MG_gene_species.cxx File Reference

#include "merge.hxx"
#include <awt_config_manager.hxx>
#include <aw_awar.hxx>
#include <aw_root.hxx>
#include <aw_msg.hxx>
#include <aw_select.hxx>
#include <arbdbt.h>
#include <arb_str.h>
#include <gb_aci.h>

Include dependency graph for MG_gene_species.cxx:

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Macros
#define	AWAR_MERGE_GENE_SPECIES_SAV   AWAR_MERGE_SAV "gene_species/"
#define	AWAR_MERGE_GENE_SPECIES_TMP   AWAR_MERGE_TMP "gene_species/"
#define	AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD   AWAR_MERGE_GENE_SPECIES_TMP "current"
#define	AWAR_MERGE_GENE_SPECIES_DEST   AWAR_MERGE_GENE_SPECIES_TMP "dest"
#define	AWAR_MERGE_GENE_SPECIES_SOURCE   AWAR_MERGE_GENE_SPECIES_TMP "source"
#define	AWAR_MERGE_GENE_SPECIES_METHOD   AWAR_MERGE_GENE_SPECIES_TMP "method"
#define	AWAR_MERGE_GENE_SPECIES_ACI   AWAR_MERGE_GENE_SPECIES_TMP "aci"
#define	AWAR_MERGE_GENE_SPECIES_EXAMPLE   AWAR_MERGE_GENE_SPECIES_TMP "example"
#define	AWAR_MERGE_GENE_SPECIES_FIELDS_SAVE   AWAR_MERGE_GENE_SPECIES_TMP "save"
#define	AWAR_MERGE_GENE_SPECIES_CREATE_FIELDS   AWAR_MERGE_GENE_SPECIES_SAV "activated"
#define	AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS   AWAR_MERGE_GENE_SPECIES_SAV "field_defs"
#define	BUFSIZE   100
#define	MAX_EQUAL_WARNINGS   10
#define	add_config(s, id)   cdef.add(field_awar(s, id), id, count)

Enumerations
enum	CreationMethod { MG_CREATE_COPY_ORGANISM, MG_CREATE_COPY_GENE, MG_CREATE_USING_ACI_ONLY }

Functions
void	MG_create_gene_species_awars (AW_root *aw_root, AW_default aw_def)
char *	strcpydest (char *dest, const char *src)
const char *	field_awar (const char *field_name, const char *subfield)
const char *	current_field_awar (AW_root *aw_root, const char *subfield)
static void	create_awars_for_field (const char *cur_field)
static char *	MG_create_field_content (GBDATA *gb_species, CreationMethod method, const char *origins_field, const char *aci, GB_ERROR &error, GB_HASH *organism_hash)
GB_ERROR	MG_export_fields (AW_root *aw_root, GBDATA *gb_src, GBDATA *gb_dst, GB_HASH *error_suppressor, GB_HASH *source_organism_hash)
static char *	MG_create_current_field_content (AW_root *aw_root, GBDATA *gb_species, GB_ERROR &error)
static void	MG_update_example (AW_root *aw_root)
static void	check_and_correct_current_field (char *&cur_field)
static void	MG_current_field_def_changed_cb (AW_root *aw_root)
static void	MG_source_field_changed_cb (AW_root *aw_root)
static void	MG_dest_field_changed_cb (AW_root *aw_root)
static void	MG_method_changed_cb (AW_root *aw_root)
static void	MG_delete_selected_field_def (AW_window *aww)
static void	MG_aci_changed_cb (AW_root *aw_root)
static void	MG_update_selection_list_on_field_transfers (AW_root *aw_root, AW_selection_list *geneSpecFieldList)
static void	init_gene_species_xfer_fields_subconfig (AWT_config_definition &cdef, char *existing_definitions)
static void	init_gene_species_xfer_fields_config (AWT_config_definition &cdef)
static char *	store_gene_species_xfer_fields ()
static void	load_or_reset_gene_species_xfer_fields (const char *stored_string, AW_selection_list *geneSpecFieldList)
AW_window *	MG_gene_species_create_field_transfer_def_window (AW_root *aw_root)

Variables
static AW_default	MG_props = NULp
static bool	allow_callbacks = true

Macro Definition Documentation

#define AWAR_MERGE_GENE_SPECIES_SAV   AWAR_MERGE_SAV "gene_species/"

Definition at line 27 of file MG_gene_species.cxx.

