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

kNumQueries =

(query_data.

());

(kNumQueries == 0) {

(

= 0;

< kNumQueries;

++) {

retval->AddInterval(query_data.

(

)->GetInt());

}

(

.NotEmpty()) {

retval->AddInterval(*

, 0,

);

rps_scale_factor(1.0);

os <<

<<

;

&core_masked_query_regions,

(masked_query_regions) {

core_masked_query_regions,

*masked_query_regions);

rps_info ? (*rps_info)() : 0,

(num_threads));

=

+

=

+

number_of_queries,

(number_of_queries), writer);

(filt_opts) {

(error_str);

partial(

);

errstr =

;

errstr =

;

errstr +=

;

( errstr !=

) {

: kNoPhiBlastPattern(-1)

Auxiliary functions for BLAST.

Declarations for indexed blast databases.

ESubjectMaskingType

Define the possible subject masking types.

#define sfree(x)

Safe free a pointer: belongs to a higher level header.

@ eTracebackSearch

Traceback stage.

@ ePrelimSearch

Preliminary stage.

BlastDiagnostics * Blast_DiagnosticsInitMT(MT_LOCK mt_lock)

Initialize the BlastDiagnostics structure for a multi-threaded search.

BlastDiagnostics * Blast_DiagnosticsInit(void)

Initialize the BlastDiagnostics structure and all its substructures.

BlastSeqLoc * BlastSeqLocFree(BlastSeqLoc *loc)

Deallocate all BlastSeqLoc objects in a chain.

BlastHSPWriter * BlastHSPWriterNew(BlastHSPWriterInfo **writer_info, BlastQueryInfo *query_info, BLAST_SequenceBlk *query)

A generic function to create writer.

BlastHSPPipe * BlastHSPPipeNew(BlastHSPPipeInfo **pipe_info, BlastQueryInfo *query_info)

A generic function to create pipe.

BlastHSPPipeInfo * BlastHSPPipeInfo_Add(BlastHSPPipeInfo **head, BlastHSPPipeInfo *node)

Adds node to the linked list starting a head, which should be NULL when initializing the linked list,...

Declaration of ADT to save and retrieve lists of HSPs in the BLAST engine.

BlastHSPStream * BlastHSPStreamNew(EBlastProgramType program, const BlastExtensionOptions *extn_opts, Boolean sort_on_read, Int4 num_queries, BlastHSPWriter *writer)

Initialize the HSP stream.

Classes that capture the state of the BLAST options (or subsets of options) and restore them later (u...

C++ version of the initialization for the mutex locking interface.

@ eMixedMBLookupTable

use when some volumes are searched with index and some are not

@ eIndexedMBLookupTable

use database index as a lookup structure

Declares class to encapsulate all BLAST options.

Boolean Blast_ProgramIsMapping(EBlastProgramType p)

Boolean Blast_ProgramIsPhiBlast(EBlastProgramType p)

Returns true if program is PHI-BLAST (i.e.

Boolean Blast_ProgramIsRpsBlast(EBlastProgramType p)

Returns true if program is RPS-BLAST (i.e.

Utility function to convert internal BLAST result structures into objects::CSeq_align_set objects.

char * BlastSeqSrcGetInitError(const BlastSeqSrc *seq_src)

Function to retrieve NULL terminated string containing the description of an initialization error or ...

BlastSeqSrc * BlastSeqSrcFree(BlastSeqSrc *seq_src)

Frees the BlastSeqSrc structure by invoking the destructor function set by the user-defined construct...

Utilities initialize/setup BLAST.

Int2 Blast_SetPHIPatternInfo(EBlastProgramType program, const SPHIPatternSearchBlk *pattern_blk, const BLAST_SequenceBlk *query, const BlastSeqLoc *lookup_segments, BlastQueryInfo *query_info, Blast_Message **blast_message)

In a PHI BLAST search, adds pattern information to the BlastQueryInfo structure.

