ARB
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#include <attributes.h>
#include <aw_base.hxx>
#include <arbdb_base.h>
Go to the source code of this file.
void AP_create_consensus_var | ( | AW_root * | aw_root, |
AW_default | aw_def | ||
) |
Definition at line 248 of file AP_consensus.cxx.
References AW_awar::add_callback(), ARB_strdup(), AWAR_CONSENSUS_ALIGNMENT, AWAR_CONSENSUS_CONSIDBOUND, AWAR_CONSENSUS_COUNTGAPS, AWAR_CONSENSUS_GAPBOUND, AWAR_CONSENSUS_GROUP, AWAR_CONSENSUS_LOWER, AWAR_CONSENSUS_MARKED_ONLY, AWAR_CONSENSUS_NAME, AWAR_CONSENSUS_UPPER, AW_root::awar_int(), AWAR_MAX_FREQ_IGNORE_GAPS, AWAR_MAX_FREQ_SAI_NAME, AW_root::awar_string(), consensus_upper_lower_changed_cb(), GB_clear_error(), NT_global::gb_main, GBT_get_default_alignment(), GLOBAL, AW_awar::set_minmax(), and ta.
Referenced by nt_create_all_awars().
Definition at line 289 of file AP_consensus.cxx.
References AW_POPDOWN(), AW_ROOT_DEFAULT, AW_SCALER_LINEAR, AWAR_CONSENSUS_ALIGNMENT, AWAR_CONSENSUS_CONSIDBOUND, AWAR_CONSENSUS_COUNTGAPS, AWAR_CONSENSUS_GAPBOUND, AWAR_CONSENSUS_GROUP, AWAR_CONSENSUS_LOWER, AWAR_CONSENSUS_MARKED_ONLY, AWAR_CONSENSUS_NAME, AWAR_CONSENSUS_UPPER, awt_create_ALI_selection_list(), AWT_create_IUPAC_info_window(), awt_create_SAI_selection_list(), AWT_insert_config_manager(), CON_calculate_cb(), CONSENSUS_CONFIG_ID, NT_global::gb_main, GLOBAL, AW_window::load_xfig(), and makeHelpCallback().
Referenced by popup_new_main_window().
Definition at line 468 of file AP_consensus.cxx.
References AW_POPDOWN(), AWAR_MAX_FREQ_IGNORE_GAPS, AWAR_MAX_FREQ_SAI_NAME, awt_create_SAI_selection_list(), CON_calc_max_freq_cb(), NT_global::gb_main, GB_pop_transaction(), GB_push_transaction(), GLOBAL, AW_window::load_xfig(), and makeHelpCallback().
Referenced by popup_new_main_window().
Definition at line 48 of file AP_pos_var_pars.cxx.
References AP_calc_pos_var_pars(), AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_PVP_SAI, AWAR_PVP_TREE, AW_root::awar_string(), awt_create_SAI_selection_list(), awt_create_TREE_selection_list(), AWT_registerTreeAwarSimple(), NT_global::gb_main, GBT_name_of_largest_tree(), GLOBAL, makeHelpCallback(), NO_TREE_SELECTED, ta, and AW_awar::write_string().
Referenced by popup_new_main_window().
Definition at line 588 of file ColumnStat_2_gnuplot.cxx.
References AW_awar::add_callback(), AW_create_fileselection_awars(), AW_create_standard_fileselection(), AW_HORIZONTAL, AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_CS2GP, AWAR_CS2GP_FILTER_NAME, AWAR_CS2GP_GNUPLOT_OVERLAY_POSTFIX, AWAR_CS2GP_GNUPLOT_OVERLAY_PREFIX, AWAR_CS2GP_NAME, AWAR_CS2GP_SMOOTH_GNUPLOT, AWAR_CS2GP_SMOOTH_VALUES, AWAR_CS2GP_SUFFIX, AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AW_root::awar_string(), awt_create_filter_awars(), awt_create_select_filter(), awt_create_select_filter_win(), colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), COLSTAT_create_selection_list(), adfiltercbstruct::def_alignment, NT_global::gb_main, GLOBAL, AW_selection_list::insert(), AW_selection_list::insert_default(), makeHelpCallback(), PLOT, PLOT_AND_VIEW, PLOT_CLEANUP, PT_PLOT_TYPES, ta, AW_awar::touch(), and AW_selection_list::update().
Referenced by popup_new_main_window().
