macke.cxx File Reference

#include "macke.h"
#include "wrap.h"
#include "parser.h"
#include "rdp_info.h"

Include dependency graph for macke.cxx:

Go to the source code of this file.

Classes
class	MackeParser

Macros
#define	MACKELIMIT   10000

Functions
static int	macke_abbrev (const char *line, char *key, int index)
static void	macke_continue_line (const char *key, char *oldname, char *&var, Reader &reader)
static void	macke_one_entry_in (Reader &reader, const char *key, char *oldname, char *&var, int index)
static void	macke_read_seq (Seq &seq, char *&seqabbr, Reader &reader)
void	macke_origin (Seq &seq, char *&seqabbr, Reader &reader)
void	macke_out_header (Writer &write)
void	macke_seq_display_out (const Macke &macke, Writer &write, Format inType, bool first_sequence)
static void	macke_print_line (Writer &write, const char *prefix, const char *content)
static void	macke_print_prefixed_line (const Macke &macke, Writer &write, const char *tag, const char *content)
static bool	macke_print_prefixed_line_if_content (const Macke &macke, Writer &write, const char *tag, const char *content)
static bool	macke_is_genbank_entry_comment (const char *Str)
static void	macke_print_keyword_rem (const Macke &macke, int index, Writer &write)
void	macke_seq_info_out (const Macke &macke, Writer &write)
int	macke_key_word (const char *line, int index, char *key)
void	macke_seq_data_out (const Seq &seq, const Macke &macke, Writer &write)

Variables
static const char *	genbankEntryComments []

Macro Definition Documentation

#define MACKELIMIT   10000

Definition at line 9 of file macke.cxx.

Referenced by macke_seq_data_out().

Function Documentation

static int macke_abbrev ( const char *  line, char *  key, int  index  )

static

Definition at line 11 of file macke.cxx.

References parse_key_word(), and Skip_white_space().

Referenced by macke_continue_line(), and macke_read_seq().

static void macke_continue_line ( const char *  key, char *  oldname, char *&  var, Reader &  reader  )

static

Definition at line 19 of file macke.cxx.

References has_content(), Reader::line(), macke_abbrev(), skip_eolnl_and_append_spaced(), str_equal(), and TOKENSIZE.

Referenced by macke_one_entry_in().

static void macke_one_entry_in ( Reader &  reader, const char *  key, char *  oldname, char *&  var, int  index  )

static

Definition at line 37 of file macke.cxx.

References has_content(), Reader::line(), macke_continue_line(), and skip_eolnl_and_append_spaced().

static void macke_read_seq ( Seq &  seq, char *&  seqabbr, Reader &  reader  )

static

Definition at line 47 of file macke.cxx.

References Seq::add(), ca_assert, Seq::get_len(), has_content(), Seq::is_empty(), Reader::line(), LINESIZE, macke_abbrev(), str_equal(), throw_errorf(), and TOKENSIZE.

Referenced by macke_origin().

void macke_origin	(	Seq &	seq,
		char *&	seqabbr,
		Reader &	reader
	)

Definition at line 72 of file macke.cxx.

References ca_assert, and macke_read_seq().

void macke_out_header

(

Writer &

write

)

Definition at line 78 of file macke.cxx.

References Writer::out(), Writer::outf(), and today_date().

Referenced by to_macke().

void macke_seq_display_out	(	const Macke &	macke,
		Writer &	write,
		Format	inType,
		bool	first_sequence
	)

Definition at line 85 of file macke.cxx.

References Writer::out(), Writer::outf(), and SWISSPROT.

Referenced by write_to_macke().

static void macke_print_line ( Writer &  write, const char *  prefix, const char *  content  )

static

Definition at line 107 of file macke.cxx.

References MACKEMAXLINE, and WrapMode::print().

Referenced by macke_print_prefixed_line().

static void macke_print_prefixed_line ( const Macke &  macke, Writer &  write, const char *  tag, const char *  content  )

static

Definition at line 112 of file macke.cxx.

References ca_assert, has_content(), LINESIZE, and macke_print_line().

Referenced by macke_print_prefixed_line_if_content(), and macke_seq_info_out().

static bool macke_print_prefixed_line_if_content ( const Macke &  macke, Writer &  write, const char *  tag, const char *  content  )

static

Definition at line 121 of file macke.cxx.

References has_content(), and macke_print_prefixed_line().

Referenced by macke_seq_info_out().

static bool macke_is_genbank_entry_comment ( const char *  Str )

static

Definition at line 145 of file macke.cxx.

References lookup_keyword, macke_key_word(), and TOKENSIZE.

Referenced by macke_seq_info_out().

static void macke_print_keyword_rem ( const Macke &  macke, int  index, Writer &  write  )

static

Definition at line 152 of file macke.cxx.

References LINESIZE, MACKEMAXLINE, WrapMode::print(), and RDP_SUBKEY_INDENT.

Referenced by macke_seq_info_out().

void macke_seq_info_out	(	const Macke &	macke,
		Writer &	write
	)

Definition at line 162 of file macke.cxx.

References macke_is_genbank_entry_comment(), macke_print_keyword_rem(), macke_print_prefixed_line(), macke_print_prefixed_line_if_content(), and Writer::name().

Referenced by macke_to_gcg(), and write_to_macke().

int macke_key_word	(	const char *	line,
		int	index,
		char *	key
	)

Definition at line 189 of file macke.cxx.

References parse_key_word().

Referenced by macke_is_genbank_entry_comment(), and mtog_decode_ref_and_remarks().

void macke_seq_data_out	(	const Seq &	seq,
		const Macke &	macke,
		Writer &	write
	)

Definition at line 196 of file macke.cxx.

References Seq::get_len(), Seq::get_seq(), MACKELIMIT, Writer::out(), Writer::outf(), and warningf().

Referenced by write_to_macke().

Variable Documentation

const char* genbankEntryComments[]

static

Initial value:

= {
    "KEYWORDS",
    "GenBank ACCESSION",
    "auth",
    "title",
    "jour",
    "standard",
    "Source of strain",
    "Former name",
    "Alternate name",
    "Common name",
    "Host organism",
    "RDP ID",
    "Sequencing methods",
    "3' end complete",
    "5' end complete",
}

Definition at line 127 of file macke.cxx.