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
	)

Definition at line 9 of file genbank.cxx.

References ca_assert, GBINDENT, and parse_key_word().

Referenced by genbank_reference(), genbank_source(), GenbankReader::get_key_word(), gtom(), and GenbankParser::parse_section().

static int genbank_check_blanks ( const char *  line, int  numb  )

static

Definition at line 17 of file genbank.cxx.

Referenced by genbank_comments(), genbank_continue_line(), and startsWithBlanks::operator()().

static void genbank_continue_line ( char *&  Str, int  numb, Reader &  reader  )

static

Definition at line 33 of file genbank.cxx.

References genbank_check_blanks(), Reader::line(), LINESIZE, skip_eolnl_and_append_spaced(), and Skip_white_space().

Referenced by genbank_one_comment_entry(), genbank_one_entry_in(), and genbank_source().

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

Definition at line 66 of file genbank.cxx.

References GBINDENT, genbank_continue_line(), genbank_key_word(), genbank_one_entry_in(), Reader::line(), NULp, Skip_white_space(), str_equal(), and TOKENSIZE.

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

Definition at line 96 of file genbank.cxx.

References ASSERT_RESULT, GenbankRef::author, GBINDENT, genbank_key_word(), genbank_one_entry_in(), genbank_skip_unidentified(), has_content(), GenbankRef::journal, Reader::line(), GenbankRef::standard, str_equal(), terminate_with(), GenbankRef::title, TOKENSIZE, and warningf().

static void genbank_comments ( GenBank &  gbk, Reader &  reader  )

static

Definition at line 138 of file genbank.cxx.

References Append(), ARB_strdup(), ca_assert, comment_subkey(), GBINDENT, genbank_check_blanks(), genbank_one_comment_entry(), Reader::line(), line, RDP_comments::others, parse_RDP_comment(), Reader::set_line(), Skip_white_space(), str0len(), and TOKENSIZE.

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

Definition at line 182 of file genbank.cxx.

References Append(), ARB_strdup(), copy(), NULp, skip_eolnl_and_append(), str_equal(), strf(), throw_errorf(), and valid_acc_char().

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

Definition at line 245 of file genbank.cxx.

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

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

Definition at line 327 of file genbank.cxx.

References GenbankRef::author, genbank_out_one_entry(), has_content(), GenbankRef::journal, NOPERIOD, GenbankRef::ref, GenbankRef::standard, GenbankRef::title, and TOKENSIZE.

Referenced by genbank_out_header().

static void genbank_print_comment_if_content ( Writer &  write, const char *  key, const char *  content  )

static

Definition at line 347 of file genbank.cxx.

References GBINDENT, GBMAXLINE, has_content(), LINESIZE, WrapMode::print(), RDP_CONTINUED_INDENT, and RDP_SUBKEY_INDENT.

Referenced by genbank_out_header().

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
	)

Definition at line 368 of file genbank.cxx.

References OrgInfo::commname, SeqInfo::comp3, SeqInfo::comp5, OrgInfo::cultcoll, OrgInfo::exists(), SeqInfo::exists(), RDP_comments::exists(), OrgInfo::formname, GBINDENT, SeqInfo::gbkentry, genbank_out_one_entry(), genbank_out_one_reference(), genbank_print_comment_if_content(), genbank_print_completeness(), Seq::get_len(), OrgInfo::hostorg, length, SeqInfo::methods, OrgInfo::nickname, NOPERIOD, RDP_comments::orginf, RDP_comments::others, Writer::out(), Writer::outf(), PERIOD, SeqInfo::RDPid, Writer::repeated(), RDP_comments::seqinf, OrgInfo::source, and str0len().

Referenced by genbank_out(), and genbank_to_gcg().

void genbank_out_base_count	(	const Seq &	seq,
		Writer &	write
	)

Definition at line 440 of file genbank.cxx.

References BaseCounts::a, BaseCounts::c, Seq::count(), BaseCounts::g, BaseCounts::other, Writer::out(), Writer::outf(), and BaseCounts::t.

Referenced by genbank_out(), and genbank_to_gcg().

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

Definition at line 450 of file genbank.cxx.

References genbank_out_base_count(), genbank_out_header(), genbank_out_origin(), and Writer::out().

Referenced by write_to_genbank().