cmaple::Alignment Class Reference

#include <alignment.h>

Public Types
enum	InputType {   IN_FASTA , IN_PHYLIP , IN_MAPLE , IN_AUTO ,   IN_UNKNOWN }

Public Member Functions
	Alignment ()
	Default constructor.
	Alignment (std::istream &aln_stream, const std::string &ref_seq="", const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)
	Constructor from a stream of an alignment in FASTA, PHYLIP, or MAPLE format.
	Alignment (const std::string &aln_filename, const std::string &ref_seq="", const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)
	Constructor from an alignment file in FASTA, PHYLIP, or MAPLE format.
	~Alignment ()
	Destructor.
void	read (std::istream &aln_stream, const std::string &ref_seq="", const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)
	Read an alignment from a stream in FASTA, PHYLIP, or MAPLE format.
void	read (const std::string &aln_filename, const std::string &ref_seq="", const InputType format=IN_AUTO, const cmaple::SeqRegion::SeqType seqtype=cmaple::SeqRegion::SEQ_AUTO)
	Read an alignment from a file in FASTA, PHYLIP, or MAPLE format.
void	write (std::ostream &aln_stream, const InputType &format=IN_MAPLE)
	Write the alignment to a stream in FASTA, PHYLIP, or MAPLE format.
void	write (const std::string &aln_filename, const InputType &format=IN_MAPLE, const bool overwrite=false)
	Write the alignment to a file in FASTA, PHYLIP, or MAPLE format.

Detailed Description

Class presents the input alignment

Member Enumeration Documentation

InputType

enum cmaple::Alignment::InputType

Alignment format

Enumerator
IN_FASTA	FASTA format
IN_PHYLIP	PHYLIP format
IN_MAPLE	MAPLE format
IN_AUTO	Auto detect
IN_UNKNOWN	Unknown format

Constructor & Destructor Documentation

Alignment() [1/2]

cmaple::Alignment::Alignment	(	std::istream &	aln_stream,
		const std::string &	ref_seq = "",
		const InputType	format = IN_AUTO,
		const cmaple::SeqRegion::SeqType	seqtype = cmaple::SeqRegion::SEQ_AUTO
	)

Constructor from a stream of an alignment in FASTA, PHYLIP, or MAPLE format.

Parameters

[in]	aln_stream	A stream of an alignment file
[in]	ref_seq	A reference sequence (optional). If not specified, it will be read from the alignment (in MAPLE format) or automatically generated from the alignment (in FASTA or PHYLIP format)
[in]	format	Format of the alignment (optional): IN_MAPLE, IN_FASTA, IN_PHYLIP, or IN_AUTO (auto detection)
[in]	seqtype	Data type of sequences (optional): SEQ_DNA (nucleotide data), SEQ_PROTEIN (amino acid data), or SEQ_AUTO (auto detection)

Exceptions

std::invalid_argument

if any of the following situations occur. the alignment is empty or in an incorrect format the sequences contain invalid states

Alignment() [2/2]

cmaple::Alignment::Alignment	(	const std::string &	aln_filename,
		const std::string &	ref_seq = "",
		const InputType	format = IN_AUTO,
		const cmaple::SeqRegion::SeqType	seqtype = cmaple::SeqRegion::SEQ_AUTO
	)

Constructor from an alignment file in FASTA, PHYLIP, or MAPLE format.

Parameters

[in]	aln_filename	Name of an alignment file
[in]	ref_seq	A reference sequence (optional). If not specified, it will be read from the alignment (in MAPLE format) or automatically generated from the alignment (in FASTA or PHYLIP format)
[in]	format	Format of the alignment (optional): IN_MAPLE, IN_FASTA, IN_PHYLIP, or IN_AUTO (auto detection)
[in]	seqtype	Data type of sequences (optional): SEQ_DNA (nucleotide data), SEQ_PROTEIN (amino acid data), or SEQ_AUTO (auto detection)

Exceptions

std::invalid_argument	if any of the following situations occur. the alignment is empty or in an incorrect format the sequences contain invalid states
std::ios_base::failure	if the alignment file is not found

Member Function Documentation

read() [1/2]

void cmaple::Alignment::read	(	std::istream &	aln_stream,
		const std::string &	ref_seq = "",
		const InputType	format = IN_AUTO,
		const cmaple::SeqRegion::SeqType	seqtype = cmaple::SeqRegion::SEQ_AUTO
	)

Read an alignment from a stream in FASTA, PHYLIP, or MAPLE format.

Parameters

[in]	aln_stream	A stream of an alignment file
[in]	ref_seq	A reference sequence (optional). If not specified, it will be read from the alignment (in MAPLE format) or automatically generated from the alignment (in FASTA or PHYLIP format)
[in]	format	Format of the alignment (optional): IN_MAPLE, IN_FASTA, IN_PHYLIP, or IN_AUTO (auto detection)
[in]	seqtype	Data type of sequences (optional): SEQ_DNA (nucleotide data), SEQ_PROTEIN (amino acid data), or SEQ_AUTO (auto detection)

Exceptions

std::invalid_argument

if any of the following situations occur. the alignment is empty or in an incorrect format the sequences contain invalid states

read() [2/2]

void cmaple::Alignment::read	(	const std::string &	aln_filename,
		const std::string &	ref_seq = "",
		const InputType	format = IN_AUTO,
		const cmaple::SeqRegion::SeqType	seqtype = cmaple::SeqRegion::SEQ_AUTO
	)

Read an alignment from a file in FASTA, PHYLIP, or MAPLE format.

Parameters

[in]	aln_filename	Name of an alignment file
[in]	ref_seq	A reference sequence (optional). If not specified, it will be read from the alignment (in MAPLE format) or automatically generated from the alignment (in FASTA or PHYLIP format)
[in]	format	Format of the alignment (optional): IN_MAPLE, IN_FASTA, IN_PHYLIP, or IN_AUTO (auto detection)
[in]	seqtype	Data type of sequences (optional): SEQ_DNA (nucleotide data), SEQ_PROTEIN (amino acid data), or SEQ_AUTO (auto detection)

Exceptions

std::invalid_argument	if any of the following situations occur. the alignment is empty or in an incorrect format the sequences contain invalid states
std::ios_base::failure	if the alignment file is not found

write() [1/2]

void cmaple::Alignment::write	(	std::ostream &	aln_stream,
		const InputType &	format = IN_MAPLE
	)

Write the alignment to a stream in FASTA, PHYLIP, or MAPLE format.

Parameters

[in]	aln_stream	A stream of the output alignment file
[in]	format	Format of the output alignment (optional): IN_MAPLE, IN_FASTA, or IN_PHYLIP

Exceptions

std::invalid_argument	if the format is unknown
std::logic_error	if the alignment is empty (i.e., nothing to write)

write() [2/2]

void cmaple::Alignment::write	(	const std::string &	aln_filename,
		const InputType &	format = IN_MAPLE,
		const bool	overwrite = false
	)

Write the alignment to a file in FASTA, PHYLIP, or MAPLE format.

Parameters

[in]	aln_filename	Name of the output alignment file
[in]	format	Format of the output alignment (optional): IN_MAPLE, IN_FASTA, or IN_PHYLIP
[in]	overwrite	TRUE to overwrite the existing output file (optional)

Exceptions

std::invalid_argument	if any of the following situations occur. aln_filename is empty format is unknown
std::logic_error	if the alignment is empty (i.e., nothing to write)
std::ios_base::failure	if aln_filename already exists and overwrite = false

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The documentation for this class was generated from the following file:

• alignment/alignment.h