global.h File Reference

#include <arb_assert.h>
#include <arb_defs.h>
#include <arbtools.h>
#include <smartptr.h>
#include <arb_string.h>
#include <arb_global_defs.h>

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Classes
class	Convaln_exception
class	Warnings

Macros
#define	ca_assert(cond)   arb_assert(cond)
#define	WORD_SEP   ",.; ?:!)]}"
#define	lookup_keyword(keyword, table)   ___lookup_keyword(keyword, table, ARRAY_ELEMS(table))

Functions
CONSTEXPR_INLINE int	min (int t1, int t2)
CONSTEXPR_INLINE int	max (int t1, int t2)
CONSTEXPR_INLINE bool	str_equal (const char *s1, const char *s2)
CONSTEXPR_INLINE bool	str_iequal (const char *s1, const char *s2)
CONSTEXPR_INLINE int	str0len (const char *str)
char *	strndup (const char *str, int len)
CONSTEXPR_INLINE int	count_spaces (const char *str)
bool	occurs_in (char ch, const char *in)
CONSTEXPR_INLINE bool	is_end_mark (char ch)
CONSTEXPR_INLINE bool	is_sequence_terminator (const char *str)
bool	is_gapchar (char ch)
bool	is_word_char (char ch)
CONSTEXPR_INLINE bool	has_no_content (const char *field)
CONSTEXPR_INLINE bool	has_content (const char *field)
char *	no_content ()
bool	copy_content (char *&entry, const char *content)

Macro Definition Documentation

#define ca_assert

(

cond

)

arb_assert(cond)

Definition at line 33 of file global.h.

Referenced by append_known_len(), Convaln_exception::catched(), GcgWriter::comment_writer(), Convaln_exception::Convaln_exception(), correct_subspecies(), embl_origin(), embl_print_completeness(), embl_print_lines(), etog_journal(), FileWriter::expect_written(), findMultipattern(), findPattern(), format2name(), gcg_date(), gcg_doc_out(), genbank_comments(), genbank_date(), genbank_key_word(), genbank_origin(), genbank_print_completeness(), genbank_print_lines(), Alignment::get(), Seq::get_id(), Alignment::get_len(), Refs< GenbankRef >::get_ref(), FINAL_TYPE< SEQTYPE >::get_rem(), Alignment::getSeqPtr(), FormattedFile::init(), macke_origin(), macke_print_prefixed_line(), macke_read_seq(), mtog_decode_ref_and_remarks(), occurs_in(), GcgCommentWriter::out(), Seq::out(), Writer::outf(), MackeParser::parse_section(), phylip_print_line(), WrapMode::print(), SetOnce::replace(), Refs< GenbankRef >::resize(), FileWriter::seq_done(), SetOnce::set(), Seq::set_id(), Reader::set_line(), strf(), terminate_with(), GcgCommentWriter::throw_write_error(), ConvertibleData::to_embl(), ConvertibleData::to_genbank(), ConvertibleData::to_macke(), to_paup(), to_phylip(), to_printable(), SetOnce::value(), GcgWriter::write_seq_data(), Convaln_exception::~Convaln_exception(), FileWriter::~FileWriter(), GcgCommentWriter::~GcgCommentWriter(), MackeReader::~MackeReader(), Reader::~Reader(), and Seq::~Seq().

#define WORD_SEP   ",.; ?:!)]}"

Definition at line 117 of file global.h.

Referenced by is_word_char().

#define lookup_keyword	(		keyword,
			table
	)		___lookup_keyword(keyword, table, ARRAY_ELEMS(table))

Definition at line 144 of file global.h.

Referenced by macke_is_genbank_entry_comment().

Function Documentation

CONSTEXPR_INLINE int min	(	int	t1,
		int	t2
	)

Definition at line 92 of file global.h.

CONSTEXPR_INLINE int max	(	int	t1,
		int	t2
	)

Definition at line 93 of file global.h.

CONSTEXPR_INLINE bool str_equal	(	const char *	s1,
		const char *	s2
	)

Definition at line 95 of file global.h.

Referenced by ___lookup_keyword(), check_consistency(), convert(), embl_continue_line(), embl_date(), embl_skip_unidentified(), etog(), etog_journal(), genbank_reference(), genbank_source(), genbank_verify_accession(), gtoe_journal(), gtom(), macke_continue_line(), macke_read_seq(), mtog_decode_ref_and_remarks(), and parse_RDP_comment().

