#include "gb_local.h"
#include <arbdbt.h>
#include <arb_strbuf.h>

Include dependency graph for aditem.cxx:

Macros
#define	GENERATE_ID(num) sprintf(generated_id, "%s%zu", default_id, num);

#define	MAX_NAME_LEN 20

Functions
GBDATA *	GBT_find_or_create_item_rel_item_data (GBDATA gb_item_data, const char itemname, const char id_field, const char id, bool markCreated)

GBDATA *	GBT_find_or_create_species_rel_species_data (GBDATA gb_species_data, const char name, bool markCreated)

GBDATA *	GBT_find_or_create_species (GBDATA gb_main, const char name, bool markCreated)

GBDATA *	GBT_find_or_create_SAI (GBDATA gb_main, const char name)

GBDATA *	GBT_find_item_rel_item_data (GBDATA gb_item_data, const char id_field, const char *id_value)

GBDATA *	GBT_expect_item_rel_item_data (GBDATA gb_item_data, const char id_field, const char *id_value)

GBDATA *	GBT_get_species_data (GBDATA *gb_main)

GBDATA *	GBT_first_marked_species_rel_species_data (GBDATA *gb_species_data)

GBDATA *	GBT_first_marked_species (GBDATA *gb_main)

GBDATA *	GBT_next_marked_species (GBDATA *gb_species)

GBDATA *	GBT_first_species_rel_species_data (GBDATA *gb_species_data)

GBDATA *	GBT_first_species (GBDATA *gb_main)

GBDATA *	GBT_next_species (GBDATA *gb_species)

GBDATA *	GBT_find_species_rel_species_data (GBDATA gb_species_data, const char name)

GBDATA *	GBT_expect_species_rel_species_data (GBDATA gb_species_data, const char name)

GBDATA *	GBT_find_species (GBDATA gb_main, const char name)

GBDATA *	GBT_expect_species (GBDATA gb_main, const char name)

GBDATA *	GBT_get_SAI_data (GBDATA *gb_main)

GBDATA *	GBT_first_SAI_rel_SAI_data (GBDATA *gb_sai_data)

GBDATA *	GBT_first_SAI (GBDATA *gb_main)

GBDATA *	GBT_next_SAI (GBDATA *gb_sai)

GBDATA *	GBT_find_SAI_rel_SAI_data (GBDATA gb_sai_data, const char name)

GBDATA *	GBT_expect_SAI_rel_SAI_data (GBDATA gb_sai_data, const char name)

GBDATA *	GBT_find_SAI (GBDATA gb_main, const char name)

GBDATA *	GBT_expect_SAI (GBDATA gb_main, const char name)

static long	GBT_get_item_count (GBDATA gb_parent_of_container, const char item_container_name)

long	GBT_get_species_count (GBDATA *gb_main)

long	GBT_get_SAI_count (GBDATA *gb_main)

static char *	GBT_create_unique_item_identifier (GBDATA gb_item_container, const char id_field, const char *default_id)

char *	GBT_create_unique_species_name (GBDATA gb_main, const char default_name)

long	GBT_mark_all (GBDATA *gb_main, int flag)

long	GBT_mark_all_that (GBDATA gb_main, int flag, bool(condition)(GBDATA , void ), void *cd)

long	GBT_count_marked_species (GBDATA *gb_main)

char *	GBT_store_marked_species (GBDATA *gb_main, bool unmark_all)

NOT4PERL GB_ERROR	GBT_with_stored_species (GBDATA gb_main, const char stored, species_callback doit, int *clientdata)

static GB_ERROR	restore_mark (GBDATA gb_species, int )

GB_ERROR	GBT_restore_marked_species (GBDATA gb_main, const char stored_marked)

GB_CSTR	GBT_get_name_or_description (GBDATA *gb_item)

const char *	GBT_get_name (GBDATA *gb_item)

NOT4PERL GB_CSTR	GBT_read_name (GBDATA *gb_item)

GBDATA **	GBT_gen_species_array (GBDATA gb_main, long speciesCountPtr)

Macro Definition Documentation

#define GENERATE_ID ( num ) sprintf(generated_id, "%s%zu", default_id, num);

Referenced by GBT_create_unique_item_identifier().

#define MAX_NAME_LEN 20

Referenced by GBT_with_stored_species().

