ARB
Classes | Macros | Functions | Variables
adGene.cxx File Reference
#include "gb_local.h"
#include <adGene.h>
#include <arbdbt.h>
#include <arb_strbuf.h>
#include <arb_strarray.h>
Include dependency graph for adGene.cxx:

Go to the source code of this file.

Classes

struct  GEN_position_mem_handler
 

Macros

#define swap(a, b, type)   do { type tmp = (a); (a) = (b); (b) = (tmp); } while (0)
 

Functions

bool GEN_is_genome_db (GBDATA *gb_main, int default_value)
 
GBDATA * GEN_findOrCreate_gene_data (GBDATA *gb_species)
 
GBDATA * GEN_find_gene_data (GBDATA *gb_species)
 
GBDATA * GEN_expect_gene_data (GBDATA *gb_species)
 
GBDATA * GEN_find_gene_rel_gene_data (GBDATA *gb_gene_data, const char *name)
 
GBDATA * GEN_find_gene (GBDATA *gb_species, const char *name)
 
GBDATA * GEN_expect_gene (GBDATA *gb_species, const char *name)
 
static GBDATA * GEN_create_nonexisting_gene_rel_gene_data (GBDATA *gb_gene_data, const char *name)
 
GBDATA * GEN_create_nonexisting_gene (GBDATA *gb_species, const char *name)
 
GBDATA * GEN_find_or_create_gene_rel_gene_data (GBDATA *gb_gene_data, const char *name)
 
GBDATA * GEN_first_gene (GBDATA *gb_species)
 
GBDATA * GEN_first_gene_rel_gene_data (GBDATA *gb_gene_data)
 
GBDATA * GEN_next_gene (GBDATA *gb_gene)
 
GBDATA * GEN_first_marked_gene (GBDATA *gb_species)
 
GBDATA * GEN_next_marked_gene (GBDATA *gb_gene)
 
GEN_position * GEN_new_position (int parts, bool joinable)
 
void GEN_use_uncertainties (GEN_position *pos)
 
void GEN_free_position (GEN_position *pos)
 
static GB_ERROR parseCSV (GBDATA *gb_gene, const char *field_name, size_t parts_expected, ConstStrArray &parseTable)
 
static GB_ERROR parsePositions (GBDATA *gb_gene, const char *field_name, int parts_expected, size_t *results, ConstStrArray &parseTable)
 
GEN_position * GEN_read_position (GBDATA *gb_gene)
 
GB_ERROR GEN_write_position (GBDATA *gb_gene, const GEN_position *pos, long seqLength)
 
static int cmp_location_parts (const void *v1, const void *v2)
 
void GEN_sortAndMergeLocationParts (GEN_position *location)
 
const char * GEN_origin_organism (GBDATA *gb_pseudo)
 
const char * GEN_origin_gene (GBDATA *gb_pseudo)
 
bool GEN_is_pseudo_gene_species (GBDATA *gb_species)
 
GB_ERROR GEN_organism_not_found (GBDATA *gb_pseudo)
 
static const char * pseudo_species_hash_key (const char *organism_name, const char *gene_name)
 
static GBDATA * GEN_read_pseudo_species_from_hash (const GB_HASH *pseudo_hash, const char *organism_name, const char *gene_name)
 
void GEN_add_pseudo_species_to_hash (GBDATA *gb_pseudo, GB_HASH *pseudo_hash)
 
GB_HASH * GEN_create_pseudo_species_hash (GBDATA *gb_main, long additionalSize)
 
GBDATA * GEN_find_pseudo_species (GBDATA *gb_main, const char *organism_name, const char *gene_name, const GB_HASH *pseudo_hash)
 
GBDATA * GEN_find_origin_organism (GBDATA *gb_pseudo, const GB_HASH *organism_hash)
 
GBDATA * GEN_find_origin_gene (GBDATA *gb_pseudo, const GB_HASH *organism_hash)
 
GBDATA * GEN_first_pseudo_species (GBDATA *gb_main)
 
GBDATA * GEN_next_pseudo_species (GBDATA *gb_species)
 
static GBDATA * GEN_next_marked_pseudo_species (GBDATA *gb_species)
 
