AW_rename.cxx File Reference

#include "AW_rename.hxx"
#include <aw_awars.hxx>
#include <aw_window.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <names_client.h>
#include <servercntrl.h>
#include <client.h>
#include <cctype>
#include <ctime>

Include dependency graph for AW_rename.cxx:

Go to the source code of this file.

Classes
class	NameServerConnection

Functions
static const char *	get_addid (GBDATA *gb_main)
static GB_ERROR	set_addid (GBDATA *gb_main, const char *addid)
const char *	AW_get_nameserver_addid (GBDATA *gb_main)
GB_ERROR	AW_select_nameserver (GBDATA *gb_main, GBDATA *gb_other_main)
GB_ERROR	AW_test_nameserver (GBDATA *gb_main)
GB_ERROR	AWTC_generate_one_name (GBDATA *gb_main, const char *full_name, const char *acc, const char *addid, char *&new_name)
GB_ERROR	AWTC_recreate_name (GBDATA *gb_species)
char *	AWTC_create_numbered_suffix (GB_HASH *species_name_hash, const char *shortname, GB_ERROR &warning)
GB_ERROR	AWTC_pars_names (GBDATA *gb_main, bool *isWarningPtr)
static void	awt_rename_cb (AW_window *aww, GBDATA *gb_main)
AW_window *	AWTC_create_rename_window (AW_root *root, GBDATA *gb_main)
static char *	makeUniqueShortName (const char *prefix, UniqueNameDetector &existing)
char *	AWTC_makeUniqueShortName (const char *prefix, UniqueNameDetector &existingNames)
char *	AWTC_generate_random_name (UniqueNameDetector &existingNames)
int	AWTC_name_quality (const char *short_name)

Variables
static NameServerConnection	name_server

Function Documentation

static const char* get_addid ( GBDATA *  gb_main )

static

Definition at line 27 of file AW_rename.cxx.

References AWAR_NAMESERVER_ADDID, GB_FIND, GB_read_char_pntr(), GB_search(), NULp, and ta.

Referenced by AW_get_nameserver_addid(), and AW_select_nameserver().

static GB_ERROR set_addid ( GBDATA *  gb_main, const char *  addid  )

static

Definition at line 33 of file AW_rename.cxx.

References AWAR_NAMESERVER_ADDID, error(), GB_end_transaction(), GB_push_transaction(), and GBT_write_string().

Referenced by AW_select_nameserver().

const char* AW_get_nameserver_addid

(

GBDATA *

gb_main

)

Definition at line 39 of file AW_rename.cxx.

References aw_assert, and get_addid().

Referenced by AWTC_pars_names(), AWTC_recreate_name(), concatenateFieldsCreateNewSpecies(), NameServerConnection::connect(), create_new_species(), and namesFilename().

GB_ERROR AW_select_nameserver	(	GBDATA *	gb_main,
		GBDATA *	gb_other_main
	)

Definition at line 49 of file AW_rename.cxx.

References aw_assert, aw_question(), error(), GB_await_error(), GBS_get_arb_tcp_entries(), GBS_global_string(), GBS_read_arb_tcp(), GBS_scan_arb_tcp_param(), get_addid(), NULp, and set_addid().

Referenced by ArbImporter::import_data().

GB_ERROR AW_test_nameserver

(

GBDATA *

gb_main

)

Definition at line 311 of file AW_rename.cxx.

References NameServerConnection::connect().

Referenced by addid_changed_cb().

GB_ERROR AWTC_generate_one_name	(	GBDATA *	gb_main,
		const char *	full_name,
		const char *	acc,
		const char *	addid,
		char *&	new_name
	)

Definition at line 317 of file AW_rename.cxx.

References aisc_get(), aisc_nput(), NameServerConnection::connect(), NameServerConnection::disconnect(), GB_export_errorf(), NameServerConnection::getLink(), NameServerConnection::getLocs(), and NULp.

Referenced by concatenateFieldsCreateNewSpecies(), create_new_species(), and gen_extract_gene_2_pseudoSpecies().

