fasta.hpp File Reference

Operators to edit gaps in sequences. More...

#include <corelib/ncbi_limits.hpp>
#include <corelib/ncbi_param.hpp>
#include <util/line_reader.hpp>
#include <util/static_map.hpp>
#include <objects/seq/Bioseq.hpp>
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seq/Seq_gap.hpp>
#include <objects/seq/Linkage_evidence.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objtools/readers/reader_base.hpp>
#include <objtools/readers/line_error.hpp>
#include <objtools/readers/message_listener.hpp>
#include <objtools/readers/source_mod_parser.hpp>
#include <objects/seq/Seq_data.hpp>
#include <objtools/readers/fasta_reader_utils.hpp>
#include <objtools/readers/mod_reader.hpp>
#include <unordered_set>
#include <stack>
#include <sstream>

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Classes
class	CFastaReader
	Base class for reading FASTA sequences. More...
struct	CFastaReader::SGap
struct	SFastaFileMap
struct	SFastaFileMap::SFastaEntry
class	IFastaEntryScan
	Callback interface to scan fasta file for entries. More...

Typedefs
typedef CFastaReader::TFlags	TReadFastaFlags

Functions
CRef< CSeq_entry >	ReadFasta (CNcbiIstream &in, CFastaReader::TFlags flags=0, int *counter=nullptr, CFastaReader::TMasks *lcv=nullptr, ILineErrorListener *pMessageListener=nullptr)
	A const-correct replacement for the deprecated ReadFasta function. More...
void	ReadFastaFileMap (SFastaFileMap *fasta_map, CNcbiIfstream &input)
	Function reads input stream (assumed that it is FASTA format) one molecule entry after another filling the map structure describing and pointing on molecule entries. More...
void	ScanFastaFile (IFastaEntryScan *scanner, CNcbiIfstream &input, CFastaReader::TFlags fread_flags)
	Scan FASTA files, call IFastaEntryScan::EntryFound (payload function) More...

Detailed Description

Operators to edit gaps in sequences.

Interfaces for reading and scanning FASTA-format sequences.

Definition in file fasta.hpp.