Function Documentation

GBDATA* GBT_find_or_create_item_rel_item_data	(	GBDATA *	gb_item_data,
		const char *	itemname,
		const char *	id_field,
		const char *	id,
		bool	markCreated
	)

Search for an existing or create a new, named item.

Parameters

gb_item_data	item container
itemname	description of itemtype (for error messages)
id_field	item-field containing ID (e.g. "name")
id	the ID itself (compare is case-insensitive)
markCreated	true -> mark item if it was created

Returns: found/created item or NULp if an error occurs (which is exported in that case)

Definition at line 18 of file aditem.cxx.

References error(), GB_await_error(), GB_create_container(), GB_end_transaction(), GB_export_errorf(), GB_push_transaction(), GB_write_flag(), GBT_find_item_rel_item_data(), GBT_write_string(), and NULp.

Referenced by EXP_find_or_create_experiment_rel_exp_data(), GBT_find_or_create_colorset(), GBT_find_or_create_SAI(), and GBT_find_or_create_species_rel_species_data().

GBDATA* GBT_find_or_create_species_rel_species_data	(	GBDATA *	gb_species_data,
		const char *	name,
		bool	markCreated
	)

Definition at line 57 of file aditem.cxx.

References GBT_find_or_create_item_rel_item_data().

Referenced by export_to_DB(), GBT_find_or_create_species(), MG_merge_tagged_field_cb(), and species_create_handler().

GBDATA* GBT_find_or_create_species	(	GBDATA *	gb_main,
		const char *	name,
		bool	markCreated
	)

Definition at line 61 of file aditem.cxx.

References GBT_find_or_create_species_rel_species_data(), and GBT_get_species_data().

Referenced by create_new_species(), and gen_extract_gene_2_pseudoSpecies().

GBDATA* GBT_find_or_create_SAI	(	GBDATA *	gb_main,
		const char *	name
	)

Search for an SAI, when SAI does not exist, create it

Definition at line 65 of file aditem.cxx.

References GBT_find_or_create_item_rel_item_data(), and GBT_get_SAI_data().

Referenced by CON_calc_max_freq(), CON_export(), create_concatInfo_SAI(), create_next_SAI(), export_to_DB(), NT_count_different_chars(), PH_create_ml_multiline_SAI(), PH_save_ml_cb(), ALI_ARBDB::put_SAI(), and AP_pos_var::save_aliEntry_to_SAI().

GBDATA* GBT_find_item_rel_item_data	(	GBDATA *	gb_item_data,
		const char *	id_field,
		const char *	id_value
	)

search for items starting at item container

Parameters

'gb_item_data'	is a container containing items
'id_field'	is a field containing a unique identifier for each item (e.g. 'name' for species)
'id_value'	expected value of 'id_field'

Returns: a pointer to an item with 'id_field' containing 'id_value' or NULp (in this case an error MAY be exported)

Note: If you expect the item to exist, use GBT_expect_item_rel_item_data()

Definition at line 74 of file aditem.cxx.

References GB_find_string(), GB_get_father(), GB_IGNORE_CASE, NULp, and SEARCH_GRANDCHILD.

Referenced by EXP_find_experiment_rel_exp_data(), GBT_create_unique_item_identifier(), GBT_expect_item_rel_item_data(), GBT_find_colorset(), GBT_find_or_create_item_rel_item_data(), GBT_find_SAI(), GBT_find_SAI_rel_SAI_data(), GBT_find_species(), GBT_find_species_rel_species_data(), and GEN_find_gene_rel_gene_data().

GBDATA* GBT_expect_item_rel_item_data	(	GBDATA *	gb_item_data,
		const char *	id_field,
		const char *	id_value
	)

like GBT_find_item_rel_item_data(), but also exports an error if the item is not present

Definition at line 91 of file aditem.cxx.

References GB_export_errorf(), GB_find(), GB_get_father(), GB_have_error(), GB_read_key_pntr(), GBT_find_item_rel_item_data(), and SEARCH_GRANDCHILD.

Referenced by GBT_expect_SAI(), GBT_expect_SAI_rel_SAI_data(), GBT_expect_species(), GBT_expect_species_rel_species_data(), and GEN_expect_gene().

GBDATA* GBT_get_species_data ( GBDATA * gb_main )

Definition at line 105 of file aditem.cxx.

