#include "gb_aci_impl.h"
#include "gb_key.h"
#include "TreeNode.h"
#include <aw_awar_defs.hxx>
#include <adGene.h>
#include <ad_cb.h>
#include <arb_defs.h>
#include <arb_strbuf.h>
#include <arb_file.h>
#include <arb_strarray.h>
#include <arb_sort.h>
#include <cctype>
#include <cmath>
#include <algorithm>

Include dependency graph for adlang1.cxx:

Classes
class	DefinedCommands

class	Tab

struct	binop_pair

struct	cached_taxonomy

struct	common_filter_params

struct	diff_params

struct	filter_params

Namespaces
	GBL_IMPL

Macros
#define	GROUP_COUNT_CHARS 6

#define	BITS_PER_HEXCHAR 4

#define	MAX_GROUPS (1 << (GROUP_COUNT_CHARS*BITS_PER_HEXCHAR))

#define	GBL_COMMON_FILTER_PARAMS

Typedefs
typedef char (	filter_fun )(const char seq, const char filter, size_t flen, void *param)

Enumerations
enum	Case { UPPER, LOWER, CAPS }

enum	GBT_ITEM_TYPE { GBT_ITEM_UNKNOWN, GBT_ITEM_SPECIES, GBT_ITEM_GENE }

enum	filter_function { FP_FILTER, FP_MODIFY }

Functions
NOT4PERL void	GB_set_export_sequence_hook (gb_export_sequence_cb escb)

void	GBL_IMPL::print_trace (const char *text)

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

static int	gbl_stricmp (const char s1, const char s2)

static int	gbl_strincmp (const char s1, const char s2, int size2)

static const char *	gbl_stristr (const char haystack, const char needle)

int	approve_pos (int pos, int len)

static GB_ERROR	gbl_mid_streams (const GBL_streams &arg_input, GBL_streams &arg_out, int start, int end)

static GB_ERROR	gbl_trace (GBL_command_arguments *args)

template<typename T >
GB_ERROR	gbl_apply_binary_operator (GBL_command_arguments args, char (op)(const char , const char *, T), T client_data)

static char *	unEscapeString (const char *escapedString)

static char *	escapeString (const char *unescapedString)

static GB_ERROR	gbl_quote (GBL_command_arguments *args)

static GB_ERROR	gbl_unquote (GBL_command_arguments *args)

static GB_ERROR	gbl_escape (GBL_command_arguments *args)

static GB_ERROR	gbl_unescape (GBL_command_arguments *args)

static GB_ERROR	gbl_command (GBL_command_arguments *args)

static GB_ERROR	gbl_eval (GBL_command_arguments *args)

static GB_ERROR	gbl_define (GBL_command_arguments *args)

static GB_ERROR	gbl_do (GBL_command_arguments *args)

static GB_ERROR	gbl_streams (GBL_command_arguments *args)

static GB_ERROR	expect_used_in_genome_db (GBL_command_arguments *args)

static GB_ERROR	apply_to_origin (GBL_command_arguments *args, bool organism)

static GB_ERROR	gbl_origin_gene (GBL_command_arguments *args)

static GB_ERROR	gbl_origin_organism (GBL_command_arguments *args)

static GB_ERROR	applyToItemFoundByKey (GBL_command_arguments args, const char itemname, GBDATA gb_item_data, const char key)

static GB_ERROR	gbl_findspec (GBL_command_arguments *args)

static GB_ERROR	gbl_findacc (GBL_command_arguments *args)

static GB_ERROR	gbl_findgene (GBL_command_arguments *args)

GB_ERROR	count_by_tab (GBL_command_arguments *args, const Tab &tab)

GB_ERROR	remove_by_tab (GBL_command_arguments *args, const Tab &tab)

static GB_ERROR	gbl_count (GBL_command_arguments *args)

static GB_ERROR	gbl_len (GBL_command_arguments *args)

static GB_ERROR	gbl_remove (GBL_command_arguments *args)

static GB_ERROR	gbl_keep (GBL_command_arguments *args)

static char *	binop_compare (const char arg1, const char arg2, bool case_sensitive)

static char *	binop_equals (const char arg1, const char arg2, bool case_sensitive)

static char *	binop_contains (const char arg1, const char arg2, bool case_sensitive)

static char *	binop_partof (const char arg1, const char arg2, bool case_sensitive)

static GB_ERROR	gbl_compare (GBL_command_arguments *args)

static GB_ERROR	gbl_icompare (GBL_command_arguments *args)

static GB_ERROR	gbl_equals (GBL_command_arguments *args)

static GB_ERROR	gbl_iequals (GBL_command_arguments *args)

static GB_ERROR	gbl_contains (GBL_command_arguments *args)

static GB_ERROR	gbl_icontains (GBL_command_arguments *args)

static GB_ERROR	gbl_partof (GBL_command_arguments *args)

static GB_ERROR	gbl_ipartof (GBL_command_arguments *args)

static GB_ERROR	gbl_isEmpty (GBL_command_arguments *args)

static GB_ERROR	gbl_inRange (GBL_command_arguments *args)

static GB_ERROR	gbl_translate (GBL_command_arguments *args)

static GB_ERROR	gbl_echo (GBL_command_arguments *args)

static GB_ERROR	gbl_dd (GBL_command_arguments *args)

static GB_ERROR	convert_case (GBL_command_arguments *args, Case convTo)

static GB_ERROR	gbl_caps (GBL_command_arguments *args)

static GB_ERROR	gbl_upper (GBL_command_arguments *args)

static GB_ERROR	gbl_lower (GBL_command_arguments *args)

static GB_ERROR	gbl_head (GBL_command_arguments *args)

static GB_ERROR	gbl_tail (GBL_command_arguments *args)

GB_ERROR	mid (GBL_command_arguments *args, int start_index)

static GB_ERROR	gbl_mid0 (GBL_command_arguments *args)

static GB_ERROR	gbl_mid (GBL_command_arguments *args)

static GB_ERROR	tab (GBL_command_arguments *args, bool pretab)

static GB_ERROR	gbl_tab (GBL_command_arguments *args)

static GB_ERROR	gbl_pretab (GBL_command_arguments *args)

static GB_ERROR	gbl_crop (GBL_command_arguments *args)

static GB_ERROR	gbl_cut (GBL_command_arguments *args)

static GB_ERROR	gbl_drop (GBL_command_arguments *args)

static GB_ERROR	gbl_dropempty (GBL_command_arguments *args)

static GB_ERROR	gbl_dropzero (GBL_command_arguments *args)

static GB_ERROR	gbl_swap (GBL_command_arguments *args)

static GB_ERROR	backfront_stream (GBL_command_arguments *args, int toback)

static GB_ERROR	gbl_toback (GBL_command_arguments *args)

static GB_ERROR	gbl_tofront (GBL_command_arguments *args)