AW_window* NT_create_branch_analysis_window | ( | AW_root * | aw_root, |
TREE_canvas * | ntw | ||
) |
Definition at line 307 of file NT_branchAnalysis.cxx.
References TREE_canvas::get_index(), BranchWindow::get_window(), and nt_assert.
Referenced by popup_new_main_window().
void NT_delete_mark_all_cb | ( | AW_window * | , |
TREE_canvas * | ntw | ||
) |
Definition at line 31 of file NT_cb.cxx.
References aw_ask_sure(), aw_message(), GB_transaction::close(), error(), GB_delete(), AWT_canvas::gb_main, GBT_first_marked_species(), GBT_next_marked_species(), NULp, AWT_canvas::request_refresh(), and ta.
Referenced by popup_new_main_window().
Definition at line 60 of file NT_cb.cxx.
References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), awt_auto_popdown_cb(), awt_create_TREE_selection_list(), NT_global::gb_main, GBS_global_string(), GLOBAL, nt_assert, and popup_tree_admin_window().
Referenced by popup_new_main_window().
Definition at line 92 of file NT_cb.cxx.
References AW_root::awar(), NT_global::gb_main, GBT_name_of_bottom_tree(), AW_window::get_root(), GLOBAL, ta, and AW_awar::write_string().
Referenced by popup_new_main_window().
void NT_create_alignment_vars | ( | AW_root * | aw_root, |
AW_default | aw_def, | ||
GBDATA * | gb_main | ||
) |
Definition at line 98 of file NT_cb.cxx.
References AWAR_DEFAULT_ALIGNMENT, AW_root::awar_string(), GB_DEFAULT_ALIGNMENT, GB_search(), GB_STRING, AW_awar::map(), and ta.
Referenced by nt_create_all_awars().
Definition at line 109 of file NT_cb.cxx.
References ALI_create_admin_window(), AWAR_DEFAULT_ALIGNMENT, NT_global::gb_main, GLOBAL, AW_window::hide(), MAIN_ADMIN, and NULp.
Referenced by NT_create_select_alignment_window(), and popup_new_main_window().
Definition at line 119 of file NT_cb.cxx.
References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_DEFAULT_ALIGNMENT, awt_auto_popdown_cb(), awt_create_ALI_selection_list(), NT_global::gb_main, GLOBAL, NT_create_alignment_admin_window(), and NULp.
Referenced by popup_new_main_window().
void NT_createConcatenationAwars | ( | AW_root * | aw_root, |
AW_default | aw_def, | ||
GBDATA * | gb_main | ||
) |
Definition at line 52 of file NT_concatenate.cxx.
References ARB_strdup(), aw_message(), AWAR_CON_ALIGNMENT_SEPARATOR, AWAR_CON_ALLOW_OVERWRITE_ALI, AWAR_CON_INSGAPS_FOR_MISS_ALIS, AWAR_CON_MERGE_FIELD, AWAR_CON_NEW_ALIGNMENT_NAME, AWAR_CON_SELECTED_ALI, AWAR_CON_SEQUENCE_TYPE, AWAR_CON_STORE_SIM_SP_NO, AW_root::awar_int(), AW_root::awar_string(), GB_await_error(), GB_clear_error(), GBS_global_string(), GBT_get_alignment_type_string(), GBT_get_default_alignment(), NULp, AW_awar::set_srt(), SRT_AUTOCORRECT_ALINAME, and ta.
Referenced by nt_create_all_awars().
Definition at line 753 of file NT_concatenate.cxx.
References createMergeSimilarSpeciesWindow(), MERGE_SPECIES_SIMPLE, and NULp.
Referenced by NT_createConcatenationWindow(), and popup_new_main_window().
Definition at line 789 of file NT_concatenate.cxx.
References AW_awar::add_callback(), alitype_changed_cb(), AW_POPDOWN(), AW_root::awar(), AWAR_CON_ALIGNMENT_SEPARATOR, AWAR_CON_ALLOW_OVERWRITE_ALI, AWAR_CON_INSGAPS_FOR_MISS_ALIS, AWAR_CON_NEW_ALIGNMENT_NAME, AWAR_CON_SELECTED_ALI, AWAR_CON_SEQUENCE_TYPE, awt_create_subset_selection_list(), concatenateAlignments(), createSelectionList(), NT_global::gb_main, AW_selection::get_sellist(), GLOBAL, AW_window::load_xfig(), makeHelpCallback(), NT_createMergeSimilarSpeciesAndConcatenateWindow(), NT_createMergeSimilarSpeciesWindow(), and useSelectedAlignment().
