util.cxx File Reference

#include <BufferedFileReader.h>
#include "fun.h"
#include "defs.h"
#include "global.h"
#include "reader.h"
#include <cstdarg>
#include <cerrno>

Include dependency graph for util.cxx:

Go to the source code of this file.

Enumerations
enum	FindMode { FIND_START, FIND_SKIP_OVER }

Functions
bool	scan_token (char *to, const char *from)
void	scan_token_or_die (char *to, const char *from)
void	scan_token_or_die (char *to, Reader &reader, int offset)
void	throw_error (int error_num, const char *error_message)
char *	strf (const char *format,...)
void	throw_errorf (int error_num, const char *error_messagef,...)
void	warning (int warning_num, const char *warning_message)
void	warningf (int warning_num, const char *warning_messagef,...)
int	Skip_white_space (const char *line, int index)
void	Getstr (char *line, int linenum)
void	append_known_len (char *&string1, int len1, const char *string2, int len2)
void	terminate_with (char *&str, char ch)
void	skip_eolnl_and_append (char *&string1, const char *string2)
void	skip_eolnl_and_append_spaced (char *&string1, const char *string2)
void	Append (char *&string1, const char *string2)
void	Append (char *&string1, char ch)
void	upcase (char *str)
int	fputs_len (const char *str, int len, Writer &write)
static int	findPattern (const char *text, const char *pattern, FindMode mode)
static int	findMultipattern (const char *str, const char **const &pattern, char expect_behind, FindMode mode)
static int	findSubspecies (const char *str, char expect_behind, FindMode mode)
static int	findStrain (const char *str, char expect_behind, FindMode mode)
int	find_pattern (const char *text, const char *pattern)
int	skip_pattern (const char *text, const char *pattern)
int	find_subspecies (const char *str, char expect_behind)
int	skip_subspecies (const char *str, char expect_behind)
int	find_strain (const char *str, char expect_behind)
int	skip_strain (const char *str, char expect_behind)
const char *	stristr (const char *str, const char *substring)
int	___lookup_keyword (const char *keyword, const char *const *lookup_table, int lookup_table_size)
int	parse_key_word (const char *line, char *key, const char *separator)

Enumeration Type Documentation

enum FindMode

Enumerator
FIND_START
FIND_SKIP_OVER

Definition at line 168 of file util.cxx.

Function Documentation

bool scan_token	(	char *	to,
		const char *	from
	)

Definition at line 10 of file util.cxx.

Referenced by gtoe_journal(), and scan_token_or_die().

void scan_token_or_die	(	char *	to,
		const char *	from
	)

Definition at line 14 of file util.cxx.

References scan_token(), and throw_error().

Referenced by etog_journal(), gtoe(), gtom(), mtog_decode_ref_and_remarks(), parse_RDP_comment(), and scan_token_or_die().

void scan_token_or_die	(	char *	to,
		Reader &	reader,
		int	offset
	)

Definition at line 19 of file util.cxx.

References Reader::line(), offset, and scan_token_or_die().

void throw_error	(	int	error_num,
		const char *	error_message
	)

Definition at line 23 of file util.cxx.

Referenced by ask_for_conversion_params(), convert(), scan_token_or_die(), throw_errorf(), throw_incomplete_entry(), and to_phylip().

char* strf	(	const char *	format,
			...
	)

Definition at line 27 of file util.cxx.

References buffer, BUFSIZE, ca_assert, strndup(), va_end(), and va_start().

Referenced by add_link_attributes(), check_specific_duplicates(), genbank_verify_accession(), gtoe(), gtoe_reference(), gtom(), and Helpfile::readHelp().

void throw_errorf	(	int	error_num,
		const char *	error_messagef,
			...
	)

Definition at line 41 of file util.cxx.

References buffer, BUFSIZE, throw_error(), va_end(), and va_start().

Referenced by ask_for_conversion_params(), command_line_conversion(), FileWriter::expect_written(), FileWriter::FileWriter(), genbank_verify_accession(), macke_read_seq(), parse_intype(), parse_outtype(), Reader::Reader(), throw_conversion_failure(), throw_conversion_not_implemented(), throw_conversion_not_supported(), throw_unsupported_input_format(), Writer::throw_write_error(), to_phylip(), valid_name_or_die(), and warningf().

void warning	(	int	warning_num,
		const char *	warning_message
	)

Definition at line 61 of file util.cxx.

References Warnings::shown().

Referenced by MG_remap::add_reference(), alignToNextRelative(), ARB_main(), awt_create_input_mask(), AWTC_pars_names(), compress_sequence_tree(), embl_date(), GB_login(), GEN_root::GEN_root(), genbank_verify_keywords(), main(), MERGE_sequences_simple(), MG_create_remap(), mtog_genbank_def_and_source(), pars_start_cb(), readCfg(), reorder_keys(), reorder_up_down(), StorableSelectionList::save(), KeySorter::save_changes(), GB_MAIN_TYPE::save_quick_as(), scan_existing_input_masks(), and warningf().

void warningf	(	int	warning_num,
		const char *	warning_messagef,
			...
	)

Definition at line 66 of file util.cxx.

References buffer, BUFSIZE, Warnings::shown(), throw_errorf(), va_end(), va_start(), and warning().

Referenced by cfgReadWarning(), check_consistency(), do_conversion(), etog_journal(), genbank_date(), genbank_reference(), macke_seq_data_out(), readCfg(), and GcgWriter::set_species_name().

int Skip_white_space	(	const char *	line,
		int	index
	)

Definition at line 84 of file util.cxx.