static GB_ERROR	gbl_merge (GBL_command_arguments *args)

static GB_ERROR	gbl_split (GBL_command_arguments *args)

static GB_ERROR	gbl_colsplit (GBL_command_arguments *args)

static char *	do_extract_words (const char source, const char chars, float minlen, bool sort_output)

static GB_ERROR	gbl_extract_words (GBL_command_arguments *args)

static GB_ERROR	gbl_extract_sequence (GBL_command_arguments *args)

static GB_ERROR	gbl_checksum (GBL_command_arguments *args)

static GB_ERROR	gbl_gcgchecksum (GBL_command_arguments *args)

static GB_ERROR	gbl_srt (GBL_command_arguments *args)

static char *	apply_numeric_binop (const char arg1, const char arg2, int(*num_bin_op)(int, int))

static char *	apply_double_binop (const char arg1, const char arg2, double(*num_bin_op)(double, double))

static char *	apply_auto_numeric_binop (const char arg1, const char arg2, binop_pair multiop)

template<typename T >
static T	binop_plus (T v1, T v2)

template<typename T >
static T	binop_minus (T v1, T v2)

template<typename T >
static T	binop_mult (T v1, T v2)

template<typename T >
static T	binop_div (T v1, T v2)

template<typename T >
static T	binop_per_cent (T v1, T v2)

static int	binop_rest (int i1, int i2)

static GB_ERROR	gbl_plus (GBL_command_arguments *args)

static GB_ERROR	gbl_fplus (GBL_command_arguments *args)

static GB_ERROR	gbl_minus (GBL_command_arguments *args)

static GB_ERROR	gbl_fminus (GBL_command_arguments *args)

static GB_ERROR	gbl_mult (GBL_command_arguments *args)

static GB_ERROR	gbl_fmult (GBL_command_arguments *args)

static GB_ERROR	gbl_div (GBL_command_arguments *args)

static GB_ERROR	gbl_fdiv (GBL_command_arguments *args)

static GB_ERROR	gbl_rest (GBL_command_arguments *args)

static GB_ERROR	gbl_per_cent (GBL_command_arguments *args)

static GB_ERROR	gbl_fper_cent (GBL_command_arguments *args)

template<typename T >
static T	binop_isAbove (T i1, T i2)

template<typename T >
static T	binop_isBelow (T i1, T i2)

template<typename T >
static T	binop_isEqual (T i1, T i2)

static GB_ERROR	gbl_isAbove (GBL_command_arguments *args)

static GB_ERROR	gbl_isBelow (GBL_command_arguments *args)

static GB_ERROR	gbl_isEqual (GBL_command_arguments *args)

double	float_shift_factor (int digits)

static GB_ERROR	gbl_round (GBL_command_arguments *args)

static GB_ERROR	gbl_not (GBL_command_arguments *args)

static GB_ERROR	gbl_and (GBL_command_arguments *args)

static GB_ERROR	gbl_or (GBL_command_arguments *args)

static GB_ERROR	gbl_select (GBL_command_arguments *args)

static GB_ERROR	gbl_readdb (GBL_command_arguments *args)

static GBT_ITEM_TYPE	identify_gb_item (GBDATA *gb_item)

static void	free_cached_taxonomy (cached_taxonomy *ct)

static void	build_taxonomy_rek (TreeNode node, GB_HASH tax_hash, const char parent_group, int group_counter)

static bool	is_cached_taxonomy (const char , long val, void cl_ct)

static const char *	tree_of_cached_taxonomy (cached_taxonomy *ct)

static void	flush_taxonomy_cb (GBDATA gbd, cached_taxonomy ct)

static void	flush_taxonomy_if_new_group_cb (GBDATA gb_tree, cached_taxonomy ct)

static cached_taxonomy *	get_cached_taxonomy (GBDATA gb_main, const char tree_name, GB_ERROR *error)

static char *	get_taxonomy_string (GB_HASH tax_hash, const char group_key, int depth, GB_ERROR *error)

static const char *	get_taxonomy (GBDATA gb_species_or_group, const char tree_name, bool is_current_tree, int depth, GB_ERROR *error)

static GB_ERROR	gbl_taxonomy (GBL_command_arguments *args)

static GB_ERROR	gbl_sequence (GBL_command_arguments *args)

static GB_ERROR	gbl_export_sequence (GBL_command_arguments *args)

static GB_ERROR	gbl_ali_name (GBL_command_arguments *args)

static GB_ERROR	gbl_sequence_type (GBL_command_arguments *args)

static GB_ERROR	format (GBL_command_arguments *args, bool simple_format)

static GB_ERROR	gbl_format (GBL_command_arguments *args)

static GB_ERROR	gbl_format_sequence (GBL_command_arguments *args)

static char *	gbl_read_seq_sai_or_species (GBDATA gb_main, const char species, const char sai, const char ali, size_t *seqLen)

static GB_ERROR	apply_filters (GBL_command_arguments args, common_filter_params common, filter_fun filter_one, void *param)

static char *	calc_diff (const char seq, const char filter, size_t, void *paramP)

static GB_ERROR	gbl_diff (GBL_command_arguments *args)

static char *	filter_seq (const char seq, const char filter, size_t flen, void *paramP)

static GB_ERROR	gbl_filter (GBL_command_arguments *args)

static GB_ERROR	gbl_change_gc (GBL_command_arguments *args)

static GB_ERROR	gbl_exec (GBL_command_arguments *args)

const GBL_command_lookup_table &	ACI_get_standard_commands ()

Variables
static gb_export_sequence_cb	get_export_sequence = NULp

int	GBL_IMPL::traceACI = 0

int	GBL_IMPL::traceIndent = 0

static DefinedCommands	defined_commands

static GB_HASH *	cached_taxonomies = NULp

static GBL_command_definition	gbl_command_table []

Macro Definition Documentation

#define GROUP_COUNT_CHARS 6

Definition at line 1504 of file adlang1.cxx.

Referenced by build_taxonomy_rek(), and get_taxonomy_string().

#define BITS_PER_HEXCHAR 4

Definition at line 1505 of file adlang1.cxx.

#define MAX_GROUPS (1 << (GROUP_COUNT_CHARS*BITS_PER_HEXCHAR))

Definition at line 1506 of file adlang1.cxx.

Referenced by build_taxonomy_rek().

#define GBL_COMMON_FILTER_PARAMS

Value:

common_filter_params common_param;                                                                                  \
    GBL_STRUCT_PARAM_STRING(common_param, align,    "align=",    NULp, "alignment to use (defaults to default alignment)"); \
    GBL_STRUCT_PARAM_STRING(common_param, sai,      "SAI=",      NULp, "Use default sequence of given SAI as a filter"); \
    GBL_STRUCT_PARAM_STRING(common_param, species,  "species=",  NULp, "Use default sequence of given species as a filter"); \
    GBL_STRUCT_PARAM_BIT   (common_param, first,    "first=",    0,    "Use 1st stream as filter for other streams");   \
    GBL_STRUCT_PARAM_BIT   (common_param, pairwise, "pairwise=", 0,    "Use 1st stream as filter for 2nd, 3rd for 4th, ...")

