NT_main.cxx File Reference

#include "NT_local.h"
#include <mg_merge.hxx>
#include <awti_import.hxx>
#include <insdel.h>
#include <macros.hxx>
#include <mod_rlimit.h>
#include <TreeDisplay.hxx>
#include <awt.hxx>
#include <awt_misc.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_TreeAwars.hxx>
#include <aw_advice.hxx>
#include <aw_question.hxx>
#include <aw_awars.hxx>
#include <aw_edit.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_global_awars.hxx>
#include <adGene.h>
#include <arb_version.h>
#include <arb_progress.h>
#include <arb_file.h>
#include <signal.h>

Include dependency graph for NT_main.cxx:

Go to the source code of this file.

Classes
class	NtreeCommandLine
class	SelectedDatabase
struct	merge_scheme

Macros
#define	MAXNAMELEN   35
#define	AWAR_DB_FILTER   AWAR_DBBASE "/filter"
#define	AWAR_DB_DIRECTORY   AWAR_DBBASE "/directory"
#define	ABORTED_BY_USER   "aborted by user"

Enumerations
enum	ArgType {   RUNNING_DB, DIRECTORY, EXISTING_DB, NEW_DB,   FILEMASK, EXISTING_FILE, UNKNOWN_ARG }
enum	RunMode { NORMAL, IMPORT, MERGE, BROWSE }

Functions
GB_ERROR	NT_format_all_alignments (GBDATA *gb_main)
static GB_ERROR	nt_check_database_consistency ()
static __ATTR__USERESULT GB_ERROR	startup_mainwindow_and_dbserver (AW_root *aw_root, const char *autorun_macro, TREE_canvas *&result_ntw)
static ARB_ERROR	load_and_startup_main_window (AW_root *aw_root, const char *autorun_macro)
static void	nt_delete_database (AW_window *aww)
static void	start_main_window_after_import (AW_root *aw_root)
static void	nt_intro_start_existing (AW_window *aw_intro)
static void	nt_intro_start_merge (AW_window *aw_intro)
static void	nt_intro_start_import (AW_window *aw_intro)
static AW_window *	nt_create_intro_window (AW_root *awr)
static void	AWAR_DB_PATH_changed_cb (AW_root *awr)
bool	has_arb_suffix (const char *arg)
static ArgType	detectArgType (const char *arg)
static ARB_ERROR	check_argument_for_mode (const char *database, char *&browser_startdir, RunMode &mode)
static void	exit_from_merge (const char *restart_args)
static void	merge_startup_abort_cb (AW_window *)
static AW_window *	merge_startup_error_window (AW_root *aw_root, GB_ERROR error)
static AW_window *	startup_merge_main_window (AW_root *aw_root, merge_scheme *ms)
static AW_window *	startup_merge_prompting_for_nonexplicit_dst_db (AW_root *aw_root, merge_scheme *ms)
static AW_window *	startup_merge_prompting_for_nonexplicit_dbs (AW_root *aw_root, merge_scheme *ms)
static void	startup_gui (NtreeCommandLine &cl, ARB_ERROR &error)
int	ARB_main (int argc, char *argv[])

Variables
AW_HEADER_MAIN NT_global	GLOBAL
static bool	merge_tool_running_as_client = true

Macro Definition Documentation

#define MAXNAMELEN   35

Referenced by load_and_startup_main_window().

#define AWAR_DB_FILTER   AWAR_DBBASE "/filter"

Definition at line 215 of file NT_main.cxx.

Referenced by nt_delete_database().

#define AWAR_DB_DIRECTORY   AWAR_DBBASE "/directory"

Definition at line 216 of file NT_main.cxx.

Referenced by AWAR_DB_PATH_changed_cb(), nt_intro_start_merge(), and startup_gui().

#define ABORTED_BY_USER   "aborted by user"

Definition at line 483 of file NT_main.cxx.

Referenced by check_argument_for_mode(), and startup_gui().

Enumeration Type Documentation

enum ArgType

Enumerator
RUNNING_DB
DIRECTORY
EXISTING_DB
NEW_DB
FILEMASK
EXISTING_FILE
UNKNOWN_ARG

Definition at line 449 of file NT_main.cxx.

enum RunMode

Enumerator
NORMAL
IMPORT
MERGE
BROWSE

Definition at line 481 of file NT_main.cxx.

Function Documentation

GB_ERROR NT_format_all_alignments

(

GBDATA *

gb_main

)

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().

static GB_ERROR nt_check_database_consistency ( )

static

Definition at line 148 of file NT_main.cxx.

References NT_global::gb_main, NT_format_all_alignments(), and NT_repair_DB().

