NT_extern.cxx File Reference

#include "map_viewer.h"
#include "NT_local.h"
#include "ad_trees.h"
#include "NT_group_search.h"
#include <seq_quality.h>
#include <multi_probe.hxx>
#include <st_window.hxx>
#include <GEN.hxx>
#include <EXP.hxx>
#include <TreeCallbacks.hxx>
#include <AW_rename.hxx>
#include <probe_gui.hxx>
#include <primer_design.hxx>
#include <gde.hxx>
#include <awtc_submission.hxx>
#include <macros.hxx>
#include <nds.h>
#include <db_query.h>
#include <dbui.h>
#include <refentries.h>
#include <insdel.h>
#include <awti_export.hxx>
#include <awti_import.hxx>
#include <awt.hxx>
#include <awt_input_mask.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_www.hxx>
#include <awt_TreeAwars.hxx>
#include <awt_misc.hxx>
#include <aw_color_groups.hxx>
#include <aw_advice.hxx>
#include <aw_preset.hxx>
#include <aw_awars.hxx>
#include <aw_global_awars.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_select.hxx>
#include <rootAsWin.h>
#include <ad_cb.h>
#include <arb_strbuf.h>
#include <arb_file.h>
#include <arb_version.h>
#include <saicalc.h>

Include dependency graph for NT_extern.cxx:

Go to the source code of this file.

Classes
class	FINAL_TYPE< SEQTYPE >
	xml element More...
class	TREE_canvas_registry

Macros
#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"
#define	AWAR_DB_TYPE   AWAR_DBBASE "/type"
#define	AWAR_DB_COMPRESSION   AWAR_DBBASE "/compression"
#define	AWAR_DB_OPTI_TREENAME   AWAR_DBBASE "/optimize_tree_name"
#define	TREE_BUTTON_OVERSIZE   6
#define	EDIT_XSIZE   50
#define	EDIT_YSIZE   30

Enumerations
enum	Export_Type { EXPORT_SPACE_PADDED_RIGHT_ALIGNED = 1, EXPORT_SPACE_PADDED_LEFT_ALIGNED = 4, EXPORT_TAB_SEPARATED = 2, EXPORT_COMMA_SEPARATED = 3 }

Functions
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)
static void	nt_changesecurity (AW_root *aw_root)
static void	export_nds_cb (AW_window *aww, bool do_print)
static AW_window *	create_nds_export_window (AW_root *root)
static void	create_export_nds_awars (AW_root *awr, AW_default def)
static void	selectedSpeciesChanged_cb (AW_root *awr)
static void	expert_mode_changed_cb (AW_root *aw_root)
static void	NT_toggle_expert_mode (AW_window *aww)
static void	NT_toggle_focus_policy (AW_window *aww)
static void	nt_create_all_awars (AW_root *awr)
static bool	nt_disconnect_from_db (AW_root *aw_root, GBDATA *&gb_main_ref)
static void	nt_run (const char *command)
void	NT_start (const char *arb_ntree_args, bool restart_with_new_ARB_PID)
static __ATTR__NORETURN void	really_exit (int exitcode, bool kill_my_clients)
void	NT_exit (AW_window *aws, int exitcode)
void	NT_restart (AW_root *aw_root, const char *arb_ntree_args)
static void	nt_start_2nd_arb (AW_window *aww, bool quit)
static void	NT_save_quick_cb (AW_window *aww)
static void	NT_save_quick_as_cb (AW_window *aww)
static void	NT_save_as_cb (AW_window *aww)
static AW_window *	NT_create_save_quick_as_window (AW_root *aw_root, const char *base_name)
static void	NT_database_optimization (AW_window *aww)
static AW_window *	NT_create_database_optimization_window (AW_root *aw_root)
static AW_window *	NT_create_save_as (AW_root *aw_root, const char *base_name)
static void	NT_undo_cb (AW_window *, GB_UNDO_TYPE undo_type, TREE_canvas *ntw)
static void	NT_infomode_cb (UNFIXED, TREE_canvas *canvas, AWT_COMMAND_MODE mode)
static void	NT_mark_duplicates (UNFIXED, TREE_canvas *ntw)
static void	NT_justify_branch_lenghs (UNFIXED, TREE_canvas *ntw)
static void	relink_pseudo_species_to_organisms (GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash)
static void	NT_pseudo_species_to_organism (AW_window *, TREE_canvas *ntw)
static void	NT_open_mask_window (AW_window *aww, int id, GBDATA *gb_main)
static void	NT_create_mask_submenu (AW_window_menu_modes *awm)
static AW_window *	create_colorize_species_window (AW_root *aw_root)
static void	NT_update_marked_counter (GBDATA *, AW_window *aww)
static void	NT_alltree_remove_leafs (AW_window *, GBT_TreeRemoveType mode, GBDATA *gb_main)
TreeNode *	NT_get_tree_root_of_canvas (TREE_canvas *ntw)
static ARB_ERROR	mark_referred_species (GBDATA *gb_main, const DBItemSet &referred)
static AW_window *	create_mark_by_refentries_window (AW_root *awr, GBDATA *gbmain)
static void	merge_from_to (AW_root *awr, const char *db_awar_name, bool merge_to)
static void	merge_from_cb (AW_window *aww, AW_CL cl_awarNamePtr)
static void	merge_into_cb (AW_window *aww, AW_CL cl_awarNamePtr)
static AW_window *	NT_create_merge_from_window (AW_root *awr)
static AW_window *	NT_create_merge_to_window (AW_root *awr)
static void	update_main_window_title (AW_root *awr, AW_window_menu_modes *aww, int clone)
static void	canvas_tree_awar_changed_cb (AW_awar *, bool, TREE_canvas *ntw)
TREE_canvas *	NT_get_canvas_by_index (int idx)
void	NT_fill_canvas_selection_list (class AW_selection_list *sellst, TREE_canvas *to_skip)
void	NT_deselect_group (AW_root *awr)
static void	group_selected_by_canvas_cb (AWT_graphic_tree *gfx)
static void	group_awar_changed_cb (AW_root *awr)
static AW_window *	popup_new_main_window (AW_root *awr, int clone, TREE_canvas **result_ntw)
TREE_canvas *	NT_create_main_window (AW_root *aw_root)

