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

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34 #ifndef ALGO_BLAST_BLASTINPUT___BLAST_SRA_INPUT__HPP 35 #define ALGO_BLAST_BLASTINPUT___BLAST_SRA_INPUT__HPP 57  bool

check_for_paires =

true

,

58  bool

cache_enabled =

false

);

62  virtual int

GetNextSequence(

CBioseq_set

& bioseq_set);

64  virtual bool

End(

void

);

86  void

x_NextAccession(

void

);

92

unique_ptr<CCSraShortReadIterator>

m_It

;

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

Base class representing a source of biological sequences.

Class for reading sequences from SRA respository or SRA file.

TSeqPos m_BasesAdded

Number of bases added so far.

bool m_IsPaired

Are queries paired.

unique_ptr< CCSraShortReadIterator > m_It

unique_ptr< CCSraDb > m_SraDb

CSraInputSource(const CSraInputSource &)

vector< string >::iterator m_ItAcc

vector< string > m_Accessions

CSraInputSource & operator=(const CSraInputSource &)

virtual ~CSraInputSource()

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.

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

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