GB_ERROR AWTC_recreate_name

(

GBDATA *

gb_species

)

Definition at line 366 of file AW_rename.cxx.

References aisc_get(), aisc_nput(), AW_get_nameserver_addid(), NameServerConnection::connect(), NameServerConnection::disconnect(), error(), GB_await_error(), GB_entry(), GB_get_root(), gb_main, GB_read_as_string(), GB_read_string(), GBS_global_string(), GBT_abort_rename_session(), GBT_begin_rename_session(), GBT_commit_rename_session(), GBT_find_species(), GBT_gen_accession_number(), GBT_get_default_alignment(), GBT_rename_species(), NameServerConnection::getLink(), NameServerConnection::getLocs(), and NULp.

Referenced by species_rename_handler().

char* AWTC_create_numbered_suffix	(	GB_HASH *	species_name_hash,
		const char *	shortname,
		GB_ERROR &	warning
	)

Definition at line 446 of file AW_rename.cxx.

References ARB_alloc(), GBS_read_hash(), and NULp.

Referenced by AWTC_pars_names(), and MERGE_sequences_simple().

GB_ERROR AWTC_pars_names	(	GBDATA *	gb_main,
		bool *	isWarningPtr
	)

Definition at line 465 of file AW_rename.cxx.

References aisc_get(), aisc_nput(), AW_get_nameserver_addid(), AWTC_create_numbered_suffix(), NameServerConnection::connect(), NameServerConnection::disconnect(), arb_progress::done(), GB_await_error(), GB_entry(), GB_IGNORE_CASE, GB_read_as_string(), GB_read_string(), GBS_create_hash(), GBS_free_hash(), GBS_incr_hash(), GBT_abort_rename_session(), GBT_begin_rename_session(), GBT_commit_rename_session(), GBT_first_species(), GBT_gen_accession_number(), GBT_get_default_alignment(), GBT_get_species_count(), GBT_next_species(), GBT_rename_species(), NameServerConnection::getLink(), NameServerConnection::getLocs(), arb_progress::inc_and_check_user_abort(), NULp, arb_progress::sub_progress_skipped(), and warning().

Referenced by awt_rename_cb(), ArbImporter::import_data(), and renameDB().

static void awt_rename_cb ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 566 of file AW_rename.cxx.

References aw_message(), AW_root::awar(), AWAR_TREE_REFRESH, AWTC_pars_names(), error(), AW_window::get_root(), NULp, and AW_awar::touch().

Referenced by AWTC_create_rename_window().

AW_window* AWTC_create_rename_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 573 of file AW_rename.cxx.

References AW_POPDOWN(), AW_popup_namesadmin_window(), awt_rename_cb(), AW_window::load_xfig(), and makeHelpCallback().

Referenced by popup_new_main_window().

static char* makeUniqueShortName ( const char *  prefix, UniqueNameDetector &  existing  )

static

Definition at line 612 of file AW_rename.cxx.

References aw_assert, UniqueNameDetector::name_known(), NULp, and result.

Referenced by AWTC_makeUniqueShortName().

char* AWTC_makeUniqueShortName	(	const char *	prefix,
		UniqueNameDetector &	existingNames
	)

Definition at line 648 of file AW_rename.cxx.

References aw_assert, GB_export_errorf(), makeUniqueShortName(), NULp, and result.

Referenced by concatenateFieldsCreateNewSpecies(), create_new_species(), DBwriter::createOrganism(), and species_copy_cb().

char* AWTC_generate_random_name

(

UniqueNameDetector &

existingNames

)

Definition at line 679 of file AW_rename.cxx.

References aw_message(), AWTC_generate_random_name(), GB_random(), UniqueNameDetector::name_known(), and NULp.

Referenced by AWTC_generate_random_name(), create_new_species(), and gen_extract_gene_2_pseudoSpecies().

int AWTC_name_quality

(

const char *

short_name

)

Definition at line 707 of file AW_rename.cxx.

Referenced by InsertDatainGDE().

Variable Documentation

NameServerConnection name_server

static

Definition at line 300 of file AW_rename.cxx.