Definition at line 2333 of file adlang1.cxx.

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

Typedef Documentation

typedef char*(* filter_fun)(const char *seq, const char *filter, size_t flen, void *param)

Definition at line 2341 of file adlang1.cxx.

Enumeration Type Documentation

enum Case

Enumerator
UPPER
LOWER
CAPS

Definition at line 861 of file adlang1.cxx.

enum GBT_ITEM_TYPE

Enumerator
GBT_ITEM_UNKNOWN
GBT_ITEM_SPECIES
GBT_ITEM_GENE

Definition at line 1465 of file adlang1.cxx.

enum filter_function

Enumerator
FP_FILTER
FP_MODIFY

Definition at line 2454 of file adlang1.cxx.

Function Documentation

NOT4PERL void GB_set_export_sequence_hook ( gb_export_sequence_cb escb )

Definition at line 35 of file adlang1.cxx.

References gb_assert, and get_export_sequence.

Referenced by SEQIO::export_by_format(), and ExportFieldScanner::scanFields().

static int gbl_stricmp	(	const char *	s1,
		const char *	s2
	)

static

Definition at line 175 of file adlang1.cxx.

Referenced by binop_compare(), and binop_equals().

static int gbl_strincmp	(	const char *	s1,
		const char *	s2,
		int	size2
	)

static

Definition at line 192 of file adlang1.cxx.

Referenced by gbl_stristr().

static const char* gbl_stristr	(	const char *	haystack,
		const char *	needle
	)

static

Definition at line 209 of file adlang1.cxx.

References gb_assert, gbl_strincmp(), and NULp.

Referenced by binop_contains().

int approve_pos	(	int	pos,
		int	len
	)

inline

Definition at line 254 of file adlang1.cxx.

Referenced by gbl_mid_streams().

static GB_ERROR gbl_mid_streams	(	const GBL_streams &	arg_input,
		GBL_streams &	arg_out,
		int	start,
		int	end
	)

static

Definition at line 256 of file adlang1.cxx.

References approve_pos(), ARB_strdup(), ARB_strpartdup(), gb_assert, GBL_streams::get(), GBL_streams::insert(), NULp, s, and GBL_streams::size().

Referenced by gbl_dd(), gbl_head(), gbl_tail(), gbl_trace(), and mid().

static GB_ERROR gbl_trace ( GBL_command_arguments * args )

static

Definition at line 278 of file adlang1.cxx.

References EXPECT_PARAMS, gbl_mid_streams(), GBS_global_string(), GBL_command_arguments::get_param(), GBL_command_arguments::input, GBL_command_arguments::output, GBL_IMPL::print_trace(), and GBL_IMPL::traceACI.

template<typename T >

GB_ERROR gbl_apply_binary_operator	(	GBL_command_arguments *	args,
		char ()(const char , const char , T)	op,
		T	client_data
	)

static char* unEscapeString ( const char * escapedString )

static

Definition at line 384 of file adlang1.cxx.

References result.

Referenced by apply_to_origin(), applyToItemFoundByKey(), gbl_command(), gbl_define(), gbl_eval(), and gbl_unescape().

static char* escapeString ( const char * unescapedString )

static

Definition at line 404 of file adlang1.cxx.

References result.

Referenced by gbl_escape().

static GB_ERROR gbl_quote ( GBL_command_arguments * args )

static

Definition at line 430 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_unquote ( GBL_command_arguments * args )

static

Definition at line 438 of file adlang1.cxx.

References ARB_strpartdup(), EXPECT_NO_PARAM, GBL_streams::get(), IN_2_OUT, GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

static GB_ERROR gbl_escape ( GBL_command_arguments * args )

static

Definition at line 455 of file adlang1.cxx.

References escapeString(), EXPECT_NO_PARAM, GBL_streams::get(), GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

static GB_ERROR gbl_unescape ( GBL_command_arguments * args )

static

Definition at line 464 of file adlang1.cxx.

References EXPECT_NO_PARAM, GBL_streams::get(), GBL_command_arguments::input, NULp, PASS_2_OUT, GBL_streams::size(), and unEscapeString().

static GB_ERROR gbl_command ( GBL_command_arguments * args )

static

Definition at line 474 of file adlang1.cxx.

References command, error(), EXPECT_PARAMS, GB_await_error(), GBS_global_string(), GBL_streams::get(), GBL_command_arguments::get_callEnv(), GBL_command_arguments::get_param(), GBL_command_arguments::input, GBL_call_env::interpret_subcommand(), NULp, PASS_2_OUT, GBL_IMPL::print_trace(), result, GBL_streams::size(), GBL_IMPL::traceACI, and unEscapeString().

static GB_ERROR gbl_eval ( GBL_command_arguments * args )

static

Definition at line 493 of file adlang1.cxx.

References command, error(), EXPECT_PARAMS, GB_await_error(), GBS_global_string(), GBL_streams::get(), GBL_command_arguments::get_callEnv(), GBL_command_arguments::get_param(), GBL_command_arguments::input, GBL_call_env::interpret_subcommand(), NULp, PASS_2_OUT, result, GBL_streams::size(), TRACE_ACI, and unEscapeString().

static GB_ERROR gbl_define ( GBL_command_arguments * args )

static

Definition at line 528 of file adlang1.cxx.

References COMMAND_DROPS_INPUT_STREAMS, EXPECT_PARAMS, GBS_global_string(), GBL_command_arguments::get_param(), NULp, DefinedCommands::set(), TRACE_ACI, and unEscapeString().

static GB_ERROR gbl_do ( GBL_command_arguments * args )

static

Definition at line 540 of file adlang1.cxx.

References error(), EXPECT_PARAMS, GB_await_error(), GBS_global_string(), GBL_streams::get(), DefinedCommands::get(), GBL_command_arguments::get_callEnv(), GBL_command_arguments::get_param(), GBL_command_arguments::input, GBL_call_env::interpret_subcommand(), NULp, PASS_2_OUT, result, GBL_streams::size(), and TRACE_ACI.

static GB_ERROR gbl_streams ( GBL_command_arguments * args )

static

Definition at line 562 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR expect_used_in_genome_db ( GBL_command_arguments * args )

static

Definition at line 569 of file adlang1.cxx.

References GBS_global_string(), GEN_is_genome_db(), GBL_command_arguments::get_cmdName(), GBL_command_arguments::get_gb_main(), and NULp.