GBDATA * GEN_first_marked_pseudo_species (GBDATA *gb_main)
 
bool GEN_is_organism (GBDATA *gb_species)
 
GBDATA * GEN_find_organism (GBDATA *gb_main, const char *name)
 
GBDATA * GEN_first_organism (GBDATA *gb_main)
 
GBDATA * GEN_next_organism (GBDATA *gb_organism)
 
long GEN_get_organism_count (GBDATA *gb_main)
 
GBDATA * GEN_first_marked_organism (GBDATA *gb_main)
 
GBDATA * GEN_next_marked_organism (GBDATA *gb_organism)
 
char * GEN_global_gene_identifier (GBDATA *gb_gene, GBDATA *gb_organism)
 

Variables

static GEN_position * lastFreedPosition = NULp
 
static struct
GEN_position_mem_handler 		GEN_position_dealloc
 
static GEN_position * location2sort = NULp
 

Macro Definition Documentation

#define swap (   a,
  b,
  type 
)    do { type tmp = (a); (a) = (b); (b) = (tmp); } while (0)

Referenced by GEN_sortAndMergeLocationParts().

Function Documentation

bool GEN_is_genome_db ( GBDATA *  gb_main,
int  default_value 
)

Definition at line 20 of file adGene.cxx.

References assert_or_exit, error(), GB_await_error(), GB_create(), GB_entry(), GB_INT, GB_read_int(), GB_write_int(), GBK_terminatef(), GENOM_DB_TYPE, and NULp.

Referenced by create_primer_design_window(), create_probe_admin_window(), create_probe_design_window(), expect_used_in_genome_db(), GBT_commit_rename_session(), GEN_is_organism(), ArbImporter::import_data(), MERGE_create_main_window(), mg_transfer_listed_species(), mg_transfer_selected_species(), NT_import_sequences(), NT_repair_DB(), pd_export_pt_server(), CheckedConsistencies::perform_item_checks(), popup_new_main_window(), primer_design_event_init(), probe_design_event(), and probe_match_event().

GBDATA* GEN_findOrCreate_gene_data ( GBDATA *  gb_species)

Definition at line 44 of file adGene.cxx.

References gb_assert, GB_CREATE_CONTAINER, and GB_search().

Referenced by GEN_create_nonexisting_gene(), and NT_fix_gene_data().

GBDATA* GEN_find_gene_data ( GBDATA *  gb_species)

Definition at line 50 of file adGene.cxx.

References GB_FIND, and GB_search().

Referenced by gbl_findgene(), GEN_find_gene(), GEN_root::GEN_root(), NT_convert_gene_locations(), NT_fix_gene_data(), and probe_match_event().

GBDATA* GEN_expect_gene_data ( GBDATA *  gb_species)

Definition at line 54 of file adGene.cxx.

References gb_assert, GB_FIND, and GB_search().

Referenced by GEN_expect_gene(), GEN_first_gene(), GEN_first_marked_gene(), GEN_get_first_gene_data(), GEN_get_local_gene_data(), GEN_get_next_gene_data(), and get_current_gene_data().

GBDATA* GEN_find_gene_rel_gene_data ( GBDATA *  gb_gene_data,
const char *  name 
)

Definition at line 60 of file adGene.cxx.

References GBT_find_item_rel_item_data().

Referenced by GEN_create_nonexisting_gene_rel_gene_data(), GEN_find_gene(), gene_copy_handler(), gene_create_cb(), and gene_rename_handler().

GBDATA* GEN_find_gene ( GBDATA *  gb_species,
const char *  name 
)

Definition at line 64 of file adGene.cxx.

References GEN_find_gene_data(), GEN_find_gene_rel_gene_data(), and NULp.

Referenced by GEN_item_type_species_selector::current(), gen_find_gene_by_id(), GEN_find_origin_gene(), GEN_get_current_gene(), primer_design_event_init(), and probe_match_event().

GBDATA* GEN_expect_gene ( GBDATA *  gb_species,
const char *  name 
)

Definition at line 72 of file adGene.cxx.

References GBT_expect_item_rel_item_data(), and GEN_expect_gene_data().

static GBDATA* GEN_create_nonexisting_gene_rel_gene_data ( GBDATA *  gb_gene_data,
const char *  name 
)
static

Definition at line 78 of file adGene.cxx.

