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NCBI C++ ToolKit: src/algo/blast/blastinput/blast_input.cpp Source File

believe_defline

,

retrieve_seq_data

,

local_id_counter

,

seqlen_thresh2guess

,

: m_Strand(strand), m_LowerCaseMask(lowercase),

m_BelieveDeflines(believe_defline),

m_SkipSeqCheck(skip_seq_check),

m_Range(range), m_DLConfig(dlconfig),

m_RetrieveSeqData(retrieve_seq_data),

m_LocalIdCounter(local_id_counter),

m_SeqLenThreshold2Guess(seqlen_thresh2guess),

m_Strand = (m_DLConfig.m_IsLoadingProteins)

SetQueryLocalIdMode();

(loc.

->IsInt()) {

}

(loc.

->IsWhole()) {

(

<< retval.size() <<

);

(

exception&) {

(loc->

()) {

(

<< retval->

() <<

);

ss <<

<< e.

() << ends;

+

(retrieve_seq_data) {

idToStore->

(*

);

retval->

().push_back(idToStore);

+

m_BatchSize(batch_size),

m_MaxNumSequences(5000000),

Interface for converting sources of sequence data into blast sequence input.

CRef< CBioseq > CreateBioseqFromId(CConstRef< CSeq_id > id, bool retrieve_seq_data)

Creates a Bioseq given a SeqId.

bool IsProtein(CConstRef< CSeq_id > id)

Checks the molecule type of the Bioseq identified by the given SeqId.

static bool IsEmptyBioseq(const CBioseq &bioseq)

Returns true if the Bioseq contained in the seq_entry is empty (i.e.

CRef< CScope > m_scope

Scope object used to retrieve the bioseqs.

bool HasSequence(CConstRef< CSeq_id > id)

Checks whether the Bioseq actually contains sequence.

CBlastInputOMF(CBlastInputSourceOMF *source, TSeqPos batch_size)

TSeqPos m_MaxNumSequences

CRef< CBioseq_set > GetNextSeqBatch(void)

CBlastInputSourceOMF * m_Source

Class that centralizes the configuration data for sequences to be converted.

virtual int GetNextSequence(CBioseq_set &bioseq_set)=0

Get one sequence (or a pair for NGS reads)

virtual CRef< CBlastSearchQuery > GetNextSequence(CScope &scope)=0

Retrieve a single sequence (in a CBlastSearchQuery container)

virtual SSeqLoc GetNextSSeqLoc(CScope &scope)=0

Retrieve a single sequence (in an SSeqLoc container)

Generalized converter from an abstract source of biological sequence data to collections of blast inp...

CBlastInput & operator=(const CBlastInput &rhs)

Prohibit assignment operator.

TSeqPos GetBatchSize() const

Retrieve the target size of a batch of sequences.

TSeqLocVector GetAllSeqLocs(CScope &scope)

Read and convert all the sequences from the source.

CBlastInput(CBlastInputSource *source, int batch_size=kMax_Int)

Constructor.

TSeqLocVector GetNextSeqLocBatch(CScope &scope)

Read and convert the next batch of sequences.

bool End()

Determine if we have reached the end of the BLAST input.

CRef< CBlastQueryVector > GetAllSeqs(CScope &scope)

Read and convert all the sequences from the source.

CRef< CBlastInputSource > m_Source

pointer to source of sequences

void do_copy(const CBlastInput &input)

Perform the actual copy for assignment operator and copy constructor.

TSeqPos m_BatchSize

total size of one block of sequences

CRef< CBlastQueryVector > GetNextSeqBatch(CScope &scope)

Read and convert the next batch of sequences.

void AddQuery(CRef< CBlastSearchQuery > q)

Add a query to the set.

size_type Size() const

Returns the number of queries found in this query vector.

Defines user input exceptions.

unsigned int TSeqPos

Type for sequence locations and lengths.

#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 AsFastaString(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

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

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool IsProtein(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

TSeqPos GetGapSizeForward(void) const

returns number of gap symbols ahead including current symbol returns 0 if current position is not in ...

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.

int64_t Int8

8-byte (64-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.

string::size_type GetPos(void) const noexcept

Get error position.

TErrCode GetErrCode(void) const

Get error code.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

const TWhole & GetWhole(void) const

Get the variant data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

@ eNa_strand_both

in forward orientation

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

TRepr GetRepr(void) const

Get the Repr member data.

TId & SetId(void)

Assign a value to Id data member.

const TInst & GetInst(void) const

Get the Inst member data.

bool CanGetMol(void) const

Check if it is safe to call GetMol method.

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

void SetInst(TInst &value)

Assign a value to Inst data member.

bool CanGetSeq_data(void) const

Check if it is safe to call GetSeq_data method.

bool CanGetInst(void) const

Check if it is safe to call GetInst method.

@ eRepr_raw

continuous sequence

const CharType(& source)[N]

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Configuration structure for the CBlastScopeSource.

Structure to represent a single sequence to be fed to BLAST.

CConstRef< objects::CSeq_loc > seqloc

Seq-loc describing the sequence to use as query/subject to BLAST The types of Seq-loc currently suppo...

CRef< objects::CScope > scope

Scope where the sequence referenced can be found by the toolkit's object manager.

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