Referenced by field_awar().

#define AWAR_MERGE_GENE_SPECIES_TMP   AWAR_MERGE_TMP "gene_species/"

Definition at line 28 of file MG_gene_species.cxx.

#define AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD   AWAR_MERGE_GENE_SPECIES_TMP "current"

Definition at line 32 of file MG_gene_species.cxx.

Referenced by current_field_awar(), load_or_reset_gene_species_xfer_fields(), MG_create_gene_species_awars(), MG_current_field_def_changed_cb(), MG_delete_selected_field_def(), MG_dest_field_changed_cb(), and MG_gene_species_create_field_transfer_def_window().

#define AWAR_MERGE_GENE_SPECIES_DEST   AWAR_MERGE_GENE_SPECIES_TMP "dest"

Definition at line 33 of file MG_gene_species.cxx.

Referenced by MG_create_gene_species_awars(), MG_current_field_def_changed_cb(), MG_dest_field_changed_cb(), and MG_gene_species_create_field_transfer_def_window().

#define AWAR_MERGE_GENE_SPECIES_SOURCE   AWAR_MERGE_GENE_SPECIES_TMP "source"

Definition at line 34 of file MG_gene_species.cxx.

Referenced by MG_create_current_field_content(), MG_create_gene_species_awars(), MG_current_field_def_changed_cb(), MG_gene_species_create_field_transfer_def_window(), MG_method_changed_cb(), and MG_source_field_changed_cb().

#define AWAR_MERGE_GENE_SPECIES_METHOD   AWAR_MERGE_GENE_SPECIES_TMP "method"

Definition at line 35 of file MG_gene_species.cxx.

Referenced by MG_create_current_field_content(), MG_create_gene_species_awars(), MG_current_field_def_changed_cb(), MG_gene_species_create_field_transfer_def_window(), MG_method_changed_cb(), and MG_source_field_changed_cb().

#define AWAR_MERGE_GENE_SPECIES_ACI   AWAR_MERGE_GENE_SPECIES_TMP "aci"

Definition at line 36 of file MG_gene_species.cxx.

Referenced by MG_aci_changed_cb(), MG_create_current_field_content(), MG_create_gene_species_awars(), MG_current_field_def_changed_cb(), and MG_gene_species_create_field_transfer_def_window().

#define AWAR_MERGE_GENE_SPECIES_EXAMPLE   AWAR_MERGE_GENE_SPECIES_TMP "example"

Definition at line 37 of file MG_gene_species.cxx.

Referenced by MG_create_gene_species_awars(), MG_gene_species_create_field_transfer_def_window(), and MG_update_example().

#define AWAR_MERGE_GENE_SPECIES_FIELDS_SAVE   AWAR_MERGE_GENE_SPECIES_TMP "save"

Definition at line 38 of file MG_gene_species.cxx.

Referenced by init_gene_species_xfer_fields_config(), load_or_reset_gene_species_xfer_fields(), MG_create_gene_species_awars(), and store_gene_species_xfer_fields().

#define AWAR_MERGE_GENE_SPECIES_CREATE_FIELDS   AWAR_MERGE_GENE_SPECIES_SAV "activated"

Definition at line 41 of file MG_gene_species.cxx.

Referenced by MG_create_gene_species_awars(), MG_export_fields(), and MG_gene_species_create_field_transfer_def_window().

#define AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS   AWAR_MERGE_GENE_SPECIES_SAV "field_defs"

Definition at line 42 of file MG_gene_species.cxx.

Referenced by init_gene_species_xfer_fields_config(), load_or_reset_gene_species_xfer_fields(), MG_create_gene_species_awars(), MG_delete_selected_field_def(), MG_dest_field_changed_cb(), MG_export_fields(), MG_gene_species_create_field_transfer_def_window(), MG_update_selection_list_on_field_transfers(), and store_gene_species_xfer_fields().

#define BUFSIZE   100

Definition at line 67 of file MG_gene_species.cxx.

