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

: m_TSeqLocVector(&v),

m_OwnTSeqLocVector(

),

m_CalculatedMasks(

),

x_AutoDetectGeneticCodes();

: m_TSeqLocVector(&v),

m_OwnTSeqLocVector(

),

m_CalculatedMasks(

),

m_Program(opts->GetProgramType())

m_OwnTSeqLocVector(

),

m_CalculatedMasks(

),

: m_QueryVector(& v),

m_OwnTSeqLocVector(

),

m_CalculatedMasks(

),

m_Program(opts->GetProgramType())

*

= sseqloc->seqloc->GetId();

desc_it(sseqloc->scope->GetBioseqHandle(*

),

* warnings)

(

)

+

(

)->AsFastaString() +

);

scope = (*m_TSeqLocVector)[

].scope;

( !seqloc->

() ) {

title = (*desc)->GetTitle();

strand_opt, messages);

vector<BLAST_SequenceBlk*>* seqblk_vec,

* max_subjlen)

[16] = {0xFF, 0x00, 0x01, 0xFF, 0x02, 0xFF, 0xFF, 0xFF,

0x03, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF, 0xFF };

* ncbi2na)

(

= 0;

< inp_bytes;

++) {

inp = ncbi4na[

];

= inp & 0xF;

c =

[

];

(

== 0 ||

== 0x0F) {

ncbi2na[

] = random.

() & 0x3;

bitcount = ((

& 1) + ((

>> 1) & 1) +

((

>> 2) & 1) + ((

>> 3) & 1));

pick = random.

() % bitcount;

(

j = 0; j < 4; j++) {

((

& (1 << j)) == 0)

objects::CScope* scope,

(sequences.empty()) {

(seq->seqloc->IsWhole()) {

}

(seq->seqloc->IsInt()) {

);

retval->AddInterval(

, range.

(), range.

());

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent ...

Definitions which are dependant on the NCBI C++ Object Manager.

#define BLAST_GENETIC_CODE

Default genetic code for query and/or database.

Declares class to encapsulate all BLAST options.

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

Boolean Blast_QueryIsNucleotide(EBlastProgramType p)

Returns true if the query is nucleotide.

EBlastProgramType

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

Boolean Blast_SubjectIsTranslated(EBlastProgramType p)

Returns true if the subject is translated.

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

Defines interface for retrieving sequence identifiers.

Declarations of auxiliary functions using IBlastSeqInfoSrc to retrieve ids and related sequence infor...

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

ncbi::TMaskedQueryRegions mask

int GetGenCode(int def=1) const

Defines BLAST error codes (user errors included)

Encapsulates ALL the BLAST algorithm's options.

Implements the object manager dependant version of the IBlastQuerySource.

CRef< objects::CScope > GetScope(size_type i) const

Get the scope containing a query by index.

TMaskedQueryRegions GetMaskedRegions(size_type i) const

Get the masked regions for a query by number.

size_type Size() const

Returns the number of queries found in this query vector.

vector< value_type >::size_type size_type

size_type type definition

CConstRef< objects::CSeq_loc > GetQuerySeqLoc(size_type i) const

Get the query Seq-loc for a query by index.

CRef< CBlastSearchQuery > GetBlastSearchQuery(size_type i) const

Get the CBlastSearchQuery object at index i.

Implementation of the IBlastSeqVector interface which obtains data from a CSeq_loc and a CScope relyi...

Thrown on an attempt to write unassigned data member.

Lightweight wrapper around sequence data which provides a CSeqVector-like interface to the data.

Collection of masked regions for a single query sequence.

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

API (CDeflineGenerator) for computing sequences' titles ("definitions").

static int base_length[29]

Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.

CRef< objects::CPacked_seqint > TSeqLocVector2Packed_seqint(const TSeqLocVector &sequences)

Converts a TSeqLocVector into a CPacked_seqint.

virtual CConstRef< objects::CSeq_loc > GetSeqLoc(int i) const

Return the CSeq_loc associated with a sequence.

virtual const objects::CSeq_id * GetSeqId(int index) const

Return the sequence identifier associated with a sequence.

int GetWindowMaskerTaxId() const

Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherw...

void SetupQueries_OMF(IBlastQuerySource &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)

ObjMgr Free version of SetupQueries.

void SetupSubjects(TSeqLocVector &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Sets up internal subject data structure for the BLAST search.

virtual TSeqPos GetLength(int i) const

Return the length of a sequence.

virtual void GetStrandData(objects::ENa_strand strand, unsigned char *buf)

@inheritDoc

EBlastEncoding

Different types of sequence encodings for sequence retrieval from the BLAST database.

SBlastSequence GetSequence_OMF(IBlastSeqVector &sv, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, std::string *warnings=0)

Object manager free version of GetSequence.

TMaskedQueryRegions PackedSeqLocToMaskedQueryRegions(CConstRef< objects::CSeq_loc > sloc, EBlastProgramType program, bool assume_both_strands=false)

Auxiliary function to convert a Seq-loc describing masked query regions to a TMaskedQueryRegions obje...

int GetDustFilteringLevel() const

void SetupSubjects_OMF(IBlastQuerySource &subjects, EBlastProgramType program, vector< BLAST_SequenceBlk * > *seqblk_vec, unsigned int *max_subjlen)

Object manager free version of SetupSubjects.

TSeqLocVector * m_TSeqLocVector

Reference to input TSeqLocVector (or NULL if not used)

virtual string GetTitle(int index) const

Return the title of a sequence.

virtual SBlastSequence GetBlastSequence(int i, EBlastEncoding encoding, objects::ENa_strand strand, ESentinelType sentinel, string *warnings=0) const

Return the sequence data for a sequence.