Referenced by apply_to_origin(), and gbl_findgene().

static GB_ERROR apply_to_origin	(	GBL_command_arguments *	args,
		bool	organism
	)

static

static GB_ERROR gbl_origin_gene ( GBL_command_arguments * args )

static

Definition at line 613 of file adlang1.cxx.

References apply_to_origin().

static GB_ERROR gbl_origin_organism ( GBL_command_arguments * args )

static

Definition at line 614 of file adlang1.cxx.

References apply_to_origin().

static GB_ERROR applyToItemFoundByKey	(	GBL_command_arguments *	args,
		const char *	itemname,
		GBDATA *	gb_item_data,
		const char *	key
	)

static

Definition at line 617 of file adlang1.cxx.

References command, error(), GB_await_error(), GB_find_string(), GB_get_father(), GB_IGNORE_CASE, GBS_global_string(), GBL_streams::get(), GBL_command_arguments::get_env(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, result, SEARCH_GRANDCHILD, GBL_streams::size(), and unEscapeString().

Referenced by gbl_findacc(), gbl_findgene(), and gbl_findspec().

static GB_ERROR gbl_findspec ( GBL_command_arguments * args )

static

Definition at line 652 of file adlang1.cxx.

References applyToItemFoundByKey(), EXPECT_PARAMS, GBT_get_species_data(), and GBL_command_arguments::get_gb_main().

static GB_ERROR gbl_findacc ( GBL_command_arguments * args )

static

Definition at line 656 of file adlang1.cxx.

References applyToItemFoundByKey(), EXPECT_PARAMS, GBT_get_species_data(), and GBL_command_arguments::get_gb_main().

static GB_ERROR gbl_findgene ( GBL_command_arguments * args )

static

Definition at line 661 of file adlang1.cxx.

References applyToItemFoundByKey(), error(), EXPECT_ITEM_REFERENCED, EXPECT_PARAMS, expect_used_in_genome_db(), GB_get_grandfather(), GB_read_key_pntr(), GBS_global_string(), GBT_get_name_or_description(), GEN_find_gene_data(), GEN_is_organism(), and GBL_command_arguments::get_item_ref().

GB_ERROR count_by_tab	(	GBL_command_arguments *	args,
		const Tab &	tab
	)

inline

Definition at line 700 of file adlang1.cxx.

References FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::input, NULp, safeCharIndex(), and GBL_streams::size().

Referenced by gbl_count(), and gbl_len().

GB_ERROR remove_by_tab	(	GBL_command_arguments *	args,
		const Tab &	tab
	)

inline

Definition at line 710 of file adlang1.cxx.

References GBS_strstruct::erase(), GBL_streams::get(), GBS_strstruct::get_copy(), GBL_command_arguments::input, NULp, PASS_2_OUT, GBS_strstruct::put(), and GBL_streams::size().

Referenced by gbl_keep(), and gbl_remove().

static GB_ERROR gbl_count ( GBL_command_arguments * args )

static

Definition at line 724 of file adlang1.cxx.

References count_by_tab(), EXPECT_PARAMS, and GBL_command_arguments::get_param().

static GB_ERROR gbl_len ( GBL_command_arguments * args )

static

Definition at line 728 of file adlang1.cxx.

References count_by_tab(), EXPECT_OPTIONAL_PARAMS, GBL_command_arguments::get_optional_param(), and NULp.

static GB_ERROR gbl_remove ( GBL_command_arguments * args )

static

Definition at line 733 of file adlang1.cxx.

References EXPECT_PARAMS, GBL_command_arguments::get_param(), and remove_by_tab().

static GB_ERROR gbl_keep ( GBL_command_arguments * args )

static

Definition at line 737 of file adlang1.cxx.

References EXPECT_PARAMS, GBL_command_arguments::get_param(), and remove_by_tab().

static char* binop_compare	(	const char *	arg1,
		const char *	arg2,
		bool	case_sensitive
	)

static

Definition at line 743 of file adlang1.cxx.

References gbl_stricmp(), GBS_global_string_copy(), and result.

Referenced by gbl_compare(), and gbl_icompare().

static char* binop_equals	(	const char *	arg1,
		const char *	arg2,
		bool	case_sensitive
	)

static

Definition at line 751 of file adlang1.cxx.

References gbl_stricmp(), GBS_global_string_copy(), and result.

Referenced by gbl_equals(), and gbl_iequals().

static char* binop_contains	(	const char *	arg1,
		const char *	arg2,
		bool	case_sensitive
	)

static

Definition at line 759 of file adlang1.cxx.

References gbl_stristr(), GBS_global_string_copy(), and NULp.

Referenced by binop_partof(), gbl_contains(), and gbl_icontains().

static char* binop_partof	(	const char *	arg1,
		const char *	arg2,
		bool	case_sensitive
	)

static

Definition at line 769 of file adlang1.cxx.

References binop_contains().

Referenced by gbl_ipartof(), and gbl_partof().

static GB_ERROR gbl_compare ( GBL_command_arguments * args )

static

Definition at line 773 of file adlang1.cxx.

References binop_compare(), and gbl_apply_binary_operator().

static GB_ERROR gbl_icompare ( GBL_command_arguments * args )

static

Definition at line 774 of file adlang1.cxx.

References binop_compare(), and gbl_apply_binary_operator().

static GB_ERROR gbl_equals ( GBL_command_arguments * args )

static

Definition at line 775 of file adlang1.cxx.

References binop_equals(), and gbl_apply_binary_operator().

static GB_ERROR gbl_iequals ( GBL_command_arguments * args )

static

Definition at line 776 of file adlang1.cxx.

References binop_equals(), and gbl_apply_binary_operator().

static GB_ERROR gbl_contains ( GBL_command_arguments * args )

static

Definition at line 777 of file adlang1.cxx.

References binop_contains(), and gbl_apply_binary_operator().

static GB_ERROR gbl_icontains ( GBL_command_arguments * args )

static

Definition at line 778 of file adlang1.cxx.

References binop_contains(), and gbl_apply_binary_operator().

static GB_ERROR gbl_partof ( GBL_command_arguments * args )

static

Definition at line 779 of file adlang1.cxx.

References binop_partof(), and gbl_apply_binary_operator().

static GB_ERROR gbl_ipartof ( GBL_command_arguments * args )

static

Definition at line 780 of file adlang1.cxx.

References binop_partof(), and gbl_apply_binary_operator().

static GB_ERROR gbl_isEmpty ( GBL_command_arguments * args )

static

Definition at line 782 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_inRange ( GBL_command_arguments * args )

static

Definition at line 790 of file adlang1.cxx.

References EXPECT_PARAMS, FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_translate ( GBL_command_arguments * args )

static

Definition at line 805 of file adlang1.cxx.