Variables
static nt_item_type_species_selector	item_type_species
static bool	track_group_selection_by_canvas = true

Macro Definition Documentation

#define AWAR_EXPORT_NDS   "tmp/export_nds"

Definition at line 71 of file NT_extern.cxx.

Referenced by create_export_nds_awars(), create_nds_export_window(), and export_nds_cb().

#define AWAR_EXPORT_NDS_SEPARATOR   AWAR_EXPORT_NDS "/delimiter"

Definition at line 72 of file NT_extern.cxx.

Referenced by create_export_nds_awars(), create_nds_export_window(), and export_nds_cb().

#define AWAR_MARKED_SPECIES_COUNTER   "tmp/disp_marked_species"

Definition at line 73 of file NT_extern.cxx.

Referenced by nt_create_all_awars(), NT_update_marked_counter(), and popup_new_main_window().

#define AWAR_NTREE_TITLE_MODE   "tmp/title_mode"

Definition at line 74 of file NT_extern.cxx.

Referenced by nt_create_all_awars().

#define AWAR_DB_TYPE   AWAR_DBBASE "/type"

Definition at line 481 of file NT_extern.cxx.

Referenced by NT_create_save_as(), and NT_save_as_cb().

#define AWAR_DB_COMPRESSION   AWAR_DBBASE "/compression"

Definition at line 482 of file NT_extern.cxx.

Referenced by NT_create_save_as(), and NT_save_as_cb().

#define AWAR_DB_OPTI_TREENAME   AWAR_DBBASE "/optimize_tree_name"

Definition at line 483 of file NT_extern.cxx.

Referenced by NT_create_database_optimization_window(), and NT_database_optimization().

#define TREE_BUTTON_OVERSIZE   6

Referenced by popup_new_main_window().

#define EDIT_XSIZE   50

Referenced by popup_new_main_window().

#define EDIT_YSIZE   30

Referenced by popup_new_main_window().

Enumeration Type Documentation

enum Export_Type

Enumerator
EXPORT_SPACE_PADDED_RIGHT_ALIGNED
EXPORT_SPACE_PADDED_LEFT_ALIGNED
EXPORT_TAB_SEPARATED
EXPORT_COMMA_SEPARATED

Definition at line 84 of file NT_extern.cxx.

Function Documentation

void create_probe_design_variables	(	AW_root *	aw_root,
		AW_default	def,
		AW_default	global
	)

Definition at line 1235 of file probe_design.cxx.

