ARB
Classes | Namespaces | Macros | Typedefs | Enumerations | Functions | Variables
adlang1.cxx File Reference
#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:

Go to the source code of this file.

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, ...")
common_filter_params
Definition: adlang1.cxx:2324
GBL_STRUCT_PARAM_STRING
#define GBL_STRUCT_PARAM_STRING(strct, member, param_name, def, help_text)
Definition: gb_aci_impl.h:106
GBL_STRUCT_PARAM_BIT
#define GBL_STRUCT_PARAM_BIT(strct,member, param_name, def, help_text)
Definition: gb_aci_impl.h:107
NULp
#define NULp
Definition: cxxforward.h:114

Definition at line 2332 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 2340 of file adlang1.cxx.

Enumeration Type Documentation

enum Case
Enumerator
UPPER 
LOWER 
CAPS 

Definition at line 860 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 2453 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 176 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 193 of file adlang1.cxx.

Referenced by gbl_stristr().

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

Definition at line 210 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 255 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 257 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 279 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 
)

Definition at line 329 of file adlang1.cxx.

References GBL_IMPL::check_optional_parameters(), error(), gb_assert, 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, GBL_command_arguments::param_count(), PASS_2_OUT, GBL_command_arguments::set_params_checked(), and GBL_streams::size().

Referenced by gbl_compare(), gbl_contains(), gbl_div(), gbl_equals(), gbl_fdiv(), gbl_fminus(), gbl_fmult(), gbl_fper_cent(), gbl_fplus(), gbl_icompare(), gbl_icontains(), gbl_iequals(), gbl_ipartof(), gbl_isAbove(), gbl_isBelow(), gbl_isEqual(), gbl_minus(), gbl_mult(), gbl_partof(), gbl_per_cent(), gbl_plus(), and gbl_rest().

static char* unEscapeString ( const char *  escapedString)
static

Definition at line 385 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 405 of file adlang1.cxx.

References result.

Referenced by gbl_escape().

static GB_ERROR gbl_quote ( GBL_command_arguments *  args)
static

Definition at line 431 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 439 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 456 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 465 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 475 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 494 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 529 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 541 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 563 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 570 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

Definition at line 575 of file adlang1.cxx.

References command, error(), EXPECT_ITEM_REFERENCED, EXPECT_PARAMS, expect_used_in_genome_db(), GB_await_error(), GBS_global_string(), GEN_find_origin_gene(), GEN_find_origin_organism(), GEN_is_pseudo_gene_species(), GBL_streams::get(), GBL_command_arguments::get_cmdName(), GBL_command_arguments::get_env(), GBL_command_arguments::get_item_ref(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, result, GBL_streams::size(), and unEscapeString().

Referenced by gbl_origin_gene(), and gbl_origin_organism().

static GB_ERROR gbl_origin_gene ( GBL_command_arguments *  args)
static

Definition at line 614 of file adlang1.cxx.

References apply_to_origin().

static GB_ERROR gbl_origin_organism ( GBL_command_arguments *  args)
static

Definition at line 615 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 618 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 653 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 657 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 662 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 701 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 711 of file adlang1.cxx.

References GBS_chrcat(), GBS_strclose(), GBS_stropen(), GBL_streams::get(), GBL_command_arguments::input, NULp, PASS_2_OUT, 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 EXPECT_OPTIONAL_PARAMS, GBS_chrcat(), GBS_global_string(), GBS_strclose(), GBS_stropen(), GBL_streams::get(), GBL_command_arguments::get_optional_param(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, PASS_2_OUT, GBL_streams::size(), and tab().

static GB_ERROR gbl_echo ( GBL_command_arguments *  args)
static

Definition at line 848 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 855 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 862 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 889 of file adlang1.cxx.

References CAPS, and convert_case().

static GB_ERROR gbl_upper ( GBL_command_arguments *  args)
static

Definition at line 890 of file adlang1.cxx.

References convert_case(), and UPPER.

static GB_ERROR gbl_lower ( GBL_command_arguments *  args)
static

Definition at line 891 of file adlang1.cxx.

References convert_case(), and LOWER.

static GB_ERROR gbl_head ( GBL_command_arguments *  args)
static

Definition at line 893 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 899 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 906 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 910 of file adlang1.cxx.

References mid().

static GB_ERROR gbl_mid ( GBL_command_arguments *  args)
static

Definition at line 911 of file adlang1.cxx.

References mid().

static GB_ERROR tab ( GBL_command_arguments *  args,
bool  pretab 
)
static

Definition at line 913 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 937 of file adlang1.cxx.

References tab().

static GB_ERROR gbl_pretab ( GBL_command_arguments *  args)
static

Definition at line 938 of file adlang1.cxx.