Referenced by popup_new_main_window().
Definition at line 1015 of file NT_dbrepair.cxx.
References GEN_is_genome_db(), NT_convert_gene_locations(), NT_del_mark_move_REF(), NT_fix_dict_compress(), NT_fix_gene_data(), NULp, CheckedConsistencies::perform_check(), CheckedConsistencies::perform_item_checks(), CheckedConsistencies::register_item_check(), remove_dup_colors(), and ta.
Referenced by nt_check_database_consistency(), and NT_rerepair_DB().
Definition at line 1040 of file NT_dbrepair.cxx.
References aw_message(), CheckedConsistencies::forgetDoneChecks(), NT_repair_DB(), and NULp.
Referenced by popup_new_main_window().
void NT_activate_configMarkers_display | ( | TREE_canvas * | ntw | ) |
Definition at line 254 of file NT_edconf.cxx.
References AW_awar::add_callback(), AWAR_CL_DISPLAY_CONFIG_MARKERS, AWAR_CL_SELECTED_CONFIGS, AW_root::awar_int(), AW_root::awar_string(), AWT_canvas::awr, gb_main, AWT_canvas::gb_main, GBS_global_string(), TREE_canvas::get_index(), install_config_change_callbacks(), selected_configs_awar_changed_cb(), selected_configs_display_awar_changed_cb(), and AW_awar::touch().
Referenced by popup_new_main_window().
void NT_popup_configuration_admin | ( | AW_window * | aw_main, |
TREE_canvas * | ntw | ||
) |
Definition at line 1253 of file NT_edconf.cxx.
References create_configuration_admin_window(), and AW_window::get_root().
Referenced by popup_new_main_window().
Definition at line 1271 of file NT_edconf.cxx.
References AW_POPDOWN(), AWAR_CONFIGURATION, awt_create_CONFIG_selection_list(), NT_global::gb_main, GLOBAL, init_config_awars(), nt_start_editor_on_configuration(), and NULp.
Referenced by popup_new_main_window().
void NT_start_editor_on_tree | ( | AW_window * | aww, |
int | use_species_aside, | ||
TREE_canvas * | ntw | ||
) |
Definition at line 1294 of file NT_edconf.cxx.
References aw_message_if(), BY_CALLING_THE_EDITOR, DEFAULT_CONFIGURATION, error(), GBK_system(), AW_window::get_root(), init_config_awars(), nt_create_configuration(), and NT_get_tree_root_of_canvas().
Referenced by popup_new_main_window().
void NT_create_config_after_import | ( | TREE_canvas * | ntw, |
bool | imported_from_scratch | ||
) |
create a new config after import
imported_from_scratch | if true -> DB was created from scratch, all species in DB are marked. if false -> data was imported into existing DB. Other species may be marked as well, imported species are "queried". |
Definition at line 1322 of file NT_edconf.cxx.
References GB_clear_user_flag(), AWT_canvas::gb_main, GB_read_flag(), GB_user_flag(), GB_USERFLAG_QUERY, GB_USERFLAG_WASMARKED, GB_write_flag(), GB_write_user_flag(), GBT_first_species(), GBT_next_species(), nt_create_config_after_import(), and ta.
Referenced by nt_seq_load_cb(), and start_main_window_after_import().
void NT_start | ( | const char * | arb_ntree_args, |
bool | restart_with_new_ARB_PID | ||
) |
Definition at line 397 of file NT_extern.cxx.
References command, GBS_global_string_copy(), and nt_run().
Referenced by exit_from_merge(), NT_restart(), and nt_start_2nd_arb().
Definition at line 410 of file NT_extern.cxx.
References AWTI_cleanup_importer(), NT_global::gb_main, GB_read_clients(), AW_window::get_root(), GLOBAL, nt_disconnect_from_db(), really_exit(), and shutdown_macro_recording().
Referenced by nt_create_intro_window(), and popup_new_main_window().
Definition at line 419 of file NT_extern.cxx.
References EXIT_SUCCESS, NT_global::gb_main, GB_read_clients(), GLOBAL, nt_disconnect_from_db(), NT_start(), and really_exit().
Referenced by exit_from_merge(), nt_intro_start_merge(), and nt_start_2nd_arb().