Referenced by field_awar().

#define MAX_EQUAL_WARNINGS   10

Referenced by MG_export_fields().

#define add_config	(		s,
			id
	)		cdef.add(field_awar(s, id), id, count)

Referenced by init_gene_species_xfer_fields_subconfig().

Enumeration Type Documentation

enum CreationMethod

Enumerator
MG_CREATE_COPY_ORGANISM
MG_CREATE_COPY_GENE
MG_CREATE_USING_ACI_ONLY

Definition at line 44 of file MG_gene_species.cxx.

Function Documentation

void MG_create_gene_species_awars	(	AW_root *	aw_root,
		AW_default	aw_def
	)

Definition at line 52 of file MG_gene_species.cxx.

References AW_root::awar_int(), AWAR_MERGE_GENE_SPECIES_ACI, AWAR_MERGE_GENE_SPECIES_CREATE_FIELDS, AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, AWAR_MERGE_GENE_SPECIES_DEST, AWAR_MERGE_GENE_SPECIES_EXAMPLE, AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, AWAR_MERGE_GENE_SPECIES_FIELDS_SAVE, AWAR_MERGE_GENE_SPECIES_METHOD, AWAR_MERGE_GENE_SPECIES_SOURCE, and AW_root::awar_string().

Referenced by MERGE_create_all_awars().

char* strcpydest ( char *  dest, const char *  src  )

inline

Definition at line 69 of file MG_gene_species.cxx.

Referenced by field_awar().

const char* field_awar ( const char *  field_name, const char *  subfield  )

inline

Definition at line 80 of file MG_gene_species.cxx.

References AWAR_MERGE_GENE_SPECIES_SAV, buffer, BUFSIZE, IF_DEBUG, mg_assert, and strcpydest().

Referenced by create_awars_for_field(), current_field_awar(), MG_current_field_def_changed_cb(), and MG_export_fields().

const char* current_field_awar ( AW_root *  aw_root, const char *  subfield  )

inline

Definition at line 92 of file MG_gene_species.cxx.

References AW_root::awar(), AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, field_awar(), NULp, and AW_awar::read_string().

Referenced by MG_aci_changed_cb(), MG_method_changed_cb(), and MG_source_field_changed_cb().

static void create_awars_for_field ( const char *  cur_field )

static

Definition at line 101 of file MG_gene_species.cxx.

References AW_root::awar_int(), AW_root::awar_string(), field_awar(), and AW_root::SINGLETON.

Referenced by init_gene_species_xfer_fields_subconfig(), and MG_export_fields().

static char* MG_create_field_content ( GBDATA *  gb_species, CreationMethod  method, const char *  origins_field, const char *  aci, GB_ERROR &  error, GB_HASH *  organism_hash  )

static

Definition at line 109 of file MG_gene_species.cxx.

References GB_await_error(), GB_command_interpreter_in_env(), GB_entry(), GB_read_as_string(), GBS_global_string(), GEN_find_origin_gene(), GEN_find_origin_organism(), GEN_is_pseudo_gene_species(), GEN_origin_gene(), GEN_origin_organism(), GLOBAL_gb_src, mg_assert, MG_CREATE_COPY_GENE, MG_CREATE_COPY_ORGANISM, MG_CREATE_USING_ACI_ONLY, NULp, and result.

Referenced by MG_create_current_field_content(), and MG_export_fields().

GB_ERROR MG_export_fields	(	AW_root *	aw_root,
		GBDATA *	gb_src,
		GBDATA *	gb_dst,
		GB_HASH *	error_suppressor,
		GB_HASH *	source_organism_hash
	)

Definition at line 177 of file MG_gene_species.cxx.

References aw_message(), aw_message_if(), AW_root::awar(), AWAR_MERGE_GENE_SPECIES_CREATE_FIELDS, AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, create_awars_for_field(), error(), field_awar(), GBS_global_string(), GBS_incr_hash(), GBS_optimize_hash(), GBS_read_hash(), GBT_get_name_or_description(), GBT_write_string(), GEN_is_pseudo_gene_species(), MAX_EQUAL_WARNINGS, mg_assert, MG_create_field_content(), NULp, AW_awar::read_int(), AW_awar::read_string(), result, and start.

