Go to the source code of this file.
Macros | |
| #define | mg_assert(bed) arb_assert(bed) |
| #define | AWAR_MERGE_SAV "merge/" |
| #define | AWAR_MERGE_TMP "tmp/" AWAR_MERGE_SAV |
| #define | AWAR_MERGE_TMP_SRC AWAR_MERGE_TMP "src/" |
| #define | AWAR_MERGE_TMP_DST AWAR_MERGE_TMP "dst/" |
| #define | AWAR_DB_SRC AWAR_MERGE_TMP_SRC "db" |
| #define | AWAR_DB_DST AWAR_MERGE_TMP_DST "db" |
| #define | AWAR_REMAP_SPECIES_LIST AWAR_MERGE_SAV "remap_species_list" |
| #define | AWAR_REMAP_ENABLE AWAR_MERGE_SAV "remap_enable" |
| #define | IS_QUERIED_SPECIES(gb_species) GB_user_flag(gb_species, GB_USERFLAG_QUERY) |
Enumerations | |
| enum | DbSel { SRC_DB = 1, DST_DB = 2 } |
Macro Definition Documentation
| #define mg_assert | ( | bed | ) | arb_assert(bed) |
Definition at line 24 of file merge.hxx.
Referenced by awar_name_tmp(), bindAdmin(), Candidate::Candidate(), field_awar(), get_gb_main(), init_gene_species_xfer_fields_subconfig(), ScopedTransporter::markTarget(), MERGE_create_main_window(), MERGE_sequences_simple(), mg_check_field_cb(), MG_copy_and_check_alignments(), MG_create_field_content(), MG_delete_selected_field_def(), MG_dest_field_changed_cb(), MG_exit(), MG_export_fields(), MG_transfer_one_species(), MG_update_selection_list_on_field_transfers(), popup_single_field_transfer_window(), MG_remap::remap(), softbase::softbase(), ViaFtsTransporter::transferOne(), and MG_remaps::~MG_remaps().
| #define AWAR_MERGE_TMP_SRC AWAR_MERGE_TMP "src/" |
Definition at line 29 of file merge.hxx.
Referenced by awar_name_tmp(), and bindAdmin().
| #define AWAR_MERGE_TMP_DST AWAR_MERGE_TMP "dst/" |
Definition at line 30 of file merge.hxx.
Referenced by awar_name_tmp(), and bindAdmin().
| #define AWAR_DB_SRC AWAR_MERGE_TMP_SRC "db" |
Definition at line 32 of file merge.hxx.
Referenced by MERGE_create_db_file_awars(), MERGE_create_main_window(), MG_create_save_as_window(), MG_exit(), and MG_save_cb().
| #define AWAR_DB_DST AWAR_MERGE_TMP_DST "db" |
Definition at line 33 of file merge.hxx.
Referenced by MERGE_create_db_file_awars(), MERGE_create_main_window(), MG_create_save_as_window(), MG_exit(), MG_save_cb(), and MG_save_quick_result_cb().
| #define AWAR_REMAP_SPECIES_LIST AWAR_MERGE_SAV "remap_species_list" |
Definition at line 76 of file merge.hxx.
Referenced by clear_references_cb(), get_reference_species_names(), MG_create_merge_species_window(), MG_create_preserves_selection_window(), read_references(), test_references_cb(), and write_references().
| #define AWAR_REMAP_ENABLE AWAR_MERGE_SAV "remap_enable" |
Definition at line 77 of file merge.hxx.
Referenced by adaption_enabled(), MG_create_merge_species_window(), MG_create_preserves_selection_window(), and write_references().
| #define IS_QUERIED_SPECIES | ( | gb_species | ) | GB_user_flag(gb_species, GB_USERFLAG_QUERY) |
Definition at line 79 of file merge.hxx.
Referenced by mg_check_field_cb(), mg_count_queried(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), transfer_field_of_listed_cb(), and ScopedTransporter::transferAllIn().
Enumeration Type Documentation
Function Documentation
|
inline |
Definition at line 37 of file merge.hxx.
References DST_DB, and SRC_DB.
Referenced by awar_name_tmp(), bindAdmin(), and get_gb_main().
Definition at line 39 of file merge.hxx.
