ARB
Public Member Functions | List of all members
Seq Class Reference

#include <seq.h>

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Collaboration diagram for Seq:
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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 charget_id () const
 
void add (char c)
 
int get_len () const
 
bool is_empty () const
 
const charget_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
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
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().


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