References ArbProbeCollection::add(), AW_awar::add_callback(), ARB_strpartdup(), auto_match_changed(), aw_message(), AW_root::awar_float(), AW_root::awar_int(), AWAR_ITARGET_STRING, AWAR_MAX_MISMATCHES, AWAR_PC_AUTO_MATCH, AWAR_PC_CURRENT_COLLECTION, AWAR_PC_MATCH_BIAS, AWAR_PC_MATCH_NHITS, AWAR_PC_MATCH_WEIGHTS, AWAR_PC_MATCH_WIDTH, AWAR_PC_MISMATCH_THRESHOLD, AWAR_PC_SELECTED_PROBE, AWAR_PC_TARGET_NAME, AWAR_PC_TARGET_STRING, AWAR_PD_COMMON_EXP_SPLIT, AWAR_PD_DESIGN_CLIPRESULT, AWAR_PD_DESIGN_EXP_DT, AWAR_PD_DESIGN_EXP_DTEDGE, AWAR_PD_DESIGN_GENE, AWAR_PD_DESIGN_MAX_ECOLIPOS, AWAR_PD_DESIGN_MAX_GC, AWAR_PD_DESIGN_MAX_LENGTH, AWAR_PD_DESIGN_MAX_TEMP, AWAR_PD_DESIGN_MAXBOND, AWAR_PD_DESIGN_MIN_ECOLIPOS, AWAR_PD_DESIGN_MIN_GC, AWAR_PD_DESIGN_MIN_LENGTH, AWAR_PD_DESIGN_MIN_TEMP, AWAR_PD_DESIGN_MINTARGETS, AWAR_PD_DESIGN_MISHIT, AWAR_PD_MATCH_ALSO_REVCOMP, AWAR_PD_MATCH_AUTOMATCH, AWAR_PD_MATCH_LIM_NMATCH, AWAR_PD_MATCH_MARKHITS, AWAR_PD_MATCH_MAX_RES, AWAR_PD_MATCH_NHITS, AWAR_PD_MATCH_NMATCHES, AWAR_PD_MATCH_RESOLVE, AWAR_PD_MATCH_SORTBY, AWAR_PD_MATCH_WRITE2TMP, AWAR_PD_SELECTED_MATCH, AWAR_PROBE_ADMIN_PT_SERVER, AWAR_PROBE_CREATE_GENE_SERVER, AWAR_PT_SERVER, AWAR_SPECIES_NAME, AWAR_SPV_ACI_COMMAND, AWAR_SPV_DB_FIELD_NAME, AWAR_SPV_DB_FIELD_WIDTH, AWAR_SPV_SAI_2_PROBE, AWAR_SPV_SELECTED_PROBE, AW_root::awar_string(), AWAR_TARGET_STRING, bond_awar_name(), buffer, ArbProbeCollection::clear(), GBS_global_string(), GBT_splitNdestroy_string(), gc_minmax_changed_cb(), get_probe_collection(), ArbProbeCollection::getParameters(), NULp, PD, probelength_changed_cb(), AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), REPLACE_TARGET_CONTROL_CHARS, resolved_probe_chosen(), selected_match_changed_cb(), seq, AW_awar::set_minmax(), AW_awar::set_srt(), ArbProbeCollection::setParameters(), CharPtrArray::size(), SPLIT_DROPEMPTY, and temp_minmax_changed_cb().

Referenced by nt_create_all_awars().

void create_insertDeleteColumn_variables	(	AW_root *	root,
		AW_default	db1
	)

Definition at line 135 of file NT_ins_col.cxx.

References AW_awar::add_callback(), AWAR_CURSOR_POSITION, AWAR_INSDEL_AFFECTED, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_CONTAINS, AWAR_INSDEL_DELETABLE, AWAR_INSDEL_DIRECTION, AWAR_INSDEL_RANGE, AWAR_INSDEL_SAI, AWAR_INSDEL_SAI_CHARS, AWAR_INSDEL_WHAT, AW_root::awar_int(), AW_root::awar_string(), BEHIND, DOESNT_CONTAIN, NT_global::gb_main, GLOBAL, info2bio(), range_changed_cb(), RANGES, AW_awar::set_minmax(), update_RangeList(), and update_RangeList_cb().

Referenced by nt_create_all_awars().

AW_window* create_insertDeleteColumn_window

(

AW_root *

root

)

Definition at line 201 of file NT_ins_col.cxx.

References AW_POPDOWN(), AWAR_CURSOR_POSITION, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_DELETABLE, DELETE, insdel_event(), INSERT, makeHelpCallback(), and NULp.

Referenced by popup_new_main_window().

AW_window* create_insertDeleteBySAI_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 268 of file NT_ins_col.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_INSDEL_AFFECTED, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_CONTAINS, AWAR_INSDEL_DELETABLE, AWAR_INSDEL_DIRECTION, AWAR_INSDEL_RANGE, AWAR_INSDEL_SAI, AWAR_INSDEL_SAI_CHARS, AWAR_INSDEL_WHAT, awt_create_SAI_selection_button(), AWT_insert_config_manager(), BEHIND, cleanup_when_closing(), CONTAINS, DELETE, DOESNT_CONTAIN, INFRONTOF, insdel_sai_event(), INSERT, makeHelpCallback(), NULp, RANGES, and SINGLE_COLUMNS.

Referenced by popup_new_main_window().

AW_window* create_tree_window	(	AW_root *	aw_root,
		AWT_graphic *	awd
	)

static void nt_changesecurity ( AW_root *  aw_root )

static

Definition at line 91 of file NT_extern.cxx.

References AW_root::awar(), AWAR_SECURITY_LEVEL, GB_change_my_security(), NT_global::gb_main, GB_pop_transaction(), GB_push_transaction(), GLOBAL, and AW_awar::read_int().

