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Classes | Macros | Functions | Variables
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 chargenbankEntryComments []
 

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
static void macke_one_entry_in ( Reader reader,
const char key,
char oldname,
char *&  var,
int  index 
)
static
static void macke_read_seq ( Seq seq,
char *&  seqabbr,
Reader reader 
)
static
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
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 
)
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.