Referenced by startup_mainwindow_and_dbserver().

static __ATTR__USERESULT GB_ERROR startup_mainwindow_and_dbserver ( AW_root *  aw_root, const char *  autorun_macro, TREE_canvas *&  result_ntw  )

static

Definition at line 158 of file NT_main.cxx.

References AWT_initTreeAwarRegistry(), configure_macro_recording(), error(), execute_macro(), GB_is_server(), NT_global::gb_main, GBK_system(), nt_check_database_consistency(), NT_create_main_window(), and NT_repair_userland_problems().

Referenced by load_and_startup_main_window(), and start_main_window_after_import().

static ARB_ERROR load_and_startup_main_window ( AW_root *  aw_root, const char *  autorun_macro  )

static

Definition at line 177 of file NT_main.cxx.

References aw_message_if(), AW_root::awar(), AWAR_DB_PATH, AWAR_SAVED_DB_PATH, error(), GB_await_error(), NT_global::gb_main, GBS_global_string(), GBT_open(), MAXNAMELEN, NULp, AW_awar::read_string(), startup_mainwindow_and_dbserver(), and AW_awar::write_string().

Referenced by nt_intro_start_existing(), and startup_gui().

static void nt_delete_database ( AW_window *  aww )

static

Definition at line 218 of file NT_main.cxx.

References aw_ask_sure(), aw_message(), AW_root::awar(), AWAR_DB_FILTER, AWAR_DB_PATH, error(), GB_delete_database(), GBS_global_string(), AW_window::get_root(), NULp, AW_awar::read_string(), and AW_awar::touch().

Referenced by nt_create_intro_window().

static void start_main_window_after_import ( AW_root *  aw_root )

static

Definition at line 239 of file NT_main.cxx.

References aw_message_if(), NT_global::aw_root, AW_root::awar(), AWAR_IMPORT_AUTOCONF, AWAR_TREE_REFRESH, AWTI_acquire_imported_DB_and_cleanup_importer(), NT_global::gb_main, nt_assert, NT_create_config_after_import(), NULp, AW_awar::read_int(), startup_mainwindow_and_dbserver(), and AW_awar::touch().

Referenced by nt_intro_start_import(), and startup_gui().

static void nt_intro_start_existing ( AW_window *  aw_intro )

static

Definition at line 256 of file NT_main.cxx.

References aw_popup_ok(), ARB_ERROR::deliver(), error(), ARB_ERROR::expect_no_error(), AW_window::get_root(), got_macro_ability(), AW_window::hide(), load_and_startup_main_window(), nt_assert, NULp, and AW_window::show().

Referenced by nt_create_intro_window().

static void nt_intro_start_merge ( AW_window *  aw_intro )

static

Definition at line 269 of file NT_main.cxx.

References AW_root::awar(), AWAR_DB_DIRECTORY, GBS_global_string_copy(), AW_window::get_root(), NT_restart(), and AW_awar::read_char_pntr().

Referenced by nt_create_intro_window().

static void nt_intro_start_import ( AW_window *  aw_intro )

static

Definition at line 277 of file NT_main.cxx.

References AWAR_DB_PATH, AW_root::awar_string(), AWTI_open_import_window(), AWTI_set_importDB_pointer(), NT_global::gb_main, AW_window::get_root(), got_macro_ability(), AW_window::hide(), nt_assert, NULp, start_main_window_after_import(), and AW_awar::write_string().

Referenced by nt_create_intro_window().

static AW_window* nt_create_intro_window ( AW_root *  awr )

static

Definition at line 289 of file NT_main.cxx.

References ARB_BUILD_DATE, ARB_BUILD_YEAR, ARB_VERSION, AW_create_standard_fileselection(), AWAR_DBBASE, AWAR_EXPERT, EXIT_SUCCESS, GBS_global_string(), AW_window::load_xfig(), makeHelpCallback(), nt_delete_database(), NT_exit(), nt_intro_start_existing(), nt_intro_start_import(), nt_intro_start_merge(), and NULp.

Referenced by startup_gui().

static void AWAR_DB_PATH_changed_cb ( AW_root *  awr )

static

Definition at line 337 of file NT_main.cxx.

References AW_root::awar(), AWAR_DB_DIRECTORY, AWAR_DB_NAME, AWAR_SAVED_DB_PATH, AW_awar::read_string(), and AW_awar::write_string().

Referenced by startup_gui().

bool has_arb_suffix ( const char *  arg )

inline

Definition at line 459 of file NT_main.cxx.

Referenced by detectArgType().

static ArgType detectArgType ( const char *  arg )

static

Definition at line 467 of file NT_main.cxx.

References DIRECTORY, EXISTING_DB, EXISTING_FILE, FILEMASK, GB_is_directory(), GB_is_regularfile(), GBT_check_arb_file(), has_arb_suffix(), NEW_DB, RUNNING_DB, and UNKNOWN_ARG.

