ARB
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#include "NT_local.h"
#include <arbdbt.h>
#include <adGene.h>
#include <items.h>
#include <GEN.hxx>
#include <EXP.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_question.hxx>
#include <arb_str.h>
#include <arb_strarray.h>
#include <map>
#include <set>
#include <string>
#include <vector>
#include <ad_colorset.h>
Go to the source code of this file.
Classes | |
class | CheckedConsistencies |
class | KeyInfo |
class | Dict |
Macros | |
#define | STATUS_PREFIX "Dictionary: " |
Typedefs | |
typedef GB_ERROR(* | item_check_fun )(GBDATA *gb_item, ItemSelector &sel) |
typedef map< string, item_check_fun > | item_check_map |
typedef item_check_map::const_iterator | item_check_iter |
typedef SmartPtr< Dict > | DictPtr |
typedef map< string, int > | KeyCounter |
typedef SmartPtr< KeyInfo > | KeyInfoPtr |
typedef map< string, KeyInfoPtr > | Keys |
typedef map< string, DictPtr > | DictMap |
typedef vector< DictPtr > | Dicts |
typedef set< string > | StringSet |
#define STATUS_PREFIX "Dictionary: " |
Definition at line 660 of file NT_dbrepair.cxx.
Referenced by NT_fix_dict_compress().
typedef GB_ERROR(* item_check_fun)(GBDATA *gb_item, ItemSelector &sel) |
Definition at line 49 of file NT_dbrepair.cxx.
typedef map<string, item_check_fun> item_check_map |
Definition at line 51 of file NT_dbrepair.cxx.
typedef item_check_map::const_iterator item_check_iter |
Definition at line 52 of file NT_dbrepair.cxx.
Definition at line 578 of file NT_dbrepair.cxx.
typedef map<string, int> KeyCounter |
Definition at line 653 of file NT_dbrepair.cxx.
typedef SmartPtr<KeyInfo> KeyInfoPtr |
Definition at line 654 of file NT_dbrepair.cxx.
typedef map<string, KeyInfoPtr> Keys |
Definition at line 655 of file NT_dbrepair.cxx.
Definition at line 656 of file NT_dbrepair.cxx.
Definition at line 657 of file NT_dbrepair.cxx.
Definition at line 658 of file NT_dbrepair.cxx.
Definition at line 187 of file NT_dbrepair.cxx.
References aw_message(), GB_transaction::close(), error(), GB_child(), GB_delete(), GB_entry(), GBS_global_string(), GBT_first_species(), GBT_get_name_or_description(), GBT_next_species(), GEN_find_gene_data(), GEN_findOrCreate_gene_data(), GENOM_ALIGNMENT, arb_progress::inc_and_check_user_abort(), NULp, and ta.
Referenced by NT_repair_DB().
Definition at line 237 of file NT_dbrepair.cxx.
References GB_entry(), GBS_global_string(), and NULp.
Referenced by NT_convert_gene_locations().
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Definition at line 246 of file NT_dbrepair.cxx.
References GB_entry(), GBS_global_string(), GBS_reuse_buffer(), and NULp.
Referenced by NT_convert_gene_locations().
Definition at line 256 of file NT_dbrepair.cxx.
References aw_message(), GEN_position::complement, disexpectField(), error(), expectField(), GB_await_error(), GB_delete(), GB_entry(), GB_read_byte(), GB_read_char_pntr(), GB_read_int(), GBS_global_string(), GBS_reuse_buffer(), GEN_find_gene_data(), GEN_first_gene_rel_gene_data(), GEN_first_organism(), GEN_free_position(), GEN_global_gene_identifier(), GEN_new_position(), GEN_next_gene(), GEN_next_organism(), GEN_use_uncertainties(), GEN_write_position(), arb_progress::inc_and_check_user_abort(), nt_assert, NULp, GEN_position::start_pos, GEN_position::start_uncertain, GEN_position::stop_pos, GEN_position::stop_uncertain, and ta.