References AWAR_MERGE_TMP_DST, AWAR_MERGE_TMP_SRC, buffer, mg_assert, SRC_DB, and validDb().
Definition at line 106 of file MG_alignment.cxx.
References AW_POPDOWN(), bindAdmin(), copy_and_check_alignments_ignoreResult(), AW_window::load_xfig(), makeHelpCallback(), SOURCE_ADMIN, and TARGET_ADMIN.
Referenced by MERGE_create_main_window().
Definition at line 173 of file MG_names.cxx.
References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_ADDID_DST, AWAR_ADDID_MATCH, AWAR_ADDID_SRC, AWAR_ALLOW_DUPS, AWAR_OVERRIDE, AWAR_RENAME_STATUS, AW_window::load_xfig(), makeHelpCallback(), NULp, override_toggle_cb(), and rename_both_databases().
Referenced by MERGE_create_main_window().
Definition at line 1188 of file MG_species.cxx.
References AW_awar::add_callback(), AW_window::at(), aw_message(), AW_POPDOWN(), AW_root::awar(), AW_root::awar_int(), AWAR_REMAP_ENABLE, AWAR_REMAP_SPECIES_LIST, AWAR_SPECIES_DST, AWAR_SPECIES_SRC, AWAR_SPECIES_XFER_FTS, AWAR_SPECIES_XFER_SCOPE, AWAR_SPECIES_XFER_TYPE, AW_root::awar_string(), AWM_ALL, AWM_DISABLED, AW_window::button_length(), QUERY::query_spec::by_pos_fig, AW_window::callback(), QUERY::query_spec::config_pos_fig, QUERY::query_spec::count_pos_fig, DbScanner::create(), AW_window::create_autosize_button(), AW_window::create_button(), AW_window::create_menu(), create_mg_check_fields_window(), create_mg_merge_tagged_fields_window(), AW_window::create_option_menu(), QUERY::create_query_box(), AW_window::create_text_field(), AW_window::create_toggle(), DB_SCANNER, QUERY::query_spec::do_delete_pos_fig, QUERY::query_spec::do_mark_pos_fig, QUERY::query_spec::do_query_pos_fig, QUERY::query_spec::do_refresh_pos_fig, QUERY::query_spec::do_set_pos_fig, QUERY::query_spec::do_unmark_pos_fig, DST_DB, QUERY::query_spec::ere_pos_fig, error(), QUERY::query_spec::expect_hit_in_ref_list, QUERY::query_spec::gb_main, QUERY::query_spec::gb_ref, GB_USERFLAG_QUERY, QUERY::query_spec::get_queried_itemtype(), AW_window::get_root(), GLOBAL_gb_dst, GLOBAL_gb_src, AW_window_simple_menu::init(), AW_window::insert_menu_topic(), AW_window::insert_option(), QUERY::query_spec::key_pos_fig, AW_window::load_xfig(), makeHelpCallback(), MG_create_preserves_selection_window(), MG_expect_renamed(), MG_gene_species_create_field_transfer_def_window(), mg_initialize_species_selectors(), MG_map_species(), MG_transfer_species(), NULp, QUERY::query_spec::open_parser_pos_fig, QUERY::query_spec::qbox_pos_fig, QUERY::query_spec::query_pos_fig, QUERY::query_spec::result_pos_fig, QUERY::query_spec::select_bit, AW_window::sens_mask(), AW_window::sep______________(), ScopedTransporter::set_query_to_update(), AW_window::shadow_width(), QUERY::query_spec::species_name, SRC_DB, SXS_LISTED_SPECIES, SXS_SELECTED_SPECIES, SXT_SINGLE_FIELD, SXT_USING_FTS, SXT_USING_FTS_SKIP_ALI, SXT_WHOLE_SPECIES, QUERY::query_spec::tree_name, AW_window::update_option_menu(), QUERY::query_spec::use_menu, AW_awar::write_int(), and XFER_select_RuleSet().
Referenced by MERGE_create_main_window().
Definition at line 398 of file MG_preserves.cxx.
