#include <gb_aci.h>

Include dependency graph for gb_aci_impl.h:

This graph shows which files directly or indirectly include this file:

Classes
struct	GBL_IMPL::gbl_param

Namespaces
	GBL_IMPL

Macros
#define	PASS_2_OUT(args, s) (args)->output.insert(s)

#define	COPY_2_OUT(args, s) PASS_2_OUT(args, ARB_strdup(s))

#define	IN_2_OUT(args, i) PASS_2_OUT(args, args->input.get_smart(i))

#define	PARAM_2_OUT(args, i) PASS_2_OUT(args, args->get_param_smart(i))

#define	FORMAT_2_OUT(args, fmt, value) PASS_2_OUT(args, GBS_global_string_copy(fmt, value))

#define	GBL_BEGIN_PARAMS gbl_param *params = NULp

#define	GBL_PARAM_TYPE(type, var, param_name, def, help_text) type var = gbl_param_##type(param_name, def, help_text, &params, &var)

#define	GBL_STRUCT_PARAM_TYPE(type, strct, member, param_name, def, help_text) strct.member = gbl_param_##type(param_name, def, help_text, &params, &strct.member)

#define	PARAM_IF(cond, param) ((cond) ? (param) : NULp)

#define	GBL_PARAM_INT(var,param_name, def, help_text) GBL_PARAM_TYPE(int, var, param_name, def, help_text)

#define	GBL_PARAM_CHAR(var,param_name, def, help_text) GBL_PARAM_TYPE(char, var, param_name, def, help_text)

#define	GBL_PARAM_UINT(var,param_name, def, help_text) GBL_PARAM_TYPE(nat, var, param_name, def, help_text)

#define	GBL_PARAM_STRING(var, param_name, def, help_text) GBL_PARAM_TYPE(String, var, param_name, def, help_text)

#define	GBL_PARAM_BIT(var,param_name, def, help_text) GBL_PARAM_TYPE(bit, var, param_name, def, help_text)

#define	GBL_STRUCT_PARAM_INT(strct,member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(int, strct, member, param_name, def, help_text)

#define	GBL_STRUCT_PARAM_CHAR(strct,member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(char, strct, member, param_name, def, help_text)

#define	GBL_STRUCT_PARAM_UINT(strct,member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(nat, strct, member, param_name, def, help_text)

#define	GBL_STRUCT_PARAM_STRING(strct, member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(String, strct, member, param_name, def, help_text)

#define	GBL_STRUCT_PARAM_BIT(strct,member, param_name, def, help_text) GBL_STRUCT_PARAM_TYPE(bit, strct, member, param_name, def, help_text)

#define	GBL_TRACE_PARAMS(args)

#define	GBL_END_PARAMS

#define	GBL_CHECK_FREE_PARAM(nr, cnt)

#define	TRACE_ACI(text) if (GBL_IMPL::traceACI) GBL_IMPL::print_trace(text)

#define	DO_AND_RETURN_ON_ERROR(cmd)

#define	EXPECT_NO_PARAM(args) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_no_parameter(args))

#define	EXPECT_PARAMS_PASSED(args, syntax) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_has_parameters(args,syntax))

#define	ACCEPT_ANY_PARAMS(args) gb_assert((args)->set_params_checked())

#define	EXPECT_PARAMS(args, cnt, help) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_parameters(args, cnt, help))

#define	EXPECT_OPTIONAL_PARAMS(args, fixCnt, fixhelp, optCnt, opthelp) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_optional_parameters(args, fixCnt, fixhelp, optCnt, opthelp, true, true))

#define	EXPECT_OPTIONAL_PARAMS_CUSTOM(args, fixCnt, fixhelp, optCnt, opthelp, trail, all) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_optional_parameters(args, fixCnt, fixhelp, optCnt, opthelp, trail, all))

#define	EXPECT_LEGAL_STREAM_INDEX(args, number)

#define	EXPECT_ITEM_REFERENCED(args) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_item_referenced(args))

#define	COMMAND_DROPS_INPUT_STREAMS(args)