Referenced by nt_create_all_awars().

static void export_nds_cb ( AW_window *  aww, bool  do_print  )

static

Definition at line 98 of file NT_extern.cxx.

References arb_assert, aw_message(), AW_refresh_fileselection(), AW_root::awar(), AWAR_EXPORT_NDS, AWAR_EXPORT_NDS_SEPARATOR, AWAR_TREE, error(), EXPORT_COMMA_SEPARATED, EXPORT_SPACE_PADDED_LEFT_ALIGNED, EXPORT_SPACE_PADDED_RIGHT_ALIGNED, fputc(), fputs(), NT_global::gb_main, GB_textprint(), GBT_count_marked_species(), GBT_first_marked_species(), GBT_next_marked_species(), GBT_split_string(), AW_window::get_root(), GLOBAL, label, max, NDS_OUTPUT_COMMA_SEPARATED, NDS_OUTPUT_TAB_SEPARATED, nt_assert, NULp, AW_awar::read_int(), AW_awar::read_string(), CharPtrArray::size(), SPLIT_KEEPEMPTY, and ta.

Referenced by create_nds_export_window().

static AW_window* create_nds_export_window ( AW_root *  root )

static

Definition at line 189 of file NT_extern.cxx.

References AW_create_standard_fileselection(), AW_POPDOWN(), AWAR_EXPORT_NDS, AWAR_EXPORT_NDS_SEPARATOR, EXPORT_COMMA_SEPARATED, export_nds_cb(), EXPORT_SPACE_PADDED_LEFT_ALIGNED, EXPORT_SPACE_PADDED_RIGHT_ALIGNED, EXPORT_TAB_SEPARATED, AW_window::load_xfig(), and makeHelpCallback().

Referenced by popup_new_main_window().

static void create_export_nds_awars ( AW_root *  awr, AW_default  def  )

static

Definition at line 224 of file NT_extern.cxx.

References AW_create_fileselection_awars(), AWAR_EXPORT_NDS, AWAR_EXPORT_NDS_SEPARATOR, AW_root::awar_int(), and EXPORT_TAB_SEPARATED.

Referenced by nt_create_all_awars().

static void selectedSpeciesChanged_cb ( AW_root *  awr )

static

Definition at line 229 of file NT_extern.cxx.

References AW_root::awar(), AWAR_GROUP, AWAR_INFO_BUTTON_TEXT, AWAR_SPECIES_NAME, fputs(), NULp, AW_awar::read_char_pntr(), AW_awar::write_pointer(), and AW_awar::write_string().

Referenced by nt_create_all_awars().

static void expert_mode_changed_cb ( AW_root *  aw_root )

static

Definition at line 240 of file NT_extern.cxx.

References AW_root::awar(), AWAR_AWM_MASK, AWAR_EXPERT, AWM_ALL, AWM_BASIC, AW_awar::read_int(), and AW_awar::write_int().

Referenced by nt_create_all_awars().

static void NT_toggle_expert_mode ( AW_window *  aww )

static

Definition at line 244 of file NT_extern.cxx.

References AW_root::awar(), AWAR_EXPERT, AW_window::get_root(), and AW_awar::toggle_toggle().

Referenced by popup_new_main_window().

static void NT_toggle_focus_policy ( AW_window *  aww )

static

Definition at line 245 of file NT_extern.cxx.

References AW_root::awar(), AWAR_AW_FOCUS_FOLLOWS_MOUSE, AW_window::get_root(), and AW_awar::toggle_toggle().

Referenced by popup_new_main_window().

static void nt_create_all_awars ( AW_root *  awr )

static

Definition at line 247 of file NT_extern.cxx.

References AW_awar::add_callback(), AP_create_consensus_var(), ARB_bind_global_awars(), ARB_format_alignment(), AW_create_namesadmin_awars(), aw_message(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_DB_COMMENT, AWAR_ERROR_MESSAGES, AWAR_EXPERT, AWAR_FOOTER, AWAR_INFO_BUTTON_TEXT, AW_root::awar_int(), AWAR_MARKED_SPECIES_COUNTER, AWAR_NTREE_TITLE_MODE, AWAR_SAI_COLOR_STR, AWAR_SAI_GLOBAL, AWAR_SAI_NAME, AWAR_SECURITY_LEVEL, AWAR_SPECIES_NAME, AW_root::awar_string(), AWAR_TOPAREA_SAIS, AWAR_TREE, awt_create_aww_vars(), AWTC_create_submission_variables(), DBUI::create_dbui_awars(), create_export_nds_awars(), create_group_search_awars(), create_insertDeleteColumn_variables(), create_primer_design_variables(), create_probe_design_variables(), RefEntries::create_refentries_awars(), create_trees_var(), error(), EXP_create_awars(), expert_mode_changed_cb(), NT_global::gb_main, GB_read_clients(), GBK_terminatef(), GDE_init(), GDE_WINDOWTYPE_DEFAULT, GEN_create_awars(), GLOBAL, NDS_create_vars(), nt_changesecurity(), NT_create_alignment_vars(), NT_create_compare_taxonomy_awars(), NT_create_extendeds_vars(), NT_create_multifurcate_tree_awars(), NT_create_resort_awars(), NT_create_trackAliChanges_Awars(), NT_create_transpro_variables(), NT_createConcatenationAwars(), NT_createValidNamesAwars(), NULp, selectedSpeciesChanged_cb(), SQ_create_awars(), AW_awar::touch(), TREE_create_awars(), and AW_awar::write_int().