References error(), gb_assert, GB_await_error(), GB_create_container(), GB_end_transaction(), GB_export_error(), GB_push_transaction(), GBT_write_string(), GEN_find_gene_rel_gene_data(), and NULp.

Referenced by GEN_create_nonexisting_gene().

GBDATA* GEN_create_nonexisting_gene ( GBDATA *  gb_species,
const char *  name 
)

Definition at line 96 of file adGene.cxx.

References GEN_create_nonexisting_gene_rel_gene_data(), and GEN_findOrCreate_gene_data().

GBDATA* GEN_find_or_create_gene_rel_gene_data ( GBDATA *  gb_gene_data,
const char *  name 
)

Definition at line 100 of file adGene.cxx.

References error(), GB_create_container(), GB_end_transaction(), GB_export_error(), GB_find_string(), GB_get_father(), GB_IGNORE_CASE, GB_push_transaction(), GBT_write_string(), NULp, and SEARCH_GRANDCHILD.

Referenced by gene_create_cb().

GBDATA* GEN_first_gene ( GBDATA *  gb_species)

Definition at line 130 of file adGene.cxx.

References GB_entry(), and GEN_expect_gene_data().

Referenced by do_hide_command_for_one_species(), do_mark_command_for_one_species(), insert_genes_of_organism(), mark_organisms_with_marked_genes(), and probe_match_event().

GBDATA* GEN_first_gene_rel_gene_data ( GBDATA *  gb_gene_data)

Definition at line 134 of file adGene.cxx.

References GB_entry().

Referenced by first_gene_in_range(), GEN_root::GEN_root(), and NT_convert_gene_locations().

GBDATA* GEN_next_gene ( GBDATA *  gb_gene)

Definition at line 138 of file adGene.cxx.

References gb_assert, GB_has_key(), and GB_nextEntry().

Referenced by do_hide_command_for_one_species(), do_mark_command_for_one_species(), GEN_root::GEN_root(), insert_genes_of_organism(), mark_organisms_with_marked_genes(), next_gene_in_range(), NT_convert_gene_locations(), and probe_match_event().

GBDATA* GEN_first_marked_gene ( GBDATA *  gb_species)

Definition at line 143 of file adGene.cxx.

References GB_first_marked(), and GEN_expect_gene_data().

Referenced by pd_get_the_gene_names(), and probe_match_event().

GBDATA* GEN_next_marked_gene ( GBDATA *  gb_gene)

Definition at line 146 of file adGene.cxx.

References GB_next_marked().

Referenced by next_gene_in_range(), pd_get_the_gene_names(), and probe_match_event().

GEN_position* GEN_new_position ( int  parts,
bool  joinable 
)

Definition at line 155 of file adGene.cxx.

References ARB_calloc(), GEN_position::complement, gb_assert, GEN_position::joinable, lastFreedPosition, NULp, GEN_position::parts, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by Location::create_GEN_position(), LocationEditor::create_GEN_position_from_fields(), GEN_read_position(), and NT_convert_gene_locations().

void GEN_use_uncertainties ( GEN_position *  pos)

Definition at line 184 of file adGene.cxx.

References GEN_position::complement, GEN_position::parts, GEN_position::start_uncertain, and GEN_position::stop_uncertain.

Referenced by Location::create_GEN_position(), LocationEditor::create_GEN_position_from_fields(), GEN_read_position(), gene_changed_cb(), and NT_convert_gene_locations().

void GEN_free_position ( GEN_position *  pos)

Definition at line 195 of file adGene.cxx.

References GEN_position::start_pos.

Referenced by GBT_read_gene_sequence_and_length(), GEN_read_position(), loadPositions4gene(), NT_convert_gene_locations(), primer_design_event_init(), scan_gene_positions(), LocationEditor::set_pos(), GEN_position_mem_handler::~GEN_position_mem_handler(), and LocationEditor::~LocationEditor().

static GB_ERROR parseCSV ( GBDATA *  gb_gene,
const char *  field_name,
size_t  parts_expected,
ConstStrArray &  parseTable 
)
static

Definition at line 211 of file adGene.cxx.

References ConstStrArray::erase(), error(), GB_await_error(), GB_entry(), GB_read_string(), GBS_global_string(), GBT_splitNdestroy_string(), NULp, and CharPtrArray::size().