CBlastQuerySourceOM(TSeqLocVector &v, EBlastProgramType prog)

Constructor which takes a TSeqLocVector.

objects::ENa_strand m_Strand

Maintains the state of the strand currently saved by the implementation of this class.

CBlastSeqVectorOM(const CSeq_loc &seqloc, CScope &scope)

void SetupQueries(TSeqLocVector &queries, BlastQueryInfo *qinfo, BLAST_SequenceBlk **seqblk, EBlastProgramType prog, objects::ENa_strand strand_opt, TSearchMessages &messages)

Populates BLAST_SequenceBlk with sequence data for use in CORE BLAST.

virtual void SetCoding(CSeq_data::E_Choice coding)

@inheritDoc

virtual SBlastSequence GetCompressedPlusStrand()

@inheritDoc

CRef< CBlastQueryVector > m_QueryVector

Reference to input CBlastQueryVector (or empty if not used)

virtual Uint1 operator[](TSeqPos pos) const

@inheritDoc

virtual TMaskedQueryRegions GetMaskedRegions(int i)

Return the filtered (masked) regions for a sequence.

const CBlastOptions * m_Options

BLAST algorithm options.

virtual TSeqPos x_Size() const

@inheritDoc

const CSeq_loc & m_SeqLoc

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

void x_SetStrand(ENa_strand s)

@inheritDoc

TAutoUint1Ptr data

Sequence data.

void x_AutoDetectGeneticCodes(void)

Tries to extract the genetic code using the CScope, if it succeeds, it supercedes what's specified in...

ESentinelType

Allows specification of whether sentinel bytes should be used or not.

bool GetDustFiltering() const

void Blast_FindWindowMaskerLoc(CBlastQueryVector &query, const CBlastOptions *opts)

Find Window Masker filtered locations using a BlastOptions.

virtual Uint4 GetGeneticCodeId(int index) const

Retrieve the genetic code associated with a sequence.

int GetQueryGeneticCode() const

void x_FixStrand(objects::ENa_strand &strand) const

If the Seq-loc is on the minus strand and the user is asking for the minus strand,...

CRef< objects::CSeq_loc > MaskedQueryRegionsToPackedSeqLoc(const TMaskedQueryRegions &sloc)

Interface to build a CSeq-loc from a TMaskedQueryRegion; note that conversion conversion in this dire...

void Blast_FindRepeatFilterLoc(TSeqLocVector &query_loc, const CBlastOptionsHandle *opts_handle)

Finds repeats locations for a given set of sequences.

static unsigned char ctable[16]

virtual objects::ENa_strand GetStrand(int i) const

Return strand for a sequence.

void SetupQueryInfo(TSeqLocVector &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)

Allocates the query information structure and fills the context offsets, in case of multiple queries,...

int GetDustFilteringLinker() const

void Blast_FindDustFilterLoc(TSeqLocVector &queries, const CBlastNucleotideOptionsHandle *nucl_handle)

Finds dust locations for a given set of sequences by calling the the symmetric dust lib.

const char * GetWindowMaskerDatabase() const

Return the name of the windowmasker database to use.

void x_CalculateMasks()

Performs filtering on the query sequences to calculate the masked locations.

bool GetRepeatFiltering() const

Returns true if repeat filtering is on.

bool m_CalculatedMasks

this flag allows for lazy initialization of the masking locations

void SetupQueryInfo_OMF(const IBlastQuerySource &queries, EBlastProgramType prog, objects::ENa_strand strand_opt, BlastQueryInfo **qinfo)

ObjMgr Free version of SetupQueryInfo.

const char * GetRepeatFilteringDB() const

Returns the name of the repeat filtering database to use.

TSeqPos size() const

Returns the length of the sequence data (in the case of nucleotides, only one strand)

int GetDustFilteringWindow() const

EBlastProgramType m_Program

BLAST program variable.

virtual CConstRef< objects::CSeq_loc > GetMask(int i)

Return the filtered (masked) regions for a sequence.

virtual TSeqPos Size() const

Return the number of elements in the sequence container.

bool m_OwnTSeqLocVector

flag to determine if the member above should or not be deleted in the destructor

virtual void x_SetMinusStrand()

@inheritDoc

virtual ~CBlastQuerySourceOM()

dtor which determines if the internal pointer to its data should be deleted or not.

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

virtual void x_SetPlusStrand()

@inheritDoc

void s_Ncbi4naToNcbi2na(const string &ncbi4na, int base_length, unsigned char *ncbi2na)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

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

ENa_strand GetStrand(void) const

Get the location's strand.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const TDescr & GetDescr(void) const

bool CanGetDescr(void) const

@ eCoding_Ncbi

Set coding to binary coding (Ncbi4na or Ncbistdaa)

ENa_strand GetStrand(void) const

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void SetCoding(TCoding coding)

const_iterator begin(void) const

const_iterator end(void) const

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.

bool NotEmpty(void) const THROWS_NONE

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

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

TValue GetRand(void)

Get the next random number in the interval [0..GetMax()] (inclusive)

TThisType & Set(position_type from, position_type to)

static TThisType GetWhole(void)

#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.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

ENa_strand

strand of nucleic acid

list< CRef< CSeqdesc > > Tdata

const TSource & GetSource(void) const

Get the variant data.

E_Choice

Choice variants.

@ e_Title

a title for this sequence

@ e_Source

source of materials, includes Org-ref

C++ implementation of repeats filtering for C++ BLAST.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Structure to hold a sequence.

The query related information.

Structure to store sequence data and its length for use in the CORE of BLAST (it's a malloc'ed array ...

Blast wrappers for WindowMasker filtering.

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