Int2 BLAST_MainSetUp(EBlastProgramType program_number, const QuerySetUpOptions *qsup_options, const BlastScoringOptions *scoring_options, BLAST_SequenceBlk *query_blk, const BlastQueryInfo *query_info, double scale_factor, BlastSeqLoc **lookup_segments, BlastMaskLoc **mask, BlastScoreBlk **sbpp, Blast_Message **blast_message, GET_MATRIX_PATH get_path)

"Main" setup routine for BLAST.

Internal auxiliary setup classes/functions for C++ BLAST APIs.

BlastScoreBlk * BlastScoreBlkFree(BlastScoreBlk *sbp)

Deallocates BlastScoreBlk as well as all associated structures.

Defines BLAST error codes (user errors included)

Wrapper class for BlastMaskLoc .

Class that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLA...

Wrapper class to manage the BlastRPSInfo structure, as currently there aren't any allocation or deall...

BlastSeqLoc * getLocs() const

Get access to the held object.

Wrapper class for Blast_Message .

Provides access (not ownership) to the C structures used to configure local BLAST search class implem...

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

@ eNoCompositionBasedStats

Don't use composition based statistics.

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

Get the Seq_loc for the sequence indicated by index.

int GetGapExtensionCost() const

Returns the gap extension cost associated with the scoring matrix above.

void Blast_GetSeqLocInfoVector(EBlastProgramType program, const objects::CPacked_seqint &queries, const BlastMaskLoc *mask, TSeqLocInfoVector &mask_v)

Converts a BlastMaskLoc internal structure into an object returned by the C++ API.

static BlastHSPPipe * CreateHspPipe(const CBlastOptionsMemento *opts_memento, BlastQueryInfo *query_info)

Create a pipe to be registered for use by stream.

DbIndexSetQueryInfoFnType GetDbIndexSetQueryInfoFn()

Return the appropriate callback to set query information in the index.

static BlastDiagnostics * CreateDiagnosticsStructure()

Create and initialize the BlastDiagnostics structure for single-threaded applications.

static CRef< CBlastRPSInfo > CreateRpsStructures(const string &rps_dbname, CRef< CBlastOptions > options)

Initializes RPS-BLAST data structures.

int GetFilteringAlgorithm() const

Accessor for the filtering algorithm ID.

static CRef< CPacked_seqint > s_LocalQueryData2Packed_seqint(ILocalQueryData &query_data)

Auxiliary function to extract the Seq-ids from the ILocalQueryData and bundle them in a Packed-seqint...

void AddMessageAllQueries(EBlastSeverity severity, int error_id, const string &message)

Add a message for all queries.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

const string GetIndexName() const

void SetGapOpeningCost(int g)

BlastSeqSrc * SeqDbBlastSeqSrcInit(const string &dbname, bool is_prot, Uint4 first_seq=0, Uint4 last_seq=0, Int4 mask_algo_id=-1, ESubjectMaskingType mask_type=eNoSubjMasking)

Initialize the sequence source structure.

double GetScalingFactor() const

Returns the scaling factor used to build RPS-BLAST database.

static void InitializeMegablastDbIndex(CRef< CBlastOptions > options)

Initialize a megablast BLAST database index.

virtual BLAST_SequenceBlk * GetSequenceBlk()=0

Accessor for the BLAST_SequenceBlk structure.

void Blast_Message2TSearchMessages(const Blast_Message *blmsg, const BlastQueryInfo *query_info, TSearchMessages &messages)

Converts the Blast_Message structure into a TSearchMessages object.

static BlastDiagnostics * CreateDiagnosticsStructureMT()

Create and initialize the BlastDiagnostics structure for multi-threaded applications.

void SetGapExtensionCost(int e)

void SetUseIndex(bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false)

static LookupTableWrap * CreateLookupTable(CRef< ILocalQueryData > query_data, const CBlastOptionsMemento *opts_memento, BlastScoreBlk *score_blk, CRef< CBlastSeqLocWrap > lookup_segments, const CBlastRPSInfo *rps_info=NULL, BlastSeqSrc *seqsrc=NULL, size_t num_threads=1)