Referenced by GEN_read_position(), and parsePositions().

static GB_ERROR parsePositions ( GBDATA *  gb_gene,
const char *  field_name,
int  parts_expected,
size_t *  results,
ConstStrArray &  parseTable 
)
static

Definition at line 232 of file adGene.cxx.

References error(), GBS_global_string(), and parseCSV().

Referenced by GEN_read_position().

GEN_position* GEN_read_position ( GBDATA *  gb_gene)

Definition at line 250 of file adGene.cxx.

References GEN_position::complement, error(), gb_assert, GB_entry(), GB_export_error(), GB_read_int(), GBS_global_string(), GEN_free_position(), GEN_new_position(), GEN_use_uncertainties(), NULp, parseCSV(), parsePositions(), CharPtrArray::reserve(), GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by GBT_read_gene_sequence_and_length(), gene_changed_cb(), loadPositions4gene(), PosGene::PosGene(), primer_design_event_init(), and scan_gene_positions().

GB_ERROR GEN_write_position ( GBDATA *  gb_gene,
const GEN_position *  pos,
long  seqLength 
)

Definition at line 325 of file adGene.cxx.

References GBS_strstruct::cat(), GEN_position::complement, error(), gb_assert, GB_await_error(), GB_delete(), GB_entry(), GB_get_grandfather(), GB_INT, GB_read_count(), GB_search(), GB_STRING, GB_write_int(), GB_write_string(), GBS_global_string(), GBT_find_sequence(), GENOM_ALIGNMENT, GBS_strstruct::get_data(), GEN_position::joinable, length, NULp, GEN_position::parts, GBS_strstruct::put(), start, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, and GEN_position::stop_uncertain.

Referenced by boundloc_changed_cb(), gene_create_cb(), NT_convert_gene_locations(), and DBwriter::writeFeature().

static int cmp_location_parts ( const void *  v1,
const void *  v2 
)
static

Definition at line 476 of file adGene.cxx.

References cmp, GEN_position::start_pos, and GEN_position::stop_pos.

Referenced by GEN_sortAndMergeLocationParts().

void GEN_sortAndMergeLocationParts ( GEN_position *  location)

Definition at line 487 of file adGene.cxx.

References cmp_location_parts(), GEN_position::complement, NULp, GEN_position::parts, GEN_position::start_pos, GEN_position::stop_pos, and swap.

Referenced by GBT_read_gene_sequence_and_length(), and scan_gene_positions().

const char* GEN_origin_organism ( GBDATA *  gb_pseudo)

Definition at line 549 of file adGene.cxx.

References GB_entry(), GB_read_char_pntr(), and NULp.

Referenced by GEN_add_pseudo_species_to_hash(), GEN_find_origin_organism(), GEN_find_pseudo_species(), GEN_is_pseudo_gene_species(), GEN_organism_not_found(), GEN_species_name_changed_cb(), MG_create_field_content(), and MG_transfer_one_species().

const char* GEN_origin_gene ( GBDATA *  gb_pseudo)

Definition at line 553 of file adGene.cxx.

References GB_entry(), GB_read_char_pntr(), and NULp.

Referenced by GEN_add_pseudo_species_to_hash(), GEN_find_origin_gene(), GEN_find_pseudo_species(), GEN_species_name_changed_cb(), and MG_create_field_content().

bool GEN_is_pseudo_gene_species ( GBDATA *  gb_species)

Definition at line 558 of file adGene.cxx.

References GEN_origin_organism().

Referenced by apply_to_origin(), GEN_find_origin_gene(), GEN_find_origin_organism(), GEN_first_marked_pseudo_species(), GEN_first_pseudo_species(), GEN_mark_organism_or_corresponding_organism(), GEN_next_marked_pseudo_species(), GEN_next_pseudo_species(), GEN_organism_not_found(), GEN_species_name_changed_cb(), MG_create_field_content(), MG_export_fields(), MG_transfer_one_species(), MG_update_example(), and relink_pseudo_species_to_organisms().

GB_ERROR GEN_organism_not_found ( GBDATA *  gb_pseudo)

Definition at line 565 of file adGene.cxx.

