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

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x_InitInputReader();

EInputFormat

= eFasta,

paired =

);

EInputFormat

= eFasta);

(

) {

m_LineReader->AtEOF();}

x_ReadFastaOrFastq(

& bioseq_set);

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

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

Class representing a text file containing sequences in fasta format.

virtual ~CBlastFastaInputSource()

Destructor.

CRef< ILineReader > m_LineReader

interface to read lines

AutoPtr< CFastaReader > m_InputReader

Reader of FASTA sequences or identifiers.

bool m_ReadProteins

read protein sequences?

CBlastInputSourceConfig m_Config

Configuration for the sequences to be read.

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)

Base class representing a source of biological sequences.

CShortReadFastaInputSource(const CShortReadFastaInputSource &)

EInputFormat m_Format

Input format: FASTA, FASTQ, FASTC.

TSeqPos m_BasesAdded

Number of bases added so far.

virtual ~CShortReadFastaInputSource()

bool m_ParseSeqIds

Should defline ids be used Bioseq objects.

CRef< ILineReader > m_SecondLineReader

unsigned int m_Id

A counter for generating local ids.

CRef< ILineReader > m_LineReader

void SetParseSeqIds(bool val)

EInputFormat

Input formats.

TSeqPos m_SeqBuffLen

string::capacity() can be used instead

CShortReadFastaInputSource & operator=(const CShortReadFastaInputSource &)

bool m_IsPaired

Are paired sequences in the input.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Operators to edit gaps in sequences.

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_BLASTINPUT_EXPORT

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

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

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