References GBT_find_or_create().

Referenced by addSpeciesToConcatenateList(), AP_tree_root::AP_tree_root(), ARB_main(), calc_and_update_alignment_errors_cb(), compress_sequence_tree(), concatenateFieldsCreateNewSpecies(), copy_move_del_alignment(), copy_SAI_to_species_cb(), create_new_species(), DI_create_matrix_variables(), experiment_field_selection_list_rescan(), export_to_DB(), gbl_findacc(), gbl_findspec(), GBT_begin_rename_session(), GBT_check_alignment(), GBT_check_data(), GBT_count_marked_species(), GBT_create_unique_species_name(), GBT_expect_species(), GBT_find_or_create_species(), GBT_find_species(), GBT_first_marked_species(), GBT_first_species(), GBT_gen_species_array(), GBT_mark_all(), gene_extract_handler(), gene_field_selection_list_rescan(), get_first_species_data(), ALI_ARBDB::get_sequence(), ALI_ARBDB::get_sequence_string(), ArbImporter::import_data(), launch_MapViewer_cb(), DI_MATRIX::load(), mark_action(), MERGE_sequences_simple(), mg_check_field_cb(), mg_get_first_species_data1(), mg_get_first_species_data2(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), mg_transfer_selected_species(), GroupSearch::perform_search(), popup_new_main_window(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), ALI_ARBDB::put_sequence(), ALI_ARBDB::put_sequence_string(), ArbImporter::read_data(), ReadArbdb(), resort_data_base(), Aligner::run(), QUERY::search_duplicated_field_content(), species_create_handler(), species_field_selection_list_rescan(), transfer_field_of_listed_cb(), and ScopedTransporter::transferAllIn().

GBDATA* GBT_first_marked_species_rel_species_data ( GBDATA * gb_species_data )

Definition at line 109 of file aditem.cxx.

References GB_first_marked().

Referenced by get_first_species(), DI_MATRIX::load(), probe_match_event(), and ReadArbdb().

GBDATA* GBT_first_marked_species ( GBDATA * gb_main )

Definition at line 113 of file aditem.cxx.

References GB_first_marked(), and GBT_get_species_data().

Referenced by aed_start_naligning(), ALI_realign_marked(), ALI_translate_marked(), arb_prm_read(), brute_force_find_next_species(), build_reverse_complement(), CON_export(), CON_insertSequences(), concatenateAlignments(), ED4_get_marked_from_menu(), export_nds_cb(), MO_Liste::fill_marked_bakts(), GBT_create_marked_species_hash(), GBT_store_marked_species(), GEN_first_marked_organism(), GEN_first_marked_pseudo_species(), PHDATA::load(), mergeSimilarSpecies(), nt_add_partial(), nt_build_conf_marked(), NT_count_different_chars(), NT_delete_mark_all_cb(), pd_get_the_names(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), SpeciesSelector::select_first(), sina_start(), species_rename_join(), split_alignment(), SQ_evaluate(), and SQ_mark_species().

GBDATA* GBT_next_marked_species ( GBDATA * gb_species )

Definition at line 116 of file aditem.cxx.

References gb_assert, GB_has_key(), and GB_next_marked().

Referenced by aed_start_naligning(), ALI_realign_marked(), ALI_translate_marked(), arb_prm_read(), brute_force_find_next_species(), build_reverse_complement(), CON_export(), CON_insertSequences(), concatenateAlignments(), ED4_get_marked_from_menu(), export_nds_cb(), MO_Liste::fill_marked_bakts(), GBT_create_marked_species_hash(), GBT_store_marked_species(), GEN_next_marked_organism(), GEN_next_marked_pseudo_species(), get_next_species(), DI_MATRIX::load(), PHDATA::load(), mergeSimilarSpecies(), nt_add_partial(), nt_build_conf_marked(), NT_count_different_chars(), NT_delete_mark_all_cb(), pd_get_the_names(), probe_match_event(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), ReadArbdb(), SpeciesSelector::select_next(), sina_start(), species_rename_join(), split_alignment(), SQ_evaluate(), and SQ_mark_species().

GBDATA* GBT_first_species_rel_species_data ( GBDATA * gb_species_data )

Definition at line 121 of file aditem.cxx.

References GB_entry().