Referenced by MG_transfer_one_species().

static char* MG_create_current_field_content ( AW_root *  aw_root, GBDATA *  gb_species, GB_ERROR &  error  )

static

Definition at line 247 of file MG_gene_species.cxx.

References AW_root::awar(), AWAR_MERGE_GENE_SPECIES_ACI, AWAR_MERGE_GENE_SPECIES_METHOD, AWAR_MERGE_GENE_SPECIES_SOURCE, MG_create_field_content(), NULp, AW_awar::read_int(), AW_awar::read_string(), and result.

Referenced by MG_update_example().

static void MG_update_example ( AW_root *  aw_root )

static

Definition at line 260 of file MG_gene_species.cxx.

References AW_root::awar(), AWAR_MERGE_GENE_SPECIES_EXAMPLE, error(), GB_export_errorf(), GBS_global_string_copy(), GBT_find_species(), GEN_is_pseudo_gene_species(), GLOBAL_gb_src, MG_create_current_field_content(), MG_left_AWAR_SPECIES_NAME(), NULp, AW_awar::read_string(), result, ta, and AW_awar::write_string().

Referenced by MG_aci_changed_cb(), MG_current_field_def_changed_cb(), MG_dest_field_changed_cb(), MG_gene_species_create_field_transfer_def_window(), MG_method_changed_cb(), and MG_source_field_changed_cb().

static void check_and_correct_current_field ( char *&  cur_field )

static

Definition at line 286 of file MG_gene_species.cxx.

References ARB_stricmp(), aw_message(), and GBS_global_string_copy().

Referenced by MG_current_field_def_changed_cb(), and MG_dest_field_changed_cb().

static void MG_current_field_def_changed_cb ( AW_root *  aw_root )

static

Definition at line 296 of file MG_gene_species.cxx.

References allow_callbacks, AW_root::awar(), AW_root::awar_int(), AWAR_MERGE_GENE_SPECIES_ACI, AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, AWAR_MERGE_GENE_SPECIES_DEST, AWAR_MERGE_GENE_SPECIES_METHOD, AWAR_MERGE_GENE_SPECIES_SOURCE, AW_root::awar_string(), check_and_correct_current_field(), field_awar(), MG_update_example(), AW_awar::read_int(), AW_awar::read_string(), AW_awar::write_int(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void MG_source_field_changed_cb ( AW_root *  aw_root )

static

Definition at line 335 of file MG_gene_species.cxx.

References allow_callbacks, aw_message(), AW_root::awar(), AWAR_MERGE_GENE_SPECIES_METHOD, AWAR_MERGE_GENE_SPECIES_SOURCE, current_field_awar(), MG_CREATE_USING_ACI_ONLY, MG_update_example(), AW_awar::read_int(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void MG_dest_field_changed_cb ( AW_root *  aw_root )

static

Definition at line 355 of file MG_gene_species.cxx.

References allow_callbacks, AW_root::awar(), AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, AWAR_MERGE_GENE_SPECIES_DEST, AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, check_and_correct_current_field(), GBS_global_string(), mg_assert, MG_update_example(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void MG_method_changed_cb ( AW_root *  aw_root )

static

Definition at line 380 of file MG_gene_species.cxx.

References allow_callbacks, AW_root::awar(), AWAR_MERGE_GENE_SPECIES_METHOD, AWAR_MERGE_GENE_SPECIES_SOURCE, current_field_awar(), MG_CREATE_USING_ACI_ONLY, MG_update_example(), AW_awar::read_int(), AW_awar::write_int(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void MG_delete_selected_field_def ( AW_window *  aww )

static

Definition at line 395 of file MG_gene_species.cxx.

References aw_message(), AW_root::awar(), AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, GBS_global_string(), AW_window::get_root(), mg_assert, AW_awar::read_string(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void MG_aci_changed_cb ( AW_root *  aw_root )

static

Definition at line 422 of file MG_gene_species.cxx.

