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NCBI C++ ToolKit: include/algo/blast/blastinput/blast_input.hpp Source File

kSeqLenThreshold2Guess = 25;

lowercase =

,

believe_defline =

,

retrieve_seq_data =

,

local_id_counter = 1,

seqlen_thresh2guess =

skip_seq_check =

);

m_SeqLenThreshold2Guess;

m_SeqLenThreshold2Guess =

;

eInvalidStrand:

;

eSeqIdNotFound:

;

eEmptyUserInput:

;

eInvalidRange:

;

eSequenceMismatch:

;

eInvalidInput:

;

: m_Source(

), m_BatchSize(batch_size), m_NumSeqs(0), m_TotalLength(0) {}

() {

m_Source->End(); }

retrieve_seq_data);

IsEmptyBioseq(

& bioseq);

(

) = 0;

(

) {

m_Source->End();}

Declares CBlastScopeSource class to create properly configured CScope objects to invoke the BLAST dat...

ncbi::TMaskedQueryRegions mask

Auxiliary class for creating Bioseqs given SeqIds.

CRef< CScope > m_scope

Scope object used to retrieve the bioseqs.

CBlastBioseqMaker(CRef< CScope > scope)

Constructor.

CBlastInputOMF & operator=(const CBlastInputOMF &rhs)

CBlastInputOMF(const CBlastInputOMF &rhs)

TSeqPos m_MaxNumSequences

TSeqPos GetBatchSize(void) const

CBlastInputSourceOMF * m_Source

CRef< CBioseq_set > m_BioseqSet

void SetMaxBatchNumSeqs(TSeqPos num)

Int8 GetTotalLengthProcessed() const

Int8 GetNumSeqsProcessed() const

void SetBatchSize(TSeqPos num)

TSeqPos GetMaxBatchNumSeqs(void) const

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

void SetConvertGapsToNs(bool val)

Turn on/off converting gaps to Ns in read FASTA sequences.

void SetLocalIdCounterInitValue(int val)

Set the local id counter initial value.

TSeqRange GetRange() const

Get range for all sequences.

bool GetConvertGapsToNs(void) const

Retrieve gaps to Ns converstion option value.

bool m_LowerCaseMask

Whether to save lowercase mask locs.

void SetRetrieveSeqData(bool value)

Turn on or off the retrieval of sequence data.

objects::ENa_strand m_Strand

Strand to assign to sequences.

void SetSkipSeqCheck(bool skip)

Turn validation of sequence on/off.

bool m_GapsToNs

Convert gaps to Ns in FASTA sequences.

bool m_BelieveDeflines

Whether to parse sequence IDs.

TSeqRange m_Range

Sequence range.

unsigned int m_SeqLenThreshold2Guess

The sequence length threshold to guess molecule type.

const string & GetLocalIdPrefix() const

Retrieve the custom prefix string used for generating local ids.

void SetLowercaseMask(bool mask)

Turn lowercase masking on/off.

~CBlastInputSourceConfig()

Destructor.

void SetLocalIdPrefix(const string &prefix)

Set the custom prefix string used for generating local ids.

void SetSubjectLocalIdMode()

Append subject-specific prefix codes to all generated local ids.

void SetRange(const TSeqRange &r)

Set range for all sequences.

objects::ENa_strand GetStrand() const

Retrieve the current strand value.

void SetBelieveDeflines(bool believe)

Turn parsing of sequence IDs on/off.

bool IsProteinInput() const

Determine if this object is for configuring reading protein sequences.

void SetSeqLenThreshold2Guess(unsigned int val)

Set the sequence length threshold to guess the molecule type.

void SetStrand(objects::ENa_strand strand)

Set the strand to a specified value.

bool m_SkipSeqCheck

Whether to validate sequence data -RMH-.

int m_LocalIdCounter

Initialization parameter to CSeqidGenerator.

int GetLocalIdCounterInitValue() const

Retrieve the local id counter initial value.

const SDataLoaderConfig & GetDataLoaderConfig()

Retrieve the data loader configuration object for read-only access.

bool GetBelieveDeflines() const

Retrieve current sequence ID parsing status.

bool m_RetrieveSeqData

Configuration for CBlastInputReader.

string m_LocalIdPrefix

Custom prefix string passed to CSeqidGenerator.

unsigned int GetSeqLenThreshold2Guess() const

Retrieve the sequence length threshold to guess the molecule type.

SDataLoaderConfig m_DLConfig

Configuration object for data loaders, used by CBlastInputReader.

SDataLoaderConfig & SetDataLoaderConfig()

Retrieve the data loader configuration object for manipulation.

bool GetSkipSeqCheck() const

Retrieve status of sequence alphabet validation.

bool GetLowercaseMask() const

Retrieve lowercase mask status.

bool RetrieveSeqData() const

True if the sequence data must be fetched.

TSeqRange & SetRange(void)

Set range for all sequences.

void SetQueryLocalIdMode()

Append query-specific prefix codes to all generated local ids.

virtual ~CBlastInputSourceOMF()

virtual int GetNextSequence(CBioseq_set &bioseq_set)=0

Get one sequence (or a pair for NGS reads)

Base class representing a source of biological sequences.

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

Retrieve a single sequence (in a CBlastSearchQuery container)

virtual bool End()=0

Signal whether there are any unread sequence left.

virtual SSeqLoc GetNextSSeqLoc(CScope &scope)=0

Retrieve a single sequence (in an SSeqLoc container)

virtual ~CBlastInputSource()

Destructor.

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

~CBlastInput()

Destructor.

Int8 GetNumSeqsProcessed() const

TSeqPos GetBatchSize() const

Retrieve the target size of a batch of sequences.

CBlastInput(CBlastInputSource *source, int batch_size=kMax_Int)

Constructor.

bool End()

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

void SetBatchSize(TSeqPos batch_size)

Set the target size of a batch of sequences.

CRef< CBlastInputSource > m_Source

pointer to source of sequences

Int8 GetTotalLengthProcessed() const

TSeqPos m_BatchSize

total size of one block of sequences

Defines user input exceptions.

NCBI_EXCEPTION_DEFAULT(CInputException, CException)

EErrCode

Error types that reading BLAST input can generate.

@ eInvalidStrand

Invalid strand specification.

@ eSequenceMismatch

Expected sequence type isn't what was expected.

@ eInvalidRange

Invalid range specification.

@ eEmptyUserInput

No input was provided.

@ eSeqIdNotFound

The sequence ID cannot be resolved.

virtual const char * GetErrCodeString(void) const override

Translate from the error code value to its string representation.

Include a standard set of the NCBI C++ Toolkit most basic headers.

unsigned int TSeqPos

Type for sequence locations and lengths.

CException & operator=(const CException &)

Private assignment operator to prohibit assignment.

TErrCode GetErrCode(void) const

Get error code.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

int64_t Int8

8-byte (64-bit) signed integer

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#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.

#define NCBI_BLASTINPUT_EXPORT

ENa_strand

strand of nucleic acid

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Definition of SSeqLoc structure.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Configuration structure for the CBlastScopeSource.

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

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