Initialize the lookup table.

static BlastScoreBlk * CreateScoreBlock(const CBlastOptionsMemento *opts_memento, CRef< ILocalQueryData > query_data, BlastSeqLoc **lookup_segments, TSearchMessages &search_messages, TSeqLocInfoVector *masked_query_regions=NULL, const CBlastRPSInfo *rps_info=NULL)

Initializes the BlastScoreBlk.

void SetMatrixName(const char *matrix)

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

static BlastSeqSrc * CreateBlastSeqSrc(const CSearchDatabase &db)

Create a BlastSeqSrc from a CSearchDatabase (uses CSeqDB)

BlastExtensionOptions * m_ExtnOpts

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

string ToString() const

Converts messages to a string, which is returned.

BLAST_SequenceBlk * m_Queries

The query sequence data, these fields are "borrowed" from the query factory (which owns them)

std::string DbIndexInit(const string &indexname, bool old_style, bool &partial, const int word_size)

BlastHitSavingOptions * m_HitSaveOpts

BlastQueryInfo * m_QueryInfo

The query information structure.

ESubjectMaskingType GetMaskType() const

char * BlastFindMatrixPath(const char *matrix_name, Boolean is_prot)

Returns the path to a specified matrix.

virtual size_t GetNumQueries()=0

Get the number of queries.

static BlastHSPWriter * CreateHspWriter(const CBlastOptionsMemento *opts_memento, BLAST_SequenceBlk *query, BlastQueryInfo *query_info)

Create a writer to be registered for use by stream.

static BlastHSPStream * CreateHspStream(const CBlastOptionsMemento *opts_memento, size_t number_of_queries, BlastHSPWriter *writer)

Create and initialize the BlastHSPStream structure.

ECompoAdjustModes GetCompositionBasedStats() const

unsigned char GetMBTemplateLength() const

Megablast only lookup table options.

EBlastProgramType m_ProgramType

bool GetMBIndexLoaded() const

virtual size_t GetSeqLength(size_t index)=0

Get the length of the sequence indicated by index.

SInternalData()

Default ctor.

const int kNoPhiBlastPattern

set to -1 in ctor, indicate that m_NumPatOccurInDB is unset or not applicable.

BlastScoringOptions * m_ScoringOpts

const char * GetMatrixName() const

Returns the name of the scoring matrix used to build the RPS-BLAST database.

QuerySetUpOptions * m_QueryOpts

LookupTableOptions * m_LutOpts

void SetMBIndexLoaded(bool index_loaded=true)

Blast_Message * Get() const

MT_LOCK Blast_CMT_LOCKInit(void)

Initialize a mutex locking mechanism for BLAST.

int m_NumPatOccurInDB

Number of times pattern found to occur in database (for phi-blast only).

bool GetIsOldStyleMBIndex() const

EOpenFlags

Flags for opening database files.

void SetLookupTableType(ELookupTableType type)

SDatabaseScanData()

Default ctor.

int GetGapOpeningCost() const

Returns the gap opening cost associated with the scoring matrix above.

@ fRpsBlastWithCBS

Flags set for RPS-BLAST running in CBS mode.

@ fRpsBlast

Flags set for RPS-BLAST.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ERR_POST_EX(err_code, err_subcode, message)

Error posting with error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

int16_t Int2

2-byte (16-bit) signed integer

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned 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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

BlastHSPPipeInfo * BlastHSPBestHitPipeInfoNew(BlastHSPBestHitParams *params)

BlastHSPWriterInfo * BlastHSPBestHitInfoNew(BlastHSPBestHitParams *params)

WriterInfo and PipeInfo to create a best hit writer/pipe.

BlastHSPBestHitParams * BlastHSPBestHitParamsNew(const BlastHitSavingOptions *hit_options, const BlastHSPBestHitOptions *best_hit_opts, Int4 compositionBasedStats, Boolean gapped_calculation)

create a set of parameters

Implementation of a number of BlastHSPWriters to save hits from a BLAST search, and subsequently retu...

