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NCBI C++ ToolKit: include/algo/blast/api/remote_blast.hpp Source File

SInteractingOptions;

SetGIList(

list<TGi> & gi_list);

SetNegativeGIList(

list<TGi> & gi_list);

SetDatabase(

& x);

SetEntrezQuery(

* x);

objects::CBlast4_get_search_results_reply::TMasks

vector<string>* warnings =

);

SubmitSync(

);

SubmitSync(

timeout);

ESearchStatus CheckStatus();

CheckDone(

);

GetErrors(

);

GetWarnings(

);

vector<string> & GetWarningVector();

vector<string> & GetErrorVector();

& GetRID(

);

list< string > GetSearchStats(

);

SetVerbose(EDebugMode verb = eDebug);

list< CRef<objects::CBioseq> > GetSubjectSequences();

GetCreatedBy();

m_DbFilteringAlgorithmId;

m_DbFilteringAlgorithmKey;

(

& client_id) { m_ClientId = client_id; }

LoadFromArchive();

GetPsiNumberOfIterations(

);

IsErrMsgArchive(

);

!m_SubjectSeqLocs.empty() || !m_SubjectSequences.empty();

x_SetDatabase(

& x);

list< CRef<objects::CBlast4_parameter> >

;

objects::CBlast4_get_search_results_reply

;

TGSRR::TMasks x_GetMasks(

);

x_DefaultTimeout(

);

& program,

& service);

x_Init(

& RID);

x_InitDiskCache(

);

x_SetAlgoOpts(

);

x_SetOneParam(objects::CBlast4Field & field,

*

);

x_SetOneParam(objects::CBlast4Field & field,

list<int> *

);

x_SetOneParam(objects::CBlast4Field & field,

list<Int8> *

);

x_SetOneParam(objects::CBlast4Field & field,

**

);

x_GetState(

);

x_IsUnknownRID(

);

TGSRR * x_GetGSRR(

);

x_GetSearchResults(

);

x_CheckConfig(

);

x_SubmitSearch(

);

x_CheckResults(

);

x_CheckResultsDC(

);

x_PollUntilDone(EImmediacy poll_immed,

seconds);

x_GetRequestInfo();

x_GetRequestInfoFromRID();

x_GetRequestInfoFromFile();

x_QueryMaskingLocationsToNetwork();

objects::CBlast4_value & v,

SInteractingOptions & io);

SInteractingOptions & io);

x_GetSubjects(

);

&

);

x_GetPsiIterationsFromServer(

);

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

ESubjectMaskingType

Define the possible subject masking types.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

ncbi::TMaskedQueryRegions mask

Defines BLAST error codes (user errors included)

Handle to the options to the BLAST algorithm.

EFormat

The formats are checked in the same order as declared here.

Exception class for the CRemoteBlast class.

API for Remote Blast Requests.

list< CRef< objects::CBlast4_parameter > > TValueList

Value list.

objects::CBlast4_get_search_results_reply TGSRR

An alias for the most commonly used part of the Blast4 search results.

ENeedConfig m_NeedConfig

Bitfield to track whether all necessary configuration is done.

list< CRef< objects::CBioseq > > m_SubjectSequences

Subject Sequences.

CRef< objects::CBlast4_queries > m_Queries

Queries associated with this search.

objects::EBlast4_frame_type FrameNumber2NetworkFrame(int frame, EBlastProgramType program)

Converts the return value of CSeqLocInfo::GetFrame into the Blast4-frame-type field.

list< CRef< objects::CBlast4_ka_block > > TKarlinAltschulBlocks

Convenience typedef for a list of CRef<CBlast4_ka_block>

void EnableDiskCacheUse()

Controls disk cache usage for results retrieval.

list< TGi > m_GiList

GI list.

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.

EErrCode

Error types that BLAST can generate.

string m_RID

Request ID of submitted or pre-existing search.

TSeqLocInfoVector m_QueryMaskingLocations

Masking locations for queries.

list< TGi > m_NegativeGiList

Negative GI list.

CFormatGuess::EFormat m_ObjectType

Type of object CBlast4_archive as determined by CFormatGuess.

bool m_use_disk_cache

Use disk cache for retrieving results default: false.

ENeedConfig

This class attempts to verify whether all necessary configuration is complete before attempting to su...

CRef< objects::CBlast4_archive > m_Archive

Archive of BLAST search and results.

set< TTaxId > & GetNegativeTaxidList()

CRemoteBlast & operator=(const CRemoteBlast &)

Prohibit assignment.

CRef< blast::CBlastOptionsHandle > m_CBOH

Options for new search.

string GetTask() const

Returns the task used to create the remote search (if any)

ESearchStatus

Represents the status of previously submitted search/RID.

vector< CConstRef< objects::CSeq_id > > TQueryIdVector

List of query ids.

CRef< objects::CBlast4_parameters > m_FormatOpts

Options relevant to the format application.

vector< string > m_Warn

List of warnings encountered.