References GBS_strstruct::erase(), EXPECT_OPTIONAL_PARAMS, GBS_global_string(), GBL_streams::get(), GBS_strstruct::get_copy(), GBL_command_arguments::get_optional_param(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, GBS_strstruct::put(), GBL_streams::size(), and tab().

static GB_ERROR gbl_echo ( GBL_command_arguments * args )

static

Definition at line 849 of file adlang1.cxx.

References ACCEPT_ANY_PARAMS, COMMAND_DROPS_INPUT_STREAMS, NULp, PARAM_2_OUT, and GBL_command_arguments::param_count().

static GB_ERROR gbl_dd ( GBL_command_arguments * args )

static

Definition at line 856 of file adlang1.cxx.

References EXPECT_NO_PARAM, gbl_mid_streams(), GBL_command_arguments::input, and GBL_command_arguments::output.

static GB_ERROR convert_case	(	GBL_command_arguments *	args,
		Case	convTo
	)

static

Definition at line 863 of file adlang1.cxx.

References ARB_strdup(), CAPS, EXPECT_NO_PARAM, gb_assert, GBL_streams::get(), GBL_command_arguments::input, LOWER, NULp, PASS_2_OUT, GBL_streams::size(), and UPPER.

Referenced by gbl_caps(), gbl_lower(), and gbl_upper().

static GB_ERROR gbl_caps ( GBL_command_arguments * args )

static

Definition at line 890 of file adlang1.cxx.

References CAPS, and convert_case().

static GB_ERROR gbl_upper ( GBL_command_arguments * args )

static

Definition at line 891 of file adlang1.cxx.

References convert_case(), and UPPER.

static GB_ERROR gbl_lower ( GBL_command_arguments * args )

static

Definition at line 892 of file adlang1.cxx.

References convert_case(), and LOWER.

static GB_ERROR gbl_head ( GBL_command_arguments * args )

static

Definition at line 894 of file adlang1.cxx.

References EXPECT_PARAMS, gbl_mid_streams(), GBL_command_arguments::get_param(), GBL_command_arguments::input, GBL_command_arguments::output, and start.

static GB_ERROR gbl_tail ( GBL_command_arguments * args )

static

Definition at line 900 of file adlang1.cxx.

References EXPECT_PARAMS, gbl_mid_streams(), GBL_command_arguments::get_param(), GBL_command_arguments::input, and GBL_command_arguments::output.

GB_ERROR mid	(	GBL_command_arguments *	args,
		int	start_index
	)

inline

Definition at line 907 of file adlang1.cxx.

References EXPECT_PARAMS, gbl_mid_streams(), GBL_command_arguments::get_param(), GBL_command_arguments::input, and GBL_command_arguments::output.

Referenced by PrefixProbabilities::find_index_near_leftsum(), gbl_mid(), gbl_mid0(), GBT_create_unique_item_identifier(), and SEC_root::paint().

static GB_ERROR gbl_mid0 ( GBL_command_arguments * args )

static

Definition at line 911 of file adlang1.cxx.

References mid().

static GB_ERROR gbl_mid ( GBL_command_arguments * args )

static

Definition at line 912 of file adlang1.cxx.

References mid().

static GB_ERROR tab	(	GBL_command_arguments *	args,
		bool	pretab
	)

static

Definition at line 914 of file adlang1.cxx.

References EXPECT_PARAMS, GBL_streams::get(), GBL_command_arguments::get_param(), IN_2_OUT, GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

Referenced by aisc_init_hash(), format(), GB_checksum(), gbl_pretab(), gbl_tab(), gbl_translate(), Memory::get(), MemBlockManager::get_block(), MG_diff_strings(), Memory::put(), ArbImporter::read_line(), readable_probe(), GBL_IMPL::search_next_separator(), and writeSeq().

static GB_ERROR gbl_tab ( GBL_command_arguments * args )

static

Definition at line 938 of file adlang1.cxx.

References tab().

static GB_ERROR gbl_pretab ( GBL_command_arguments * args )

static

Definition at line 939 of file adlang1.cxx.

References tab().

static GB_ERROR gbl_crop ( GBL_command_arguments * args )

static

Definition at line 941 of file adlang1.cxx.

References EXPECT_PARAMS, gb_assert, GBL_streams::get(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, s, and GBL_streams::size().

static GB_ERROR gbl_cut ( GBL_command_arguments * args )

static

Definition at line 969 of file adlang1.cxx.

References bio2info(), EXPECT_LEGAL_STREAM_INDEX, EXPECT_PARAMS_PASSED, GBL_command_arguments::get_param(), IN_2_OUT, NULp, and GBL_command_arguments::param_count().

static GB_ERROR gbl_drop ( GBL_command_arguments * args )

static

Definition at line 979 of file adlang1.cxx.

References bio2info(), GBL_IMPL::check_valid_stream_index(), error(), EXPECT_PARAMS_PASSED, GBL_command_arguments::get_param(), IN_2_OUT, GBL_command_arguments::input, NULp, GBL_command_arguments::param_count(), and GBL_streams::size().

static GB_ERROR gbl_dropempty ( GBL_command_arguments * args )

static

Definition at line 1003 of file adlang1.cxx.

References EXPECT_NO_PARAM, GBL_streams::get(), IN_2_OUT, GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_dropzero ( GBL_command_arguments * args )

static

Definition at line 1014 of file adlang1.cxx.

References EXPECT_NO_PARAM, GBL_streams::get(), IN_2_OUT, GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_swap ( GBL_command_arguments * args )

static

Definition at line 1025 of file adlang1.cxx.

References bio2info(), EXPECT_LEGAL_STREAM_INDEX, EXPECT_OPTIONAL_PARAMS, gb_assert, GBL_command_arguments::get_param(), IN_2_OUT, GBL_command_arguments::input, NULp, GBL_command_arguments::param_count(), and GBL_streams::size().

static GB_ERROR backfront_stream	(	GBL_command_arguments *	args,
		int	toback
	)

static

Definition at line 1057 of file adlang1.cxx.

References bio2info(), EXPECT_LEGAL_STREAM_INDEX, EXPECT_PARAMS, GBL_command_arguments::get_param(), IN_2_OUT, GBL_command_arguments::input, NULp, and GBL_streams::size().

Referenced by gbl_toback(), and gbl_tofront().

static GB_ERROR gbl_toback ( GBL_command_arguments * args )

static

Definition at line 1073 of file adlang1.cxx.

References backfront_stream().

static GB_ERROR gbl_tofront ( GBL_command_arguments * args )

static

Definition at line 1074 of file adlang1.cxx.

References backfront_stream().

static GB_ERROR gbl_merge ( GBL_command_arguments * args )

static

Definition at line 1076 of file adlang1.cxx.

References GBS_strstruct::cat(), EXPECT_OPTIONAL_PARAMS, GBL_streams::get(), GBL_command_arguments::get_optional_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, GBS_strstruct::release(), and GBL_streams::size().

static GB_ERROR gbl_split ( GBL_command_arguments * args )

static

Definition at line 1094 of file adlang1.cxx.

