandle &opts, const TValueList &L, struct SInteractingOptions &io) |
| Add algorithm and program options to the provided handle. More... | |
| EProgram | x_AdjustProgram (const TValueList &L, const string &pstr, EProgram program) |
| Adjust the EProgram based on option values. More... | |
| void | x_GetSubjects (void) |
| string | x_GetStringFromSearchInfoReply (CRef< CBlast4_reply > reply, const string &name, const string &value) |
| unsigned int | x_GetPsiIterationsFromServer (void) |
| CRemoteBlast (const CRemoteBlast &) | |
| Prohibit copy construction. More... | |
| CRemoteBlast & | operator= (const CRemoteBlast &) |
| Prohibit assignment. More... | |
Private Attributes | |
| CRef< blast::CBlastOptionsHandle > | m_CBOH |
| Options for new search. More... | |
| CRef< objects::CBlast4_queue_search_request > | m_QSR |
| Request object for new search. More... | |
| CRef< objects::CBlast4_reply > | m_Reply |
| Results of BLAST search. More... | |
| CRef< objects::CBlast4_archive > | m_Archive |
| Archive of BLAST search and results. More... | |
| bool | m_ReadFile |
| true if a CBlast4_archive should be read in. More... | |
| unique_ptr< CObjectIStream > | m_ObjectStream |
| Use to ready CBlast4_archive. More... | |
| CFormatGuess::EFormat | m_ObjectType |
| Type of object CBlast4_archive as determined by CFormatGuess. More... | |
| vector< string > | m_Errs |
| List of errors encountered. More... | |
| vector< string > | m_Warn |
| List of warnings encountered. More... | |
| string | m_RID |
| Request ID of submitted or pre-existing search. More... | |
| int | m_ErrIgn |
| Count of server glitches (communication errors) to ignore. More... | |
| bool | m_Pending |
| Pending state: indicates that search still needs to be queued. More... | |
| EDebugMode | m_Verbose |
| Verbosity mode: whether to produce debugging info on stdout. More... | |
| ENeedConfig | m_NeedConfig |
| Bitfield to track whether all necessary configuration is done. More... | |
| CRef< objects::CBlast4_database > | m_Dbs |
| Databases. More... | |
| list< CRef< objects::CBioseq > > | m_SubjectSequences |
| Subject Sequences. More... | |
| CBlast4_subject::TSeq_loc_list | m_SubjectSeqLocs |
| This field is populated when dealing with a remote bl2seq search (e.g. More... | |
| string | m_Program |
| Program value used when submitting this search. More... | |
| string | m_Service |
| Service value used when submitting this search. More... | |
| string | m_CreatedBy |
| Created-by attribution for this search. More... | |
| CRef< objects::CBlast4_queries > | m_Queries |
| Queries associated with this search. More... | |
| CRef< objects::CBlast4_parameters > | m_AlgoOpts |
| Options relevant to the search algorithm. More... | |
| CRef< objects::CBlast4_parameters > | m_ProgramOpts |
| Options relevant to the search application. More... | |
| CRef< objects::CBlast4_parameters > | m_FormatOpts |
| Options relevant to the format application. More... | |
| TSeqLocInfoVector | m_QueryMaskingLocations |
| Masking locations for queries. More... | |
| string | m_EntrezQuery |
| Entrez Query, if any. More... | |
| string | m_FirstDbSeq |
| First database sequence. More... | |
| string | m_FinalDbSeq |
| Final database sequence. More... | |
| list< TGi > | m_GiList |
| GI list. More... | |
| list< TGi > | m_NegativeGiList |
| Negative GI list. More... | |
| int | m_DbFilteringAlgorithmId |
| filtering algorithm to use in the database More... | |
| string | m_DbFilteringAlgorithmKey |
| filtering algorithm key to use in the database More... | |
| ESubjectMaskingType | m_SubjectMaskingType |
| string | m_Task |
| Task used when the search was submitted (recovered via CBlastOptionsBuilder) More... | |
| string | m_ClientId |
| Client ID submitting requests throw this interface. More... | |
| bool | m_use_disk_cache |
| Use disk cache for retrieving results default: false. More... | |
| bool | m_disk_cache_error_flag |
| disk cache error flag More... | |
| string | m_disk_cache_error_msg |
| disk cache error message More... | |
| set< TTaxId > | m_TaxidList |
| set< TTaxId > | m_NegativeTaxidList |
Additional Inherited Members | |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Detailed Description
API for Remote Blast Requests.
API Class to facilitate submission of Remote Blast requests. Provides an interface to build a Remote Blast request given an object of a subclass of CBlastOptionsHandle.
Definition at line 93 of file remote_blast.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/remote_blast.hpp
- src/algo/blast/api/remote_blast.cpp