References tab().

static GB_ERROR gbl_crop ( GBL_command_arguments *  args)
static

Definition at line 940 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 968 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 978 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 1002 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 1013 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 1024 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 1056 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 1072 of file adlang1.cxx.

References backfront_stream().

static GB_ERROR gbl_tofront ( GBL_command_arguments *  args)
static

Definition at line 1073 of file adlang1.cxx.

References backfront_stream().

static GB_ERROR gbl_merge ( GBL_command_arguments *  args)
static

Definition at line 1075 of file adlang1.cxx.

References EXPECT_OPTIONAL_PARAMS, GBS_strcat(), GBS_strclose(), GBS_stropen(), 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_split ( GBL_command_arguments *  args)
static

Definition at line 1093 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 1140 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 1164 of file adlang1.cxx.

References ARB_strdup(), GB_sort(), GB_string_comparator(), GBS_chrcat(), GBS_strcat(), GBS_strclose(), GBS_stropen(), NULp, 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 COMMAND_DROPS_INPUT_STREAMS, EXPECT_ITEM_REFERENCED, EXPECT_PARAMS_PASSED, GBS_strcat(), GBS_strclose(), GBS_stropen(), GBT_read_as_string(), GBL_command_arguments::get_item_ref(), GBL_command_arguments::get_param(), NULp, GBL_command_arguments::param_count(), PASS_2_OUT, 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(), 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 1581 of file adlang1.cxx.

Referenced by tree_of_cached_taxonomy().

static const char* tree_of_cached_taxonomy ( cached_taxonomy *  ct)
static

Definition at line 1588 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 1599 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 1643 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

Definition at line 1680 of file adlang1.cxx.

References ARB_strdup(), build_taxonomy_rek(), CASTSIG, destroy(), flush_taxonomy_cb(), flush_taxonomy_if_new_group_cb(), GB_add_callback(), gb_assert, GB_await_error(), GB_CB_CHANGED_OR_DELETED, GB_CB_SON_CREATED, GB_entry(), GB_IGNORE_CASE, GB_nextEntry(), GB_remove_all_callbacks_to(), GBS_create_dynaval_hash(), GBS_create_hash(), GBS_dynaval_free(), GBS_global_string(), GBS_read_hash(), GBS_write_hash(), GBT_count_leafs(), GBT_find_tree(), GBT_link_tree(), GBT_read_tree(), cached_taxonomy::groups, long, NULp, cached_taxonomy::taxonomy, and cached_taxonomy::tree_name.

Referenced by get_taxonomy().

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

Definition at line 1753 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 1789 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 1864 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

Definition at line 1907 of file adlang1.cxx.

References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, COPY_2_OUT, error(), EXPECT_ITEM_REFERENCED, GB_await_error(), GB_read_string(), GBT_find_sequence(), GBT_get_default_alignment(), GBT_ITEM_GENE, GBT_ITEM_SPECIES, GBT_ITEM_UNKNOWN, GBT_read_gene_sequence(), GBL_command_arguments::get_gb_main(), GBL_command_arguments::get_item_ref(), identify_gb_item(), PASS_2_OUT, and seq.

static GB_ERROR gbl_export_sequence ( GBL_command_arguments *  args)
static

Definition at line 1947 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 1981 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 1994 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 2009 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 2247 of file adlang1.cxx.

References format().

static GB_ERROR gbl_format_sequence ( GBL_command_arguments *  args)
static

Definition at line 2248 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 2251 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 2347 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 2405 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 2436 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 2466 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(), GBS_chrcat(), GBS_strclose(), GBS_strncat(), GBS_stropen(), and filter_params::include.

Referenced by gbl_change_gc(), and gbl_filter().

static GB_ERROR gbl_filter ( GBL_command_arguments *  args)
static

Definition at line 2537 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 2558 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

Definition at line 2583 of file adlang1.cxx.

References error(), EXPECT_PARAMS_PASSED, gb_assert, GB_await_error(), GB_fopen_tempfile(), GB_is_privatefile(), GB_unique_filename(), GB_unlink_or_warn(), GBS_chrcat(), GBS_global_string(), GBS_strcat(), GBS_strclose(), GBS_stropen(), GBL_streams::get(), GBL_command_arguments::get_param(), GBL_command_arguments::input, NULp, GBL_command_arguments::param_count(), PASS_2_OUT, result, and GBL_streams::size().

const GBL_command_lookup_table& ACI_get_standard_commands ( )

Definition at line 2748 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 527 of file adlang1.cxx.

GB_HASH* cached_taxonomies = NULp
static

Definition at line 1579 of file adlang1.cxx.

GBL_command_definition gbl_command_table[]
static

Definition at line 2653 of file adlang1.cxx.

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