References ARB_strndup(), copy(), COPY_2_OUT, EXPECT_OPTIONAL_PARAMS_CUSTOM, GBS_global_string(), GBL_streams::get(), GBL_command_arguments::get_optional_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

static GB_ERROR gbl_colsplit ( GBL_command_arguments * args )

static

Definition at line 1141 of file adlang1.cxx.

References ARB_strpartdup(), EXPECT_OPTIONAL_PARAMS, GBL_streams::get(), GBL_command_arguments::get_optional_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

static char* do_extract_words	(	const char *	source,
		const char *	chars,
		float	minlen,
		bool	sort_output
	)

static

Definition at line 1165 of file adlang1.cxx.

References ARB_strdup(), GBS_strstruct::cat(), GB_sort(), GB_string_comparator(), NULp, GBS_strstruct::put(), GBS_strstruct::release_memfriendly(), and s.

Referenced by gbl_extract_sequence(), and gbl_extract_words().

static GB_ERROR gbl_extract_words ( GBL_command_arguments * args )

static

Definition at line 1216 of file adlang1.cxx.

References do_extract_words(), EXPECT_PARAMS, gb_assert, GBL_streams::get(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

static GB_ERROR gbl_extract_sequence ( GBL_command_arguments * args )

static

Definition at line 1228 of file adlang1.cxx.

References chars, do_extract_words(), EXPECT_PARAMS, gb_assert, GBS_global_string(), GBL_streams::get(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, and GBL_streams::size().

static GB_ERROR gbl_checksum ( GBL_command_arguments * args )

static

Definition at line 1244 of file adlang1.cxx.

References FORMAT_2_OUT, GBL_BEGIN_PARAMS, GBL_END_PARAMS, GBL_PARAM_BIT, GBL_PARAM_STRING, GBL_TRACE_PARAMS, GBS_checksum(), GBL_streams::get(), GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_gcgchecksum ( GBL_command_arguments * args )

static

Definition at line 1258 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBS_gcgchecksum(), GBL_streams::get(), GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_srt ( GBL_command_arguments * args )

static

Definition at line 1271 of file adlang1.cxx.

References error(), EXPECT_PARAMS_PASSED, GB_await_error(), GBS_string_eval_in_env(), GBL_streams::get(), GBL_command_arguments::get_callEnv(), GBL_command_arguments::get_param(), IN_2_OUT, GBL_command_arguments::input, NULp, GBL_command_arguments::param_count(), PASS_2_OUT, and GBL_streams::size().

static char* apply_numeric_binop	(	const char *	arg1,
		const char *	arg2,
		int(*)(int, int)	num_bin_op
	)

static

Definition at line 1305 of file adlang1.cxx.

References GBS_global_string_copy(), and result.

Referenced by gbl_div(), gbl_minus(), gbl_mult(), gbl_per_cent(), gbl_plus(), and gbl_rest().

static char* apply_double_binop	(	const char *	arg1,
		const char *	arg2,
		double(*)(double, double)	num_bin_op
	)

static

Definition at line 1313 of file adlang1.cxx.

References GBS_global_string_copy(), NULp, and result.

Referenced by gbl_fdiv(), gbl_fminus(), gbl_fmult(), gbl_fper_cent(), and gbl_fplus().

static char* apply_auto_numeric_binop	(	const char *	arg1,
		const char *	arg2,
		binop_pair	multiop
	)

static

Definition at line 1321 of file adlang1.cxx.

References binop_pair::DOUBLE, GBS_global_string_copy(), binop_pair::INT, NULp, and result.

Referenced by gbl_isAbove(), gbl_isBelow(), and gbl_isEqual().

template<typename T >

static T binop_plus	(	T	v1,
		T	v2
	)

static

Definition at line 1340 of file adlang1.cxx.

template<typename T >

static T binop_minus	(	T	v1,
		T	v2
	)

static

Definition at line 1341 of file adlang1.cxx.

template<typename T >

static T binop_mult	(	T	v1,
		T	v2
	)

static

Definition at line 1342 of file adlang1.cxx.

template<typename T >

static T binop_div	(	T	v1,
		T	v2
	)

static

Definition at line 1343 of file adlang1.cxx.

template<typename T >

static T binop_per_cent	(	T	v1,
		T	v2
	)

static

Definition at line 1344 of file adlang1.cxx.

static int binop_rest	(	int	i1,
		int	i2
	)

static

Definition at line 1346 of file adlang1.cxx.

Referenced by gbl_rest().

static GB_ERROR gbl_plus ( GBL_command_arguments * args )

static

Definition at line 1349 of file adlang1.cxx.

References apply_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_fplus ( GBL_command_arguments * args )

static

Definition at line 1350 of file adlang1.cxx.

References apply_double_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_minus ( GBL_command_arguments * args )

static

Definition at line 1351 of file adlang1.cxx.

References apply_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_fminus ( GBL_command_arguments * args )

static

Definition at line 1352 of file adlang1.cxx.

References apply_double_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_mult ( GBL_command_arguments * args )

static

Definition at line 1353 of file adlang1.cxx.

References apply_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_fmult ( GBL_command_arguments * args )

static

Definition at line 1354 of file adlang1.cxx.

References apply_double_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_div ( GBL_command_arguments * args )

static

Definition at line 1355 of file adlang1.cxx.

References apply_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_fdiv ( GBL_command_arguments * args )

static

Definition at line 1356 of file adlang1.cxx.

References apply_double_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_rest ( GBL_command_arguments * args )

static

Definition at line 1357 of file adlang1.cxx.

References apply_numeric_binop(), binop_rest(), and gbl_apply_binary_operator().

static GB_ERROR gbl_per_cent ( GBL_command_arguments * args )

static

Definition at line 1358 of file adlang1.cxx.

References apply_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_fper_cent ( GBL_command_arguments * args )

static

Definition at line 1359 of file adlang1.cxx.

References apply_double_binop(), and gbl_apply_binary_operator().

template<typename T >

static T binop_isAbove	(	T	i1,
		T	i2
	)

static

Definition at line 1361 of file adlang1.cxx.

template<typename T >

static T binop_isBelow	(	T	i1,
		T	i2
	)

static

Definition at line 1362 of file adlang1.cxx.

template<typename T >

static T binop_isEqual	(	T	i1,
		T	i2
	)

static

Definition at line 1363 of file adlang1.cxx.

static GB_ERROR gbl_isAbove ( GBL_command_arguments * args )

static

Definition at line 1365 of file adlang1.cxx.

References apply_auto_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_isBelow ( GBL_command_arguments * args )

static

Definition at line 1366 of file adlang1.cxx.