References allow_callbacks, AW_root::awar(), AWAR_MERGE_GENE_SPECIES_ACI, current_field_awar(), MG_update_example(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void MG_update_selection_list_on_field_transfers ( AW_root *  aw_root, AW_selection_list *  geneSpecFieldList  )

static

Definition at line 434 of file MG_gene_species.cxx.

References AW_root::awar(), AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, AW_selection_list::clear(), AW_selection_list::insert(), AW_selection_list::insert_default(), mg_assert, AW_awar::read_string(), start, and AW_selection_list::update().

Referenced by load_or_reset_gene_species_xfer_fields(), and MG_gene_species_create_field_transfer_def_window().

static void init_gene_species_xfer_fields_subconfig ( AWT_config_definition &  cdef, char *  existing_definitions  )

static

Definition at line 462 of file MG_gene_species.cxx.

References add_config, create_awars_for_field(), mg_assert, and start.

Referenced by load_or_reset_gene_species_xfer_fields(), and store_gene_species_xfer_fields().

static void init_gene_species_xfer_fields_config ( AWT_config_definition &  cdef )

static

Definition at line 491 of file MG_gene_species.cxx.

References AWT_config_definition::add(), AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, and AWAR_MERGE_GENE_SPECIES_FIELDS_SAVE.

Referenced by load_or_reset_gene_species_xfer_fields(), and store_gene_species_xfer_fields().

static char* store_gene_species_xfer_fields ( )

static

Definition at line 495 of file MG_gene_species.cxx.

References AW_root::awar(), AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, AWAR_MERGE_GENE_SPECIES_FIELDS_SAVE, init_gene_species_xfer_fields_config(), init_gene_species_xfer_fields_subconfig(), AWT_config_definition::read(), AW_awar::read_string(), AW_root::SINGLETON, and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

static void load_or_reset_gene_species_xfer_fields ( const char *  stored_string, AW_selection_list *  geneSpecFieldList  )

static

Definition at line 516 of file MG_gene_species.cxx.

References AW_root::awar(), AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, AWAR_MERGE_GENE_SPECIES_FIELDS_SAVE, init_gene_species_xfer_fields_config(), init_gene_species_xfer_fields_subconfig(), MG_update_selection_list_on_field_transfers(), AW_awar::read_string(), AWT_config_definition::reset(), AW_root::SINGLETON, AWT_config_definition::write(), and AW_awar::write_string().

Referenced by MG_gene_species_create_field_transfer_def_window().

AW_window* MG_gene_species_create_field_transfer_def_window

(

AW_root *

aw_root

)

Definition at line 549 of file MG_gene_species.cxx.

References AW_awar::add_callback(), AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_MERGE_GENE_SPECIES_ACI, AWAR_MERGE_GENE_SPECIES_CREATE_FIELDS, AWAR_MERGE_GENE_SPECIES_CURRENT_FIELD, AWAR_MERGE_GENE_SPECIES_DEST, AWAR_MERGE_GENE_SPECIES_EXAMPLE, AWAR_MERGE_GENE_SPECIES_FIELDS_DEFS, AWAR_MERGE_GENE_SPECIES_METHOD, AWAR_MERGE_GENE_SPECIES_SOURCE, AWT_insert_config_manager(), load_or_reset_gene_species_xfer_fields(), makeHelpCallback(), MG_aci_changed_cb(), MG_CREATE_COPY_GENE, MG_CREATE_COPY_ORGANISM, MG_CREATE_USING_ACI_ONLY, MG_current_field_def_changed_cb(), MG_delete_selected_field_def(), MG_dest_field_changed_cb(), MG_left_AWAR_SPECIES_NAME(), MG_method_changed_cb(), MG_source_field_changed_cb(), MG_update_example(), MG_update_selection_list_on_field_transfers(), NULp, and store_gene_species_xfer_fields().

Referenced by MG_create_merge_species_window().

Variable Documentation

AW_default MG_props = NULp

static

Definition at line 50 of file MG_gene_species.cxx.

bool allow_callbacks = true

static

Definition at line 294 of file MG_gene_species.cxx.

Referenced by MG_aci_changed_cb(), MG_current_field_def_changed_cb(), MG_dest_field_changed_cb(), MG_method_changed_cb(), and MG_source_field_changed_cb().