Referenced by SelectedDatabase::reselect_file().

static ARB_ERROR check_argument_for_mode ( const char *  database, char *&  browser_startdir, RunMode &  mode  )

static

Definition at line 485 of file NT_main.cxx.

References ABORTED_BY_USER, AW_extract_directory(), aw_question(), AW_unfold_path(), BROWSE, error(), FALLTHROUGH, GB_is_directory(), GB_is_regularfile(), GBS_global_string(), GBT_check_arb_file(), IMPORT, nt_assert, and NULp.

Referenced by startup_gui().

static void exit_from_merge ( const char *  restart_args )

static

Definition at line 744 of file NT_main.cxx.

References EXIT_SUCCESS, merge_tool_running_as_client, nt_assert, NT_restart(), NT_start(), and AW_root::SINGLETON.

Referenced by merge_startup_abort_cb(), and startup_merge_main_window().

static void merge_startup_abort_cb ( AW_window *  )

static

Definition at line 755 of file NT_main.cxx.

References exit_from_merge(), fputs(), and NULp.

Referenced by merge_startup_error_window(), startup_merge_prompting_for_nonexplicit_dbs(), and startup_merge_prompting_for_nonexplicit_dst_db().

static AW_window* merge_startup_error_window ( AW_root *  aw_root, GB_ERROR  error  )

static

Definition at line 760 of file NT_main.cxx.

References AW_RESIZE_DEFAULT, merge_startup_abort_cb(), NULp, and AW_window::recalc_size_atShow().

Referenced by startup_merge_main_window().

static AW_window* startup_merge_main_window ( AW_root *  aw_root, merge_scheme *  ms  )

static

Definition at line 779 of file NT_main.cxx.

References SelectedDatabase::arg_type(), AW_ROOT_DEFAULT, merge_scheme::dst, merge_scheme::error, exit_from_merge(), merge_scheme::fix_dst(), merge_scheme::fix_src(), SelectedDatabase::get_fullname(), got_macro_ability(), merge_scheme::knows_dbs(), MERGE_create_db_file_awars(), MERGE_create_main_window(), merge_startup_error_window(), NEW_DB, nt_assert, merge_scheme::open_dbs(), and merge_scheme::src.

Referenced by startup_merge_prompting_for_nonexplicit_dst_db().

static AW_window* startup_merge_prompting_for_nonexplicit_dst_db ( AW_root *  aw_root, merge_scheme *  ms  )

static

Definition at line 805 of file NT_main.cxx.

References merge_scheme::awar_dst, awt_create_load_box(), merge_scheme::dst, SelectedDatabase::get_dir(), SelectedDatabase::get_mask(), SelectedDatabase::get_role(), AW_window::makeWindowReplacer(), merge_startup_abort_cb(), SelectedDatabase::needs_to_prompt(), and startup_merge_main_window().

Referenced by startup_merge_prompting_for_nonexplicit_dbs().

static AW_window* startup_merge_prompting_for_nonexplicit_dbs ( AW_root *  aw_root, merge_scheme *  ms  )

static

Definition at line 820 of file NT_main.cxx.

References merge_scheme::awar_src, awt_create_load_box(), SelectedDatabase::get_dir(), SelectedDatabase::get_mask(), SelectedDatabase::get_role(), AW_window::makeWindowReplacer(), merge_startup_abort_cb(), SelectedDatabase::needs_to_prompt(), merge_scheme::src, and startup_merge_prompting_for_nonexplicit_dst_db().

Referenced by startup_gui().

static void startup_gui ( NtreeCommandLine &  cl, ARB_ERROR &  error  )

static

Definition at line 838 of file NT_main.cxx.

References ABORTED_BY_USER, AW_awar::add_callback(), ARB_declare_global_awars(), ARB_strdup(), SelectedDatabase::arg_type(), NtreeCommandLine::autorun_macro(), AW_create_fileselection_awars(), AW_edit(), aw_popup_ok(), NT_global::aw_root, AW_ROOT_DEFAULT, AW_root::awar(), AWAR_DB_DIRECTORY, AWAR_DB_NAME, AWAR_DB_PATH, AWAR_DB_PATH_changed_cb(), AWAR_DBBASE, AWAR_EXPERT, AW_root::awar_int(), AWAR_SAVED_DB_PATH, AW_root::awar_string(), AWT_install_cb_guards(), AWT_system_cb(), AWTI_open_import_window(), AWTI_set_importDB_pointer(), BROWSE, check_argument_for_mode(), merge_scheme::dst, NtreeCommandLine::free_args(), GB_find_latest_file(), NT_global::gb_main, GB_path_in_ARBLIB(), GB_path_in_arbprop(), GB_time_of_file(), GBS_global_string(), NtreeCommandLine::get_arg(), GLOBAL_gb_dst, GLOBAL_gb_src, got_macro_ability(), IMPORT, load_and_startup_main_window(), AW_root::main_loop(), MERGE, MERGE_create_all_awars(), merge_tool_running_as_client, message(), NORMAL, nt_assert, nt_create_intro_window(), NULp, ARB_ERROR::preserve(), RUNNING_DB, AW_root::setUserActionTracker(), AW_window::show(), merge_scheme::src, start_main_window_after_import(), startup_merge_prompting_for_nonexplicit_dbs(), NtreeCommandLine::wants_help(), NtreeCommandLine::wants_import(), NtreeCommandLine::wants_merge(), and AW_awar::write_string().