Referenced by NT_create_main_window().

static bool nt_disconnect_from_db ( AW_root *  aw_root, GBDATA *&  gb_main_ref  )

static

Definition at line 331 of file NT_extern.cxx.

References aw_question(), AWT_destroy_input_masks(), GB_close(), GB_last_saved_clock(), GB_last_saved_time(), gb_main, GB_read_clients(), GB_read_clock(), GB_time_of_day(), GBCMS_shutdown(), GBS_global_string_copy(), nt_assert, NULp, and AW_root::unlink_awars_from_DB().

Referenced by NT_exit(), and NT_restart().

static void nt_run ( const char *  command )

static

Definition at line 387 of file NT_extern.cxx.

References error(), GBK_dump_backtrace(), and GBK_system().

Referenced by NT_start(), and really_exit().

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().

static __ATTR__NORETURN void really_exit ( int  exitcode, bool  kill_my_clients  )

static

Definition at line 403 of file NT_extern.cxx.

References nt_run().

Referenced by NT_exit(), and NT_restart().

void NT_exit	(	AW_window *	aws,
		int	exitcode
	)

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().

void NT_restart	(	AW_root *	aw_root,
		const char *	arb_ntree_args
	)

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().

static void nt_start_2nd_arb ( AW_window *  aww, bool  quit  )

static

Definition at line 428 of file NT_extern.cxx.

References ARB_strdup(), AW_root::awar(), AWAR_SAVED_DB_PATH, GB_split_full_path(), AW_window::get_root(), NT_restart(), NT_start(), NULp, and AW_awar::read_char_pntr().

Referenced by popup_new_main_window().

static void NT_save_quick_cb ( AW_window *  aww )

static

Definition at line 448 of file NT_extern.cxx.

References aw_message(), AW_refresh_fileselection(), AW_root::awar(), AWAR_DB_PATH, AWAR_DBBASE, AWAR_SAVED_DB_PATH, AW_root::dont_save_awars_with_default_value(), error(), NT_global::gb_main, GB_save_quick(), AW_window::get_root(), GLOBAL, AW_awar::read_string(), and AW_awar::write_string().

Referenced by popup_new_main_window().

static void NT_save_quick_as_cb ( AW_window *  aww )

static

Definition at line 465 of file NT_extern.cxx.

References AW_refresh_fileselection(), AW_root::awar(), AWAR_DB_PATH, AWAR_DBBASE, AWAR_SAVED_DB_PATH, error(), NT_global::gb_main, GB_save_quick_as(), AW_window::get_root(), GLOBAL, AW_window::hide_or_notify(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by NT_create_save_quick_as_window().

static void NT_save_as_cb ( AW_window *  aww )

static

Definition at line 485 of file NT_extern.cxx.

References AW_refresh_fileselection(), AW_root::awar(), AWAR_DB_COMPRESSION, AWAR_DB_PATH, AWAR_DB_TYPE, AWAR_DBBASE, AWAR_SAVED_DB_PATH, AW_root::dont_save_awars_with_default_value(), error(), NT_global::gb_main, GB_save(), GBS_global_string_copy(), AW_window::get_root(), GLOBAL, AW_window::hide_or_notify(), AW_awar::read_char_pntr(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by NT_create_save_as().

static AW_window* NT_create_save_quick_as_window ( AW_root *  aw_root, const char *  base_name  )

static

Definition at line 505 of file NT_extern.cxx.

References AW_create_standard_fileselection(), AW_POPDOWN(), AWAR_DB_COMMENT, makeHelpCallback(), NT_save_quick_as_cb(), and NULp.

Referenced by popup_new_main_window().

static void NT_database_optimization ( AW_window *  aww )

static

Definition at line 532 of file NT_extern.cxx.

References arb_progress::allow_title_reuse(), AW_root::awar(), AWAR_DB_OPTI_TREENAME, error(), GB_begin_transaction(), GB_end_transaction(), NT_global::gb_main, GB_optimize(), GBT_check_data(), GBT_compress_sequence_tree2(), GBT_get_alignment_names(), AW_window::get_root(), GLOBAL, AW_window::hide_or_notify(), arb_progress::inc_and_check_user_abort(), NULp, AW_awar::read_string(), CharPtrArray::size(), and WEIGHTED.

