// =============================================================== // // // // File : NT_extern.cxx // // Purpose : // // // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include "map_viewer.h" #include "NT_local.h" #include "ad_trees.h" #include "NT_group_search.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #if defined(DEVEL_RALF) # define TRACE_GROUP_SELECTION #endif #define AWAR_EXPORT_NDS "tmp/export_nds" #define AWAR_EXPORT_NDS_SEPARATOR AWAR_EXPORT_NDS "/delimiter" #define AWAR_MARKED_SPECIES_COUNTER "tmp/disp_marked_species" #define AWAR_NTREE_TITLE_MODE "tmp/title_mode" void create_probe_design_variables(AW_root *aw_root, AW_default def, AW_default global); void create_insertDeleteColumn_variables(AW_root *root, AW_default db1); AW_window *create_insertDeleteColumn_window(AW_root *root); AW_window *create_insertDeleteBySAI_window(AW_root *root, GBDATA *gb_main); AW_window *create_tree_window(AW_root *aw_root, AWT_graphic *awd); enum Export_Type { EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, // format info (using spaces). slow - uses one extra pass for column width detection. EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, // dito, but left aligned EXPORT_TAB_SEPARATED = 2, // format info (using 1 tab per column - for easy import into star-calc, excel, etc. ) EXPORT_COMMA_SEPARATED = 3, // like EXPORT_TAB_SEPARATED, but using commas }; static void nt_changesecurity(AW_root *aw_root) { int level = aw_root->awar(AWAR_SECURITY_LEVEL)->read_int(); GB_push_transaction(GLOBAL.gb_main); GB_change_my_security(GLOBAL.gb_main, level); // changes user security GB_pop_transaction(GLOBAL.gb_main); } static void export_nds_cb(AW_window *aww, bool do_print) { AW_root *aw_root = aww->get_root(); char *name = aw_root->awar(AWAR_EXPORT_NDS"/file_name")->read_string(); FILE *out = fopen(name, "w"); if (!out) { aw_message("Error: Cannot open and write to file"); } else { GB_transaction ta(GLOBAL.gb_main); char *tree_name = aw_root->awar(AWAR_TREE)->read_string(); const Export_Type export_type = (Export_Type)aw_root->awar(AWAR_EXPORT_NDS_SEPARATOR)->read_int(); const NDS_Type nds_type = export_type == EXPORT_COMMA_SEPARATED ? NDS_OUTPUT_COMMA_SEPARATED : NDS_OUTPUT_TAB_SEPARATED; const bool spacePadded = export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED || export_type == EXPORT_SPACE_PADDED_RIGHT_ALIGNED; const int passesNeeded = spacePadded ? 2 : 1; NDS_Labeler labeler(nds_type); arb_progress progress("Exporting data using NDS", passesNeeded*GBT_count_marked_species(GLOBAL.gb_main)); const size_t max_col = std::max(labeler.max_columns(GLOBAL.gb_main), 1L); size_t col_max_len[max_col]; const char *col_format = NULp; if (spacePadded) { for (size_t i = 0; i0); // otherwise empty, unused column (might be ok, but might need different handling) arb_assert(col_max_len[i]<=INT_MAX); // (protect cast below) if (export_type == EXPORT_SPACE_PADDED_LEFT_ALIGNED && i == (col_count-1)) { // left aligned and last column fputs(parts[i], out); } else { fprintf(out, col_format, int(col_max_len[i]), parts[i]); } } fputc('\n', out); } } else { fprintf(out, "%s\n", label); } ++progress; } } AW_refresh_fileselection(aw_root, AWAR_EXPORT_NDS); fclose(out); if (do_print) { GB_ERROR error = GB_textprint(name); if (error) aw_message(error); } free(tree_name); } free(name); } static AW_window *create_nds_export_window(AW_root *root) { AW_window_simple *aws = new AW_window_simple; aws->init(root, "EXPORT_NDS_OF_MARKED", "EXPORT NDS OF MARKED SPECIES"); aws->load_xfig("sel_box_nds.fig"); aws->callback(AW_POPDOWN); aws->at("close"); aws->create_button("CLOSE", "CLOSE", "C"); aws->callback(makeHelpCallback("arb_export_nds.hlp")); aws->at("help"); aws->create_button("HELP", "HELP", "H"); aws->at("save"); aws->callback(makeWindowCallback(export_nds_cb, false)); aws->create_button("SAVE", "SAVE", "S"); aws->at("print"); aws->callback(makeWindowCallback(export_nds_cb, true)); aws->create_button("PRINT", "PRINT", "P"); aws->at("toggle1"); aws->label("Column output"); aws->create_option_menu(AWAR_EXPORT_NDS_SEPARATOR); aws->insert_option ("Space padded (left aligned)", "S", EXPORT_SPACE_PADDED_LEFT_ALIGNED); aws->insert_option ("Space padded (right aligned)", "r", EXPORT_SPACE_PADDED_RIGHT_ALIGNED); aws->insert_default_option("TAB separated", "T", EXPORT_TAB_SEPARATED); aws->insert_option ("Comma separated", "C", EXPORT_COMMA_SEPARATED); aws->update_option_menu(); AW_create_standard_fileselection(aws, AWAR_EXPORT_NDS); return aws; } static void create_export_nds_awars(AW_root *awr, AW_default def) { AW_create_fileselection_awars(awr, AWAR_EXPORT_NDS, "", ".nds", "export.nds"); awr->awar_int(AWAR_EXPORT_NDS_SEPARATOR, EXPORT_TAB_SEPARATED, def); } static void selectedSpeciesChanged_cb(AW_root *awr) { const char *value = awr->awar(AWAR_SPECIES_NAME)->read_char_pntr(); awr->awar(AWAR_INFO_BUTTON_TEXT)->write_string(value[0] ? value : "Species Info"); if (value[0]) { awr->awar(AWAR_GROUP)->write_pointer(NULp); // deselect group when species gets selected #if defined(TRACE_GROUP_SELECTION) fputs("clear AWAR_GROUP (because species selected)\n", stderr); #endif } } static void expert_mode_changed_cb(AW_root *aw_root) { aw_root->awar(AWAR_AWM_MASK)->write_int(aw_root->awar(AWAR_EXPERT)->read_int() ? AWM_ALL : AWM_BASIC); // publish expert-mode globally } static void NT_toggle_expert_mode(AW_window *aww) { aww->get_root()->awar(AWAR_EXPERT)->toggle_toggle(); } static void NT_toggle_focus_policy(AW_window *aww) { aww->get_root()->awar(AWAR_AW_FOCUS_FOLLOWS_MOUSE)->toggle_toggle(); } static void nt_create_all_awars(AW_root *awr) { // creates awars for all modules reachable from ARB_NT main window awr->awar_string(AWAR_FOOTER, "", AW_ROOT_DEFAULT); if (GB_read_clients(GLOBAL.gb_main)>=0) { awr->awar_string(AWAR_TREE, "", GLOBAL.gb_main); } else { awr->awar_string(AWAR_TREE, "", AW_ROOT_DEFAULT); } awr->awar_string(AWAR_TOPAREA_SAIS, "ECOLI;HELIX;HELIX_NR", AW_ROOT_DEFAULT); awr->awar_string(AWAR_SPECIES_NAME, "", GLOBAL.gb_main); awr->awar_string(AWAR_SAI_NAME, "", GLOBAL.gb_main); awr->awar_string(AWAR_SAI_GLOBAL, "", GLOBAL.gb_main); awr->awar_string(AWAR_INFO_BUTTON_TEXT, "Species Info", GLOBAL.gb_main); awr->awar(AWAR_SPECIES_NAME)->add_callback(selectedSpeciesChanged_cb); awr->awar_int(AWAR_NTREE_TITLE_MODE, 1); awr->awar_string(AWAR_SAI_COLOR_STR, "", GLOBAL.gb_main); // sai visualization in probe match GEN_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); EXP_create_awars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); #if defined(DEBUG) AWT_create_db_browser_awars(awr, AW_ROOT_DEFAULT); #endif // DEBUG AW_create_namesadmin_awars(awr, GLOBAL.gb_main); awr->awar_int(AWAR_SECURITY_LEVEL, 0, AW_ROOT_DEFAULT); awr->awar(AWAR_SECURITY_LEVEL)->add_callback(nt_changesecurity); #if defined(DEBUG) && 0 awr->awar(AWAR_SECURITY_LEVEL)->write_int(6); // no security for debugging.. #endif // DEBUG create_insertDeleteColumn_variables(awr, AW_ROOT_DEFAULT); create_probe_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); create_primer_design_variables(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); create_trees_var(awr, AW_ROOT_DEFAULT); DBUI::create_dbui_awars(awr); AP_create_consensus_var(awr, AW_ROOT_DEFAULT); { GB_ERROR gde_err = GDE_init(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main, NULp, ARB_format_alignment, GDE_WINDOWTYPE_DEFAULT); if (gde_err) GBK_terminatef("Fatal: %s", gde_err); } NT_create_transpro_variables(awr, AW_ROOT_DEFAULT); NT_create_resort_awars(awr, AW_ROOT_DEFAULT); NT_create_compare_taxonomy_awars(awr, AW_ROOT_DEFAULT); NT_create_trackAliChanges_Awars(awr, AW_ROOT_DEFAULT); NT_create_alignment_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); NT_create_extendeds_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); NDS_create_vars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); create_export_nds_awars(awr, AW_ROOT_DEFAULT); create_group_search_awars(awr, AW_ROOT_DEFAULT); TREE_create_awars(awr, GLOBAL.gb_main); awr->awar_string(AWAR_ERROR_MESSAGES, "", GLOBAL.gb_main); awr->awar_string(AWAR_DB_COMMENT, "", GLOBAL.gb_main); AWTC_create_submission_variables(awr, GLOBAL.gb_main); NT_createConcatenationAwars(awr, AW_ROOT_DEFAULT, GLOBAL.gb_main); NT_createValidNamesAwars(awr, AW_ROOT_DEFAULT); // lothar