References apply_auto_numeric_binop(), and gbl_apply_binary_operator().

static GB_ERROR gbl_isEqual ( GBL_command_arguments * args )

static

Definition at line 1367 of file adlang1.cxx.

References apply_auto_numeric_binop(), and gbl_apply_binary_operator().

double float_shift_factor ( int digits )

inline

Definition at line 1369 of file adlang1.cxx.

References digits().

Referenced by gbl_round().

static GB_ERROR gbl_round ( GBL_command_arguments * args )

static

Definition at line 1381 of file adlang1.cxx.

References digits(), EXPECT_PARAMS, float_shift_factor(), FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, and GBL_streams::size().

static GB_ERROR gbl_not ( GBL_command_arguments * args )

static

Definition at line 1398 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::input, NULp, s, and GBL_streams::size().

static GB_ERROR gbl_and ( GBL_command_arguments * args )

static

Definition at line 1409 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::input, NULp, s, and GBL_streams::size().

static GB_ERROR gbl_or ( GBL_command_arguments * args )

static

Definition at line 1419 of file adlang1.cxx.

References EXPECT_NO_PARAM, FORMAT_2_OUT, GBL_streams::get(), GBL_command_arguments::input, NULp, s, and GBL_streams::size().

static GB_ERROR gbl_select ( GBL_command_arguments * args )

static

Definition at line 1430 of file adlang1.cxx.

References ACCEPT_ANY_PARAMS, GBL_IMPL::check_valid_param_index(), error(), GB_await_error(), GBL_streams::get(), GBL_command_arguments::get_callEnv(), GBL_command_arguments::get_param(), GBL_command_arguments::input, GBL_call_env::interpret_subcommand(), NULp, PASS_2_OUT, result, and GBL_streams::size().

static GB_ERROR gbl_readdb ( GBL_command_arguments * args )

static

Definition at line 1446 of file adlang1.cxx.

References GBS_strstruct::cat(), COMMAND_DROPS_INPUT_STREAMS, EXPECT_ITEM_REFERENCED, EXPECT_PARAMS_PASSED, GBT_read_as_string(), GBL_command_arguments::get_item_ref(), GBL_command_arguments::get_param(), NULp, GBL_command_arguments::param_count(), PASS_2_OUT, GBS_strstruct::release(), and GBL_command_arguments::track_field_access().

static GBT_ITEM_TYPE identify_gb_item ( GBDATA * gb_item )

static

Definition at line 1471 of file adlang1.cxx.

References GB_get_father(), GB_KEY(), GBT_ITEM_GENE, GBT_ITEM_SPECIES, and GBT_ITEM_UNKNOWN.

Referenced by gbl_export_sequence(), and gbl_sequence().

static void free_cached_taxonomy ( cached_taxonomy * ct )

static

Definition at line 1522 of file adlang1.cxx.

References GBS_free_hash(), cached_taxonomy::taxonomy, and cached_taxonomy::tree_name.

Referenced by flush_taxonomy_cb().

static void build_taxonomy_rek	(	TreeNode *	node,
		GB_HASH *	tax_hash,
		const char *	parent_group,
		int *	group_counter
	)

static

Definition at line 1528 of file adlang1.cxx.

References ARB_strdup(), gb_assert, TreeNode::gb_node, GBS_global_string(), GBS_global_string_copy(), GBS_write_hash(), GBT_get_name(), GROUP_COUNT_CHARS, TreeNode::has_group_info(), TreeNode::is_leaf(), TreeNode::is_leftson(), KEELED_INDICATOR, TreeNode::keelTarget(), MAX_GROUPS, and TreeNode::name.

Referenced by get_cached_taxonomy().

static bool is_cached_taxonomy	(	const char *	,
		long	val,
		void *	cl_ct
	)

static

Definition at line 1582 of file adlang1.cxx.

Referenced by tree_of_cached_taxonomy().

static const char* tree_of_cached_taxonomy ( cached_taxonomy * ct )

static

Definition at line 1589 of file adlang1.cxx.

References GBS_hash_next_element_that(), is_cached_taxonomy(), NULp, tree, and cached_taxonomy::tree_name.

Referenced by flush_taxonomy_cb(), and flush_taxonomy_if_new_group_cb().

static void flush_taxonomy_cb	(	GBDATA *	gbd,
		cached_taxonomy *	ct
	)

static

Definition at line 1600 of file adlang1.cxx.

References AWAR_TREE_REFRESH, CASTSIG, error(), free_cached_taxonomy(), GB_await_error(), GB_CB_CHANGED_OR_DELETED, GB_CB_DELETE, GB_get_gb_main_during_cb(), GB_inside_callback(), GB_INT, gb_main, GB_remove_all_callbacks_to(), GB_search(), GB_touch(), GBS_global_string(), GBS_write_hash(), NULp, and tree_of_cached_taxonomy().

Referenced by flush_taxonomy_if_new_group_cb(), and get_cached_taxonomy().

static void flush_taxonomy_if_new_group_cb	(	GBDATA *	gb_tree,
		cached_taxonomy *	ct
	)

static

Definition at line 1644 of file adlang1.cxx.

References flush_taxonomy_cb(), fputs(), GB_entry(), GB_nextEntry(), cached_taxonomy::groups, and tree_of_cached_taxonomy().

Referenced by get_cached_taxonomy().

static cached_taxonomy* get_cached_taxonomy	(	GBDATA *	gb_main,
		const char *	tree_name,
		GB_ERROR *	error
	)

static

static char* get_taxonomy_string	(	GB_HASH *	tax_hash,
		const char *	group_key,
		int	depth,
		GB_ERROR *	error
	)

static

Definition at line 1754 of file adlang1.cxx.

References ARB_strdup(), gb_assert, GBS_global_string(), GBS_global_string_copy(), GBS_read_hash(), GROUP_COUNT_CHARS, NULp, and result.

Referenced by get_taxonomy().

static const char* get_taxonomy	(	GBDATA *	gb_species_or_group,
		const char *	tree_name,
		bool	is_current_tree,
		int	depth,
		GB_ERROR *	error
	)

static

Definition at line 1790 of file adlang1.cxx.

References GB_entry(), GB_get_root(), gb_main, GB_read_string(), GBS_global_string(), GBS_read_hash(), get_cached_taxonomy(), get_taxonomy_string(), NULp, result, and cached_taxonomy::taxonomy.

Referenced by gbl_taxonomy().

static GB_ERROR gbl_taxonomy ( GBL_command_arguments * args )

static

Definition at line 1865 of file adlang1.cxx.