Referenced by NT_create_database_optimization_window().

static AW_window* NT_create_database_optimization_window ( AW_root *  aw_root )

static

Definition at line 568 of file NT_extern.cxx.

References AW_POPDOWN(), AWAR_DB_OPTI_TREENAME, AW_root::awar_string(), awt_create_TREE_selection_list(), NT_global::gb_main, GBT_name_of_largest_tree(), GLOBAL, makeHelpCallback(), NT_database_optimization(), NULp, and ta.

Referenced by NT_create_save_as(), and popup_new_main_window().

static AW_window* NT_create_save_as ( AW_root *  aw_root, const char *  base_name  )

static

Definition at line 597 of file NT_extern.cxx.

References AW_create_standard_fileselection(), AW_POPDOWN(), AWAR_DB_COMMENT, AWAR_DB_COMPRESSION, AWAR_DB_TYPE, AWT_insert_DBcompression_selector(), AWT_insert_DBsaveType_selector(), makeHelpCallback(), NT_create_database_optimization_window(), NT_save_as_cb(), and NULp.

Referenced by popup_new_main_window().

static void NT_undo_cb ( AW_window *  , GB_UNDO_TYPE  undo_type, TREE_canvas *  ntw  )

static

Definition at line 636 of file NT_extern.cxx.

References aw_message(), error(), NT_global::gb_main, GB_undo(), GLOBAL, AWT_canvas::request_refresh(), and ta.

Referenced by popup_new_main_window().

static void NT_infomode_cb ( UNFIXED  , TREE_canvas *  canvas, AWT_COMMAND_MODE  mode  )

static

Definition at line 646 of file NT_extern.cxx.

References AWT_canvas::awr, AWT_canvas::gb_main, nt_mode_event(), NULp, and DBUI::popup_species_info_window().

Referenced by popup_new_main_window().

static void NT_mark_duplicates ( UNFIXED  , TREE_canvas *  ntw  )

static

Definition at line 651 of file NT_extern.cxx.

References AWT_TREE, AWT_canvas::gb_main, AP_tree::mark_duplicates(), NT_mark_all_cb(), NULp, AWT_canvas::request_structure_update(), and ta.

Referenced by popup_new_main_window().

static void NT_justify_branch_lenghs ( UNFIXED  , TREE_canvas *  ntw  )

static

Definition at line 663 of file NT_extern.cxx.

References AWT_TREE, AWT_canvas::gb_main, AP_tree::justify_branch_lenghs(), AWT_canvas::request_save_and_zoom_reset(), and ta.

Referenced by popup_new_main_window().

static void relink_pseudo_species_to_organisms ( GBDATA *&  ref_gb_node, char *&  ref_name, GB_HASH *  organism_hash  )

static

Definition at line 682 of file NT_extern.cxx.

References GBT_read_string(), GEN_find_origin_organism(), and GEN_is_pseudo_gene_species().

Referenced by NT_pseudo_species_to_organism().

static void NT_pseudo_species_to_organism ( AW_window *  , TREE_canvas *  ntw  )

static

Definition at line 699 of file NT_extern.cxx.

References AWT_TREE, AWT_canvas::gb_main, GBS_free_hash(), GBT_create_organism_hash(), relink_pseudo_species_to_organisms(), AP_tree::relink_tree(), AWT_canvas::request_save(), and ta.

Referenced by popup_new_main_window().

static void NT_open_mask_window ( AW_window *  aww, int  id, GBDATA *  gb_main  )

static

Definition at line 751 of file NT_extern.cxx.

References AWT_initialize_input_mask(), AWT_look_input_mask(), gb_main, AW_window::get_root(), item_type_species, and nt_assert.

Referenced by NT_create_mask_submenu().

static void NT_create_mask_submenu ( AW_window_menu_modes *  awm )

static

Definition at line 757 of file NT_extern.cxx.

References AWT_create_mask_submenu(), AWT_IT_SPECIES, NT_global::gb_main, GLOBAL, and NT_open_mask_window().

Referenced by popup_new_main_window().

static AW_window* create_colorize_species_window ( AW_root *  aw_root )

static

Definition at line 760 of file NT_extern.cxx.

References QUERY::create_colorize_items_window(), NT_global::gb_main, GLOBAL, and SPECIES_get_selector().

Referenced by popup_new_main_window().

static void NT_update_marked_counter ( GBDATA *  , AW_window *  aww  )

static

Updates marked counter and issues redraw on tree if number of marked species changes. Called on any change of species_information container.

Definition at line 764 of file NT_extern.cxx.

References AW_root::awar(), AWAR_MARKED_SPECIES_COUNTER, AWAR_TREE_REFRESH, buffer, NT_global::gb_main, GBS_global_string(), GBT_count_marked_species(), AW_window::get_root(), GLOBAL, AW_awar::read_string(), AW_awar::touch(), and AW_awar::write_string().