Typedefs
typedef const char *	GBL_IMPL::String

typedef int	GBL_IMPL::bit

typedef unsigned int	GBL_IMPL::nat

Functions
const char *	GBL_IMPL::search_matching_parenthesis (const char *source)

char *	GBL_IMPL::search_matching_parenthesis (char *source)

void	GBL_IMPL::gbl_new_param (gbl_param *pp, GB_TYPES type, void vaddr, const char param_name, const char help_text)

int	GBL_IMPL::gbl_param_int (const char param_name, int def, const char help_text, gbl_param *pp, int vaddr)

char	GBL_IMPL::gbl_param_char (const char param_name, char def, const char help_text, gbl_param *pp, char vaddr)

nat	GBL_IMPL::gbl_param_nat (const char param_name, nat def, const char help_text, gbl_param *pp, nat vaddr)

const char *	GBL_IMPL::gbl_param_String (const char param_name, const char def, const char help_text, gbl_param pp, String vaddr)

int	GBL_IMPL::gbl_param_bit (const char param_name, int def, const char help_text, gbl_param *pp, bit vaddr)

GB_ERROR	GBL_IMPL::trace_params (const GBL_streams &param, gbl_param ppara, const char com)

void	GBL_IMPL::print_trace (const char *text)

void	GBL_IMPL::modify_trace_indent (int diff)

GB_ERROR	GBL_IMPL::check_no_parameter (GBL_command_arguments *args)

GB_ERROR	GBL_IMPL::check_has_parameters (GBL_command_arguments args, const char param_syntax)

GB_ERROR	GBL_IMPL::check_parameters (GBL_command_arguments args, int expected, const char parameterList)

GB_ERROR	GBL_IMPL::check_optional_parameters (GBL_command_arguments args, int fix, const char fixParam, int opt, const char *optParam, bool opt_trailing, bool opt_expect_all)

GB_ERROR	GBL_IMPL::check_valid_index (int number, const char *what, int min, int max)

GB_ERROR	GBL_IMPL::check_valid_stream_index (GBL_command_arguments *args, int number)

GB_ERROR	GBL_IMPL::check_valid_param_index (GBL_command_arguments *args, int number)

GB_ERROR	GBL_IMPL::check_item_referenced (GBL_command_arguments *args)

Macro Definition Documentation

#define PASS_2_OUT	(	args,
		s
	)	(args)->output.insert(s)

#define COPY_2_OUT	(	args,
		s
	)	PASS_2_OUT(args, ARB_strdup(s))

Definition at line 20 of file gb_aci_impl.h.

Referenced by gbl_sequence(), and gbl_split().

#define IN_2_OUT	(	args,
		i
	)	PASS_2_OUT(args, args->input.get_smart(i))

Definition at line 21 of file gb_aci_impl.h.

Referenced by backfront_stream(), gbl_cut(), gbl_drop(), gbl_dropempty(), gbl_dropzero(), gbl_srt(), gbl_swap(), gbl_unquote(), and tab().

#define PARAM_2_OUT	(	args,
		i
	)	PASS_2_OUT(args, args->get_param_smart(i))

Definition at line 22 of file gb_aci_impl.h.

Referenced by gbl_echo().

#define FORMAT_2_OUT	(	args,
		fmt,
		value
	)	PASS_2_OUT(args, GBS_global_string_copy(fmt, value))

Definition at line 24 of file gb_aci_impl.h.

Referenced by count_by_tab(), gbl_and(), gbl_checksum(), gbl_gcgchecksum(), gbl_inRange(), gbl_isEmpty(), gbl_not(), gbl_or(), gbl_quote(), gbl_round(), gbl_streams(), grl_aid(), grl_groupsize(), grl_hitcount(), grl_hitidx(), grl_markedingroup(), and grl_nesting().

#define GBL_BEGIN_PARAMS gbl_param *params = NULp

Definition at line 45 of file gb_aci_impl.h.

Referenced by format(), gbl_change_gc(), gbl_checksum(), gbl_diff(), and gbl_filter().

#define GBL_PARAM_TYPE	(	type,
		var,
		param_name,
		def,
		help_text
	)	type var = gbl_param_##type(param_name, def, help_text, &params, &var)

Definition at line 91 of file gb_aci_impl.h.

#define GBL_STRUCT_PARAM_TYPE	(	type,
		strct,
		member,
		param_name,
		def,
		help_text
	)	strct.member = gbl_param_##type(param_name, def, help_text, &params, &strct.member)

Definition at line 92 of file gb_aci_impl.h.

#define PARAM_IF	(	cond,
		param
	)	((cond) ? (param) : NULp)

Definition at line 95 of file gb_aci_impl.h.