BlastHSPCollectorParams * BlastHSPCollectorParamsNew(const BlastHitSavingOptions *hit_options, Int4 compositionBasedStats, Boolean gapped_calculation)

Sets up parameter set for use by collector.

BlastHSPWriterInfo * BlastHSPCollectorInfoNew(BlastHSPCollectorParams *params)

WriterInfo to create a default writer: the collecter.

Implementation of the BlastHSPWriter interface to perform culling.

BlastHSPWriterInfo * BlastHSPCullingInfoNew(BlastHSPCullingParams *params)

WriterInfo and PipeInfo to create a best hit writer/pipe.

BlastHSPCullingParams * BlastHSPCullingParamsNew(const BlastHitSavingOptions *hit_options, const BlastHSPCullingOptions *best_hit_opts, Int4 compositionBasedStats, Boolean gapped_calculation)

create a set of parameters

BlastHSPPipeInfo * BlastHSPCullingPipeInfoNew(BlastHSPCullingParams *params)

Implementation of a number of BlastHSPWriters to save the best chain of RNA-Seq hits to a genome.

BlastHSPWriterInfo * BlastHSPMapperInfoNew(BlastHSPMapperParams *params)

WriterInfo to create a default writer: the collecter.

BlastHSPMapperParams * BlastHSPMapperParamsNew(const BlastHitSavingOptions *hit_options, const BlastScoringOptions *scoring_options)

Sets up parameter set for use by collector.

Int2 LookupTableWrapInit_MT(BLAST_SequenceBlk *query, const LookupTableOptions *lookup_options, const QuerySetUpOptions *query_options, BlastSeqLoc *lookup_segments, BlastScoreBlk *sbp, LookupTableWrap **lookup_wrap_ptr, const BlastRPSInfo *rps_info, Blast_Message **error_msg, BlastSeqSrc *seqsrc, Uint4 num_threads)

Create the lookup table for all query words (possibly multithreaded, depends on implementation).

#define TRUE

bool replacment for C indicating true.

vector< TMaskedQueryRegions > TSeqLocInfoVector

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

Implementation of the BlastSeqSrc interface using the C++ BLAST databases API.

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

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

Structure to hold a sequence.

Return statistics from the BLAST search.

Int4 compositionBasedStats

mode of compositional adjustment to use; if zero then compositional adjustment is not used

Keeps parameters used in best hit algorithm.

double overhang

overhang used in condition 1.

Keeps prelim_hitlist_size and HitSavingOptions together.

Keeps parameters used in best hit algorithm.

Int4 culling_max

number of HSPs allowed per query region.

Structure containing the HSP filtering/writing options.

EBlastStage culling_stage

BlastHSPBestHitOptions * best_hit

Best Hit algorithm.

EBlastStage best_hit_stage

BlastHSPCullingOptions * culling_opts

culling algorithm

Keeps prelim_hitlist_size and HitSavingOptions together.

A wrap of data structure used to create a pipe.

ADT definition of BlastHSPPipe.

Default implementation of BlastHSPStream.

A wrap of data structure used to create a writer.

ADT definition of BlastHSPWriter.

BlastHSPFilteringOptions * hsp_filt_opt

Contains options to configure the HSP filtering/writering structures If not set, the default HSP filt...

The query related information.

Structure used for scoring calculations.

Boolean gapped_calculation

gap-free search if FALSE

char * matrix

Name of the matrix containing all scores: needed for finding neighboring words.

Used to hold a set of positions, mostly used for filtering.

Complete type definition of Blast Sequence Source ADT.

EBlastSeverity severity

severity code

Wrapper structure for different types of BLAST lookup tables.

void * lut

Pointer to the actual lookup table structure.

Structure containing all auxiliary information needed in a pattern search.

Uniform BLAST Search Interface.

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