Referenced by popup_new_main_window().

static void NT_alltree_remove_leafs ( AW_window *  , GBT_TreeRemoveType  mode, GBDATA *  gb_main  )

static

Definition at line 781 of file NT_extern.cxx.

References aw_message(), aw_message_if(), GB_transaction::close(), destroy(), CharPtrArray::empty(), error(), GBS_free_hash(), GBS_global_string(), GBT_create_species_hash(), GBT_get_tree_names(), GBT_read_tree(), GBT_remove_leafs(), GBT_REMOVE_MARKED, GBT_REMOVE_ZOMBIES, GBT_write_tree(), arb_progress::inc_and_check_user_abort(), nt_assert, NULp, CharPtrArray::size(), arb_progress::subtitle(), ta, and UNCOVERED.

Referenced by popup_new_main_window().

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().

static ARB_ERROR mark_referred_species ( GBDATA *  gb_main, const DBItemSet &  referred  )

static

Definition at line 869 of file NT_extern.cxx.

References GB_write_flag(), GBT_mark_all(), s, and ta.

Referenced by create_mark_by_refentries_window().

static AW_window* create_mark_by_refentries_window ( AW_root *  awr, GBDATA *  gbmain  )

static

Definition at line 880 of file NT_extern.cxx.

References RefEntries::create_refentries_window(), mark_referred_species(), NULp, and SPECIES_get_selector().

Referenced by popup_new_main_window().

static void merge_from_to ( AW_root *  awr, const char *  db_awar_name, bool  merge_to  )

static

Definition at line 891 of file NT_extern.cxx.

References AW_root::awar(), AWT_system_cb(), GBK_singlequote(), GBS_global_string(), and AW_awar::read_char_pntr().

Referenced by merge_from_cb(), and merge_into_cb().

static void merge_from_cb ( AW_window *  aww, AW_CL  cl_awarNamePtr  )

static

Definition at line 906 of file NT_extern.cxx.

References AW_window::get_root(), and merge_from_to().

Referenced by NT_create_merge_from_window().

static void merge_into_cb ( AW_window *  aww, AW_CL  cl_awarNamePtr  )

static

Definition at line 907 of file NT_extern.cxx.

References AW_window::get_root(), and merge_from_to().

Referenced by NT_create_merge_to_window().

static AW_window* NT_create_merge_from_window ( AW_root *  awr )

static

Definition at line 909 of file NT_extern.cxx.

References awt_create_load_box(), merge_from_cb(), and NULp.

Referenced by popup_new_main_window().

static AW_window* NT_create_merge_to_window ( AW_root *  awr )

static

Definition at line 917 of file NT_extern.cxx.

References AW_POPDOWN(), awt_create_load_box(), merge_into_cb(), and NULp.

Referenced by popup_new_main_window().

static void update_main_window_title ( AW_root *  awr, AW_window_menu_modes *  aww, int  clone  )

static

Definition at line 929 of file NT_extern.cxx.

References AW_root::awar(), AWAR_DB_NAME, GBS_global_string(), AW_awar::read_char_pntr(), and AW_window::set_window_title().

Referenced by popup_new_main_window().

static void canvas_tree_awar_changed_cb ( AW_awar *  , bool  , TREE_canvas *  ntw  )

static

Definition at line 939 of file NT_extern.cxx.

References AP_JUMP_REASON_TREE, AW_root::awar(), AWAR_NTREE_MAIN_WINDOW_COUNT, NT_reload_tree_event(), NULp, AW_root::SINGLETON, AW_awar::touch(), and TREE_auto_jump_cb().

Referenced by popup_new_main_window().

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().

static void group_selected_by_canvas_cb ( AWT_graphic_tree *  gfx )

static

Definition at line 1027 of file NT_extern.cxx.

References AW_root::awar(), AWAR_GROUP, Group::get_group_data(), TREE_canvas::get_index(), Group::get_name(), AWT_graphic_tree::get_root(), AWT_graphic_tree::get_selected_group(), group, Group::is_valid(), and AW_awar::write_pointer().

Referenced by popup_new_main_window().

static void group_awar_changed_cb ( AW_root *  awr )

static

Definition at line 1047 of file NT_extern.cxx.

References AP_JUMP_REASON_GROUP, AW_root::awar(), AWAR_GROUP, AWAR_SPECIES_NAME, AWT_TREE, AWT_graphic_tree::deselect_group(), fputc(), fputs(), GB_entry(), GB_get_father(), GB_read_char_pntr(), TREE_canvas_registry::get_canvas(), TREE_canvas_registry::get_count(), ARB_seqtree_root::get_gb_tree(), Group::get_group_data(), AWT_graphic_tree::get_selected_group(), AWT_graphic_tree::get_tree_root(), TREE_canvas_registry::instance(), Group::is_valid(), NULp, AW_awar::read_pointer(), AWT_canvas::request_refresh(), ta, TREE_auto_jump_cb(), and AW_awar::write_string().