Referenced by format().

#define GBL_PARAM_INT	(	var,
		param_name,
		def,
		help_text
	)	GBL_PARAM_TYPE(int, var, param_name, def, help_text)

Definition at line 97 of file gb_aci_impl.h.

Referenced by format().

#define GBL_PARAM_CHAR	(	var,
		param_name,
		def,
		help_text
	)	GBL_PARAM_TYPE(char, var, param_name, def, help_text)

Definition at line 98 of file gb_aci_impl.h.

#define GBL_PARAM_UINT	(	var,
		param_name,
		def,
		help_text
	)	GBL_PARAM_TYPE(nat, var, param_name, def, help_text)

Definition at line 99 of file gb_aci_impl.h.

Referenced by format().

#define GBL_PARAM_STRING	(	var,
		param_name,
		def,
		help_text
	)	GBL_PARAM_TYPE(String, var, param_name, def, help_text)

Definition at line 100 of file gb_aci_impl.h.

Referenced by format(), and gbl_checksum().

#define GBL_PARAM_BIT	(	var,
		param_name,
		def,
		help_text
	)	GBL_PARAM_TYPE(bit, var, param_name, def, help_text)

Definition at line 101 of file gb_aci_impl.h.

Referenced by format(), and gbl_checksum().

#define GBL_STRUCT_PARAM_INT	(	strct,
		member,
		param_name,
		def,
		help_text
	)	GBL_STRUCT_PARAM_TYPE(int, strct, member, param_name, def, help_text)

Definition at line 103 of file gb_aci_impl.h.

Referenced by gbl_change_gc().

#define GBL_STRUCT_PARAM_CHAR	(	strct,
		member,
		param_name,
		def,
		help_text
	)	GBL_STRUCT_PARAM_TYPE(char, strct, member, param_name, def, help_text)

Definition at line 104 of file gb_aci_impl.h.

Referenced by gbl_diff().

#define GBL_STRUCT_PARAM_UINT	(	strct,
		member,
		param_name,
		def,
		help_text
	)	GBL_STRUCT_PARAM_TYPE(nat, strct, member, param_name, def, help_text)

Definition at line 105 of file gb_aci_impl.h.

#define GBL_STRUCT_PARAM_STRING	(	strct,
		member,
		param_name,
		def,
		help_text
	)	GBL_STRUCT_PARAM_TYPE(String, strct, member, param_name, def, help_text)

Definition at line 106 of file gb_aci_impl.h.

Referenced by gbl_change_gc(), and gbl_filter().

#define GBL_STRUCT_PARAM_BIT	(	strct,
		member,
		param_name,
		def,
		help_text
	)	GBL_STRUCT_PARAM_TYPE(bit, strct, member, param_name, def, help_text)

Definition at line 107 of file gb_aci_impl.h.

#define GBL_TRACE_PARAMS ( args )

Value:

do {                                                                                \
        GB_ERROR def_error =                                                            \
            trace_params((args)->get_param_streams(), params, (args)->get_cmdName());   \
        gb_assert((args)->set_params_checked());                                        \
        if (def_error) { GBL_END_PARAMS; return def_error; }                            \
    } while(0)

Definition at line 109 of file gb_aci_impl.h.

Referenced by format(), gbl_change_gc(), gbl_checksum(), gbl_diff(), and gbl_filter().

#define GBL_END_PARAMS

Value:

do {                                                                \
        gbl_param *_gblp;                                               \
        while (params) {                                                \
            _gblp = params;                                             \
            params = params->next;                                      \
            free(_gblp);                                                \
        }                                                               \
    } while (0)

Definition at line 117 of file gb_aci_impl.h.

Referenced by format(), gbl_change_gc(), gbl_checksum(), gbl_diff(), and gbl_filter().

#define GBL_CHECK_FREE_PARAM	(	nr,
		cnt
	)

Value:

do {                                        \
        if ((nr)+(cnt) >= GBL_MAX_ARGUMENTS) {  \
            /* gb_assert(0); */                 \
            return "max. parameters exceeded";  \
        }                                       \
    } while (0)

Definition at line 127 of file gb_aci_impl.h.

#define TRACE_ACI ( text ) if (GBL_IMPL::traceACI) GBL_IMPL::print_trace(text)

Definition at line 195 of file gb_aci_impl.h.

Referenced by apply_ACI(), gbl_define(), gbl_do(), and gbl_eval().