Referenced by embl_comments(), embl_continue_line(), embl_date(), embl_one_comment_entry(), embl_one_entry(), genbank_comments(), genbank_continue_line(), genbank_one_comment_entry(), genbank_one_entry_in(), genbank_source(), get_atcc(), get_string(), and macke_abbrev().

void Getstr	(	char *	line,
		int	linenum
	)

Definition at line 92 of file util.cxx.

Referenced by ask_for_conversion_params().

void append_known_len ( char *&  string1, int  len1, const char *  string2, int  len2  )

inline

Definition at line 102 of file util.cxx.

References ARB_realloc(), and ca_assert.

Referenced by Append(), skip_eolnl_and_append(), skip_eolnl_and_append_spaced(), and terminate_with().

void terminate_with	(	char *&	str,
		char	ch
	)

Definition at line 110 of file util.cxx.

References append_known_len(), ca_assert, and str0len().

Referenced by embl_correct_title(), etog(), genbank_reference(), genbank_verify_keywords(), gtoe(), gtoe_journal(), gtoe_reference(), mtog(), mtog_decode_ref_and_remarks(), and mtog_genbank_def_and_source().

void skip_eolnl_and_append	(	char *&	string1,
		const char *	string2
	)

Definition at line 127 of file util.cxx.

References append_known_len(), and str0len().

Referenced by genbank_verify_accession(), mtog_genbank_def_and_source(), and partial_mtoe().

void skip_eolnl_and_append_spaced	(	char *&	string1,
		const char *	string2
	)

Definition at line 135 of file util.cxx.

References append_known_len(), and str0len().

Referenced by FINAL_TYPE< SEQTYPE >::copy_multi_rem(), embl_continue_line(), embl_one_comment_entry(), genbank_continue_line(), macke_continue_line(), and macke_one_entry_in().

void Append	(	char *&	string1,
		const char *	string2
	)

Definition at line 141 of file util.cxx.

References append_known_len(), and str0len().

Referenced by FINAL_TYPE< SEQTYPE >::add_remark(), embl_comments(), embl_correct_title(), etog_author(), etog_journal(), genbank_comments(), genbank_verify_accession(), gtoe_author(), gtom(), mtog_decode_ref_and_remarks(), mtog_genbank_def_and_source(), and partial_mtoe().

void Append	(	char *&	string1,
		char	ch
	)

Definition at line 145 of file util.cxx.

References append_known_len(), and str0len().

void upcase

(

char *

str

)

Definition at line 149 of file util.cxx.

Referenced by gtoe().

int fputs_len	(	const char *	str,
		int	len,
		Writer &	write
	)

Definition at line 155 of file util.cxx.

References Writer::out().

static int findPattern ( const char *  text, const char *  pattern, FindMode  mode  )

static

Definition at line 170 of file util.cxx.

References ca_assert, FIND_SKIP_OVER, and FIND_START.

Referenced by find_pattern(), findMultipattern(), and skip_pattern().

static int findMultipattern ( const char *  str, const char **const &  pattern, char  expect_behind, FindMode  mode  )

static

Definition at line 195 of file util.cxx.

References ca_assert, FIND_SKIP_OVER, FIND_START, findPattern(), offset, and str0len().

Referenced by findStrain(), and findSubspecies().

static int findSubspecies ( const char *  str, char  expect_behind, FindMode  mode  )

static

Definition at line 231 of file util.cxx.

References findMultipattern(), and NULp.

Referenced by find_subspecies(), and skip_subspecies().

static int findStrain ( const char *  str, char  expect_behind, FindMode  mode  )

static

Definition at line 236 of file util.cxx.

References findMultipattern(), and NULp.

Referenced by find_strain(), and skip_strain().

int find_pattern	(	const char *	text,
		const char *	pattern
	)

Definition at line 241 of file util.cxx.

References FIND_START, and findPattern().

Referenced by correct_subspecies(), genbank_get_strain(), genbank_get_subspecies(), get_atcc(), gtoe_author(), and stristr().

int skip_pattern	(	const char *	text,
		const char *	pattern
	)

Definition at line 242 of file util.cxx.

References FIND_SKIP_OVER, and findPattern().

Referenced by genbank_get_strain(), genbank_get_subspecies(), and partial_mtoe().

int find_subspecies	(	const char *	str,
		char	expect_behind
	)

Definition at line 244 of file util.cxx.

References FIND_START, and findSubspecies().

Referenced by partial_mtoe().

int skip_subspecies	(	const char *	str,
		char	expect_behind
	)

Definition at line 245 of file util.cxx.

References FIND_SKIP_OVER, and findSubspecies().

Referenced by genbank_get_subspecies().

int find_strain	(	const char *	str,
		char	expect_behind
	)

Definition at line 247 of file util.cxx.

References FIND_START, and findStrain().

Referenced by correct_subspecies().

int skip_strain	(	const char *	str,
		char	expect_behind
	)

Definition at line 248 of file util.cxx.

References FIND_SKIP_OVER, and findStrain().

Referenced by check_strain_from().

const char* stristr	(	const char *	str,
		const char *	substring
	)

Definition at line 250 of file util.cxx.

References find_pattern(), NULp, and offset.

Referenced by partial_mtoe().

int ___lookup_keyword	(	const char *	keyword,
		const char *const *	lookup_table,
		int	lookup_table_size
	)

Definition at line 255 of file util.cxx.

References str_equal().

int parse_key_word	(	const char *	line,
		char *	key,
		const char *	separator
	)

Definition at line 265 of file util.cxx.

References occurs_in(), and TOKENSIZE.

Referenced by comment_subkey(), embl_key_word(), genbank_key_word(), macke_abbrev(), and macke_key_word().