Referenced by ARB_main().

int ARB_main	(	int	argc,
		char *	argv[]
	)

Definition at line 946 of file NT_main.cxx.

References aw_initstatus(), NT_global::aw_root, AWT_create_root(), ARB_ERROR::deliver(), error(), EXIT_FAILURE, EXIT_SUCCESS, ARB_ERROR::expect_no_error(), GB_set_verbose(), need_macro_ability(), NtreeCommandLine::parse(), NtreeCommandLine::print_help(), startup_gui(), TREEDISP_STACKSIZE, and NtreeCommandLine::wants_help().

Variable Documentation

AW_HEADER_MAIN NT_global GLOBAL

Definition at line 46 of file NT_main.cxx.

Referenced by ad_move_tree_info(), ad_tree_set_security(), addSpeciesToConcatenateList(), AP_calc_pos_var_pars(), AP_create_con_expert_window(), AP_create_consensus_var(), AP_create_max_freq_window(), AP_create_pos_var_pars_window(), colstat_2_gnuplot_cb(), colstat_ali_changed_cb(), CON_calc_max_freq_cb(), CON_calculate_cb(), concatenateAlignments(), concatenateFieldsCreateNewSpecies(), config_comment_changed_cb(), copy_SAI_cb(), copy_SAI_to_species_cb(), create_colorize_species_window(), create_configuration_admin_window(), create_configuration_marker_window(), create_consense_tree_cb(), create_insertDeleteColumn_variables(), create_select_other_tree_window(), createMergeSimilarSpeciesWindow(), delete_SAI_cb(), edit_SAI_description(), export_nds_cb(), fillSelNamList(), init_config_admin_awars(), init_config_awars(), insdel_event(), insdel_sai_event(), launch_MapViewer_cb(), map_SAI_to_scanner(), mergeSimilarSpecies(), modify_configurations(), nt_changesecurity(), NT_create_alignment_admin_window(), nt_create_all_awars(), NT_create_colstat_2_gnuplot_window(), nt_create_configuration(), NT_create_consense_window(), NT_create_database_optimization_window(), NT_create_dna_2_pro_window(), NT_create_extendeds_window(), NT_create_main_window(), NT_create_mask_submenu(), NT_create_realign_dna_window(), NT_create_resort_window(), NT_create_sai_from_pfold(), NT_create_searchManuallyNames_window(), NT_create_select_alignment_window(), NT_create_select_tree_window(), NT_create_species_join_window(), NT_create_splitAlignment_window(), NT_create_startEditorOnOldConfiguration_window(), NT_create_trackAliChanges_Awars(), NT_create_trackAliChanges_window(), NT_create_twoTreeSelection(), NT_createConcatenationWindow(), NT_database_optimization(), nt_delete_configuration(), NT_deleteValidNames(), NT_exit(), nt_extract_configuration(), NT_import_sequences(), NT_importValidNames(), nt_rename_configuration(), NT_resort_data_by_phylogeny(), NT_resort_data_by_user_criteria(), NT_restart(), NT_save_as_cb(), NT_save_quick_as_cb(), NT_save_quick_cb(), NT_select_bottom_tree(), nt_seq_load_cb(), NT_suggestValidNames(), NT_undo_cb(), NT_update_marked_counter(), popup_new_main_window(), popup_tree_admin_window(), realign_event(), rename_SAI_cb(), reorder_trees_cb(), selected_config_changed_cb(), selectValidNameFromList(), sort_dtree_by_other_tree_cb(), species_rename_join(), split_ali_cb(), trackAlignmentChanges(), transpro_event(), tree_load_cb(), tree_save_cb(), tree_vars_callback(), update_default_treename_cb(), and update_RangeList_cb().

bool merge_tool_running_as_client = true

static

Definition at line 743 of file NT_main.cxx.

Referenced by exit_from_merge(), and startup_gui().