#define DO_AND_RETURN_ON_ERROR ( cmd )

Value:

do {                            \
        GB_ERROR perr = (cmd);                                      \
        if (perr) return perr;                                      \
    } while(0)

Definition at line 197 of file gb_aci_impl.h.

#define EXPECT_NO_PARAM ( args ) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_no_parameter(args))

Definition at line 202 of file gb_aci_impl.h.

Referenced by convert_case(), gbl_and(), gbl_dd(), gbl_dropempty(), gbl_dropzero(), gbl_escape(), gbl_gcgchecksum(), gbl_isEmpty(), gbl_not(), gbl_or(), gbl_quote(), gbl_streams(), gbl_unescape(), and gbl_unquote().

#define EXPECT_PARAMS_PASSED	(	args,
		syntax
	)	DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_has_parameters(args,syntax))

Definition at line 203 of file gb_aci_impl.h.

Referenced by gbl_cut(), gbl_drop(), gbl_exec(), gbl_readdb(), and gbl_srt().

#define ACCEPT_ANY_PARAMS ( args ) gb_assert((args)->set_params_checked())

Definition at line 204 of file gb_aci_impl.h.

Referenced by gbl_echo(), and gbl_select().

#define EXPECT_PARAMS	(	args,
		cnt,
		help
	)	DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_parameters(args, cnt, help))

Definition at line 206 of file gb_aci_impl.h.

Referenced by apply_to_origin(), backfront_stream(), gbl_command(), gbl_count(), gbl_crop(), gbl_define(), gbl_do(), gbl_eval(), gbl_extract_sequence(), gbl_extract_words(), gbl_findacc(), gbl_findgene(), gbl_findspec(), gbl_head(), gbl_inRange(), gbl_keep(), gbl_remove(), gbl_round(), gbl_tail(), gbl_trace(), mid(), and tab().

#define EXPECT_OPTIONAL_PARAMS	(	args,
		fixCnt,
		fixhelp,
		optCnt,
		opthelp
	)	DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_optional_parameters(args, fixCnt, fixhelp, optCnt, opthelp, true, true))

Definition at line 207 of file gb_aci_impl.h.

Referenced by gbl_colsplit(), gbl_len(), gbl_merge(), gbl_swap(), and gbl_translate().

#define EXPECT_OPTIONAL_PARAMS_CUSTOM	(	args,
		fixCnt,
		fixhelp,
		optCnt,
		opthelp,
		trail,
		all
	)	DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_optional_parameters(args, fixCnt, fixhelp, optCnt, opthelp, trail, all))

Definition at line 208 of file gb_aci_impl.h.

Referenced by gbl_split().

#define EXPECT_LEGAL_STREAM_INDEX	(	args,
		number
	)

Value:

do {                             \
        GB_ERROR serr = GBL_IMPL::check_valid_stream_index(args, number);       \
        if (serr) return serr;                                                  \
    } while(0)

Definition at line 210 of file gb_aci_impl.h.

Referenced by backfront_stream(), gbl_cut(), and gbl_swap().

#define EXPECT_ITEM_REFERENCED ( args ) DO_AND_RETURN_ON_ERROR(GBL_IMPL::check_item_referenced(args))

Definition at line 215 of file gb_aci_impl.h.

Referenced by apply_to_origin(), gbl_export_sequence(), gbl_findgene(), gbl_readdb(), gbl_sequence(), and gbl_taxonomy().

#define COMMAND_DROPS_INPUT_STREAMS ( args )

Value:

do {                                                                          \
        if (GBL_IMPL::traceACI && args->input.size()>0) {                                                              \
            if (args->input.size()>1 || args->input.get(0)[0]) {                                                        \
                GBL_IMPL::print_trace(GBS_global_string("Warning: Dropped %i input streams\n", args->input.size())); \
            }                                                                                                           \
        }                                                                                                               \
    } while(0)

Definition at line 218 of file gb_aci_impl.h.

Referenced by gbl_ali_name(), gbl_define(), gbl_echo(), gbl_export_sequence(), gbl_readdb(), gbl_sequence(), gbl_sequence_type(), gbl_taxonomy(), grl_aid(), grl_groupsize(), grl_hitcount(), grl_hitidx(), grl_markedingroup(), and grl_nesting().

Classes

Namespaces

Macros

Typedefs

Functions

Macro Definition Documentation