Referenced by ARB_main(), compress_sequence_tree(), GBT_check_alignment(), GBT_check_data(), GBT_gen_species_array(), get_first_species(), DI_MATRIX::load(), mg_check_field_cb(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), and ReadArbdb().

GBDATA* GBT_first_species ( GBDATA * gb_main )

Definition at line 124 of file aditem.cxx.

References GB_entry(), and GBT_get_species_data().

Referenced by awtc_mark_hits(), awtc_nn_search_all_listed(), AWTC_pars_names(), brute_force_find_next_species(), CON_export(), CON_insertSequences(), QUERY::copy_selection_list_2_query_box(), ImportTestData::countSpeciesAndData(), create_ref_hash(), di_mark_by_distance(), EXP_get_first_experiment_data(), find_species_candidates(), GBT_convert_changekey(), GBT_create_species_hash_sized(), GBT_mark_all(), GBT_mark_all_that(), GEN_first_organism(), GEN_first_pseudo_species(), main(), mg_count_queried(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), MP_mark_probes_in_tree(), NT_create_config_after_import(), NT_del_mark_move_REF(), NT_fix_gene_data(), NT_suggestValidNames(), ImportTestData::refill_species_list(), rerun_importTest_cb(), SpeciesSelector::select_first(), set_marks_of(), split_alignment(), SQ_evaluate(), SQ_mark_species(), SQ_pass1_no_tree(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), st_remove_entries(), trackAlignmentChanges(), transfer_field_of_listed_cb(), ScopedTransporter::transferAllIn(), QUERY::unquery_all(), and FilteredExport::write_fasta().

GBDATA* GBT_next_species ( GBDATA * gb_species )

Definition at line 128 of file aditem.cxx.

References gb_assert, GB_has_key(), and GB_nextEntry().

Referenced by ARB_main(), awtc_mark_hits(), awtc_nn_search_all_listed(), AWTC_pars_names(), brute_force_find_next_species(), compress_sequence_tree(), CON_export(), CON_insertSequences(), QUERY::copy_selection_list_2_query_box(), ImportTestData::countSpeciesAndData(), create_ref_hash(), di_mark_by_distance(), EXP_get_next_experiment_data(), find_species_candidates(), GBT_check_alignment(), GBT_check_data(), GBT_convert_changekey(), GBT_create_species_hash_sized(), GBT_gen_species_array(), GBT_mark_all(), GBT_mark_all_that(), GEN_next_organism(), GEN_next_pseudo_species(), get_next_species(), DI_MATRIX::load(), main(), mg_check_field_cb(), mg_count_queried(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), MP_mark_probes_in_tree(), NT_create_config_after_import(), NT_del_mark_move_REF(), NT_fix_gene_data(), NT_suggestValidNames(), probe_match_event(), PT_init_input_data(), PT_prepare_data(), ReadArbdb(), ImportTestData::refill_species_list(), SpeciesSelector::select_next(), set_marks_of(), split_alignment(), SQ_evaluate(), SQ_mark_species(), SQ_pass1_no_tree(), SQ_pass2_no_tree(), SQ_remove_quality_entries(), st_remove_entries(), trackAlignmentChanges(), transfer_field_of_listed_cb(), ScopedTransporter::transferAllIn(), QUERY::unquery_all(), and FilteredExport::write_fasta().

GBDATA* GBT_find_species_rel_species_data	(	GBDATA *	gb_species_data,
		const char *	name
	)

GBDATA* GBT_expect_species_rel_species_data	(	GBDATA *	gb_species_data,
		const char *	name
	)

Definition at line 136 of file aditem.cxx.

References GBT_expect_item_rel_item_data().

GBDATA* GBT_find_species	(	GBDATA *	gb_main,
		const char *	name
	)

Definition at line 139 of file aditem.cxx.

References GBT_find_item_rel_item_data(), and GBT_get_species_data().