CONSTEXPR_INLINE bool str_iequal	(	const char *	s1,
		const char *	s2
	)

Definition at line 96 of file global.h.

Referenced by ismonth().

CONSTEXPR_INLINE int str0len

(

const char *

str

)

Definition at line 98 of file global.h.

Referenced by Append(), ask_for_conversion_params(), change_file_suffix(), embl_correct_title(), etog(), etog_author(), etog_convert_references(), etog_journal(), find_date(), find_date_long_form(), findMultipattern(), gcg_doc_out(), genbank_comments(), genbank_date(), genbank_out_header(), genbank_verify_keywords(), get_atcc(), get_atcc_string(), get_string(), gtoe(), gtoe_author(), gtoe_journal(), gtom(), is_genbank_date(), isdatenum(), FINAL_TYPE< SEQTYPE >::locus_contains_date(), mtog(), paren_string(), partial_mtoe(), paup_verify_name(), phylip_print_line(), printable_print_line(), skip_eolnl_and_append(), skip_eolnl_and_append_spaced(), terminate_with(), and valid_name_or_die().

char* strndup ( const char *  str, int  len  )

inline

Definition at line 102 of file global.h.

References result.

Referenced by etog_journal(), FINAL_TYPE< SEQTYPE >::get_date(), and strf().

CONSTEXPR_INLINE int count_spaces

(

const char *

str

)

Definition at line 109 of file global.h.

Referenced by embl_one_comment_entry().

bool occurs_in ( char  ch, const char *  in  )

inline

Definition at line 111 of file global.h.

References ca_assert.

Referenced by is_word_char(), and parse_key_word().

CONSTEXPR_INLINE bool is_end_mark

(

char

ch

)

Definition at line 113 of file global.h.

Referenced by get_string(), and partial_mtoe().

CONSTEXPR_INLINE bool is_sequence_terminator

(

const char *

str

)

Definition at line 115 of file global.h.

Referenced by embl_origin(), and genbank_origin().

bool is_gapchar ( char  ch )

inline

Definition at line 119 of file global.h.

References GAP::is_import_gap().

Referenced by Seq::count_gaps(), gcg_checksum(), gcg_out_origin(), and to_printable().

bool is_word_char ( char  ch )

inline

Definition at line 120 of file global.h.

References occurs_in(), and WORD_SEP.

CONSTEXPR_INLINE bool has_no_content

(

const char *

field

)

Definition at line 122 of file global.h.

Referenced by has_content().

CONSTEXPR_INLINE bool has_content

(

const char *

field

)

Definition at line 127 of file global.h.

References has_no_content().

Referenced by check_consistency(), check_strain_from(), copy_content(), embl_continue_line(), embl_out_header(), embl_print_comment_if_content(), embl_print_lines_if_content(), etog(), etog_author(), etog_convert_references(), OrgInfo::exists(), SeqInfo::exists(), RDP_comments::exists(), genbank_get_atcc(), genbank_get_strain(), genbank_get_subspecies(), genbank_origin(), genbank_out_one_entry(), genbank_out_one_reference(), genbank_print_comment_if_content(), genbank_reference(), gtoe(), gtom(), macke_continue_line(), macke_one_entry_in(), macke_print_prefixed_line(), macke_print_prefixed_line_if_content(), macke_read_seq(), mtog(), mtog_decode_ref_and_remarks(), mtog_genbank_def_and_source(), Parser::parse_entry(), partial_mtoe(), and WrapMode::print().

char* no_content ( )

inline

Definition at line 129 of file global.h.

Referenced by FINAL_TYPE< SEQTYPE >::Embl(), etog_convert_references(), etog_journal(), FINAL_TYPE< SEQTYPE >::GenBank(), gtoe_reference(), FINAL_TYPE< SEQTYPE >::Macke(), OrgInfo::OrgInfo(), and SeqInfo::SeqInfo().

bool copy_content ( char *&  entry, const char *  content  )

inline

Definition at line 136 of file global.h.

References copy(), and has_content().

Referenced by etog(), gtoe(), gtom(), mtog(), mtog_genbank_def_and_source(), OrgInfo::set_content_from(), SeqInfo::set_content_from(), and RDP_comments::set_content_from().