EDebugMode

Debugging support can be turned on with eDebug or off with eSilent.

void SetClientId(const string &client_id)

Sets the client ID used by this object to send requests.

int m_DbFilteringAlgorithmId

filtering algorithm to use in the database

EDebugMode m_Verbose

Verbosity mode: whether to produce debugging info on stdout.

EImmediacy

Indicates whether to use async mode.

set< TTaxId > m_NegativeTaxidList

vector< string > m_Errs

List of errors encountered.

string GetDiskCacheErrorMessahe(void)

virtual const char * GetErrCodeString(void) const override

Translate from the error code value to its string representation.

void FlattenBioseqSet(const CBioseq_set &bss, list< CRef< CBioseq > > &seqs)

void SetQueries(TSeqLocList &seqlocs)

Set the query as a list of Seq_locs.

unique_ptr< CObjectIStream > m_ObjectStream

Use to ready CBlast4_archive.

CRef< objects::CBlast4_request > ExtractBlast4Request(CNcbiIstream &in)

Extract a Blast4-request (a.k.a.

string m_Service

Service value used when submitting this search.

bool m_ReadFile

true if a CBlast4_archive should be read in.

CBlast4_subject::TSeq_loc_list m_SubjectSeqLocs

This field is populated when dealing with a remote bl2seq search (e.g.

string m_FinalDbSeq

Final database sequence.

CRef< objects::CBlast4_parameters > m_AlgoOpts

Options relevant to the search algorithm.

string m_FirstDbSeq

First database sequence.

CRemoteBlast(const CRemoteBlast &)

Prohibit copy construction.

NCBI_EXCEPTION_DEFAULT(CRemoteBlastException, CBlastException)

bool IsDiskCacheActive(void)

CRef< objects::CBlast4_database > m_Dbs

Databases.

EBlastProgramType NetworkProgram2BlastProgramType(const string &program, const string &service)

Function to convert from program and service name into the CORE BLAST program type This is based on t...

string m_ClientId

Client ID submitting requests throw this interface.

CRef< objects::CBlast4_parameters > m_ProgramOpts

Options relevant to the search application.

string GetDbFilteringAlgorithmKey() const

Returns the filtering algorithm key used in the database.

vector< CRef< objects::CSeq_data > > TSeqDataVector

Defines a std::vector of CRef<CSeq_data>

EProgram x_AdjustProgram(const TValueList &L, const string &pstr, EProgram program)

Adjust the EProgram based on option values.

CRef< objects::CBlast4_queue_search_request > m_QSR

Request object for new search.

set< TTaxId > m_TaxidList

string m_DbFilteringAlgorithmKey

filtering algorithm key to use in the database

CRef< objects::CBlast4_reply > m_Reply

Results of BLAST search.

void DisableDiskCacheUse()

list< CRef< objects::CSeq_loc > > TSeqLocList

Typedef for a list of Seq-locs.

void x_ProcessOptions(CBlastOptionsHandle &opts, const TValueList &L, struct SInteractingOptions &io)

Add algorithm and program options to the provided handle.

vector< CRef< objects::CSeq_interval > > TSeqIntervalVector

Defines a std::vector of CRef<CSeq_interval>

string m_disk_cache_error_msg

disk cache error message

void SetQueries(TSeqLocList &seqlocs, const TSeqLocInfoVector &masking_locations)

Set the query as a list of Seq_locs.

set< TTaxId > & GetTaxidList()

bool m_Pending

Pending state: indicates that search still needs to be queued.

string m_Task

Task used when the search was submitted (recovered via CBlastOptionsBuilder)

bool m_disk_cache_error_flag

disk cache error flag

Int4 GetDbFilteringAlgorithmId() const

Returns the filtering algorithm ID used in the database.

ESubjectMaskingType m_SubjectMaskingType

string m_Program

Program value used when submitting this search.

string m_EntrezQuery

Entrez Query, if any.

bool x_HasRetrievedSubjects() const

string m_CreatedBy

Created-by attribution for this search.

string GetClientId() const

Retrieves the client ID used by this object to send requests.

int m_ErrIgn

Count of server glitches (communication errors) to ignore.

bool IsDiskCacheError(void)

disk cache error handling

void ClearDiskCacheError(void)

CSeqLocInfo::ETranslationFrame NetworkFrame2FrameNumber(objects::EBlast4_frame_type frame, EBlastProgramType program)

Converts Blast4-frame-type into CSeqLocInfo::ETranslationFrame.

@ eStatus_Pending

Not completed yet.

@ eStatus_Unknown

Never submitted or purged from the system.

@ eStatus_Done

Completed successfully.

@ eServiceNotAvailable

Service is not available.

@ eIncompleteConfig

Remote BLAST object not fully configured.

TErrCode GetErrCode(void) const

Get error code.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

EBlast4_frame_type

Access to EBlast4_frame_type's attributes (values, names) as defined in spec.

list< CRef< CSeq_loc > > TSeq_loc_list

Names used in blast4 network communications.

const GenericPointer< typename T::ValueType > T2 value

std::istream & in(std::istream &in_, double &x_)

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

Uniform BLAST Search Interface.

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