Referenced by alignToNextRelative(), awt_create_select_filter_window_aw_cb(), awt_create_select_filter_window_gb_cb(), awt_openDefaultURL_on_selected_species(), awtc_nn_search(), AWTC_recreate_name(), build_reverse_complement(), calculateEndPosition(), create_primer_design_window(), EXP_item_type_species_selector::current(), FINAL_TYPE< SEQTYPE >::current(), GEN_item_type_species_selector::current(), di_mark_by_distance(), do_sth_with_species(), ed_submit_info_event(), EXP_get_first_experiment_data(), expect_species_selected(), EDB_root_bact::fill_data(), find_species_by_id(), gbl_read_seq_sai_or_species(), GBT_with_stored_species(), GEN_find_organism(), GEN_get_current_organism(), GEN_get_local_gene_data(), GEN_root::GEN_root(), GEN_species_name_changed_cb(), MO_Liste::get_all_species(), get_selected_imported_species(), get_selected_species(), insert_new_species_terminal(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MG_create_remap(), mg_get_selected_species1(), mg_get_selected_species2(), MG_map_species(), MG_update_example(), move_species_to_extended(), nt_add(), NT_create_sai_from_pfold(), nt_extract_configuration(), primer_design_event_go(), primer_design_event_init(), probe_design_event(), PV_WriteTranslatedSequenceToDB(), rerun_importTest_cb(), SpeciesSelector::select_first(), selectValidNameFromList(), st_ml_add_quality_string_to_species(), transfer_field_of_selected_cb(), TranslateGeneToAminoAcidSequence(), translateSAItoColors(), and update_exportTest_result_cb().

GBDATA* GBT_expect_species	(	GBDATA *	gb_main,
		const char *	name
	)

Definition at line 146 of file aditem.cxx.

References GBT_expect_item_rel_item_data(), and GBT_get_species_data().

Referenced by GetDisplayInfo().

GBDATA* GBT_get_SAI_data ( GBDATA * gb_main )

GBDATA* GBT_first_SAI_rel_SAI_data ( GBDATA * gb_sai_data )

Definition at line 159 of file aditem.cxx.

References GB_entry().

Referenced by GBT_check_alignment(), get_first_SAI(), and nt_build_sai_string().

GBDATA* GBT_first_SAI ( GBDATA * gb_main )

Definition at line 162 of file aditem.cxx.

References GB_entry(), and GBT_get_SAI_data().

Referenced by awt_create_select_filter_window_gb_cb(), ED4_pfold_select_SAI_and_update_option_menu(), SAI_selection::fill(), find_SAI_candidates(), GBT_create_SAI_hash(), get_SAI_groups(), NT_del_mark_move_REF(), and split_alignment().

GBDATA* GBT_next_SAI ( GBDATA * gb_sai )

Definition at line 166 of file aditem.cxx.

References gb_assert, GB_has_key(), and GB_nextEntry().

Referenced by awt_create_select_filter_window_gb_cb(), ED4_pfold_select_SAI_and_update_option_menu(), SAI_selection::fill(), find_SAI_candidates(), GBT_check_alignment(), GBT_create_SAI_hash(), get_next_SAI(), get_SAI_groups(), nt_build_sai_string(), NT_del_mark_move_REF(), and split_alignment().

GBDATA* GBT_find_SAI_rel_SAI_data	(	GBDATA *	gb_sai_data,
		const char *	name
	)

Definition at line 171 of file aditem.cxx.

References GBT_find_item_rel_item_data().

Referenced by copy_SAI_cb(), extended_rename_handler(), BI_helix::init(), MG_transfer_extended(), move_species_to_extended(), nt_build_sai_string(), NT_create_sai_from_pfold(), and PT_init_input_data().

GBDATA* GBT_expect_SAI_rel_SAI_data	(	GBDATA *	gb_sai_data,
		const char *	name
	)

Definition at line 174 of file aditem.cxx.

References GBT_expect_item_rel_item_data().

Referenced by saiHasDataInAli().

GBDATA* GBT_find_SAI	(	GBDATA *	gb_main,
		const char *	name
	)

Definition at line 177 of file aditem.cxx.

References GBT_find_item_rel_item_data(), and GBT_get_SAI_data().

