ARB
Classes | Macros | Functions
genbank.cxx File Reference
#include "genbank.h"
#include "wrap.h"
Include dependency graph for genbank.cxx:

Go to the source code of this file.

Classes

class  startsWithBlanks
 

Macros

#define NOPERIOD   0
 
#define PERIOD   1
 

Functions

void genbank_key_word (const char *line, int index, char *key)
 
static int genbank_check_blanks (const char *line, int numb)
 
static void genbank_continue_line (char *&Str, int numb, Reader &reader)
 
static void genbank_one_entry_in (char *&datastring, Reader &reader)
 
static void genbank_one_comment_entry (char *&datastring, int start_index, Reader &reader)
 
static void genbank_source (GenBank &gbk, Reader &reader)
 
static void genbank_skip_unidentified (Reader &reader, int blank_num)
 
static void genbank_reference (GenBank &gbk, Reader &reader)
 
static void genbank_comments (GenBank &gbk, Reader &reader)
 
bool valid_acc_char (char ch)
 
static void genbank_verify_accession (GenBank &gbk)
 
static void genbank_verify_keywords (GenBank &gbk)
 
static void genbank_origin (Seq &seq, Reader &reader)
 
static void genbank_print_lines (Writer &write, const char *key, const char *content, const WrapMode &wrapMode)
 
static void genbank_out_one_entry (Writer &write, const char *key, const char *content, const WrapMode &wrapMode, int period)
 
static void genbank_out_one_reference (Writer &write, const GenbankRef &gbk_ref, int gbk_ref_num)
 
static void genbank_print_comment_if_content (Writer &write, const char *key, const char *content)
 
static void genbank_out_origin (const Seq &seq, Writer &write)
 
void genbank_print_completeness (Writer &write, char compX, char X)
 
void genbank_out_header (const GenBank &gbk, const Seq &seq, Writer &write)
 
void genbank_out_base_count (const Seq &seq, Writer &write)
 
void genbank_out (const GenBank &gbk, const Seq &seq, Writer &write)
 

Macro Definition Documentation

#define NOPERIOD   0

Definition at line 6 of file genbank.cxx.

Referenced by genbank_out_header(), and genbank_out_one_reference().

#define PERIOD   1

Definition at line 7 of file genbank.cxx.

Referenced by genbank_out_header().

Function Documentation

void genbank_key_word ( const char line,
int  index,
char key 
)
static int genbank_check_blanks ( const char line,
int  numb 
)
static
static void genbank_continue_line ( char *&  Str,
int  numb,
Reader reader 
)
static
static void genbank_one_entry_in ( char *&  datastring,
Reader reader 
)
static

Definition at line 55 of file genbank.cxx.

References GBINDENT, genbank_continue_line(), Reader::line(), and Skip_white_space().

Referenced by genbank_reference(), and genbank_source().

static void genbank_one_comment_entry ( char *&  datastring,
int  start_index,
Reader reader 
)
static

Definition at line 60 of file genbank.cxx.

References genbank_continue_line(), Reader::line(), and Skip_white_space().

Referenced by genbank_comments().

static void genbank_source ( GenBank &  gbk,
Reader reader 
)
static
static void genbank_skip_unidentified ( Reader reader,
int  blank_num 
)
static

Definition at line 89 of file genbank.cxx.

References Reader::skipOverLinesThat().

Referenced by genbank_reference().

static void genbank_reference ( GenBank &  gbk,
Reader reader 
)
static
static void genbank_comments ( GenBank &  gbk,
Reader reader 
)
static
bool valid_acc_char ( char  ch)
inline

Definition at line 180 of file genbank.cxx.

Referenced by genbank_verify_accession().

static void genbank_verify_accession ( GenBank &  gbk)
static
static void genbank_verify_keywords ( GenBank &  gbk)
static

Definition at line 220 of file genbank.cxx.

References Warnings::shown(), str0len(), terminate_with(), and warning().

static void genbank_origin ( Seq seq,
Reader reader 
)
static
static void genbank_print_lines ( Writer write,
const char key,
const char content,
const WrapMode wrapMode 
)
static

Definition at line 306 of file genbank.cxx.

References ca_assert, GBINDENT, GBMAXLINE, and WrapMode::print().

Referenced by genbank_out_one_entry().

static void genbank_out_one_entry ( Writer write,
const char key,
const char content,
const WrapMode wrapMode,
int  period 
)
static

Definition at line 315 of file genbank.cxx.

References genbank_print_lines(), and has_content().

Referenced by genbank_out_header(), and genbank_out_one_reference().

static void genbank_out_one_reference ( Writer write,
const GenbankRef gbk_ref,
int  gbk_ref_num 
)
static
static void genbank_print_comment_if_content ( Writer write,
const char key,
const char content 
)
static
static void genbank_out_origin ( const Seq seq,
Writer write 
)
static

Definition at line 357 of file genbank.cxx.

References GENBANK, and Seq::out().

Referenced by genbank_out().

void genbank_print_completeness ( Writer write,
char  compX,
char  X 
)
inline

Definition at line 362 of file genbank.cxx.

References ca_assert, and Writer::outf().

Referenced by genbank_out_header().

void genbank_out_header ( const GenBank &  gbk,
const Seq seq,
Writer write 
)
void genbank_out_base_count ( const Seq seq,
Writer write 
)
void genbank_out ( const GenBank &  gbk,
const Seq seq,
Writer write 
)