ARB
Functions
embl.cxx File Reference
#include "embl.h"
#include "genbank.h"
#include "macke.h"
#include "wrap.h"
Include dependency graph for embl.cxx:

Go to the source code of this file.

Functions

static void embl_continue_line (const char *pattern, char *&Str, Reader &reader)
 
static void embl_one_entry (Reader &reader, char *&entry, const char *key)
 
static void embl_date (Embl &embl, Reader &reader)
 
static void embl_correct_title (Emblref &ref)
 
int comment_subkey (const char *line, char *key)
 
bool is_embl_comment (const char *line)
 
static void embl_one_comment_entry (char *&datastring, int start_index, Reader &reader)
 
static void embl_comments (Embl &embl, Reader &reader)
 
static void embl_skip_unidentified (const char *pattern, Reader &reader)
 
static void embl_origin (Seq &seq, Reader &reader)
 
void embl_key_word (const char *line, int index, char *key)
 
static void embl_print_lines (Writer &write, const char *key, const char *content, const WrapMode &wrapMode)
 
static bool embl_print_lines_if_content (Writer &write, const char *key, const char *content, const WrapMode &wrapMode, bool followed_by_spacer)
 
static void embl_print_comment_if_content (Writer &write, const char *key, const char *content)
 
void embl_print_completeness (Writer &write, char compX, char X)
 
static void embl_out_comments (const Embl &embl, const Seq &seq, Writer &write)
 
static void embl_out_origin (const Seq &seq, Writer &write)
 
void embl_out_header (const Embl &embl, const Seq &seq, Writer &write)
 
void embl_out (const Embl &embl, const Seq &seq, Writer &write)
 
static charetog_author (char *Str)
 
static charetog_journal (const char *eJournal)
 
static void etog_convert_references (const Embl &embl, GenBank &gbk)
 
int etog (const Embl &embl, GenBank &gbk, const Seq &seq)
 
int etom (const Embl &embl, Macke &macke, const Seq &seq)
 
static chargtoe_author (char *author)
 
static chargtoe_journal (char *Str)
 
static void gtoe_reference (const GenBank &gbk, Embl &embl)
 
int gtoe (const GenBank &gbk, Embl &embl, const Seq &seq)
 
static int partial_mtoe (const Macke &macke, Embl &embl)
 
int mtoe (const Macke &macke, Embl &embl, const Seq &seq)
 

Function Documentation

static void embl_continue_line ( const char pattern,
char *&  Str,
Reader reader 
)
static
static void embl_one_entry ( Reader reader,
char *&  entry,
const char key 
)
static

Definition at line 26 of file embl.cxx.

References embl_continue_line(), Reader::line(), p_nonkey_start, and Skip_white_space().

static void embl_date ( Embl &  embl,
Reader reader 
)
static
static void embl_correct_title ( Emblref ref)
static

Definition at line 59 of file embl.cxx.

References Append(), ARB_strdup(), NULp, str0len(), terminate_with(), and Emblref::title.

Referenced by gtoe_reference().

int comment_subkey ( const char line,
char key 
)

Definition at line 83 of file embl.cxx.

References parse_key_word().

Referenced by embl_comments(), and genbank_comments().

bool is_embl_comment ( const char line)
inline

Definition at line 95 of file embl.cxx.

Referenced by embl_comments(), and embl_one_comment_entry().

static void embl_one_comment_entry ( char *&  datastring,
int  start_index,
Reader reader 
)
static
static void embl_comments ( Embl &  embl,
Reader reader 
)
static
static void embl_skip_unidentified ( const char pattern,
Reader reader 
)
static

Definition at line 138 of file embl.cxx.

References embl_key_word(), Reader::line(), str_equal(), and TOKENSIZE.

static void embl_origin ( Seq seq,
Reader reader 
)
static

Definition at line 156 of file embl.cxx.

References Seq::add(), ca_assert, Seq::is_empty(), is_sequence_terminator(), Reader::line(), and line.

void embl_key_word ( const char line,
int  index,
char key 
)
static void embl_print_lines ( Writer write,
const char key,
const char content,
const WrapMode wrapMode 
)
static

Definition at line 240 of file embl.cxx.

References ca_assert, EMBLINDENT, EMBLMAXLINE, WrapMode::print(), and TOKENSIZE.

Referenced by embl_out_header(), and embl_print_lines_if_content().

static bool embl_print_lines_if_content ( Writer write,
const char key,
const char content,
const WrapMode wrapMode,
bool  followed_by_spacer 
)
static

Definition at line 250 of file embl.cxx.

References embl_print_lines(), has_content(), and Writer::out().

Referenced by embl_out_comments(), and embl_out_header().

static void embl_print_comment_if_content ( Writer write,
const char key,
const char content 
)
static
void embl_print_completeness ( Writer write,
char  compX,
char  X 
)
inline

Definition at line 269 of file embl.cxx.

References ca_assert, and Writer::outf().

Referenced by embl_out_comments().

static void embl_out_comments ( const Embl &  embl,
const Seq seq,
Writer write 
)
static
static void embl_out_origin ( const Seq seq,
Writer write 
)
static
void embl_out_header ( const Embl &  embl,
const Seq seq,
Writer write 
)
void embl_out ( const Embl &  embl,
const Seq seq,
Writer write 
)

Definition at line 360 of file embl.cxx.

References embl_out_header(), and embl_out_origin().

Referenced by write_to_embl().

static char* etog_author ( char Str)
static

Definition at line 366 of file embl.cxx.

References Append(), ARB_strdup(), has_content(), str0len(), and TOKENSIZE.

Referenced by etog_convert_references().

static char* etog_journal ( const char eJournal)
static
static void etog_convert_references ( const Embl &  embl,
GenBank &  gbk 
)
static
int etog ( const Embl &  embl,
GenBank &  gbk,
const Seq seq 
)
int etom ( const Embl &  embl,
Macke &  macke,
const Seq seq 
)

Definition at line 543 of file embl.cxx.

References etog(), and gtom().

Referenced by ConvertibleData::to_macke().

static char* gtoe_author ( char author)
static

Definition at line 579 of file embl.cxx.

References Append(), find_pattern(), and str0len().

Referenced by gtoe_reference().

static char* gtoe_journal ( char Str)
static

Definition at line 611 of file embl.cxx.

References scan_token(), str0len(), str_equal(), terminate_with(), and TOKENSIZE.

Referenced by gtoe_reference().

static void gtoe_reference ( const GenBank &  gbk,
Embl &  embl 
)
static
int gtoe ( const GenBank &  gbk,
Embl &  embl,
const Seq seq 
)
static int partial_mtoe ( const Macke &  macke,
Embl &  embl 
)
static
int mtoe ( const Macke &  macke,
Embl &  embl,
const Seq seq 
)

Definition at line 772 of file embl.cxx.

References gtoe(), mtog(), and partial_mtoe().

Referenced by ConvertibleData::to_embl().