Referenced by ARB_main(), awt_create_select_filter_window_aw_cb(), awt_set_awar_to_valid_filter_good_for_tree_methods(), ColumnStat::calculate(), copy_SAI_to_species_cb(), create_next_SAI(), AP_pos_var::delete_aliEntry_from_SAI(), delete_SAI_cb(), ED4_getSaiColorString(), ED4_pfold_set_SAI(), edit_SAI_description(), EDB_root_bact::fill_data(), find_SAI_by_id(), Structure3D::FindTypeOfRNA(), gbl_read_seq_sai_or_species(), get_helix_string(), get_SAI_group(), get_selected_SAI(), BI_ecoli_ref::init(), insert_new_species_terminal(), map_extended(), map_SAI_to_scanner(), Structure3D::MapCurrentSpeciesToEcoliTemplate(), MG_create_remap(), MG_extended_delete_cb(), mg_get_selected_sai1(), mg_get_selected_sai2(), MG_transfer_extended(), modsai_cb(), NT_del_mark_move_REF(), rename_SAI_cb(), saiChanged_callback(), set_SAI_group(), and translateSAItoColors().

GBDATA* GBT_expect_SAI	(	GBDATA *	gb_main,
		const char *	name
	)

Definition at line 184 of file aditem.cxx.

References GBT_expect_item_rel_item_data(), and GBT_get_SAI_data().

Referenced by dot_missing_bases(), FastAligner_start(), FilterDefinition::make_filter(), and update_RangeList().

static long GBT_get_item_count	(	GBDATA *	gb_parent_of_container,
		const char *	item_container_name
	)

static

Definition at line 193 of file aditem.cxx.

References GB_entry(), GB_number_of_subentries(), GB_pop_transaction(), and GB_push_transaction().

Referenced by GBT_get_SAI_count(), and GBT_get_species_count().

long GBT_get_species_count ( GBDATA * gb_main )

long GBT_get_SAI_count ( GBDATA * gb_main )

Definition at line 211 of file aditem.cxx.

References GBT_get_item_count().

Referenced by CheckedConsistencies::CheckedConsistencies(), and GBT_create_SAI_hash().

static char* GBT_create_unique_item_identifier	(	GBDATA *	gb_item_container,
		const char *	id_field,
		const char *	default_id
	)

static

Definition at line 217 of file aditem.cxx.

References ARB_strdup(), gb_assert, GB_number_of_subentries(), GB_random(), GBT_find_item_rel_item_data(), GENERATE_ID, and mid().

Referenced by GBT_create_unique_species_name().

char* GBT_create_unique_species_name	(	GBDATA *	gb_main,
		const char *	default_name
	)

Definition at line 287 of file aditem.cxx.

References GBT_create_unique_item_identifier(), and GBT_get_species_data().

Referenced by GBT_check_alignment(), and write_entry().

long GBT_mark_all	(	GBDATA *	gb_main,
		int	flag
	)

long GBT_mark_all_that	(	GBDATA *	gb_main,
		int	flag,
		bool()(GBDATA , void *)	condition,
		void *	cd
	)

Definition at line 334 of file aditem.cxx.

References gb_assert, GB_pop_transaction(), GB_push_transaction(), GB_read_flag(), GB_write_flag(), GBT_first_species(), and GBT_next_species().

Referenced by mark_nontree_cb(), and NT_mark_all_cb().

long GBT_count_marked_species ( GBDATA * gb_main )

char* GBT_store_marked_species	(	GBDATA *	gb_main,
		bool	unmark_all
	)

stores the currently marked species in a string

Parameters

gb_main	database
unmark_all	if true -> unmark species

Returns: ';'-separated list of species names

Note: a faster (but less robust) way to temporarily store species marks, is to use the flag GB_USERFLAG_WASMARKED together with GB_write_user_flag

Definition at line 377 of file aditem.cxx.

References GBS_strstruct::cat(), GBS_strstruct::cut_tail(), GB_write_flag(), GBT_first_marked_species(), GBT_get_name(), GBT_next_marked_species(), GBS_strstruct::put(), and GBS_strstruct::release_memfriendly().

Referenced by EXP_get_first_experiment_data(), and GEN_get_first_gene_data().

NOT4PERL GB_ERROR GBT_with_stored_species	(	GBDATA *	gb_main,
		const char *	stored,
		species_callback	doit,
		int *	clientdata
	)

call a function with each species of a list

Parameters

gb_main	database
stored	';'-separated list of species names
doit	function to call with each species in 'stored'
clientdata	is passed to 'doit'

Returns: error if sth goes wrong (or if 'doit' reports error)

Definition at line 404 of file aditem.cxx.

References error(), gb_assert, GBT_find_species(), MAX_NAME_LEN, and NULp.