References gb_assert, GB_export_errorf(), GBT_get_name_or_description(), GEN_find_origin_organism(), GEN_is_pseudo_gene_species(), GEN_origin_organism(), and NULp.

Referenced by GEN_mark_organism_or_corresponding_organism().

static const char* pseudo_species_hash_key ( const char *  organism_name,
const char *  gene_name 
)
static

Definition at line 581 of file adGene.cxx.

References GBS_global_string().

Referenced by GEN_add_pseudo_species_to_hash(), and GEN_read_pseudo_species_from_hash().

static GBDATA* GEN_read_pseudo_species_from_hash ( const GB_HASH *  pseudo_hash,
const char *  organism_name,
const char *  gene_name 
)
static

Definition at line 585 of file adGene.cxx.

References GBS_read_hash(), and pseudo_species_hash_key().

Referenced by GEN_find_pseudo_species().

void GEN_add_pseudo_species_to_hash ( GBDATA *  gb_pseudo,
GB_HASH *  pseudo_hash 
)

Definition at line 589 of file adGene.cxx.

References gb_assert, GBS_write_hash(), GEN_origin_gene(), GEN_origin_organism(), and pseudo_species_hash_key().

Referenced by GEN_create_pseudo_species_hash(), and gen_extract_gene_2_pseudoSpecies().

GB_HASH* GEN_create_pseudo_species_hash ( GBDATA *  gb_main,
long  additionalSize 
)

Definition at line 599 of file adGene.cxx.

References GB_IGNORE_CASE, GBS_create_hash(), GBT_get_species_count(), GEN_add_pseudo_species_to_hash(), GEN_first_pseudo_species(), and GEN_next_pseudo_species().

Referenced by EG2PS_data::EG2PS_data().

GBDATA* GEN_find_pseudo_species ( GBDATA *  gb_main,
const char *  organism_name,
const char *  gene_name,
const GB_HASH *  pseudo_hash 
)

Definition at line 613 of file adGene.cxx.

References GEN_first_pseudo_species(), GEN_next_pseudo_species(), GEN_origin_gene(), GEN_origin_organism(), and GEN_read_pseudo_species_from_hash().

Referenced by auto_select_pseudo_species(), and gen_extract_gene_2_pseudoSpecies().

GBDATA* GEN_find_origin_organism ( GBDATA *  gb_pseudo,
const GB_HASH *  organism_hash 
)

Definition at line 643 of file adGene.cxx.

References gb_assert, GB_get_father(), GBS_read_hash(), GBT_find_species_rel_species_data(), GEN_is_pseudo_gene_species(), GEN_origin_organism(), and NULp.

Referenced by apply_to_origin(), GEN_find_origin_gene(), GEN_mark_organism_or_corresponding_organism(), GEN_organism_not_found(), MG_create_field_content(), and relink_pseudo_species_to_organisms().

GBDATA* GEN_find_origin_gene ( GBDATA *  gb_pseudo,
const GB_HASH *  organism_hash 
)

Definition at line 666 of file adGene.cxx.

References gb_assert, GEN_find_gene(), GEN_find_origin_organism(), GEN_is_pseudo_gene_species(), GEN_origin_gene(), and NULp.

Referenced by apply_to_origin(), mark_gene_species_of_marked_genes(), mark_genes_of_marked_gene_species(), and MG_create_field_content().

GBDATA* GEN_first_pseudo_species ( GBDATA *  gb_main)

Definition at line 684 of file adGene.cxx.

References GBT_first_species(), GEN_is_pseudo_gene_species(), and GEN_next_pseudo_species().

Referenced by GBT_commit_rename_session(), GEN_create_pseudo_species_hash(), GEN_find_pseudo_species(), mark_gene_species(), mark_gene_species_of_marked_genes(), mark_gene_species_using_current_alignment(), and mark_genes_of_marked_gene_species().

GBDATA* GEN_next_pseudo_species ( GBDATA *  gb_species)

Definition at line 691 of file adGene.cxx.

References GBT_next_species(), and GEN_is_pseudo_gene_species().