TreeNode* NT_get_tree_root_of_canvas | ( | TREE_canvas * | ntw | ) |
Definition at line 858 of file NT_extern.cxx.
References AWT_TREE, AWT_graphic_tree::get_root_node(), and NULp.
Referenced by nt_create_config_after_import(), NT_resort_data_by_phylogeny(), NT_start_editor_on_tree(), and nt_store_configuration().
TREE_canvas* NT_get_canvas_by_index | ( | int | idx | ) |
return canvas with index 'idx' [0...MAX_NT_WINDOWS-1]
Definition at line 978 of file NT_extern.cxx.
References TREE_canvas_registry::get_canvas(), TREE_canvas_registry::instance(), MAX_NT_WINDOWS, and nt_assert.
Referenced by CanvasRef::get_canvas(), NT_get_canvas_showing_tree(), and sync_changed_cb().
void NT_fill_canvas_selection_list | ( | class AW_selection_list * | sellst, |
TREE_canvas * | to_skip | ||
) |
insert canvases into selection list (using canvas-indices as values)
Definition at line 999 of file NT_extern.cxx.
References GBS_global_string(), TREE_canvas::get_awar_tree(), TREE_canvas_registry::get_canvas(), TREE_canvas_registry::get_count(), AW_selection_list::insert(), TREE_canvas_registry::instance(), nt_assert, and AW_awar::read_char_pntr().
Referenced by refill_syncWithList_cb().
void NT_deselect_group | ( | AW_root * | awr | ) |
Definition at line 1021 of file NT_extern.cxx.
References AW_root::awar(), AWAR_GROUP, NULp, and AW_awar::write_pointer().
Referenced by ad_move_tree_info().
TREE_canvas* NT_create_main_window | ( | AW_root * | aw_root | ) |
Definition at line 1856 of file NT_extern.cxx.
References aw_message(), error(), NT_global::gb_main, GB_request_undo_type(), GB_UNDO_NONE, GB_UNDO_UNDO, GLOBAL, nt_create_all_awars(), NT_install_treeShader(), NULp, popup_new_main_window(), and AW_window::show().
Referenced by startup_mainwindow_and_dbserver().
TREE_canvas* NT_get_canvas_showing_tree | ( | const char * | tree_name, |
bool | forceDisplay | ||
) |
Definition at line 369 of file NT_group_search.cxx.
References AW_window::activate(), AWT_canvas::aww, TREE_canvas::get_awar_tree(), AWT_canvas::is_shown(), MAX_NT_WINDOWS, nt_assert, NT_get_canvas_by_index(), NULp, AW_awar::read_char_pntr(), and AW_awar::write_string().
Referenced by ad_move_tree_info(), and get_canvas_able_to_show().
void NT_import_sequences | ( | AW_window * | aww, |
TREE_canvas * | ntw | ||
) |
Opens the "Import Sequences" dialog from the ARB main window (ARB_NTREE)
Definition at line 48 of file NT_import.cxx.
References aw_message(), AW_root::awar(), AWAR_IMPORT_GENOM_DB, AWTI_import_set_ali_and_type(), AWTI_open_import_window(), AWTI_set_importDB_pointer(), GB_await_error(), NT_global::gb_main, GBT_get_alignment_type_string(), GBT_get_default_alignment(), GEN_is_genome_db(), AW_window::get_root(), GLOBAL, GLOBAL_gb_src, got_macro_ability(), IF_ASSERTION_USED, IMP_GENOME_FLATFILE, IMP_PLAIN_SEQUENCE, nt_assert, nt_seq_load_cb(), NULp, ta, and AW_awar::write_int().
Referenced by popup_new_main_window().
Definition at line 143 of file NT_join.cxx.
References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_SPECIES_JOIN_FIELD, AWAR_SPECIES_JOIN_SEP, AWAR_SPECIES_JOIN_SEP2, AW_root::awar_string(), create_itemfield_selection_button(), FIELD_FILTER_STRING_READABLE, NT_global::gb_main, GLOBAL, makeHelpCallback(), NULp, SPECIES_get_selector(), and species_rename_join().
Referenced by popup_new_main_window().
Definition at line 54 of file NT_main.cxx.
References ARB_format_alignment(), GB_transaction::close(), arb_progress::done(), GB_entry(), GB_INT, GB_nextEntry(), GB_read_char_pntr(), GB_read_int(), GB_search(), GB_write_int(), GBS_global_string_copy(), GBT_check_data(), GBT_count_alignments(), GBT_get_presets(), GBT_write_int(), GENOM_ALIGNMENT, arb_progress::inc_and_check_user_abort(), NULp, and ta.