Referenced by EXP_get_first_experiment_data(), GBT_restore_marked_species(), and GEN_get_first_gene_data().

static GB_ERROR restore_mark	(	GBDATA *	gb_species,
		int *
	)

static

Definition at line 441 of file aditem.cxx.

References GB_write_flag(), and NULp.

Referenced by GBT_restore_marked_species().

GB_ERROR GBT_restore_marked_species	(	GBDATA *	gb_main,
		const char *	stored_marked
	)

restores marked species.

Parameters

gb_main	database
stored_marked	contains a ';'-separated list of species names to mark (as returned by GBT_store_marked_species)

Returns: error if sth goes wrong

Definition at line 446 of file aditem.cxx.

References GBT_mark_all(), GBT_with_stored_species(), NULp, and restore_mark().

Referenced by exp_restore_old_species_marks(), and gen_restore_old_species_marks().

GB_CSTR GBT_get_name_or_description ( GBDATA * gb_item )

returns the value of the "name" field of any database item or "<unnamed_item>" or similar.

See also: GBT_get_name

Definition at line 459 of file aditem.cxx.

References GB_read_key_pntr(), GBS_global_string(), GBT_read_char_pntr(), and result.

Referenced by adaptCopiedAlignment(), aed_start_naligning(), ALI_realign_marked(), alignToNextRelative(), appendNameAndUsedBasePositions(), are_not_in_tree(), auto_select_pseudo_species(), awt_add_sequences_to_list(), awtc_mark_hits(), AP_sequence::bind_to_species(), concatenateAlignments(), QUERY::copy_selection_list_2_query_box(), AP_sequence::do_lazy_load(), dot_sequence_by_consensus(), ED4_get_marked_from_menu(), ED4_pfold_select_SAI_and_update_option_menu(), EXP_get_experiment_id(), expect_entry(), FastAligner_delete_temp_entries(), SAI_selection::fill(), MO_Liste::fill_marked_bakts(), filter_columnstat_SAIs(), find_SAI_candidates(), find_species_candidates(), gbl_findgene(), GBT_convert_changekey(), GBT_read_name(), gbt_rename_alignment_of_item(), gde_filter_weights(), gen_extract_gene_2_pseudoSpecies(), gen_get_gene_id(), GEN_global_gene_identifier(), GEN_organism_not_found(), gene_requires(), get_SAI_description(), export_sequence_data::get_seq_data(), launch_MapViewer_cb(), ListDisplayRow::ListDisplayRow(), PHDATA::load(), mergeSimilarSpecies(), mg_check_field_cb(), MG_export_fields(), MP_mark_probes_in_tree(), nt_add_partial(), NT_fix_gene_data(), perform_query_cb(), PT_prepare_species_sequence(), PV_AddOrfTerminalsToLoadedSpecies(), PV_ManageTerminals(), readCompactedSequence(), reverseComplement(), set_marks_of(), species_requires(), ScopedTransporter::transferAllIn(), translate_getInfo(), FilteredExport::write_fasta(), and writeStringToAlignment().

const char* GBT_get_name ( GBDATA * gb_item )

returns the value of the "name" field of any database item or NULp.

See also: GBT_get_name_or_description

Definition at line 468 of file aditem.cxx.

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

Referenced by build_taxonomy_rek(), ED4_terminal::event_sent_by_parent(), filter_loadable_SAIs(), GroupBuilder::find_best_matching_subtree(), GBT_add_item_to_hash(), GBT_check_data(), GBT_get_colorset_names(), GBT_store_marked_species(), insert_genes_of_organism(), MG_transfer_one_species(), PARS_map_viewer(), read_name(), ImportTestData::refill_species_list(), rerun_importTest_cb(), select_representative(), TopologyShader::shade(), species_rename_handler(), and transfer_field_of_listed_cb().

NOT4PERL GB_CSTR GBT_read_name ( GBDATA * gb_item )

Definition at line 477 of file aditem.cxx.

References GBT_get_name_or_description().

GBDATA** GBT_gen_species_array	(	GBDATA *	gb_main,
		long *	speciesCountPtr
	)

Definition at line 485 of file aditem.cxx.

References ARB_alloc(), gb_species_data, GBT_first_species_rel_species_data(), GBT_get_species_data(), GBT_next_species(), NULp, and result.

Referenced by resort_data_base().

Macros

Functions

Macro Definition Documentation

Function Documentation