Referenced by GBT_commit_rename_session(), GEN_create_pseudo_species_hash(), GEN_find_pseudo_species(), GEN_first_pseudo_species(), mark_gene_species(), mark_gene_species_of_marked_genes(), mark_gene_species_using_current_alignment(), and mark_genes_of_marked_gene_species().

static GBDATA* GEN_next_marked_pseudo_species ( GBDATA *  gb_species)
static

Definition at line 701 of file adGene.cxx.

References GBT_next_marked_species(), and GEN_is_pseudo_gene_species().

Referenced by GEN_first_marked_pseudo_species().

GBDATA* GEN_first_marked_pseudo_species ( GBDATA *  gb_main)

Definition at line 711 of file adGene.cxx.

References GBT_first_marked_species(), GEN_is_pseudo_gene_species(), and GEN_next_marked_pseudo_species().

Referenced by EXP_get_first_experiment_data(), and GEN_get_first_gene_data().

bool GEN_is_organism ( GBDATA *  gb_species)

Definition at line 721 of file adGene.cxx.

References gb_assert, GB_entry(), GB_get_root(), GEN_is_genome_db(), and GENOM_ALIGNMENT.

Referenced by gbl_findgene(), GEN_find_organism(), GEN_first_marked_organism(), GEN_first_organism(), GEN_mark_organism_or_corresponding_organism(), GEN_next_marked_organism(), and GEN_next_organism().

GBDATA* GEN_find_organism ( GBDATA *  gb_main,
const char *  name 
)

Definition at line 728 of file adGene.cxx.

References GBT_find_species(), GEN_is_organism(), and NULp.

Referenced by EXP_find_experiment_by_id(), gen_find_gene_by_id(), GEN_get_first_gene_data(), get_selected_organism(), MG_transfer_one_species(), and GEN_graphic::reinit_gen_root().

GBDATA* GEN_first_organism ( GBDATA *  gb_main)

Definition at line 739 of file adGene.cxx.

References GBT_first_species(), GEN_is_organism(), and GEN_next_organism().

Referenced by GBT_create_organism_hash(), GEN_get_first_gene_data(), GEN_get_organism_count(), GEN_perform_command(), get_first_organism(), mark_organisms(), mark_organisms_with_marked_genes(), NT_convert_gene_locations(), and pd_get_the_gene_names().

GBDATA* GEN_next_organism ( GBDATA *  gb_organism)

Definition at line 745 of file adGene.cxx.

References GBT_next_species(), and GEN_is_organism().

Referenced by GBT_create_organism_hash(), GEN_first_organism(), GEN_get_next_gene_data(), GEN_get_organism_count(), GEN_perform_command(), get_next_organism(), mark_organisms(), mark_organisms_with_marked_genes(), NT_convert_gene_locations(), and pd_get_the_gene_names().

long GEN_get_organism_count ( GBDATA *  gb_main)

Definition at line 756 of file adGene.cxx.

References GEN_first_organism(), and GEN_next_organism().

Referenced by GBT_create_organism_hash().

GBDATA* GEN_first_marked_organism ( GBDATA *  gb_main)

Definition at line 767 of file adGene.cxx.

References GBT_first_marked_species(), GEN_is_organism(), and GEN_next_marked_organism().

Referenced by EXP_get_first_experiment_data(), GEN_get_first_gene_data(), GEN_perform_command(), and get_first_organism().

GBDATA* GEN_next_marked_organism ( GBDATA *  gb_organism)

Definition at line 773 of file adGene.cxx.

References GBT_next_marked_species(), and GEN_is_organism().

Referenced by EXP_get_next_experiment_data(), GEN_first_marked_organism(), GEN_get_next_gene_data(), GEN_perform_command(), and get_next_organism().

char* GEN_global_gene_identifier ( GBDATA *  gb_gene,
GBDATA *  gb_organism 
)

Definition at line 783 of file adGene.cxx.

References gb_assert, GB_get_grandfather(), GBS_global_string_copy(), and GBT_get_name_or_description().

Referenced by GBT_read_gene_sequence_and_length(), GEN_root::GEN_root(), and NT_convert_gene_locations().

Variable Documentation

GEN_position* lastFreedPosition = NULp
static

Definition at line 153 of file adGene.cxx.

Referenced by GEN_new_position().

struct GEN_position_mem_handler GEN_position_dealloc
static
GEN_position* location2sort = NULp
static

Definition at line 474 of file adGene.cxx.

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