alnread.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbistr.hpp>
#include <objtools/readers/reader_error_codes.hpp>
#include <objtools/readers/message_listener.hpp>
#include <objtools/readers/alnread.hpp>
#include "aln_errors.hpp"
#include "aln_formatguess.hpp"
#include "aln_peek_ahead.hpp"
#include "aln_scanner_clustal.hpp"
#include "aln_scanner_nexus.hpp"
#include "aln_scanner_phylip.hpp"
#include "aln_scanner_sequin.hpp"
#include "aln_scanner_fastagap.hpp"
#include "aln_scanner_multalign.hpp"

Include dependency graph for alnread.cpp:

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Functions
CAlnScanner *	GetScannerForFormat (EAlignFormat format)
bool	ReadAlignmentFile (istream &istr, bool gen_local_ids, bool use_nexus_info, CSequenceInfo &sequenceInfo, SAlignmentFile &alignmentInfo, ILineErrorListener *pErrorListener)
bool	ReadAlignmentFile (istream &istr, CSequenceInfo &sequenceInfo, SAlignmentFile &alignmentInfo)
bool	ReadAlignmentFile (istream &istr, EAlignFormat &alignFormat, CSequenceInfo &sequenceInfo, SAlignmentFile &alignmentInfo)

Function Documentation

GetScannerForFormat()

CAlnScanner* GetScannerForFormat

(

EAlignFormat

format

)

Definition at line 53 of file alnread.cpp.

References CLUSTAL, FASTAGAP, format, MULTALIN, NEXUS, PHYLIP, and SEQUIN.

Referenced by ReadAlignmentFile().

ReadAlignmentFile() [1/3]

bool ReadAlignmentFile	(	istream &	istr,
		bool	gen_local_ids,
		bool	use_nexus_info,
		CSequenceInfo &	sequenceInfo,
		SAlignmentFile &	alignmentInfo,
		ILineErrorListener *	pErrorListener
	)

Definition at line 78 of file alnread.cpp.

References CSequenceInfo::Alphabet(), format, CAlnFormatGuesser::GetFormat(), GetScannerForFormat(), and theErrorReporter.

Referenced by ReadAlignmentFile().

ReadAlignmentFile() [2/3]

bool ReadAlignmentFile	(	istream &	istr,
		CSequenceInfo &	sequenceInfo,
		SAlignmentFile &	alignmentInfo
	)

Definition at line 106 of file alnread.cpp.

References dummy, and ReadAlignmentFile().

ReadAlignmentFile() [3/3]

bool ReadAlignmentFile	(	istream &	istr,
		EAlignFormat &	alignFormat,
		CSequenceInfo &	sequenceInfo,
		SAlignmentFile &	alignmentInfo
	)

Definition at line 117 of file alnread.cpp.

References CSequenceInfo::Alphabet(), CAlnFormatGuesser::GetFormat(), and GetScannerForFormat().