Referenced by nt_check_database_consistency(), and nt_seq_load_cb().
void NT_install_treeShader | ( | TREE_canvas * | ntw, |
GBDATA * | gb_main | ||
) |
Definition at line 145 of file NT_shadeTree.cxx.
References AP_tree::set_tree_shader().
Referenced by NT_create_main_window().
void NT_configure_treeShader | ( | void | ) |
Definition at line 149 of file NT_shadeTree.cxx.
References DOWNCAST, AP_tree::get_tree_shader(), and nt_assert.
Referenced by popup_new_main_window().
void NT_resort_data_by_phylogeny | ( | AW_window * | , |
TREE_canvas * | ntw | ||
) |
Definition at line 167 of file NT_sort.cxx.
References aw_message(), error(), NT_global::gb_main, GLOBAL, NT_get_tree_root_of_canvas(), NULp, and resort_data_base().
Referenced by popup_new_main_window().
void NT_create_resort_awars | ( | AW_root * | awr, |
AW_default | aw_def | ||
) |
Definition at line 199 of file NT_sort.cxx.
References AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE_REV1, AWAR_TREE_REV2, AWAR_TREE_REV3, AWAR_TREE_SORT1, AWAR_TREE_SORT2, AWAR_TREE_SORT3, and NO_FIELD_SELECTED.
Referenced by nt_create_all_awars().
Definition at line 209 of file NT_sort.cxx.
References AW_POPDOWN(), AWAR_TREE_REV1, AWAR_TREE_REV2, AWAR_TREE_REV3, AWAR_TREE_SORT1, AWAR_TREE_SORT2, AWAR_TREE_SORT3, create_itemfield_selection_button(), FIELD_FILTER_RESORT, NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), NT_resort_data_by_user_criteria(), and SPECIES_get_selector().
Referenced by popup_new_main_window().
Definition at line 549 of file NT_split_ali.cxx.
References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_RANGE, AWAR_SPLIT_ALI_MARKED, AWAR_SPLIT_ALI_OVERWRITE, AWAR_SPLIT_ALI_POSITIONS, AWAR_SPLIT_ALI_TARGET, create_splitAlignment_awars(), NT_global::gb_main, GLOBAL, makeHelpCallback(), NULp, split_ali_cb(), and use_editor_range_cb().
Referenced by popup_new_main_window().
AW_window* NT_create_syncScroll_window | ( | AW_root * | awr, |
TREE_canvas * | ntw | ||
) |
Definition at line 89 of file NT_sync_scroll.cxx.
References AW_awar::add_callback(), AW_POPDOWN(), AW_ROOT_DEFAULT, AW_root::awar(), AW_root::awar_int(), AW_awar::awar_name, AWAR_NTREE_MAIN_WINDOW_COUNT, AWAR_TEMPL_AUTO_SYNCED, AWAR_TEMPL_SYNCED_WITH_WINDOW, awarname(), explicit_scroll_sync_cb(), GBS_global_string(), GBS_global_string_copy(), TREE_canvas::get_index(), makeHelpCallback(), NO_SCROLL_SYNC, nt_assert, refill_syncWithList_cb(), and sync_changed_cb().
Referenced by popup_new_main_window().
Definition at line 220 of file NT_syncroot.cxx.
References AW_POPDOWN(), AWAR_TREE_SYNCROOT_SELECTED, awt_create_subset_selection_list(), awt_create_TREE_selection_list(), create_syncroot_awars(), AW_selection::get_sellist(), makeHelpCallback(), multiroot_sync_subsetTrees(), NULp, and rootsync_subsetTrees_vs_selected().
Referenced by popup_new_main_window().
void NT_create_compare_taxonomy_awars | ( | AW_root * | aw_root, |
AW_default | props | ||
) |
Definition at line 335 of file NT_taxonomy.cxx.
References AW_root::awar(), AW_root::awar_int(), AW_root::awar_string(), AWAR_TREE_COMPARE_ACTION, AWAR_TREE_COMPARE_MIN_TAX_LEVELS, AWAR_TREE_COMPARE_WRITE_FIELD, AWAR_TREE_NAME, MARK, NO_FIELD_SELECTED, and AW_awar::read_string().
Referenced by nt_create_all_awars().