Referenced by NT_repair_DB().
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Definition at line 469 of file NT_dbrepair.cxx.
References arb_test::all(), aw_message(), GB_transaction::close(), error(), GB_await_error(), GB_create(), GB_delete(), GB_entry(), GB_read_string(), GB_STRING, GB_write_string(), GBS_global_string(), GBT_find_SAI(), GBT_first_SAI(), GBT_first_species(), GBT_get_alignment_names(), GBT_get_default_helix(), GBT_next_SAI(), GBT_next_species(), arb_progress::inc_and_check_user_abort(), NULp, and ta.
Referenced by NT_repair_DB().
Definition at line 547 of file NT_dbrepair.cxx.
References GB_child(), GB_DB, GB_get_quark(), GB_is_dictionary_compressed(), GB_nextChild(), GB_read_char_pntr(), GB_read_type(), GB_STRING, and nt_assert.
Referenced by Dict::canDecompress(), and KeyInfo::testCompressed().
bool contains | ( | const CONT & | container, |
const KEY & | key | ||
) |
Definition at line 663 of file NT_dbrepair.cxx.
Referenced by NT_fix_dict_compress(), and update_RangeList().
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Definition at line 667 of file NT_dbrepair.cxx.
References ARB_strdup(), ARB_strlower(), error(), GB_await_error(), GB_entry(), GB_get_dictionary(), GB_get_root(), GB_nextEntry(), GB_read_char_pntr(), GBS_global_string(), and NULp.
Referenced by NT_fix_dict_compress().
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Definition at line 707 of file NT_dbrepair.cxx.
References error(), GB_child(), GB_DB, GB_delete(), GB_get_db_path(), GB_get_quark(), GB_is_dictionary_compressed(), GB_nextChild(), GB_read_type(), GB_STRING, and NULp.
Referenced by NT_fix_dict_compress().
Definition at line 737 of file NT_dbrepair.cxx.
References GB_child(), GB_DB, GB_get_quark(), GB_is_dictionary_compressed(), GB_nextChild(), GB_read_as_string(), GB_read_type(), GB_STRING, and NULp.
Referenced by NT_fix_dict_compress().
Definition at line 760 of file NT_dbrepair.cxx.
References Dict::assignToKey(), aw_message(), aw_question(), Dict::canDecompress(), GB_transaction::close(), contains(), deleteDataOfKey(), findAffectedKeys(), GB_FIND, GB_find_or_create_quark(), gb_main, GB_search(), GB_SYSTEM_FOLDER, GB_SYSTEM_KEY_DATA, GBS_global_string(), GBS_global_string_copy(), Dict::getOriginalKey(), Dict::mayBeUsedWith(), nt_assert, NULp, readFirstCompressedDataOf(), STATUS_PREFIX, ta, and Dict::unassignFromKey().
Referenced by NT_repair_DB().
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Definition at line 978 of file NT_dbrepair.cxx.
References error(), GB_COLORGROUP_ENTRY, GB_delete(), GB_entry(), GB_get_root(), GB_nextEntry(), MutableItemSelector::generate_item_id, MutableItemSelector::item_name, and NULp.
Referenced by NT_repair_DB().
Definition at line 1015 of file NT_dbrepair.cxx.
References GEN_is_genome_db(), NT_convert_gene_locations(), NT_del_mark_move_REF(), NT_fix_dict_compress(), NT_fix_gene_data(), NULp, CheckedConsistencies::perform_check(), CheckedConsistencies::perform_item_checks(), CheckedConsistencies::register_item_check(), remove_dup_colors(), and ta.
Referenced by nt_check_database_consistency(), and NT_rerepair_DB().
Definition at line 1040 of file NT_dbrepair.cxx.
References aw_message(), CheckedConsistencies::forgetDoneChecks(), NT_repair_DB(), and NULp.
Referenced by popup_new_main_window().