ARB
|
#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>
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 } |
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 [] |
#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 |
Definition at line 2330 of file adlang1.cxx.
Referenced by gbl_change_gc(), gbl_diff(), and gbl_filter().
Definition at line 2338 of file adlang1.cxx.
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 2451 of file adlang1.cxx.
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().
Definition at line 176 of file adlang1.cxx.
Referenced by binop_compare(), and binop_equals().
Definition at line 193 of file adlang1.cxx.
Referenced by gbl_stristr().
Definition at line 210 of file adlang1.cxx.
References gb_assert, gbl_strincmp(), and NULp.
Referenced by binop_contains().
Definition at line 255 of file adlang1.cxx.
Referenced by gbl_mid_streams().
|
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 |
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.
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().
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Definition at line 614 of file adlang1.cxx.
References apply_to_origin().
|
static |
Definition at line 615 of file adlang1.cxx.
References apply_to_origin().
|
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 |
Definition at line 653 of file adlang1.cxx.
References applyToItemFoundByKey(), EXPECT_PARAMS, GBT_get_species_data(), and GBL_command_arguments::get_gb_main().
|
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 |
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().
|
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().
|
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 |
Definition at line 724 of file adlang1.cxx.
References count_by_tab(), EXPECT_PARAMS, and GBL_command_arguments::get_param().
|
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 |
Definition at line 733 of file adlang1.cxx.
References EXPECT_PARAMS, GBL_command_arguments::get_param(), and remove_by_tab().
|
static |
Definition at line 737 of file adlang1.cxx.
References EXPECT_PARAMS, GBL_command_arguments::get_param(), and remove_by_tab().
Definition at line 743 of file adlang1.cxx.
References gbl_stricmp(), GBS_global_string_copy(), and result.
Referenced by gbl_compare(), and gbl_icompare().
Definition at line 751 of file adlang1.cxx.
References gbl_stricmp(), GBS_global_string_copy(), and result.
Referenced by gbl_equals(), and gbl_iequals().
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().
Definition at line 769 of file adlang1.cxx.
References binop_contains().
Referenced by gbl_ipartof(), and gbl_partof().
|
static |
Definition at line 773 of file adlang1.cxx.
References binop_compare(), and gbl_apply_binary_operator().
|
static |
Definition at line 774 of file adlang1.cxx.
References binop_compare(), and gbl_apply_binary_operator().
|
static |
Definition at line 775 of file adlang1.cxx.
References binop_equals(), and gbl_apply_binary_operator().
|
static |
Definition at line 776 of file adlang1.cxx.
References binop_equals(), and gbl_apply_binary_operator().
|
static |
Definition at line 777 of file adlang1.cxx.
References binop_contains(), and gbl_apply_binary_operator().
|
static |
Definition at line 778 of file adlang1.cxx.
References binop_contains(), and gbl_apply_binary_operator().
|
static |
Definition at line 779 of file adlang1.cxx.
References binop_partof(), and gbl_apply_binary_operator().
|
static |
Definition at line 780 of file adlang1.cxx.
References binop_partof(), and gbl_apply_binary_operator().
|
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 |
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 |
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 |
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 |
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 |
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 |
Definition at line 889 of file adlang1.cxx.
References CAPS, and convert_case().
|
static |
Definition at line 890 of file adlang1.cxx.
References convert_case(), and UPPER.
|
static |
Definition at line 891 of file adlang1.cxx.
References convert_case(), and LOWER.
|
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 |
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.
|
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 |
Definition at line 910 of file adlang1.cxx.
References mid().
|
static |
Definition at line 911 of file adlang1.cxx.
References mid().
|
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 |
Definition at line 937 of file adlang1.cxx.
References tab().
|
static |
Definition at line 938 of file adlang1.cxx.
References tab().
|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Definition at line 1072 of file adlang1.cxx.
References backfront_stream().
|
static |
Definition at line 1073 of file adlang1.cxx.
References backfront_stream().
|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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().
Definition at line 1340 of file adlang1.cxx.
Definition at line 1341 of file adlang1.cxx.
Definition at line 1342 of file adlang1.cxx.
Definition at line 1343 of file adlang1.cxx.
Definition at line 1344 of file adlang1.cxx.
Definition at line 1346 of file adlang1.cxx.
Referenced by gbl_rest().
|
static |
Definition at line 1349 of file adlang1.cxx.
References apply_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1350 of file adlang1.cxx.
References apply_double_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1351 of file adlang1.cxx.
References apply_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1352 of file adlang1.cxx.
References apply_double_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1353 of file adlang1.cxx.
References apply_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1354 of file adlang1.cxx.
References apply_double_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1355 of file adlang1.cxx.
References apply_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1356 of file adlang1.cxx.
References apply_double_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1357 of file adlang1.cxx.
References apply_numeric_binop(), binop_rest(), and gbl_apply_binary_operator().
|
static |
Definition at line 1358 of file adlang1.cxx.
References apply_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1359 of file adlang1.cxx.
References apply_double_binop(), and gbl_apply_binary_operator().
Definition at line 1361 of file adlang1.cxx.
Definition at line 1362 of file adlang1.cxx.
Definition at line 1363 of file adlang1.cxx.
|
static |
Definition at line 1365 of file adlang1.cxx.
References apply_auto_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1366 of file adlang1.cxx.
References apply_auto_numeric_binop(), and gbl_apply_binary_operator().
|
static |
Definition at line 1367 of file adlang1.cxx.
References apply_auto_numeric_binop(), and gbl_apply_binary_operator().
|
inline |
Definition at line 1369 of file adlang1.cxx.
Referenced by gbl_round().
|
static |
Definition at line 1381 of file adlang1.cxx.
References 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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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().
Definition at line 1581 of file adlang1.cxx.
Referenced by tree_of_cached_taxonomy().
|
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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_have_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 |
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 |
Definition at line 1981 of file adlang1.cxx.
References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, error(), gb_main, GBT_get_default_alignment(), GBL_command_arguments::get_gb_main(), and PASS_2_OUT.
|
static |
Definition at line 1993 of file adlang1.cxx.
References GBL_IMPL::check_no_parameter(), COMMAND_DROPS_INPUT_STREAMS, error(), gb_main, GBT_get_alignment_type_string(), GBT_get_default_alignment(), GBL_command_arguments::get_gb_main(), and PASS_2_OUT.
|
static |
Definition at line 2007 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 |
Definition at line 2245 of file adlang1.cxx.
References format().
|
static |
Definition at line 2246 of file adlang1.cxx.
References format().
|
static |
Definition at line 2249 of file adlang1.cxx.
References error(), gb_assert, 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 |
Definition at line 2345 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().
Definition at line 2403 of file adlang1.cxx.
References ARB_strdup(), diff_params::diffC, diff_params::equalC, and result.
Referenced by gbl_diff().
|
static |
Definition at line 2434 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 |
Definition at line 2464 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 |
Definition at line 2535 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 |
Definition at line 2556 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 |
Definition at line 2581 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 2746 of file adlang1.cxx.
References ARRAY_ELEMS.
Referenced by get_GroupRename_customized_ACI_commands(), and get_GroupXfer_customized_ACI_commands().
|
static |
Definition at line 33 of file adlang1.cxx.
Referenced by GB_set_export_sequence_hook(), and gbl_export_sequence().
|
static |
Definition at line 527 of file adlang1.cxx.
Definition at line 1579 of file adlang1.cxx.
|
static |
Definition at line 2651 of file adlang1.cxx.