SQ_create_awars(awr, AW_ROOT_DEFAULT); RefEntries::create_refentries_awars(awr, AW_ROOT_DEFAULT); NT_create_multifurcate_tree_awars(awr, AW_ROOT_DEFAULT); GB_ERROR error = ARB_bind_global_awars(GLOBAL.gb_main); if (!error) { AW_awar *awar_expert = awr->awar(AWAR_EXPERT); awar_expert->add_callback(expert_mode_changed_cb); awar_expert->touch(); awt_create_aww_vars(awr, AW_ROOT_DEFAULT); } if (error) aw_message(error); } // -------------------------------------------------------------------------------- static void nt_run(const char *command) { GB_ERROR error = GBK_system(command); if (error) { fprintf(stderr, "nt_run: Failed to run '%s' (Reason: %s)\n", command, error); #if defined(DEBUG) GBK_dump_backtrace(stderr, "nt_run-error"); #endif } } void NT_start_if(const char *arb_ntree_args) { if (arb_ntree_args && arb_ntree_args[0]) { char *command = GBS_global_string_copy("arb_launcher --async arb %s", arb_ntree_args); nt_run(command); free(command); } } void NT_exit_now_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args) { // goes to header: __ATTR__NORETURN // Exit arb_ntree + optionally restart arb. // // 'exitcode': exit with this code. // 'restart_ntree_args': if null or empty -> just exit; // otherwise -> restarts arb_ntree (with new ARB_PID). AWTI_cleanup_importer(aw_root); bool is_server_and_has_clients = GLOBAL.gb_main && GB_read_clients(GLOBAL.gb_main)>0; ARB_disconnect_from_db(aw_root, GLOBAL.gb_main); NT_start_if(restart_ntree_args); if (is_server_and_has_clients) { nt_run("(arb_clean session; echo ARB done) &"); // kills all clients } exit(exitcode); } class NT_MacroExitor: public MacroExitor { int exitcode; std::string restart_ntree_args; // [if non-empty] restart arb with these arguments __ATTR__NORETURN void perform_exit() OVERRIDE { NT_exit_now_restart_if(get_root(), exitcode, restart_ntree_args.c_str()); } GBDATA* get_gbmain_checked_for_save() OVERRIDE { return GLOBAL.gb_main; } public: NT_MacroExitor(AW_root *aw_root_, int exitcode_, const char *restart_ntree_args_) : MacroExitor(aw_root_, "ARB"), exitcode(exitcode_), restart_ntree_args(null2empty(restart_ntree_args_)) // restart arb if not empty/null {} }; void NT_confirm_exit_restart_if(AW_root *aw_root, int exitcode, const char *restart_ntree_args) { // finally (may) exit ARB using NT_exit_now_restart_if(). see there for arguments. // // Beforehand this will happen: // - if no macro running -> asks user to confirm quit (and maybe aborts exit/restart). // - otherwise waits for macro to finish, then quits w/o question. static SmartPtr exitor; if (exitor.isNull()) exitor = new NT_MacroExitor(aw_root, exitcode, restart_ntree_args); exitor->maybe_exit_delayed(); if (!exitor->is_performing_delayed_exit()) exitor.setNull(); } void NT_confirm_exit(AW_window *aws, int exitcode) { NT_confirm_exit_restart_if(aws->get_root(), exitcode, NULp); } static void nt_start_2nd_arb(AW_window *aww, bool quit) { // start 2nd arb with intro window AW_root *aw_root = aww->get_root(); char *dir4intro; GB_split_full_path(aw_root->awar(AWAR_SAVED_DB_PATH)->read_char_pntr(), &dir4intro, NULp, NULp, NULp); if (!dir4intro) { dir4intro = ARB_strdup("."); } if (quit) { NT_confirm_exit_restart_if(aww->get_root(), EXIT_SUCCESS, dir4intro); } else { NT_start_if(dir4intro); } free(dir4intro); } // -------------------------------------------------------------------------------- static void NT_save_quick_cb(AW_window *aww) { AW_root *awr = aww->get_root(); char *filename = awr->awar(AWAR_DB_PATH)->read_string(); awr->dont_save_awars_with_default_value(GLOBAL.gb_main); GB_ERROR error = GB_save_quick(GLOBAL.gb_main, filename); if (error) aw_message(error); else { awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename); AW_refresh_fileselection(awr, AWAR_DBBASE); } free(filename); } static void NT_save_quick_as_cb(AW_window *aww) { AW_root *awr = aww->get_root(); char *filename = awr->awar(AWAR_DB_PATH)->read_string(); // @@@ also use dont_save_awars_with_default_value here? GB_ERROR error = GB_save_quick_as(GLOBAL.gb_main, filename); if (!error) { awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename); AW_refresh_fileselection(awr, AWAR_DBBASE); } aww->hide_or_notify(error); free(filename); } #define AWAR_DB_TYPE AWAR_DBBASE "/type" // created by AWT_insert_DBsaveType_selector #define AWAR_DB_COMPRESSION AWAR_DBBASE "/compression" // created by AWT_insert_DBcompression_selector #define AWAR_DB_OPTI_TREENAME AWAR_DBBASE "/optimize_tree_name" static void NT_save_as_cb(AW_window *aww) { AW_root *awr = aww->get_root(); char *filename = awr->awar(AWAR_DB_PATH)->read_string(); const char *atype = awr->awar(AWAR_DB_TYPE)->read_char_pntr(); const char *ctype = awr->awar(AWAR_DB_COMPRESSION)->read_char_pntr(); char *savetype = GBS_global_string_copy("%s%s", atype, ctype); awr->dont_save_awars_with_default_value(GLOBAL.gb_main); GB_ERROR error = GB_save(GLOBAL.gb_main, filename, savetype); if (!error) { awr->awar(AWAR_SAVED_DB_PATH)->write_string(filename); AW_refresh_fileselection(awr, AWAR_DBBASE); } aww->hide_or_notify(error); free(savetype); free(filename); } static AW_window *NT_create_save_quick_as_window(AW_root *aw_root, const char *base_name) { static AW_window_simple *aws = NULp; if (!aws) { aws = new AW_window_simple; aws->init(aw_root, "SAVE_CHANGES_TO", "Quicksave changes as"); aws->load_xfig("save_as.fig"); aws->at("close"); aws->callback(AW_POPDOWN); aws->create_button("CLOSE", "CLOSE", "C"); aws->callback(makeHelpCallback("save.hlp")); aws->at("help"); aws->create_button("HELP", "HELP", "H"); AW_create_standard_fileselection(aws, base_name); aws->at("comment"); aws->create_text_field(AWAR_DB_COMMENT); aws->at("save"); aws->callback(NT_save_quick_as_cb); aws->create_button("SAVE", "SAVE", "S"); } return aws; } static void NT_database_optimization(AW_window *aww) { arb_progress progress(WEIGHTED, "Optimizing database compression", 0.38); // 38% for seq-compression is just a rough guess made with silvaNR99138 // (a real guess would have to depend on ali-count, ali-length + field-count) GB_topSecurityLevel unsecured(GLOBAL.gb_main); GB_ERROR error = GB_begin_transaction(GLOBAL.gb_main); if (!error) { ConstStrArray ali_names; GBT_get_alignment_names(ali_names, GLOBAL.gb_main); arb_progress ali_progress("Optimizing sequence data", ali_names.size()); ali_progress.allow_title_reuse(); error = GBT_check_data(GLOBAL.gb_main, NULp); error = GB_end_transaction(GLOBAL.gb_main, error); if (!error) { char *tree_name = aww->get_root()->awar(AWAR_DB_OPTI_TREENAME)->read_string(); for (int i = 0; ali_names[i]; ++i) { error = GBT_compress_sequence_tree2(GLOBAL.gb_main, tree_name, ali_names[i]); ali_progress.inc_and_check_user_abort(error); } free(tree_name); } } progress.inc_and_check_user_abort(error); if (!error) { error = GB_optimize(GLOBAL.gb_main); progress.inc_and_check_user_abort(error); } aww->hide_or_notify(error); } static AW_window *NT_create_database_optimization_window(AW_root *aw_root) { static AW_window_simple *aws = NULp; if (aws) return aws; GB_transaction ta(GLOBAL.gb_main); const char *largest_tree = GBT_name_of_largest_tree(GLOBAL.gb_main); aw_root->awar_string(AWAR_DB_OPTI_TREENAME, largest_tree); aws = new AW_window_simple; aws->init(aw_root, "OPTIMIZE_DATABASE", "Optimize database compression"); aws->load_xfig("optimize.fig"); aws->at("trees"); awt_create_TREE_selection_list(GLOBAL.gb_main, aws, AWAR_DB_OPTI_TREENAME); aws->at("close"); aws->callback(AW_POPDOWN); aws->create_button("CLOSE", "CLOSE", "C"); aws->callback(makeHelpCallback("optimize.hlp")); aws->at("help"); aws->create_button("HELP", "HELP", "H"); aws->at("go"); aws->callback(NT_database_optimization); aws->create_button("GO", "GO"); return