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NCBI C++ ToolKit: src/algo/blast/api/local_blast.cpp Source File

* chunk_sz_str = getenv(

);

(

<< retval);

);

: m_QueryFactory (qf),

m_Opts (const_cast<

*>(&opts_handle->GetOptions())),

: m_QueryFactory (qf),

m_Opts (const_cast<

*>(&opts_handle->GetOptions())),

m_LocalDbAdapter (db.GetNonNullPointer())

: m_QueryFactory (qf),

m_Opts (const_cast<

*>(&opts_handle->GetOptions())),

m_SeqInfoSrc (seqInfoSrc)

db_name.assign(seqsrc_name);

(db_name.empty()) {

vector< CConstRef<objects::CSeq_id> > seqid_vec;

vector< CRef<CBlastAncillaryData> > ancill_vec;

num_subjects = 0;

(subject_infosrc !=

) {

num_subjects =

(subject_infosrc->

());

(index=0; index<local_query_data->

(); index++)

msg_vec.push_back(q_msg);

seqid_vec.push_back(query_id);

sa_vec.push_back(tmp_align);

pair<double, double> tmp_pair(-1.0, -1.0);

ancill_vec.push_back(tmp_ancillary_data);

(

=1;

< num_subjects;

++)

msg_vec.push_back(

);

seqid_vec.push_back(query_id);

sa_vec.push_back(tmp_align);

ancill_vec.push_back(tmp_ancillary_data);

(std::exception & e) {

User-defined methods of the data storage class.

Auxiliary functions for BLAST.

Declarations for indexed blast databases.

#define CODON_LENGTH

Codons are always of length 3.

BlastDiagnostics * Blast_DiagnosticsCopy(const BlastDiagnostics *diagnostics)

Free the BlastDiagnostics structure and all substructures.

#define BLASTERR_DB_MEMORY_MAP

Database file error.

#define BLASTERR_DB_TOO_MANY_OPEN_FILES

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

EBlastProgramType

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

Boolean Blast_SubjectIsPssm(EBlastProgramType p)

Returns true if the subject is PSSM.

Defines interface for retrieving sequence identifiers.

Boolean BlastSeqSrcGetIsProt(const BlastSeqSrc *seq_src)

Find if the Blast Sequence Source contains protein or nucleotide sequences.

const char * BlastSeqSrcGetName(const BlastSeqSrc *seq_src)

Get the Blast Sequence source name (e.g.

vector< CRef< objects::CSeq_align_set > > TSeqAlignVector

Vector of Seq-align-sets.

EResultType

Specifies the style of Seq-aligns that should be built from the internal BLAST data structures.

@ eDatabaseSearch

Seq-aligns in the style of a database search.

@ eSequenceComparison

Seq-aligns in the BLAST 2 Sequence style (one alignment per query-subject pair)

EProgram

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

@ eVecScreen

Vector screening.

@ eTblastx

Translated nucl-Translated nucl.

@ eBlastn

Nucl-Nucl (traditional blastn)

@ eBlastp

Protein-Protein.

@ eMapper

Jumper alignment for mapping.

@ eTblastn

Protein-Translated nucl.

@ eMegablast

Nucl-Nucl (traditional megablast)

@ eDiscMegablast

Nucl-Nucl using discontiguous megablast.

@ eBlastx

Translated nucl-Protein.

Class used to return ancillary data from a blast search, i.e.

Defines BLAST error codes (user errors included)

Encapsulates ALL the BLAST algorithm's options.

Search class to perform the preliminary stage of the BLAST search.

Index wrapper exceptions.

Search Results for All Queries.

@ eTooManyOpenFiles

Too many open files.

Implementation of the IBlastSeqInfoSrc interface to encapsulate retrieval of sequence identifiers and...

Abstract base class to encapsulate retrieval of sequence identifiers.

Class for the messages for an individual query sequence.

typedef for the messages for an entire BLAST search, which could be comprised of multiple query seque...

virtual CConstRef< objects::CSeq_loc > GetSeq_loc(size_t index)=0

Get the Seq_loc for the sequence indicated by index.

int CheckInternalData()

Checks that internal data is valid.

size_t GetNumberOfThreads(void) const

Accessor for the number of threads to use.

