Seq Class Reference

#include <seq.h>

Inheritance diagram for Seq:

Collaboration diagram for Seq:

Public Member Functions
	Seq (const char *id_, const char *seq_, int len_)
	Seq ()
	~Seq ()
void	set_id (const char *id_)
void	replace_id (const char *id_)
const char *	get_id () const
void	add (char c)
int	get_len () const
bool	is_empty () const
const char *	get_seq () const
void	count (BaseCounts &counter) const
int	count_gaps () const
void	out (Writer &write, Format outType) const

Detailed Description

Definition at line 43 of file seq.h.

Constructor & Destructor Documentation

Seq::Seq ( const char *  id_, const char *  seq_, int  len_  )

inline

Definition at line 64 of file seq.h.

Seq::Seq ( )

inline

Definition at line 72 of file seq.h.

Seq::~Seq ( )

inline

Definition at line 78 of file seq.h.

References ca_assert.

Member Function Documentation

void Seq::set_id ( const char *  id_ )

inline

Definition at line 84 of file seq.h.

References ca_assert.

Referenced by Parser::parse_entry(), MackeReader::read_one_entry(), and replace_id().

void Seq::replace_id ( const char *  id_ )

inline

Definition at line 89 of file seq.h.

References set_id().

const char* Seq::get_id ( ) const

inline

Definition at line 93 of file seq.h.

References ca_assert.

Referenced by paup_print_line(), phylip_print_line(), and to_printable().

void Seq::add ( char  c )

inline

Definition at line 98 of file seq.h.

References ARB_realloc().

Referenced by embl_origin(), genbank_origin(), and macke_read_seq().

int Seq::get_len ( ) const

inline

Definition at line 107 of file seq.h.

Referenced by embl_out_comments(), embl_out_origin(), etog(), gcg_out_origin(), gcg_seq_out(), genbank_out_header(), gtoe(), macke_read_seq(), macke_seq_data_out(), mtog(), out(), paup_print_line(), phylip_print_line(), and to_printable().

bool Seq::is_empty ( ) const

inline

Definition at line 108 of file seq.h.

Referenced by embl_origin(), genbank_origin(), and macke_read_seq().

const char* Seq::get_seq ( ) const

inline

Definition at line 110 of file seq.h.

Referenced by gcg_out_origin(), gcg_seq_out(), macke_seq_data_out(), out(), paup_print_line(), phylip_print_line(), and to_printable().

void Seq::count ( BaseCounts &  counter ) const

inline

Definition at line 115 of file seq.h.

References BaseCounts::add().

Referenced by embl_out_origin(), and genbank_out_base_count().

int Seq::count_gaps ( ) const

inline

Definition at line 120 of file seq.h.

References is_gapchar().

Referenced by gcg_seq_out().

void Seq::out	(	Writer &	write,
		Format	outType
	)		const

Definition at line 12 of file seq.cxx.

References ca_assert, EMBL, GENBANK, get_len(), get_seq(), Writer::out(), and Writer::outf().

Referenced by embl_out_origin(), and genbank_out_origin().

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

• CONVERTALN/seq.h
• CONVERTALN/seq.cxx