aws; } static AW_window *NT_create_save_as(AW_root *aw_root, const char *base_name) { static AW_window_simple *aws = NULp; if (aws) return aws; aws = new AW_window_simple; aws->init(aw_root, "SAVE_DB", "SAVE ARB DB"); aws->load_xfig("save_as.fig"); aws->at("close"); aws->callback(AW_POPDOWN); aws->create_button("CLOSE", "CLOSE", "C"); aws->at("help"); aws->callback(makeHelpCallback("save.hlp")); aws->create_button("HELP", "HELP", "H"); AW_create_standard_fileselection(aws, base_name); aws->at("type"); AWT_insert_DBsaveType_selector(aws, AWAR_DB_TYPE); aws->at("compression"); AWT_insert_DBcompression_selector(aws, AWAR_DB_COMPRESSION); aws->at("optimize"); aws->callback(NT_create_database_optimization_window); aws->help_text("optimize.hlp"); aws->create_autosize_button("OPTIMIZE", "Optimize database compression"); aws->at("save"); aws->callback(NT_save_as_cb); aws->create_button("SAVE", "SAVE", "S"); aws->at("comment"); aws->create_text_field(AWAR_DB_COMMENT); return aws; } static void NT_undo_cb(AW_window*, GB_UNDO_TYPE undo_type, TREE_canvas *ntw) { GB_ERROR error = GB_undo(GLOBAL.gb_main, undo_type); if (error) aw_message(error); else { GB_transaction ta(GLOBAL.gb_main); AWT_auto_refresh allowed_on(ntw); ntw->request_refresh(); } } static void NT_infomode_cb(UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode) { DBUI::popup_species_info_window(canvas->awr, canvas->gb_main); nt_mode_event(NULp, canvas, mode); } static void NT_mark_duplicates(UNFIXED, TREE_canvas *ntw) { AP_tree *tree_root = AWT_TREE(ntw)->get_root_node(); if (tree_root) { AWT_auto_refresh allowed_on(ntw); GB_transaction ta(ntw->gb_main); NT_mark_all_cb(NULp, ntw, 0); // unmark all tree_root->mark_duplicates(); ntw->request_structure_update(); } } static void NT_justify_branch_lenghs(UNFIXED, TREE_canvas *ntw) { GB_transaction ta(ntw->gb_main); AP_tree *tree_root = AWT_TREE(ntw)->get_root_node(); if (tree_root) { AWT_auto_refresh allowed_on(ntw); tree_root->justify_branch_lenghs(ntw->gb_main); ntw->request_save_and_zoom_reset(); } } #if defined(DEBUG) static void NT_fix_database(AW_window *) { GB_ERROR err = NULp; err = GB_fix_database(GLOBAL.gb_main); if (err) aw_message(err); } #endif static void relink_pseudo_species_to_organisms(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash) { if (ref_gb_node) { if (GEN_is_pseudo_gene_species(ref_gb_node)) { GBDATA *gb_organism = GEN_find_origin_organism(ref_gb_node, organism_hash); if (gb_organism) { char *name = GBT_read_string(gb_organism, "name"); if (name) { freeset(ref_name, name); ref_gb_node = gb_organism; } } } } } static void NT_pseudo_species_to_organism(AW_window *, TREE_canvas *ntw) { GB_transaction ta(ntw->gb_main); AP_tree *tree_root = AWT_TREE(ntw)->get_root_node(); if (tree_root) { AWT_auto_refresh allowed_on(ntw); GB_HASH *organism_hash = GBT_create_organism_hash(ntw->gb_main); tree_root->relink_tree(ntw->gb_main, relink_pseudo_species_to_organisms, organism_hash); GBS_free_hash(organism_hash); ntw->request_save(); } } // ######################################### // ######################################### // ### ### // ## user mask section ## // ### ### // ######################################### // ######################################### struct nt_item_type_species_selector FINAL_TYPE : public awt_item_type_selector { nt_item_type_species_selector() : awt_item_type_selector(AWT_IT_SPECIES) {} ~nt_item_type_species_selector() OVERRIDE {} const char *get_self_awar() const OVERRIDE { return AWAR_SPECIES_NAME; } size_t get_self_awar_content_length() const OVERRIDE { return 12; // should be enough for "nnaammee.999" } GBDATA *current(AW_root *root, GBDATA *gb_main) const OVERRIDE { // give the current item char *species_name = root->awar(get_self_awar())->read_string(); GBDATA *gb_species = NULp; if (species_name[0]) { GB_transaction ta(gb_main); gb_species = GBT_find_species(gb_main, species_name); } free(species_name); return gb_species; } const char *getKeyPath() const OVERRIDE { // give the keypath for items return CHANGE_KEY_PATH; } }; static nt_item_type_species_selector item_type_species; static void NT_open_mask_window(AW_window *aww, int id, GBDATA *gb_main) { const awt_input_mask_descriptor *descriptor = AWT_look_input_mask(id); nt_assert(descriptor); if (descriptor) AWT_initialize_input_mask(aww->get_root(), gb_main, &item_type_species, descriptor->get_internal_maskname(), descriptor->is_local_mask()); } static void NT_create_mask_submenu(AW_window_menu_modes *awm) { AWT_create_mask_submenu(awm, AWT_IT_SPECIES, NT_open_mask_window, GLOBAL.gb_main); } static AW_window *create_colorize_species_window(AW_root *aw_root) { return QUERY::create_colorize_items_window(aw_root, GLOBAL.gb_main, SPECIES_get_selector()); } // -------------------------------------------------------------------------------------------------- static void NT_alltree_remove_leafs(AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main) { GB_ERROR error = NULp; GB_transaction ta(gb_main); ConstStrArray tree_names; GBT_get_tree_names(tree_names, gb_main, false); if (!tree_names.empty()) { long treeCount = tree_names.size(); const char *whats_removed = NULp; switch (mode) { case GBT_REMOVE_ZOMBIES: whats_removed = "zombies"; break; case GBT_REMOVE_MARKED: whats_removed = "marked"; break; default: nt_assert(0); break; } const char *task = GBS_global_string("Deleting %s from %li trees", whats_removed, treeCount); arb_progress progress(task, treeCount); GB_HASH *species_hash = GBT_create_species_hash(gb_main); int modified = 0; for (int t = 0; t= groups_removed); if (!tree) { aw_message(GBS_global_string("'%s' would disappear. Please delete tree manually.", tree_names[t])); } else { if (removed>0) { error = GBT_write_tree(gb_main, tree_names[t], tree); if (error) { aw_message(GBS_global_string("Failed to write '%s' (Reason: %s)", tree_names[t], error)); } else { if (groups_removed>0) { aw_message(GBS_global_string("Removed %i species and %i groups from '%s'", removed, groups_removed, tree_names[t])); } else { aw_message(GBS_global_string("Removed %i species from '%s'", removed, tree_names[t])); } modified++; } } UNCOVERED(); destroy(tree); } } progress.inc_and_check_user_abort(error); } if (modified) { aw_message(GBS_global_string("Changed %i of %li trees.", modified, treeCount)); } else { aw_message("No tree modified"); } GBS_free_hash(species_hash); } aw_message_if(ta.close(error)); } // -------------------------------------------------------------------------------------------------- static ARB_ERROR mark_referred_species(GBDATA *gb_main, const DBItemSet& referred) { GB_transaction ta(gb_main); GBT_mark_all(gb_main, 0); DBItemSetIter end = referred.end(); for (DBItemSetIter s = referred.begin(); s != end; ++s) { GB_write_flag(*s, 1); } return ARB_ERROR(); } static AW_window *create_mark_by_refentries_window(AW_root *awr, GBDATA *gbmain) { static AW_window *aws = NULp; if (!aws) { static RefEntries::ReferringEntriesHandler reh(gbmain, SPECIES_get_selector()); aws = RefEntries::create_refentries_window(awr, &reh, "markbyref", "Mark by reference", "markbyref.hlp", NULp, "Mark referenced", mark_referred_species); } return aws; } // -------------------------------------------------------------------------------------------------- static void merge_from_to(AW_root *awr, const char *db_awar_name, bool merge_to) { const char *db_name = awr->awar(db_awar_name)->read_char_pntr(); char *quotedDB = GBK_singlequote(db_name); AW_system( GBS_global_string( merge_to ? "arb_ntree : %s &" : "arb_ntree %s : &", quotedDB) ); free(quotedDB); } static void merge_from_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, false); } static void merge_into_cb(AW_window *aww, AW_CL cl_awarNamePtr) { merge_from_to(aww->get_root(), *(const char**)cl_awarNamePtr, true); } static AW_window *NT_create_merge_from_window(AW_root *awr) { static