CRef< IBlastSeqInfoSrc > m_SeqInfoSrc

User-specified IBlastSeqInfoSrc implementation (may be used for non-standard databases,...

virtual void SetNumberOfThreads(size_t nthreads)

Mutator for the number of threads.

CRef< SInternalData > m_InternalData

Internal core data structures which are used in the preliminary and traceback stages of the search.

CRef< CBlastPrelimSearch > m_PrelimSearch

Object which runs the preliminary stage of the search.

string BlastErrorCode2String(Int2 error_code)

Returns a string containing a human-readable interpretation of the error_code passed as this function...

CLocalBlast(CRef< IQueryFactory > query_factory, CRef< CBlastOptionsHandle > opts_handle, const CSearchDatabase &dbinfo)

Constructor with database description.

CRef< SInternalData > Run()

Borrow the internal data and results results.

CRef< TBlastSeqSrc > m_SeqSrc

The source of subject sequence data.

TSearchMessages GetSearchMessages() const

Retrieve any error/warning messages that occurred during the search.

CRef< CSearchResultSet > Run()

Executes the search.

CRef< CSearchResultSet > Run()

Run the traceback search.

CRef< CBlastOptions > m_Opts

Options to use.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

TSearchMessages m_Messages

Warnings and error messages.

bool IsBlastDb() const

Returns true if this object represents a BLAST database.

BlastDiagnostics * GetDiagnostics()

Get the diagnostics structure (deep copy, needs to be deleted by caller)

void SetResultType(EResultType type)

Specifies how the Seq-align-set returned as part of the results is formatted.

virtual void SetNumberOfThreads(size_t nthreads)

@inheritDoc

EBlastProgramType EProgramToEBlastProgramType(EProgram p)

Convert EProgram to EBlastProgramType.

static IBlastSeqInfoSrc * s_InitSeqInfoSrc(const BlastSeqSrc *seqsrc)

FIXME: this should be removed as soon as we safely can We will be able to do this once we are guarant...

size_t SplitQuery_GetChunkSize(EProgram program)

Returns the optimal chunk size for a given task.

void Combine(const TSearchMessages &other_msgs)

Combine another set of search messages with this one.

void SetFilteredQueryRegions(const TSeqLocInfoVector &masks)

Sets the filtered query regions.

CRef< CBlastTracebackSearch > m_TbackSearch

Object which runs the traceback stage of the search.

IBlastSeqInfoSrc * MakeSeqInfoSrc()

Retrieves or constructs the IBlastSeqInfoSrc.

string EProgramToTaskName(EProgram p)

Convert a EProgram enumeration value to a task name (as those used in the BLAST command line binaries...

std::string m_batch_num_str

virtual size_t GetNumQueries()=0

Get the number of queries.

TSeqLocInfoVector GetFilteredQueryRegions() const

Retrieve the filtered/masked query regions.

virtual size_t Size() const =0

Returns the size of the underlying container of sequences.

void GetQueryMessages(size_t index, TQueryMessages &qmsgs)

Retrieve error/warning messages for a specific query.

CRef< TBlastDiagnostics > m_Diagnostics

Diagnostic output from preliminary and traceback stages.

TSearchMessages GetSearchMessages() const

Retrieve any error/warning messages that occurred during the search.

Int4 GetNumExtensions()

Retrieve the number of extensions performed during the search.

CRef< CLocalDbAdapter > m_LocalDbAdapter

Local DB adaptor (if one was) passed to constructor.

CRef< IQueryFactory > m_QueryFactory

Query factory from which to obtain the query sequence data.

bool IsDbScanMode() const

Returns true if this is not a database but is database scanning mode.

@ eCoreBlastError

FIXME: need to interpret CORE errors.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

int32_t Int4

4-byte (32-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

Main class to perform a BLAST search on the local machine.

#define BLAST_PROF_MARK2(marker_val)

Defines a concrete strategy for the IBlastSeqInfoSrc interface for sequence identifiers retrieval fro...

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Return statistics from the BLAST search.

BlastUngappedStats * ungapped_stat

Ungapped extension counts.

Complete type definition of Blast Sequence Source ADT.

Int4 good_init_extends

Number of successful initial extensions, i.e.

Uniform BLAST Search Interface.

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