AW_window* NT_create_compare_taxonomy_window | ( | AW_root * | aw_root, |
TREE_canvas * | ntw | ||
) |
Definition at line 345 of file NT_taxonomy.cxx.
References ALL, AW_POPDOWN(), AWAR_TREE_COMPARE_ACTION, AWAR_TREE_COMPARE_MIN_TAX_LEVELS, AWAR_TREE_COMPARE_WRITE_FIELD, COMMON, create_itemfield_selection_button(), FIELD_FILTER_INT_WRITEABLE, AWT_canvas::gb_main, INVERT, AW_window::load_xfig(), makeHelpCallback(), MARK, mark_action(), MISSING_LEFT, MISSING_RIGHT, NT_create_twoTreeSelection(), SF_ALLOW_NEW, SPECIES_get_selector(), TAX, and UNMARK.
Referenced by popup_new_main_window().
void NT_create_trackAliChanges_Awars | ( | AW_root * | root, |
AW_default | properties | ||
) |
Definition at line 152 of file NT_trackAliChanges.cxx.
References AW_root::awar_string(), AWAR_TRACK_ALI, AWAR_TRACK_INITIALS, GB_getenvUSER(), NT_global::gb_main, and GLOBAL.
Referenced by nt_create_all_awars().
Definition at line 157 of file NT_trackAliChanges.cxx.
References AW_POPDOWN(), AWAR_TRACK_ALI, AWAR_TRACK_INITIALS, awt_create_ALI_selection_list(), NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), and trackAlignmentChanges().
Referenced by popup_new_main_window().
void NT_repair_userland_problems | ( | void | ) |
Definition at line 54 of file NT_userland_fixes.cxx.
References UserlandCheck::Run().
Referenced by startup_mainwindow_and_dbserver().
void NT_createValidNamesAwars | ( | AW_root * | aw_root, |
AW_default | aw_def | ||
) |
Definition at line 36 of file NT_validManual.cxx.
References AWAR_INPUT_INITIALS, AWAR_SELECTED_VALNAME, and AW_root::awar_string().
Referenced by nt_create_all_awars().
Definition at line 154 of file NT_validManual.cxx.
References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_INPUT_INITIALS, AWAR_SELECTED_VALNAME, createValNameList(), NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), selectValidNameFromList(), and updateValNameList().
Referenced by popup_new_main_window().
void NT_deleteValidNames | ( | AW_window * | ) |
Definition at line 28 of file NT_validNames.cxx.
References aw_message(), error(), GB_begin_transaction(), GB_commit_transaction(), GB_CREATE_CONTAINER, GB_delete(), NT_global::gb_main, GB_search(), GB_write_security_delete(), and GLOBAL.
Referenced by popup_new_main_window().
void NT_importValidNames | ( | AW_window * | ) |
Definition at line 49 of file NT_validNames.cxx.
References aw_message(), validNames::determineType(), error(), GB_await_error(), GB_begin_transaction(), GB_create_container(), GB_end_transaction(), GB_entry(), NT_global::gb_main, GB_path_in_ARBLIB(), GBT_write_string(), GLOBAL, nt_assert, NULp, and string().
Referenced by popup_new_main_window().
void NT_suggestValidNames | ( | AW_window * | ) |
Definition at line 162 of file NT_validNames.cxx.
References aw_message(), GB_await_error(), GB_begin_transaction(), GB_CREATE_CONTAINER, GB_end_transaction_show_error(), GB_entry(), NT_global::gb_main, GB_nextEntry(), GB_read_string(), GB_search(), GBT_first_species(), GBT_next_species(), GBT_read_string(), GBT_write_string(), GLOBAL, nt_assert, and NULp.
Referenced by popup_new_main_window().
void NT_create_extendeds_vars | ( | AW_root * | aw_root, |
AW_default | aw_def, | ||
GBDATA * | gb_main | ||
) |
Definition at line 286 of file ad_ext.cxx.
References AW_awar::add_callback(), AW_root::awar(), AW_root::awar_int(), AWAR_SAI_GROUP, AWAR_SAI_NAME, AWAR_SAI_REFRESH_GROUPS, AW_root::awar_string(), get_SAI_group(), AW_awar::read_char_pntr(), refresh_group_cb(), refresh_SAI_groups_cb(), and set_SAI_group_cb().
Referenced by nt_create_all_awars().
Definition at line 318 of file ad_ext.cxx.
References AW_POPDOWN(), AWAR_SAI_NAME, AWAR_TOPAREA_SAIS, awt_create_SAI_selection_list(), copy_SAI_cb(), copy_SAI_to_species_cb(), DbScanner::create(), create_SAI_group_window(), DB_SCANNER, delete_SAI_cb(), edit_SAI_description(), NT_global::gb_main, GLOBAL, makeHelpCallback(), map_SAI_to_scanner(), NULp, rename_SAI_cb(), and SAI_get_selector().
Referenced by NT_create_sai_from_pfold(), and popup_new_main_window().
Definition at line 30 of file ad_spec.cxx.
References alignment_name, aw_message(), error(), GB_await_error(), GB_begin_transaction(), GB_end_transaction_show_error(), GB_entry(), GB_read_char_pntr(), GB_STRING, GB_write_string(), GBT_add_data(), GBT_count_marked_species(), GBT_find_or_create_SAI(), GBT_first_marked_species(), GBT_get_alignment_len(), GBT_get_default_alignment(), GBT_is_alignment_protein(), GBT_next_marked_species(), arb_progress::inc_and_check_user_abort(), result, and seq.
Referenced by popup_new_main_window().
void NT_create_sai_from_pfold | ( | AW_window * | aww | ) |
Creates an SAI from protein secondary structure of a selected species.
[in] | aww | AW_window |
The function takes the currently selected species and searches for the field "sec_struct". A new SAI is created using the data in this field. A simple input window allows the user to change the default name ([species name]_pfold) for the new SAI.
Definition at line 127 of file ad_spec.cxx.
References AW_window::activate(), aw_input(), aw_message(), AW_root::awar(), AWAR_SAI_NAME, AWAR_SPECIES_NAME, error(), GB_await_error(), GB_begin_transaction(), GB_child(), GB_copy_dropProtectMarksAndTempstate(), GB_CREATE_CONTAINER, GB_create_container(), GB_delete(), GB_end_transaction_show_error(), GB_entry(), GB_FIND, NT_global::gb_main, GB_nextChild(), GB_read_key(), GB_read_string(), GB_read_type(), GB_search(), GB_write_string(), GBS_global_string_copy(), GBT_find_SAI_rel_SAI_data(), GBT_find_species(), GBT_gen_accession_number(), GBT_get_default_alignment(), GBT_get_SAI_data(), GBT_write_string(), AW_window::get_root(), GLOBAL, NT_create_extendeds_window(), NULp, AW_awar::read_string(), and AW_awar::write_string().
Referenced by popup_new_main_window().
Definition at line 72 of file ad_transpro.cxx.
References AUTODETECT_STARTPOS, AW_POPDOWN(), AWAR_CURSOR_POSITION, AW_root::awar_int(), AWAR_PROTEIN_TYPE, AWAR_PROTEIN_TYPE_bacterial_code_index, AWAR_TRANSPRO_DEST, AWAR_TRANSPRO_MODE, AWAR_TRANSPRO_POS, AWAR_TRANSPRO_SOURCE, AWAR_TRANSPRO_WRITE, AWAR_TRANSPRO_XSTART, AWT_CODON_TABLES, awt_create_ALI_selection_list(), AWT_get_codon_code_name(), bio2info(), NT_global::gb_main, GLOBAL, label, makeHelpCallback(), nt_trans_cursorpos_changed(), ta, and transpro_event().
Referenced by popup_new_main_window().
Definition at line 180 of file ad_transpro.cxx.
References AW_POPDOWN(), AWAR_REALIGN_CUTOFF, AWAR_REALIGN_INCALI, AWAR_REALIGN_UNMARK, AWAR_TRANSPRO_DEST, AWAR_TRANSPRO_SOURCE, awt_create_ALI_selection_button(), awt_create_ALI_selection_list(), NT_global::gb_main, GLOBAL, AW_window::load_xfig(), makeHelpCallback(), and realign_event().
Referenced by popup_new_main_window().
void NT_create_transpro_variables | ( | AW_root * | root, |
AW_default | props | ||
) |
Definition at line 215 of file ad_transpro.cxx.
References AW_root::awar_int(), AWAR_REALIGN_CUTOFF, AWAR_REALIGN_INCALI, AWAR_REALIGN_UNMARK, AW_root::awar_string(), AWAR_TRANSPRO_DEST, AWAR_TRANSPRO_MODE, AWAR_TRANSPRO_POS, AWAR_TRANSPRO_SOURCE, AWAR_TRANSPRO_WRITE, and AWAR_TRANSPRO_XSTART.
Referenced by nt_create_all_awars().
void NT_create_twoTreeSelection | ( | AW_window * | aws | ) |
Definition at line 574 of file ad_trees.cxx.
References AW_window::at(), AW_window::auto_space(), AW_root::awar(), AW_awar::awar_name, AWAR_TREE_NAME, awt_create_TREE_selection_list(), AW_window::callback(), copy_tree_awar_cb(), AW_window::create_autosize_button(), TreeAdmin::dest_tree_awar(), NT_global::gb_main, AW_window::get_root(), GLOBAL, AW_awar::read_char_pntr(), TreeAdmin::source_tree_awar(), swap_source_dest_cb(), and AW_awar::write_string().
Referenced by NT_create_compare_taxonomy_window(), NT_create_compareTopologies_window(), and NT_create_moveGroupInfo_window().
Definition at line 636 of file ad_trees.cxx.
References ad_move_tree_info(), AW_POPDOWN(), AW_window::load_xfig(), makeHelpCallback(), and NT_create_twoTreeSelection().
Referenced by popup_new_main_window().
Definition at line 691 of file ad_trees.cxx.
References ad_move_tree_info(), AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_GROUPXFER_ACI, AWAR_GROUPXFER_INGROUP_ABS, AWAR_GROUPXFER_INGROUP_LIM, AWAR_GROUPXFER_INGROUP_REL, AWAR_GROUPXFER_KEELING, AWAR_GROUPXFER_OUTGROUP_ABS, AWAR_GROUPXFER_OUTGROUP_LIM, AWAR_GROUPXFER_OUTGROUP_REL, AWAR_GROUPXFER_OVERWRITE_MODE, AWAR_GROUPXFER_SOURCE, AWAR_GROUPXFER_UNKNOWN_ABS, AWT_insert_config_manager(), KEEP_OLD_NAMES, AW_window::load_xfig(), makeHelpCallback(), NT_create_twoTreeSelection(), NULp, REMOVE_EXISTING_GROUPS, XFER_ALL_GROUPS, and XFER_GROUPS_WITH_MARKED.
Referenced by popup_new_main_window().
Definition at line 948 of file ad_trees.cxx.
References AW_POPDOWN(), AWAR_TREE_CONSENSE_SELECTED, AWAR_TREE_CONSENSE_TREE, awt_create_subset_selection_list(), awt_create_TREE_selection_list(), create_consense_tree_cb(), NT_global::gb_main, AW_selection::get_sellist(), GLOBAL, makeHelpCallback(), NULp, and use_selected_as_target_cb().
Referenced by popup_new_main_window().
AW_window* NT_create_sort_tree_by_other_tree_window | ( | AW_root * | aw_root, |
TREE_canvas * | ntw | ||
) |
Definition at line 1087 of file ad_trees.cxx.
References AWT_canvas::aww, create_select_other_tree_window(), TREE_canvas::get_awar_tree(), AW_window::local_id(), and sort_tree_by_other_tree_cb().
Referenced by popup_new_main_window().
void NT_create_multifurcate_tree_awars | ( | AW_root * | aw_root, |
AW_default | props | ||
) |
Definition at line 1106 of file ad_trees.cxx.
References AW_root::awar_float(), AW_root::awar_int(), AWAR_MFURC_BOOTSTRAP_LIMIT, AWAR_MFURC_CONSIDER_BOOTSTRAP, AWAR_MFURC_CONSIDER_LENGTH, AWAR_MFURC_CONSIDER_TERMINALS, and AWAR_MFURC_LENGTH_LIMIT.
Referenced by nt_create_all_awars().
AW_window* NT_create_multifurcate_tree_window | ( | AW_root * | aw_root, |
TREE_canvas * | ntw | ||
) |
Definition at line 1125 of file ad_trees.cxx.
References AW_window::at(), AW_POPDOWN(), AWAR_MFURC_BOOTSTRAP_LIMIT, AWAR_MFURC_CONSIDER_BOOTSTRAP, AWAR_MFURC_CONSIDER_LENGTH, AWAR_MFURC_CONSIDER_TERMINALS, AWAR_MFURC_LENGTH_LIMIT, AWT_canvas::aww, AW_window::local_id(), makeHelpCallback(), and multifurcation_cb().
Referenced by popup_new_main_window().