References AW_awar::add_callback(), add_selected_cb(), preserve_para::alignmentList, AW_POPDOWN(), AW_root::awar(), awar_list, AWAR_REMAP_ALIGNMENT, AWAR_REMAP_CANDIDATE, AWAR_REMAP_ENABLE, AWAR_REMAP_SEL_REFERENCE, AWAR_REMAP_SPECIES_LIST, calculate_preserves_cb(), clear_candidates(), clear_references_cb(), del_reference_cb(), GLOBAL_gb_dst, GLOBAL_gb_src, init_alignments(), init_preserve_awars(), lower_reference_cb(), makeHelpCallback(), raise_reference_cb(), preserve_para::refCandidatesList, refresh_reference_list_cb(), test_references_cb(), AW_awar::touch(), and preserve_para::usedRefsList.
Referenced by MG_create_merge_species_window().
Definition at line 163 of file MG_extendeds.cxx.
References AW_POPDOWN(), AWAR_EX_NAME_DST, AWAR_EX_NAME_SRC, awt_create_SAI_selection_list(), DbScanner::create(), DB_SCANNER, DST_DB, extended_rename_cb(), GLOBAL_gb_dst, GLOBAL_gb_src, makeHelpCallback(), map_extended(), MG_extended_delete_cb(), mg_initialize_SAI_selectors(), MG_transfer_extended(), NULp, and SRC_DB.
Referenced by MERGE_create_main_window().
Definition at line 207 of file MG_trees.cxx.
References aw_message(), AW_POPDOWN(), AWAR_TREE_NAME_DST, AWAR_TREE_NAME_SRC, AWAR_TREE_OVERWRITE, AWAR_TREE_XFER_WHAT, awt_create_TREE_selection_list(), TreeAdmin::create_rename_window(), TreeAdmin::delete_tree_cb(), error(), GLOBAL_gb_dst, GLOBAL_gb_src, makeHelpCallback(), MG_expect_renamed(), MG_transfer_tree(), NULp, XFER_ALL, XFER_EXISTING, XFER_MISSING, and XFER_SELECTED.
Referenced by MERGE_create_main_window().
Definition at line 122 of file MG_configs.cxx.
References aw_message(), AW_POPDOWN(), AWAR_CONFIG_NAME_DST, AWAR_CONFIG_NAME_SRC, awt_create_CONFIG_selection_list(), config_rename_cb(), DST_DB, error(), GLOBAL_gb_dst, GLOBAL_gb_src, makeHelpCallback(), MG_config_delete_cb(), MG_expect_renamed(), MG_transfer_config(), NULp, and SRC_DB.
Referenced by MERGE_create_main_window().
Definition at line 330 of file MG_checkfield.cxx.
References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_COMPARE_FIELD, AWAR_CORRECT, AWAR_ETAG, AWAR_EXCLUDE, AW_root::awar_int(), AWAR_REPORT_FIELD, AW_root::awar_string(), AWAR_TOUPPER, create_itemfield_selection_button(), FIELD_FILTER_STRING_READABLE, FIELD_FILTER_STRING_WRITEABLE, GLOBAL_gb_dst, makeHelpCallback(), mg_check_field_cb(), NO_FIELD_SELECTED, SF_ALLOW_NEW, and SPECIES_get_selector().
Referenced by MG_create_merge_species_window().
| void MG_create_config_awar | ( | AW_root * | aw_root, |
| AW_default | aw_def | ||
| ) |
Definition at line 31 of file MG_configs.cxx.
References AWAR_CONFIG_NAME_DST, AWAR_CONFIG_NAME_SRC, and AW_root::awar_string().
Referenced by MERGE_create_all_awars().
| void MG_create_trees_awar | ( | AW_root * | aw_root, |
| AW_default | aw_def | ||
| ) |
Definition at line 33 of file MG_trees.cxx.
References AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE_NAME_DST, AWAR_TREE_NAME_SRC, AWAR_TREE_OVERWRITE, AWAR_TREE_XFER_WHAT, TreeAdmin::create_awars(), NO_TREE_SELECTED, and XFER_SELECTED.
Referenced by MERGE_create_all_awars().
| void MG_create_extendeds_awars | ( | AW_root * | aw_root, |
| AW_default | aw_def | ||
| ) |
Definition at line 24 of file MG_extendeds.cxx.
References AWAR_EX_NAME_DST, AWAR_EX_NAME_SRC, and AW_root::awar_string().
Referenced by MERGE_create_all_awars().
| void MG_create_species_awars | ( | AW_root * | aw_root, |
| AW_default | aw_def | ||
| ) |
Definition at line 65 of file MG_species.cxx.
References AWAR_APPEND, AWAR_FIELD_DST, AWAR_FIELD_SRC, AW_root::awar_int(), AWAR_SPECIES_DST, AWAR_SPECIES_SRC, AWAR_SPECIES_XFER_FTS, AWAR_SPECIES_XFER_SCOPE, AWAR_SPECIES_XFER_TYPE, AW_root::awar_string(), NO_FIELD_SELECTED, SXS_LISTED_SPECIES, and SXT_WHOLE_SPECIES.
Referenced by MERGE_create_all_awars().
| void MG_create_rename_awars | ( | AW_root * | aw_root, |
| AW_default | aw_def | ||
| ) |
Definition at line 32 of file MG_names.cxx.
References AWAR_ADDID_MATCH, AWAR_ALLOW_DUPS, AW_root::awar_int(), AWAR_OVERRIDE, AWAR_RENAME_STATUS, and AW_root::awar_string().
Referenced by MERGE_create_all_awars().
Definition at line 58 of file MG_names.cxx.
References AW_awar::add_callback(), addids_match_info_refresh_cb(), aw_message(), AWAR_ADDID_DST, AWAR_ADDID_SRC, AWAR_NAMESERVER_ADDID, AW_root::awar_string(), GB_transaction::close(), error(), GB_await_error(), GB_create(), GB_read_char_pntr(), GB_search(), GB_STRING, GB_write_string(), AW_awar::map(), NULp, and AW_awar::unmap().
Referenced by MG_create_db_dependent_awars().
Definition at line 114 of file MG_names.cxx.
References AW_root::awar(), AWAR_RENAME_STATUS, was_renamed, and AW_awar::write_string().
Referenced by addids_match_info_refresh_cb(), MERGE_create_main_window(), override_toggle_cb(), and rename_both_databases().
| GB_ERROR MG_expect_renamed | ( | ) |
Definition at line 119 of file MG_names.cxx.
References error(), NULp, and was_renamed.
Referenced by MG_create_merge_configs_window(), MG_create_merge_species_window(), and MG_create_merge_trees_window().
| int MG_copy_and_check_alignments | ( | ) |
Definition at line 25 of file MG_alignment.cxx.
References aw_message(), error(), GB_await_error(), GB_begin_transaction(), GB_clear_error(), GB_copy_dropProtectMarksAndTempstate(), GB_create_container(), GB_end_transaction(), GBS_global_string(), GBT_add_alignment_changekeys(), GBT_get_alignment(), GBT_get_alignment_names(), GBT_get_alignment_type_string(), GBT_get_presets(), GLOBAL_gb_dst, GLOBAL_gb_src, mg_assert, names, and NULp.
Referenced by copy_and_check_alignments_ignoreResult(), mg_transfer_listed_species(), mg_transfer_selected_species(), mg_xfer_via_fts(), transfer_field_of_listed_cb(), and transfer_field_of_selected_cb().
| 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().
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().
| 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().
Definition at line 179 of file MG_checkfield.cxx.
References GBT_first_species(), GBT_next_species(), and IS_QUERIED_SPECIES.
Referenced by mg_check_field_cb(), MG_merge_tagged_field_cb(), mg_transfer_listed_species(), transfer_field_of_listed_cb(), and ScopedTransporter::transferAllIn().
| const char* MG_left_AWAR_SPECIES_NAME | ( | ) |
Definition at line 63 of file MG_species.cxx.
References AWAR_SPECIES_SRC.
Referenced by MG_gene_species_create_field_transfer_def_window(), and MG_update_example().
Definition at line 88 of file merge.hxx.
References GLOBAL_gb_dst, GLOBAL_gb_src, mg_assert, SRC_DB, and validDb().
Referenced by AWT_initTreeAwarRegistry(), bindAdmin(), PH_filter::calculate_column_homology(), config_rename_handler(), awt_string_handler::db_changed(), PH_display::display(), extended_rename_handler(), AWT_tree_selection::fill(), awt_input_handler::link_to(), map_extended(), MG_config_delete_cb(), MG_extended_delete_cb(), MG_map_species(), and AP_tree::relink().