char *awar_name = NULp; // do not free, bound to callback AW_window *aw_from = awt_create_load_box(awr, "Merge data from", "other ARB database", ".", ".arb", &awar_name, makeWindowCallback(merge_from_cb, AW_CL(&awar_name))); return aw_from; } static AW_window *NT_create_merge_to_window(AW_root *awr) { static char *awar_name = NULp; // do not free, bound to callback AW_window *aw_to = awt_create_load_box(awr, "Merge data to", "other or new ARB database", ".", ".arb", &awar_name, makeWindowCallback(merge_into_cb, AW_CL(&awar_name)), makeWindowCallback(AW_POPDOWN), NULp); return aw_to; } // -------------------------------------------------------------------------------------------------- static void update_main_window_title(AW_root *awr, AW_window_menu_modes *aww, int clone) { const char *filename = awr->awar(AWAR_DB_NAME)->read_char_pntr(); const char *base_title = GBS_global_string("%s - ARB", filename); aww->set_window_title(TREE_canvas::suffixed_title_for_index(base_title, clone)); } static void canvas_tree_awar_changed_cb(AW_awar *, bool, TREE_canvas *ntw) { NT_reload_tree_event(AW_root::SINGLETON, ntw, true); AW_root::SINGLETON->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->touch(); // refresh canvas selection lists TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_TREE); } class TREE_canvas_registry { int count; TREE_canvas *canvas[MAX_NT_WINDOWS]; static TREE_canvas_registry *SINGLETON; TREE_canvas_registry() : count(0) { AW_root::SINGLETON->awar_int(AWAR_NTREE_MAIN_WINDOW_COUNT, 0, AW_ROOT_DEFAULT); } public: static TREE_canvas_registry& instance() { if (!SINGLETON) SINGLETON = new TREE_canvas_registry; return *SINGLETON; } void register_canvas(TREE_canvas *ntw) { nt_assert(countget_index()); // you have to register TREE_canvas'es in order of creation! canvas[count++] = ntw; ntw->awr->awar(AWAR_NTREE_MAIN_WINDOW_COUNT)->write_int(count); // trigger callbacks } int get_count() const { return count; } TREE_canvas *get_canvas(int idx) const { if (idx<0 || idx>=count) return NULp; return canvas[idx]; } }; TREE_canvas_registry *TREE_canvas_registry::SINGLETON = NULp; TREE_canvas *NT_get_canvas_by_index(int idx) { /*! return canvas with index 'idx' [0...MAX_NT_WINDOWS-1] */ nt_assert(idx>=0 && idxgfx == agt) return ntw; } return NULp; } #endif 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) */ const TREE_canvas_registry& reg = TREE_canvas_registry::instance(); int maxIdx = reg.get_count(); for (int32_t i = 0; iget_awar_tree()); const char *treename = ntw->get_awar_tree()->read_char_pntr(); const char *description = i ? GBS_global_string("%s: %s", TREE_canvas::suffixed_title_for_index("ARB", i), treename) : GBS_global_string("ARB main: %s", treename); sellst->insert(description, i); } } } // ---------------------------------- // group-selection handlers void NT_deselect_group(AW_root *awr) { awr->awar(AWAR_GROUP)->write_pointer(NULp); } static bool track_group_selection_by_canvas = true; static void group_selected_by_canvas_cb(AWT_graphic_tree *gfx) { const Group& group = gfx->get_selected_group(); #if defined(TRACE_GROUP_SELECTION) fprintf(stderr, "[%s] ", track_group_selection_by_canvas ? "track" : "dont track"); TREE_canvas *ntw = find_canvas_showing(gfx); if (group.is_valid()) { fprintf(stderr, "canvas %i selects group '%s'\n", ntw->get_index(), group.get_name()); } else { fprintf(stderr, "canvas %i de-selects group\n", ntw->get_index()); } #endif if (track_group_selection_by_canvas) { // set group-awar: gfx->get_root()->awar(AWAR_GROUP)->write_pointer(group.get_group_data()); // writes NULp if !group.is_valid() } } static void group_awar_changed_cb(AW_root *awr) { AW_awar *awar_group = awr->awar(AWAR_GROUP); GBDATA *gb_wanted_group = awar_group->read_pointer(); GBDATA *gb_wanted_tree = NULp; { if (gb_wanted_group) { GB_transaction ta(gb_wanted_group); gb_wanted_tree = GB_get_father(gb_wanted_group); awr->awar(AWAR_SPECIES_NAME)->write_string(""); // deselect species when group gets selected #if defined(TRACE_GROUP_SELECTION) fputs("clear AWAR_SPECIES_NAME (because group selected)\n", stderr); #endif } #if defined(TRACE_GROUP_SELECTION) const char *group_name = NULp; if (gb_wanted_group) { GB_transaction ta(gb_wanted_group); GBDATA *gb_name = GB_entry(gb_wanted_group, "group_name"); if (gb_name) group_name = GB_read_char_pntr(gb_name); } fprintf(stderr, "group awar changed to %p", gb_wanted_group); if (group_name) fprintf(stderr, " (='%s')", group_name); fputc('\n', stderr); #endif } LocallyModify ignore_group_selection_by_canvas(track_group_selection_by_canvas, false); { const TREE_canvas_registry& reg = TREE_canvas_registry::instance(); int maxIdx = reg.get_count(); for (int32_t i = 0; iget_selected_group(); GBDATA *gb_curr_tree = agt->get_tree_root()->get_gb_tree(); if (gb_curr_tree == gb_wanted_tree) { AWT_auto_refresh allowed_on(ntw); if (!curr_group.is_valid() || // no group selected curr_group.get_group_data() != gb_wanted_group) // wrong group selected { agt->select_group(gb_wanted_group); ntw->request_refresh(); } // perform auto-jump (also if group was already selected, otherwise group-traversal keys will not follow the selected group) TREE_auto_jump_cb(NULp, ntw, AP_JUMP_REASON_GROUP); } else { if (curr_group.is_valid()) { AWT_auto_refresh allowed_on(ntw); agt->deselect_group(); ntw->request_refresh(); } } } } } // ---------------------------- // create main window static AW_window *popup_new_main_window(AW_root *awr, int clone, TREE_canvas **result_ntw) { /*! create ARB_NTREE main window * @param awr application root * @param clone == 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality) * @param result_ntw is set to the created TREE_canvas (passed pointer may be NULp if result is not needed) */ GB_push_transaction(GLOBAL.gb_main); const char *awar_tree = NULp; AW_window_menu_modes *awm = new AW_window_menu_modes; { char window_id[256]; if (clone) { awar_tree = ARB_keep_string(GBS_global_string_copy(AWAR_TREE "_%i", clone)); sprintf(window_id, "ARB_NT_%i", clone); } else { awar_tree = AWAR_TREE; sprintf(window_id, "ARB_NT"); } awm->init(awr, window_id, "[starting arb]", 0, 0); // effective title is generated by update_main_window_title } awr->awar(AWAR_DB_NAME) ->add_callback(makeRootCallback(update_main_window_title, awm, clone)) ->update(); awm->button_length(5); if (!clone) AW_init_color_group_defaults("arb_ntree"); AWT_graphic_tree *tree = TREE_generate_display(awr, GLOBAL.gb_main, launch_MapViewer_cb); if (!clone) { // while creating initial window AWT_graphic_tree::install_group_changed_callback(makeGraphicTreeCallback(group_selected_by_canvas_cb)); awr->awar(AWAR_GROUP)->add_callback(group_awar_changed_cb); } TREE_canvas *ntw; { AW_awar *tree_awar = awr->awar_string(awar_tree); { AP_tree_display_style prev_style = tree->get_tree_style(); tree->set_tree_style(AP_LIST_SIMPLE, NULp); // avoid NDS warnings during startup ntw = new TREE_canvas(GLOBAL.gb_main, awm, "ARB_NT", tree, tree_awar); nt_assert(ntw->get_index() == clone); // required for proper title enumeration. tree->set_tree_style(prev_style, ntw); ntw->set_mode(AWT_MODE_SELECT); } if (result_ntw) *result_ntw = ntw; { const char *tree_name = tree_awar->read_char_pntr(); const char *existing_tree_name = GBT_existing_tree(GLOBAL.gb_main, tree_name); if (existing_tree_name) { tree_awar->write_string(existing_tree_name); NT_reload_tree_event(awr, ntw, true); // load first tree } else { AW_advice("Your database contains no tree.", AW_ADVICE_TOGGLE_AND_HELP, NULp, "no_tree.hlp"); tree->set_tree_style(AP_LIST_NDS, ntw); // no tree -> show NDS list } TREE_canvas_registry::instance().register_canvas(ntw); AWT_registerTreeAwarCallback(tree_awar, makeTreeAwarCallback(canvas_tree_awar_changed_cb, ntw), false); } } TREE_install_update_callbacks(ntw); bool is_genome_db = GEN_is_genome_db(GLOBAL.gb_main, 0); // is this a genome database ? (default = 0 = not a genom db) WindowCallback popupinfo_wcb = RootAsWindowCallback::simple(DBUI::popup_species_info_window, GLOBAL.gb_main); // -------------- // File #if defined(DEBUG) AWT_create_debug_menu(awm); #endif // DEBUG bool allow_new_window = (ntw->get_index()+1) < MAX_NT_WINDOWS; if (clone) { awm->create_menu("File", "F", AWM_ALL); if (allow_new_window) { awm->insert_menu_topic(awm->local_id("new_window"), "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULp)); } awm->insert_menu_topic("close", "Close", "C", NULp, AWM_ALL, AW_POPDOWN); } else { #if defined(DEBUG) // add more to debug-menu awm->sep______________(); awm->insert_menu_topic("fix_db", "Fix database", "F", NULp, AWM_ALL, NT_fix_database); awm->insert_menu_topic("debug_arbdb", "Print debug information", "d", NULp, AWM_ALL, makeWindowCallback(GB_print_debug_information, GLOBAL.gb_main)); awm->insert_menu_topic("test_compr", "Test compression", "T", NULp, AWM_ALL, makeWindowCallback(GBT_compression_test, GLOBAL.gb_main)); #endif // DEBUG awm->create_menu("File", "F", AWM_ALL); { // keep the following entries in sync with ../EDIT4/ED4_root.cxx@common_save_menu_entries awm->insert_menu_topic("save_changes", "Quicksave changes", "s", "save.hlp", AWM_ALL, NT_save_quick_cb); awm->insert_menu_topic("save_all_as", "Save whole database as ...", "w", "save.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE)); if (allow_new_window) { awm->sep______________(); awm->insert_menu_topic("new_window", "New window (same database)", "N", "newwindow.hlp", AWM_ALL, makeCreateWindowCallback(popup_new_main_window, clone+1, (TREE_canvas**)NULp)); } awm->sep______________(); awm->insert_menu_topic("optimize_db", "Optimize database compression", "O", "optimize.hlp", AWM_ALL, NT_create_database_optimization_window); awm->sep______________(); awm->insert_sub_menu("Import", "I"); { awm->insert_menu_topic("merge_from", "Merge from other ARB database", "d", "arb_merge_into.hlp", AWM_ALL, NT_create_merge_from_window); awm->insert_menu_topic("import_seq", "Import from external format", "I", "arb_import.hlp", AWM_ALL, makeWindowCallback(NT_import_sequences, ntw)); GDE_load_menu(awm, AWM_EXP, "Import"); } awm->close_sub_menu(); awm->insert_sub_menu("Export", "E"); { awm->insert_menu_topic("export_to_ARB", "Merge to other or new ARB database", "A", "arb_merge_outof.hlp", AWM_ALL, NT_create_merge_to_window); awm->insert_menu_topic("export_seqs", "Export to external format", "f", "arb_export.hlp", AWM_ALL, makeCreateWindowCallback(create_AWTC_export_window, GLOBAL.gb_main)); GDE_load_menu(awm, AWM_ALL, "Export"); awm->insert_menu_topic("export_nds", "Export fields (to calc-sheet using NDS)", "N", "arb_export_nds.hlp", AWM_ALL, create_nds_export_window); } awm->close_sub_menu(); awm->sep______________(); insert_macro_menu_entry(awm, false); awm->insert_sub_menu("VersionInfo/Bugreport/MailingList", "V"); { awm->insert_menu_topic("version_info", "Version info (" ARB_VERSION_DETAILED ")", "V", "version.hlp", AWM_ALL, makeHelpCallback ("version.hlp")); awm->insert_menu_topic("bug_report", "Report bug", "b", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/BugReport")); awm->insert_menu_topic("mailing_list", "Mailing list", "M", NULp, AWM_ALL, makeWindowCallback(AWT_openURL, "http://bugs.arb-home.de/wiki/ArbMailingList")); } awm->close_sub_menu(); awm->sep______________(); awm->insert_menu_topic("new_arb", "Start second database", "d", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, false)); awm->insert_menu_topic("restart_arb", "Quit + load other database", "l", "quit.hlp", AWM_ALL, makeWindowCallback(nt_start_2nd_arb, true)); awm->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS)); } // ----------------- // Species awm->create_menu("Species", "c", AWM_ALL); { awm->insert_menu_topic("species_search", "Search and query", "q", "sp_search.hlp", AWM_ALL, makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main)); awm->insert_menu_topic("species_info", "Species information", "i", "sp_info.hlp", AWM_ALL, popupinfo_wcb); awm->sep______________(); NT_insert_mark_submenus(awm, ntw, 1); awm->insert_menu_topic("mark_by_ref", "Mark by reference..", "r", "markbyref.hlp", AWM_EXP, makeCreateWindowCallback(create_mark_by_refentries_window, GLOBAL.gb_main)); awm->insert_menu_topic("species_colors", "Colors ...", "l", "colorize.hlp", AWM_ALL, create_colorize_species_window); awm->insert_menu_topic("selection_admin", "Selections ...", "o", "species_configs.hlp", AWM_ALL, makeWindowCallback(NT_popup_configuration_admin, ntw)); awm->sep______________(); awm->insert_sub_menu("Database fields admin", "f"); DBUI::insert_field_admin_menuitems(awm, GLOBAL.gb_main); awm->close_sub_menu(); NT_create_mask_submenu(awm); awm->sep______________(); awm->insert_menu_topic("del_marked", "Delete Marked Species", "D", "sp_del_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_delete_mark_all_cb, ntw)); awm->insert_sub_menu("Sort Species", "s"); { awm->insert_menu_topic("$sort_by_field", "According to Database Entries", "D", "sp_sort_fld.hlp", AWM_ALL, NT_create_resort_window); awm->insert_menu_topic("$sort_by_tree", "According to Phylogeny", "P", "sp_sort_phyl.hlp", AWM_ALL, makeWindowCallback(NT_resort_data_by_phylogeny, ntw)); } awm->close_sub_menu(); awm->insert_sub_menu("Merge Species", "g", AWM_EXP); { awm->insert_menu_topic("merge_species", "Create merged species from similar species", "m", "merge_species.hlp", AWM_EXP, NT_createMergeSimilarSpeciesWindow); awm->insert_menu_topic("join_marked", "Join Marked Species", "J", "species_join.hlp", AWM_EXP, NT_create_species_join_window); } awm->close_sub_menu(); awm->sep______________(); awm->insert_menu_topic("species_submission", "Submit Species", "b", "submission.hlp", AWM_EXP, makeCreateWindowCallback(AWTC_create_submission_window, GLOBAL.gb_main)); awm->sep______________(); awm->insert_menu_topic("new_names", "Synchronize IDs", "e", "rename.hlp", AWM_ALL, makeCreateWindowCallback(AWTC_create_rename_window, GLOBAL.gb_main)); awm->insert_sub_menu("Valid Names ...", "V", AWM_EXP); { awm->insert_menu_topic("imp_names", "Import names from file", "I", "vn_import.hlp", AWM_EXP, NT_importValidNames); awm->insert_menu_topic("del_names", "Delete names from DB", "D", "vn_delete.hlp", AWM_EXP, NT_deleteValidNames); awm->insert_menu_topic("sug_names", "Suggest valid names", "v", "vn_suggest.hlp", AWM_EXP, NT_suggestValidNames); awm->insert_menu_topic("search_names", "Search manually", "m", "vn_search.hlp", AWM_EXP, NT_create_searchManuallyNames_window); } awm->close_sub_menu(); } // ---------------------------- // Genes + Experiment if (is_genome_db) GEN_create_genes_submenu(awm, GLOBAL.gb_main, true); // ------------------ // Sequence awm->create_menu("Sequence", "S", AWM_ALL); { awm->insert_menu_topic("seq_admin", "Sequence/Alignment Admin", "A", "ad_align.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_alignment_admin_window, (AW_window*)NULp)); awm->insert_sub_menu("Insert/delete", "I"); { awm->insert_menu_topic("ins_del_col", ".. column", "c", "insdel.hlp", AWM_ALL, create_insertDeleteColumn_window); awm->insert_menu_topic("ins_del_sai", ".. using SAI", "S", "insdel_sai.hlp", AWM_ALL, makeCreateWindowCallback(create_insertDeleteBySAI_window, GLOBAL.gb_main)); } awm->close_sub_menu(); awm->sep______________(); awm->insert_sub_menu("Edit Sequences", "E"); { awm->insert_menu_topic("new_arb_edit4", "Using marked species and tree", "m", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, 0, ntw)); awm->insert_menu_topic("new2_arb_edit4", "... plus relatives", "r", "arb_edit4.hlp", AWM_ALL, makeWindowCallback(NT_start_editor_on_tree, -1, ntw)); awm->insert_menu_topic("old_arb_edit4", "Using earlier configuration", "c", "arb_edit4.hlp", AWM_ALL, NT_create_startEditorOnOldConfiguration_window); } awm->close_sub_menu(); awm->sep______________(); awm->insert_sub_menu("Align sequences", "l"); { awm->insert_menu_topic("realign_dna", "Realign DNA according to aligned protein", "R", "realign_dna.hlp", AWM_ALL, NT_create_realign_dna_window); GDE_load_menu(awm, AWM_ALL, "Align"); } awm->close_sub_menu(); awm->insert_menu_topic("seq_concat", "Concatenate sequences", "C", "concatenate.hlp", AWM_ALL, NT_createConcatenationWindow); awm->insert_menu_topic("seq_split", "Split sequences", "S", "split.hlp", AWM_ALL, NT_create_splitAlignment_window); awm->insert_menu_topic("track_changes", "Track alignment changes", "k", "track_ali_changes.hlp", AWM_EXP, NT_create_trackAliChanges_window); awm->sep______________(); awm->insert_menu_topic("dna_2_pro", "Perform translation", "t", "translate_dna_2_pro.hlp", AWM_ALL, NT_create_dna_2_pro_window); awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "D", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist")); awm->sep______________(); awm->insert_menu_topic("seq_quality", "Check Sequence Quality", "Q", "seq_quality.hlp", AWM_EXP, makeCreateWindowCallback(SQ_create_seq_quality_window, GLOBAL.gb_main)); awm->insert_menu_topic("chimera_check", "Chimera Check", "m", "chimera_check.hlp", AWM_EXP, makeCreateWindowCallback(STAT_create_chimera_check_window, GLOBAL.gb_main)); awm->sep______________(); GDE_load_menu(awm, AWM_ALL, "Print"); } // ------------- // SAI awm->create_menu("SAI", "A", AWM_ALL); { awm->insert_menu_topic("sai_admin", "SAI Admin", "S", "ad_extended.hlp", AWM_ALL, NT_create_extendeds_window); awm->insert_menu_topic("sai_calc", "Combine SAIs", "b", "saicalc.hlp", AWM_ALL, makeWindowCallback(SAI_popup_calculator_window, GLOBAL.gb_main)); awm->insert_sub_menu("Create SAI using ...", "C"); { awm->insert_menu_topic("sai_max_freq", "Max. Frequency", "M", "max_freq.hlp", AWM_EXP, AP_create_max_freq_window); awm->insert_menu_topic("sai_consensus", "Consensus", "C", "consensus.hlp", AWM_ALL, AP_create_con_expert_window); awm->insert_menu_topic("pos_var_pars", "Positional variability + Column statistic (parsimony method)", "a", "pos_var_pars.hlp", AWM_ALL, AP_create_pos_var_pars_window); awm->insert_menu_topic("arb_phyl", "Filter by base frequency", "F", "phylo.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_phylo")); awm->insert_menu_topic("sai_pfold", "Protein secondary structure (field \"sec_struct\")", "P", "pfold.hlp", AWM_EXP, NT_create_sai_from_pfold); GDE_load_menu(awm, AWM_EXP, "SAI"); } awm->close_sub_menu(); awm->insert_sub_menu("Other functions", "O"); { awm->insert_menu_topic("count_different_chars", "Count different chars/column", "C", "count_chars.hlp", AWM_EXP, makeWindowCallback(NT_count_different_chars, GLOBAL.gb_main)); awm->insert_menu_topic("corr_mutat_analysis", "Compute clusters of correlated positions", "m", "", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_rnacma", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main))); awm->insert_menu_topic("export_pos_var", "Export Column Statistic (GNUPLOT format)", "E", "csp_2_gnuplot.hlp", AWM_ALL, NT_create_colstat_2_gnuplot_window); } awm->close_sub_menu(); } // ---------------- // Probes awm->create_menu("Probes", "P", AWM_ALL); { awm->insert_menu_topic("probe_design", "Design Probes", "D", "probedesign.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_design_window, GLOBAL.gb_main)); awm->insert_menu_topic("probe_multi", "Calculate Multi-Probes", "u", "multiprobe.hlp", AWM_ALL, makeCreateWindowCallback(create_multiprobe_window, ntw)); awm->insert_menu_topic("probe_match", "Match Probes", "M", "probematch.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_window, GLOBAL.gb_main)); awm->sep______________(); awm->insert_menu_topic("probe_match_sp", "Match Probes with Specificity", "f", "probespec.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_match_with_specificity_window, ntw)); awm->sep______________(); awm->insert_menu_topic("primer_design_new", "Design Primers", "P", "primer_new.hlp", AWM_EXP, makeCreateWindowCallback(create_primer_design_window, GLOBAL.gb_main)); awm->insert_menu_topic("primer_design", "Design Sequencing Primers", "S", "primer.hlp", AWM_EXP, makeWindowCallback(ARB_system_in_console_cb, "arb_primer", new XCmdType(XCMD_SERVSYNC_WAIT_ON_ERROR, GLOBAL.gb_main))); awm->sep______________(); awm->insert_menu_topic("pt_server_admin", "PT_SERVER Admin", "A", "probeadmin.hlp", AWM_ALL, makeCreateWindowCallback(create_probe_admin_window, GLOBAL.gb_main)); } } // -------------- // Tree awm->create_menu("Tree", "T", AWM_ALL); { if (!clone) { awm->insert_menu_topic("tree_admin", "Tree admin", "i", "treeadm.hlp", AWM_ALL, popup_tree_admin_window); awm->insert_menu_topic("nds", "NDS (Node display setup)", "N", "props_nds.hlp", AWM_ALL, makeCreateWindowCallback(NDS_create_window, GLOBAL.gb_main)); awm->sep______________(); awm->insert_sub_menu("Add Species to Existing Tree", "A"); { awm->insert_menu_topic("arb_pars_quick", "ARB Parsimony (Quick add marked)", "Q", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars -add_marked -quit")); awm->insert_menu_topic("arb_pars", "ARB Parsimony interactive", "i", "pars.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_pars")); GDE_load_menu(awm, AWM_EXP, "Incremental phylogeny"); } awm->close_sub_menu(); } awm->insert_sub_menu("Remove Species from Tree", "R"); { awm->insert_menu_topic(awm->local_id("tree_remove_deleted"), "Remove zombies", "z", "trm_del.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_REMOVE_ZOMBIES)); awm->insert_menu_topic(awm->local_id("tree_remove_marked"), "Remove marked", "m", "trm_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_REMOVE_MARKED)); awm->insert_menu_topic(awm->local_id("tree_keep_marked"), "Keep marked", "K", "tkeep_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_remove_leafs, ntw, AWT_KEEP_MARKED)); awm->sep______________(); awm->insert_menu_topic("all_tree_remove_deleted", "Remove zombies from ALL trees", "A", "trm_del.hlp", AWM_ALL, makeWindowCallback(NT_alltree_remove_leafs, GBT_REMOVE_ZOMBIES, GLOBAL.gb_main)); awm->insert_menu_topic("all_tree_remove_marked", "Remove marked from ALL trees", "L", "trm_mrkd.hlp", AWM_ALL, makeWindowCallback(NT_alltree_remove_leafs, GBT_REMOVE_MARKED, GLOBAL.gb_main)); } awm->close_sub_menu(); if (!clone) { awm->insert_sub_menu("Build tree from sequence data", "B"); { awm->insert_sub_menu("Distance matrix methods", "D"); awm->insert_menu_topic("arb_dist", "Distance Matrix + ARB NJ", "J", "dist.hlp", AWM_ALL, makeWindowCallback(AW_system_async_cb, "arb_dist")); GDE_load_menu(awm, AWM_ALL, "Phylogeny Distance Matrix"); awm->close_sub_menu(); awm->insert_sub_menu("Maximum Parsimony methods", "P"); GDE_load_menu(awm, AWM_ALL, "Phylogeny max. parsimony"); awm->close_sub_menu(); awm->insert_sub_menu("Maximum Likelihood methods", "L"); GDE_load_menu(awm, AWM_EXP, "Phylogeny max. Likelihood EXP"); GDE_load_menu(awm, AWM_ALL, "Phylogeny max. Likelihood"); awm->close_sub_menu(); awm->insert_sub_menu("Other methods", "O", AWM_EXP); GDE_load_menu(awm, AWM_EXP, "Phylogeny (Other)"); awm->close_sub_menu(); } awm->close_sub_menu(); } awm->insert_menu_topic(awm->local_id("consense_tree"), "Build consensus tree", "c", "consense_tree.hlp", AWM_ALL, NT_create_consense_window); awm->sep______________(); awm->insert_sub_menu("Reset zoom", "z"); { awm->insert_menu_topic(awm->local_id("reset_logical_zoom"), "Logical zoom", "L", "rst_log_zoom.hlp", AWM_ALL, makeWindowCallback(NT_reset_lzoom_cb, ntw)); awm->insert_menu_topic(awm->local_id("reset_physical_zoom"), "Physical zoom", "P", "rst_phys_zoom.hlp", AWM_ALL, makeWindowCallback(NT_reset_pzoom_cb, ntw)); } awm->close_sub_menu(); awm->sep______________(); // taxonomic groups NT_insert_collapse_submenu(awm, ntw); if (!clone) { awm->insert_menu_topic("group_search", "Search groups...", "g", "group_search.hlp", AWM_ALL, makeWindowCallback (popup_group_search_window, GLOBAL.gb_main)); awm->insert_menu_topic("compare_taxonomy", "Compare taxonomy...", "x", "compare_taxonomy.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compare_taxonomy_window, ntw)); awm->insert_menu_topic("move_groups", "Move groups...", "v", "move_groups.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_moveGroupInfo_window)); } awm->sep______________(); if (!clone) { awm->insert_menu_topic("compare_topology", "Compare topology...", "o", "compare_topo.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_compareTopologies_window)); } awm->insert_sub_menu("Modify branches", "M"); { awm->insert_menu_topic(awm->local_id("tree_remove_remark"), "Remove bootstraps", "b", "trm_boot.hlp", AWM_ALL, makeWindowCallback(NT_remove_bootstrap, ntw)); awm->insert_menu_topic(awm->local_id("tree_edit_remark"), "Edit bootstraps", "E", "ted_boot.hlp", AWM_ALL, makeWindowCallback(NT_edit_bootstrap, ntw)); awm->sep______________(); awm->insert_menu_topic(awm->local_id("tree_reset_lengths"), "Reset branchlengths", "R", "tbl_reset.hlp", AWM_ALL, makeWindowCallback(NT_reset_branchlengths, ntw)); awm->insert_menu_topic(awm->local_id("justify_branch_lengths"), "Justify branchlengths", "J", "tbl_justify.hlp", AWM_ALL, makeWindowCallback(NT_justify_branch_lenghs, ntw)); awm->insert_menu_topic(awm->local_id("tree_scale_lengths"), "Scale Branchlengths", "S", "tbl_scale.hlp", AWM_ALL, makeWindowCallback(NT_scale_tree, ntw)); awm->sep______________(); awm->insert_menu_topic(awm->local_id("tree_multifurcate"), "Multifurcate...", "M", "multifurcate.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_multifurcate_tree_window, ntw)); awm->sep______________(); awm->insert_menu_topic(awm->local_id("tree_boot2len"), "Bootstraps -> Branchlengths", "l", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 0)); awm->insert_menu_topic(awm->local_id("tree_len2boot"), "Bootstraps <- Branchlengths", "o", "tbl_boot2len.hlp", AWM_ALL, makeWindowCallback(NT_move_boot_branch, ntw, 1)); } awm->close_sub_menu(); awm->insert_sub_menu("Beautify tree", "u"); { awm->insert_menu_topic(awm->local_id("beautifyt_tree"), "#beautifyt.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_TOP)); awm->insert_menu_topic(awm->local_id("beautifyc_tree"), "#beautifyc.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_EDGE)); awm->insert_menu_topic(awm->local_id("beautifyb_tree"), "#beautifyb.xpm", "", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_BOTTOM)); awm->insert_menu_topic(awm->local_id("beautifyr_tree"), "Radial tree (1)", "1", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_TO_CENTER)); awm->insert_menu_topic(awm->local_id("beautifyr2_tree"), "Radial tree (2)", "2", "resorttree.hlp", AWM_ALL, makeWindowCallback(NT_resort_tree_cb, ntw, BIG_BRANCHES_ALTERNATING)); awm->sep______________(); awm->insert_menu_topic(awm->local_id("sort_by_other"), "By other tree", "o", "resortbyother.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_sort_tree_by_other_tree_window, ntw)); } awm->close_sub_menu(); awm->insert_menu_topic(awm->local_id("branch_analysis"), "Branch analysis", "h", "branch_analysis.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_branch_analysis_window, ntw)); awm->insert_menu_topic(awm->local_id("syncroots"), "Adjust roots...", "j", "syncroots.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncroot_window, GLOBAL.gb_main)); awm->insert_menu_topic(awm->local_id("mark_duplicates"), "Mark duplicates", "k", "mark_duplicates.hlp", AWM_ALL, makeWindowCallback (NT_mark_duplicates, ntw)); awm->sep______________(); awm->insert_menu_topic(awm->local_id("shade"), "Tree shading...", "s", "tree_shading.hlp", AWM_ALL, makeWindowCallback (NT_configure_treeShader)); awm->insert_menu_topic(awm->local_id("syncscroll"), "Sync tree scrolling..", "e", "syncscroll.hlp", AWM_ALL, makeCreateWindowCallback(NT_create_syncScroll_window, ntw)); awm->sep______________(); awm->insert_menu_topic(awm->local_id("tree_select_latest"), "Select Last Tree", "L", NULp, AWM_ALL, makeWindowCallback(NT_select_bottom_tree, awar_tree)); awm->sep______________(); awm->insert_menu_topic("transversion", "Transversion analysis", "y", "trans_anal.hlp", AWM_EXP, makeHelpCallback("trans_anal.hlp")); if (is_genome_db) { awm->sep______________(); awm->insert_menu_topic(awm->local_id("tree_pseudo_species_to_organism"), "Relink tree to organisms", "i", "tree_pseudo.hlp", AWM_EXP, makeWindowCallback(NT_pseudo_species_to_organism, ntw)); } if (!clone) { awm->sep______________(); awm->insert_menu_topic("print_tree", "Print tree", "P", "tree2prt.hlp", AWM_ALL, makeWindowCallback(AWT_popup_print_window, static_cast(ntw))); awm->insert_menu_topic("tree_2_xfig", "Export tree to XFIG", "F", "tree2file.hlp", AWM_ALL, makeWindowCallback(AWT_popup_tree_export_window, static_cast(ntw))); } } if (!clone) { // --------------- // Tools awm->create_menu("Tools", "o", AWM_ALL); { awm->insert_menu_topic("names_admin", "Nameserver admin (IDs)", "s", "namesadmin.hlp", AWM_ALL, makeWindowCallback(AW_popup_namesadmin_window, GLOBAL.gb_main)); awm->insert_sub_menu("DB admin", "D", AWM_EXP); { awm->insert_menu_topic("db_admin", "Re-repair DB", "R", "rerepair.hlp", AWM_EXP, makeWindowCallback(NT_rerepair_DB, GLOBAL.gb_main)); } awm->close_sub_menu(); awm->sep______________(); awm->insert_sub_menu("GDE specials", "G", AWM_EXP); { GDE_load_menu(awm, AWM_EXP, NULp); } awm->close_sub_menu(); awm->sep______________(); awm->insert_menu_topic("xterm", "Start XTERM", "X", "xterm.hlp", AWM_ALL, AW_console_cb); XCmdType *showlog_cmdtype = new XCmdType(XCMD_ASYNC_WAIT_ON_ERROR, GLOBAL.gb_main); // do not free (used in callback) awm->insert_menu_topic("viewlog", "View ARB log", "l", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl run", showlog_cmdtype)); // ../SH/arb_show_log.pl awm->insert_menu_topic("viewserv", "View server log", "V", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl server", showlog_cmdtype)); awm->insert_menu_topic("viewsys", "View sysinfo", "i", "console.hlp", AWM_ALL, makeWindowCallback(ARB_system_in_console_cb, "arb_show_log.pl sysinf", showlog_cmdtype)); awm->sep______________(); GDE_load_menu(awm, AWM_EXP, "User"); } // -------------------- // Properties awm->create_menu("Properties", "r", AWM_ALL); { awm->insert_menu_topic("props_menu", "Frame settings ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window); awm->insert_menu_topic(awm->local_id("props_tree2"), "Tree options", "o", "nt_tree_settings.hlp", AWM_ALL, TREE_create_settings_window); awm->insert_menu_topic("props_tree", "Tree colors & fonts", "c", "color_props.hlp", AWM_ALL, makeCreateWindowCallback(AW_create_gc_window, ntw->gc_manager)); awm->insert_menu_topic("props_www", "Search world wide web (WWW)", "b", "props_www.hlp", AWM_ALL, makeCreateWindowCallback(AWT_create_www_window, GLOBAL.gb_main)); awm->sep______________(); awm->insert_menu_topic("!toggle_expert", "Toggle expert mode", "x", NULp, AWM_ALL, NT_toggle_expert_mode); awm->insert_menu_topic("!toggle_focus", "Toggle focus follows mouse", "m", NULp, AWM_ALL, NT_toggle_focus_policy); awm->sep______________(); AW_insert_common_property_menu_entries(awm); awm->sep______________(); awm->insert_menu_topic("save_props", "Save properties (ntree.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties); } } awm->insert_help_topic("ARB NTREE help", "N", "arb_ntree.hlp", AWM_ALL, makeHelpCallback("arb_ntree.hlp")); // ---------------------- // mode buttons // // keep them synchronized as far as possible with those in ARB_PARSIMONY // see ../PARSIMONY/PARS_main.cxx@keepModesSynchronized awm->create_mode("mode_select.xpm", "mode_select.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SELECT)); awm->create_mode("mode_mark.xpm", "mode_mark.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MARK)); awm->create_mode("mode_group.xpm", "mode_group.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_GROUP)); awm->create_mode("mode_zoom.xpm", "mode_pzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ZOOM)); awm->create_mode("mode_lzoom.xpm", "mode_lzoom.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LZOOM)); awm->create_mode("mode_info.xpm", "mode_info.hlp", AWM_ALL, makeWindowCallback(NT_infomode_cb, ntw, AWT_MODE_INFO)); awm->create_mode("mode_www.xpm", "mode_www.