References ARB_strdup(), GBL_IMPL::check_optional_parameters(), COMMAND_DROPS_INPUT_STREAMS, error(), EXPECT_ITEM_REFERENCED, gb_assert, GBS_global_string(), GBL_command_arguments::get_item_ref(), GBL_command_arguments::get_param(), get_taxonomy(), GBL_command_arguments::get_treename(), NULp, GBL_command_arguments::param_count(), PASS_2_OUT, and result.

static GB_ERROR gbl_sequence ( GBL_command_arguments * args )

static

static GB_ERROR gbl_export_sequence ( GBL_command_arguments * args )

static

Definition at line 1948 of file adlang1.cxx.

References ARB_strduplen(), GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, error(), EXPECT_ITEM_REFERENCED, gb_assert, GBT_ITEM_GENE, GBT_ITEM_SPECIES, GBT_ITEM_UNKNOWN, get_export_sequence, GBL_command_arguments::get_item_ref(), identify_gb_item(), PASS_2_OUT, and seq.

static GB_ERROR gbl_ali_name ( GBL_command_arguments * args )

static

Definition at line 1982 of file adlang1.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, error(), GB_await_error(), gb_main, GBT_get_default_alignment(), GBL_command_arguments::get_gb_main(), and PASS_2_OUT.

static GB_ERROR gbl_sequence_type ( GBL_command_arguments * args )

static

Definition at line 1995 of file adlang1.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, error(), GB_await_error(), gb_main, GBT_get_alignment_type_string(), GBT_get_default_alignment(), GBL_command_arguments::get_gb_main(), and PASS_2_OUT.

static GB_ERROR format	(	GBL_command_arguments *	args,
		bool	simple_format
	)

static

Definition at line 2010 of file adlang1.cxx.

References ARB_realloc(), ARB_strdup(), calc_digits(), error(), gb_assert, GBL_BEGIN_PARAMS, GBL_END_PARAMS, GBL_PARAM_BIT, GBL_PARAM_INT, GBL_PARAM_STRING, GBL_PARAM_UINT, GBL_TRACE_PARAMS, GBS_global_string(), GBS_global_string_copy(), GBL_streams::get(), GBL_command_arguments::input, arb_test::nl(), NULp, PARAM_IF, PASS_2_OUT, result, GBL_streams::size(), and tab().

Referenced by gbl_format(), and gbl_format_sequence().

static GB_ERROR gbl_format ( GBL_command_arguments * args )

static

Definition at line 2248 of file adlang1.cxx.

References format().

static GB_ERROR gbl_format_sequence ( GBL_command_arguments * args )

static

Definition at line 2249 of file adlang1.cxx.

References format().

static char* gbl_read_seq_sai_or_species	(	GBDATA *	gb_main,
		const char *	species,
		const char *	sai,
		const char *	ali,
		size_t *	seqLen
	)

static

Definition at line 2252 of file adlang1.cxx.

References error(), gb_assert, GB_await_error(), GB_BITS, GB_child(), GB_entry(), GB_export_error(), GB_nextChild(), GB_read_bits(), GB_read_bits_count(), GB_read_string(), GB_read_string_count(), GB_read_type(), GB_STRING, GBS_global_string(), GBT_find_SAI(), GBT_find_species(), GBT_get_default_alignment(), NULp, seq, and type.

Referenced by apply_filters().

static GB_ERROR apply_filters	(	GBL_command_arguments *	args,
		common_filter_params *	common,
		filter_fun	filter_one,
		void *	param
	)

static

Definition at line 2348 of file adlang1.cxx.

References common_filter_params::align, ARB_strduplen(), error(), common_filter_params::first, gb_assert, GB_await_error(), gbl_read_seq_sai_or_species(), GBL_streams::get(), GBL_command_arguments::get_gb_main(), GBL_command_arguments::input, NULp, common_filter_params::pairwise, PASS_2_OUT, common_filter_params::sai, GBL_streams::size(), and common_filter_params::species.

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

static char* calc_diff	(	const char *	seq,
		const char *	filter,
		size_t	,
		void *	paramP
	)

static

Definition at line 2406 of file adlang1.cxx.

References ARB_strdup(), diff_params::diffC, diff_params::equalC, and result.

Referenced by gbl_diff().

static GB_ERROR gbl_diff ( GBL_command_arguments * args )

static

Definition at line 2437 of file adlang1.cxx.

References apply_filters(), calc_diff(), GBL_BEGIN_PARAMS, GBL_COMMON_FILTER_PARAMS, GBL_END_PARAMS, GBL_STRUCT_PARAM_CHAR, and GBL_TRACE_PARAMS.

static char* filter_seq	(	const char *	seq,
		const char *	filter,
		size_t	flen,
		void *	paramP
	)

static

Definition at line 2467 of file adlang1.cxx.

References filter_params::change_pc, filter_params::change_to, filter_params::exclude, FP_FILTER, FP_MODIFY, filter_params::function, gb_assert, GB_random(), filter_params::include, GBS_strstruct::ncat(), GBS_strstruct::put(), and GBS_strstruct::release().

Referenced by gbl_change_gc(), and gbl_filter().

static GB_ERROR gbl_filter ( GBL_command_arguments * args )

static

Definition at line 2538 of file adlang1.cxx.

References apply_filters(), error(), filter_params::exclude, filter_seq(), FP_FILTER, filter_params::function, GBL_BEGIN_PARAMS, GBL_COMMON_FILTER_PARAMS, GBL_END_PARAMS, GBL_STRUCT_PARAM_STRING, GBL_TRACE_PARAMS, filter_params::include, and NULp.

static GB_ERROR gbl_change_gc ( GBL_command_arguments * args )

static

Definition at line 2559 of file adlang1.cxx.

References apply_filters(), error(), filter_params::exclude, filter_seq(), FP_MODIFY, filter_params::function, GBL_BEGIN_PARAMS, GBL_COMMON_FILTER_PARAMS, GBL_END_PARAMS, GBL_STRUCT_PARAM_INT, GBL_STRUCT_PARAM_STRING, GBL_TRACE_PARAMS, filter_params::include, and NULp.

static GB_ERROR gbl_exec ( GBL_command_arguments * args )

static

const GBL_command_lookup_table& ACI_get_standard_commands ( )

Definition at line 2749 of file adlang1.cxx.

References ARRAY_ELEMS.

Referenced by get_GroupRename_customized_ACI_commands(), and get_GroupXfer_customized_ACI_commands().

Variable Documentation

gb_export_sequence_cb get_export_sequence = NULp

static

Definition at line 33 of file adlang1.cxx.

Referenced by GB_set_export_sequence_hook(), and gbl_export_sequence().

DefinedCommands defined_commands

static

Definition at line 526 of file adlang1.cxx.

GB_HASH* cached_taxonomies = NULp

static

Definition at line 1580 of file adlang1.cxx.

GBL_command_definition gbl_command_table[]

static

Definition at line 2654 of file adlang1.cxx.

Classes

Namespaces

Macros

Typedefs

Enumerations

Functions

Variables

Macro Definition Documentation

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation