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:

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< DictDictPtr
 
typedef map< string, intKeyCounter
 
typedef SmartPtr< KeyInfoKeyInfoPtr
 
typedef map< string, KeyInfoPtrKeys
 
typedef map< string, DictPtrDictMap
 
typedef vector< DictPtrDicts
 
typedef set< stringStringSet
 

Functions

static GB_ERROR NT_fix_gene_data (GBDATA *gb_main, size_t species_count, size_t)
 
static GBDATAexpectField (GBDATA *gb_gene, const char *field, GB_ERROR &data_error)
 
static GBDATAdisexpectField (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 charreadFirstCompressedDataOf (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 662 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 51 of file NT_dbrepair.cxx.

Definition at line 53 of file NT_dbrepair.cxx.

typedef item_check_map::const_iterator item_check_iter

Definition at line 54 of file NT_dbrepair.cxx.

typedef SmartPtr<Dict> DictPtr

Definition at line 580 of file NT_dbrepair.cxx.

typedef map<string, int> KeyCounter

Definition at line 655 of file NT_dbrepair.cxx.

Definition at line 656 of file NT_dbrepair.cxx.

typedef map<string, KeyInfoPtr> Keys

Definition at line 657 of file NT_dbrepair.cxx.

typedef map<string, DictPtr> DictMap

Definition at line 658 of file NT_dbrepair.cxx.

typedef vector<DictPtr> Dicts

Definition at line 659 of file NT_dbrepair.cxx.

typedef set<string> StringSet

Definition at line 660 of file NT_dbrepair.cxx.

Function Documentation

static GB_ERROR NT_fix_gene_data ( GBDATA gb_main,
size_t  species_count,
size_t   
)
static
static GBDATA* expectField ( GBDATA gb_gene,
const char field,
GB_ERROR data_error 
)
static

Definition at line 239 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 248 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
static GB_ERROR NT_del_mark_move_REF ( GBDATA gb_main,
size_t  species_count,
size_t  sai_count 
)
static
static bool testDictionaryCompression ( GBDATA gbd,
GBQUARK  key_quark,
bool  testUse 
)
static
template<typename CONT , typename KEY >
bool contains ( const CONT &  container,
const KEY &  key 
)

Definition at line 665 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
static GB_ERROR deleteDataOfKey ( GBDATA gbd,
GBQUARK  key_quark,
StringSet deletedData,
long deleted,
long notDeleted 
)
static
static char* readFirstCompressedDataOf ( GBDATA gbd,
GBQUARK  key_quark 
)
static
static GB_ERROR NT_fix_dict_compress ( GBDATA gb_main,
size_t  ,
size_t   
)
static
static GB_ERROR remove_dup_colors ( GBDATA gb_item,
ItemSelector IF_DEBUGsel 
)
static
GB_ERROR NT_repair_DB ( GBDATA gb_main)
void NT_rerepair_DB ( AW_window ,
GBDATA gb_main 
)