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_WWW)); // topology-modification-modes awm->create_mode("mode_setroot.xpm", "mode_setroot.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SETROOT)); awm->create_mode("mode_swap.xpm", "mode_swap.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SWAP)); awm->create_mode("mode_move.xpm", "mode_move.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MOVE)); awm->create_mode("mode_length.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LENGTH)); awm->create_mode("mode_multifurc.xpm", "mode_length.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_MULTIFURC)); // layout-modes awm->create_mode("mode_line.xpm", "mode_width.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_LINE)); awm->create_mode("mode_rotate.xpm", "mode_rotate.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_ROTATE)); awm->create_mode("mode_spread.xpm", "mode_spread.hlp", AWM_ALL, makeWindowCallback(nt_mode_event, ntw, AWT_MODE_SPREAD)); awm->set_info_area_height(250); awm->at(5, 2); awm->auto_space(-2, -2); awm->shadow_width(1); // ------------------------- // create top area int first_liney; int leftx; awm->get_at_position(&leftx, &first_liney); // --------------------- // quit + help awm->button_length(0); if (clone) { awm->callback(AW_POPDOWN); awm->create_button("CLOSE", "#close.xpm"); } else { awm->callback(makeWindowCallback(NT_confirm_exit, EXIT_SUCCESS)); awm->help_text("quit.hlp"); awm->create_button("QUIT", "#quit.xpm"); } int db_pathx = awm->get_at_xposition(); // now fetch the yposition for the 2nd button line awm->at_newline(); int second_liney = awm->get_at_yposition(); awm->callback(AW_help_entry_pressed); awm->help_text("arb_ntree.hlp"); awm->create_button("?", "#help.xpm"); // -------------------------- // save + undo/redo awm->callback(NT_save_quick_cb); awm->help_text("save.hlp"); awm->create_button("SAVE", "#save.xpm"); awm->callback(makeCreateWindowCallback(NT_create_save_as, AWAR_DBBASE)); awm->help_text("save.hlp"); awm->create_button("SAVE_AS", "#saveAs.xpm"); // undo/redo: awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_UNDO, ntw)); awm->help_text("undo.hlp"); awm->create_button("UNDO", "#undo.xpm"); awm->callback(makeWindowCallback(NT_undo_cb, GB_UNDO_REDO, ntw)); awm->help_text("undo.hlp"); awm->create_button("REDO", "#redo.xpm"); int db_pathx2 = awm->get_at_xposition(); // fetch position for mode help-line: awm->at_newline(); int third_liney = awm->get_at_yposition(); awm->at(db_pathx, first_liney); // size of DB-name button is determined by buttons below: awm->at_attach_to(false, false, db_pathx2-db_pathx-1, second_liney-first_liney+1); awm->callback(makeCreateWindowCallback(NT_create_save_quick_as_window, AWAR_DBBASE)); awm->help_text("save.hlp"); awm->create_button("QUICK_SAVE_AS", AWAR_DB_NAME); // ----------------------------- // tree + tree display #define TREE_BUTTON_OVERSIZE 6 int db_treex = awm->get_at_xposition(); int second_uppery = second_liney-TREE_BUTTON_OVERSIZE; awm->at(db_treex, second_uppery); awm->button_length(0); awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_RADIAL)); awm->help_text("tr_type_radial.hlp"); awm->create_button("RADIAL_TREE_TYPE", "#radial.xpm"); awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_NORMAL)); awm->help_text("tr_type_dendro.hlp"); awm->create_button("LIST_TREE_TYPE", "#dendro.xpm"); awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_TREE_IRS)); awm->help_text("tr_type_irs.hlp"); awm->create_button("FOLDED_LIST_TREE_TYPE", "#dendroIrs.xpm"); awm->callback(makeWindowCallback(NT_set_tree_style, ntw, AP_LIST_NDS)); awm->help_text("tr_type_nds.hlp"); awm->create_button("NO_TREE_TYPE", "#listdisp.xpm"); int db_treex2 = awm->get_at_xposition(); awm->at(db_treex, first_liney); // size of tree-name button is determined by buttons below: awm->at_attach_to(false, false, db_treex2-db_treex-1, second_uppery-first_liney+1); awm->callback(makeCreateWindowCallback(NT_create_select_tree_window, awar_tree, ntw)); awm->help_text("nt_tree_select.hlp"); awm->create_button("SELECT_A_TREE", awar_tree); // --------------------------------------------------------------- // protection, alignment + editor (and maybe Genome Map) int db_alignx = awm->get_at_xposition(); // editor and genemap buttons have to be 44x24 sized #define EDIT_XSIZE 50 #define EDIT_YSIZE 30 // same as 'save as' buttons // first draw protection: int protectx = db_alignx + 2*EDIT_XSIZE; awm->at(protectx+2, first_liney+1); awm->button_length(0); awm->create_button(NULp, "#protect.xpm"); awm->at(protectx, second_liney+2); awm->create_option_menu(AWAR_SECURITY_LEVEL); awm->insert_option ("0", NULp, 0); awm->insert_option ("1", NULp, 1); awm->insert_option ("2", NULp, 2); awm->insert_option ("3", NULp, 3); awm->insert_option ("4", NULp, 4); awm->insert_option ("5", NULp, 5); awm->insert_default_option("6", NULp, 6); awm->update_option_menu(); int db_searchx = awm->get_at_xposition() - 7; // draw ali/editor buttons AFTER protect menu (to get rid of it's label) awm->at(db_alignx, second_liney); awm->at_attach_to(false, false, ((2-is_genome_db)*EDIT_XSIZE), EDIT_YSIZE); awm->callback(makeWindowCallback(NT_start_editor_on_tree, 0, ntw)); awm->help_text("arb_edit4.hlp"); if (is_genome_db) awm->create_button("EDIT_SEQUENCES", "#editor_small.xpm"); else awm->create_button("EDIT_SEQUENCES", "#editor.xpm"); if (is_genome_db) { awm->at_attach_to(false, false, EDIT_XSIZE, EDIT_YSIZE); awm->callback(makeCreateWindowCallback(GEN_create_first_map, GLOBAL.gb_main)); // initial gene map awm->help_text("gene_map.hlp"); awm->create_button("OPEN_GENE_MAP", "#gen_map.xpm"); } int db_alignx2 = awm->get_at_xposition(); awm->at(db_alignx, first_liney); awm->at_attach_to(false, false, db_alignx2-db_alignx-1, second_liney-first_liney+1); awm->callback(NT_create_select_alignment_window); awm->help_text("nt_align_select.hlp"); awm->create_button("SELECT_AN_ALIGNMENT", AWAR_DEFAULT_ALIGNMENT); // ------------------------------- // create mode-help line awm->at(leftx, third_liney); awm->button_length(AWAR_FOOTER_MAX_LEN); awm->create_button(NULp, AWAR_FOOTER); awm->at_newline(); int bottomy = awm->get_at_yposition(); // --------------------------------------- // Info / marked / Search / Jump awm->button_length(7); awm->at(db_searchx, first_liney); awm->callback(makeCreateWindowCallback(DBUI::create_species_query_window, GLOBAL.gb_main)); awm->help_text("sp_search.hlp"); awm->create_button("SEARCH", "Search"); awm->at(db_searchx, second_uppery); awm->callback(makeWindowCallback(NT_jump_cb, ntw, AP_JUMP_BY_BUTTON)); awm->help_text("tr_jump.hlp"); awm->create_button("JUMP", "Jump"); int db_infox = awm->get_at_xposition(); awm->at(db_infox, first_liney); awm->button_length(13); awm->callback(popupinfo_wcb); awm->help_text("sp_info.hlp"); awm->create_button("INFO", AWAR_INFO_BUTTON_TEXT); awm->at(db_infox, second_uppery); create_species_selection_button(awm, makeWindowCallback(NT_popup_configuration_admin, ntw), "selection_admin2", AWAR_MARKED_SPECIES_COUNTER, GLOBAL.gb_main); // set height of top area: awm->set_info_area_height(bottomy+2); awm->set_bottom_area_height(0); NT_activate_configMarkers_display(ntw); // ------------------------------------ // Autostarts for development #if defined(DEVEL_RALF) // if (is_genome_db) GEN_map_first(awr)->show(); #endif // DEVEL_RALF GB_pop_transaction(GLOBAL.gb_main); #if defined(DEBUG) AWT_check_action_ids(awr, is_genome_db ? "_genome" : ""); #endif return awm; } TREE_canvas *NT_create_main_window(AW_root *aw_root) { GB_ERROR error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_NONE); if (error) aw_message(error); nt_create_all_awars(aw_root); TREE_canvas *ntw = NULp; AW_window *aww = popup_new_main_window(aw_root, 0, &ntw); NT_install_treeShader(ntw, GLOBAL.gb_main); aww->show(); error = GB_request_undo_type(GLOBAL.gb_main, GB_UNDO_UNDO); if (error) aw_message(error); return ntw; }