ARB
Classes | Macros | Typedefs | Functions
NT_dbrepair.cxx File Reference
#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>
Include dependency graph for NT_dbrepair.cxx:

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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
 

Functions

static GB_ERROR NT_fix_gene_data (GBDATA *gb_main, size_t species_count, size_t)
 
static GBDATA * expectField (GBDATA *gb_gene, const char *field, GB_ERROR &data_error)
 
static GBDATA * disexpectField (GBDATA *gb_gene, const char *field, GB_ERROR &data_error)
 
static GB_ERROR NT_convert_gene_locations (GBDATA *gb_main, size_t species_count, size_t)
 
static GB_ERROR NT_del_mark_move_REF (GBDATA *gb_main, size_t species_count, size_t sai_count)
 
static bool testDictionaryCompression (GBDATA *gbd, GBQUARK key_quark, bool testUse)
 
template<typename CONT , typename KEY >
bool contains (const CONT &container, const KEY &key)
 
static GB_ERROR findAffectedKeys (GBDATA *gb_key_data, KeyCounter &kcount, Keys &keys, Dicts &dicts)
 
static GB_ERROR deleteDataOfKey (GBDATA *gbd, GBQUARK key_quark, StringSet &deletedData, long &deleted, long &notDeleted)
 
static char * readFirstCompressedDataOf (GBDATA *gbd, GBQUARK key_quark)
 
static GB_ERROR NT_fix_dict_compress (GBDATA *gb_main, size_t, size_t)
 
static GB_ERROR remove_dup_colors (GBDATA *gb_item, ItemSelector &IF_DEBUG(sel))
 
GB_ERROR NT_repair_DB (GBDATA *gb_main)
 
void NT_rerepair_DB (AW_window *, GBDATA *gb_main)
 

Macro Definition Documentation

#define STATUS_PREFIX   "Dictionary: "

Definition at line 660 of file NT_dbrepair.cxx.

Referenced by NT_fix_dict_compress().

Typedef Documentation

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.

typedef SmartPtr<Dict> DictPtr

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.

typedef map<string, DictPtr> DictMap

Definition at line 656 of file NT_dbrepair.cxx.

typedef vector<DictPtr> Dicts

Definition at line 657 of file NT_dbrepair.cxx.

typedef set<string> StringSet

Definition at line 658 of file NT_dbrepair.cxx.

Function Documentation

static GB_ERROR NT_fix_gene_data ( GBDATA *  gb_main,
size_t  species_count,
size_t   
)
static

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().

static GBDATA* expectField ( GBDATA *  gb_gene,
const char *  field,
GB_ERROR &  data_error 
)
static

Definition at line 237 of file NT_dbrepair.cxx.

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

Referenced by NT_convert_gene_locations().

static GBDATA* disexpectField ( GBDATA *  gb_gene,
const char *  field,
GB_ERROR &  data_error 
)
static

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().

static GB_ERROR NT_convert_gene_locations ( GBDATA *  gb_main,
size_t  species_count,
size_t   
)
static

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().

static GB_ERROR NT_del_mark_move_REF ( GBDATA *  gb_main,
size_t  species_count,
size_t  sai_count 
)
static

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().

static bool testDictionaryCompression ( GBDATA *  gbd,
GBQUARK  key_quark,
bool  testUse 
)
static

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().

template<typename CONT , typename KEY >
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().

static GB_ERROR findAffectedKeys ( GBDATA *  gb_key_data,
KeyCounter &  kcount,
Keys &  keys,
Dicts &  dicts 
)
static

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().

static GB_ERROR deleteDataOfKey ( GBDATA *  gbd,
GBQUARK  key_quark,
StringSet &  deletedData,
long &  deleted,
long &  notDeleted 
)
static

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().

static char* readFirstCompressedDataOf ( GBDATA *  gbd,
GBQUARK  key_quark 
)
static

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().

static GB_ERROR NT_fix_dict_compress ( GBDATA *  gb_main,
size_t  ,
size_t   
)
static

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().

static GB_ERROR remove_dup_colors ( GBDATA *  gb_item,
ItemSelector &  IF_DEBUGsel 
)
static

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().

GB_ERROR NT_repair_DB ( GBDATA *  gb_main)

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().

void NT_rerepair_DB ( AW_window *  ,
GBDATA *  gb_main 
)

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().

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