Referenced by popup_new_main_window().

static AW_window* popup_new_main_window ( AW_root *  awr, int  clone, TREE_canvas **  result_ntw  )

static

create ARB_NTREE main window

Parameters

awr	application root
clone	== 0 -> first window (full functionality); >0 -> additional tree views (restricted functionality)
result_ntw	is set to the created TREE_canvas (passed pointer may be NULp if result is not needed)

Definition at line 1111 of file NT_extern.cxx.

References AW_awar::add_callback(), AP_create_con_expert_window(), AP_create_max_freq_window(), AP_create_pos_var_pars_window(), AP_JUMP_BY_BUTTON, AP_LIST_NDS, AP_LIST_SIMPLE, AP_TREE_IRS, AP_TREE_NORMAL, AP_TREE_RADIAL, ARB_keep_string(), ARB_VERSION_DETAILED, AW_window::at(), AW_window::at_attach_to(), AW_window::at_newline(), AW_window::auto_space(), AW_advice(), AW_ADVICE_TOGGLE_AND_HELP, AW_create_gc_window(), AW_help_entry_pressed(), AW_init_color_group_defaults(), AW_insert_common_property_menu_entries(), AW_POPDOWN(), AW_popup_namesadmin_window(), AW_preset_window(), AW_save_properties(), AW_root::awar(), AWAR_DB_NAME, AWAR_DBBASE, AWAR_DEFAULT_ALIGNMENT, AWAR_FOOTER, AWAR_FOOTER_MAX_LEN, AWAR_GROUP, AWAR_INFO_BUTTON_TEXT, AWAR_MARKED_SPECIES_COUNTER, AWAR_SECURITY_LEVEL, AW_root::awar_string(), AWAR_TREE, awm, AWM_ALL, AWM_EXP, AWT_console(), AWT_create_www_window(), AWT_KEEP_MARKED, AWT_MODE_GROUP, AWT_MODE_INFO, AWT_MODE_LENGTH, AWT_MODE_LINE, AWT_MODE_LZOOM, AWT_MODE_MARK, AWT_MODE_MOVE, AWT_MODE_MULTIFURC, AWT_MODE_ROTATE, AWT_MODE_SELECT, AWT_MODE_SETROOT, AWT_MODE_SPREAD, AWT_MODE_SWAP, AWT_MODE_WWW, AWT_MODE_ZOOM, AWT_openURL(), AWT_popup_print_window(), AWT_popup_tree_export_window(), AWT_registerTreeAwarCallback(), AWT_REMOVE_MARKED, AWT_REMOVE_ZOMBIES, AWT_system_cb(), AWT_system_in_console_cb(), AWTC_create_rename_window(), AWTC_create_submission_window(), BIG_BRANCHES_ALTERNATING, BIG_BRANCHES_TO_BOTTOM, BIG_BRANCHES_TO_CENTER, BIG_BRANCHES_TO_EDGE, BIG_BRANCHES_TO_TOP, AW_window::button_length(), AW_window::callback(), canvas_tree_awar_changed_cb(), AW_window::close_sub_menu(), create_AWTC_export_window(), AW_window::create_button(), create_colorize_species_window(), create_insertDeleteBySAI_window(), create_insertDeleteColumn_window(), create_mark_by_refentries_window(), AW_window::create_menu(), AW_window::create_mode(), create_multiprobe_window(), create_nds_export_window(), AW_window::create_option_menu(), create_primer_design_window(), create_probe_admin_window(), create_probe_design_window(), create_probe_match_window(), create_probe_match_with_specificity_window(), DBUI::create_species_query_window(), EDIT_XSIZE, EDIT_YSIZE, EXIT_SUCCESS, GB_add_callback(), GB_CB_CHANGED, NT_global::gb_main, GB_pop_transaction(), GB_print_debug_information(), GB_push_transaction(), gb_species_data, GB_UNDO_REDO, GB_UNDO_UNDO, GBS_global_string_copy(), GBT_compression_test(), GBT_existing_tree(), GBT_get_species_data(), GBT_REMOVE_MARKED, GBT_REMOVE_ZOMBIES, AWT_canvas::gc_manager, GDE_load_menu(), GEN_create_first_map(), GEN_create_genes_submenu(), GEN_is_genome_db(), AW_window::get_at_position(), AW_window::get_at_xposition(), AW_window::get_at_yposition(), TREE_canvas::get_index(), AWT_graphic_tree::get_tree_style(), GLOBAL, group_awar_changed_cb(), group_selected_by_canvas_cb(), AW_window::help_text(), AW_window_menu_modes::init(), AW_window::insert_default_option(), DBUI::insert_field_admin_menuitems(), AW_window::insert_help_topic(), insert_macro_menu_entry(), AW_window::insert_menu_topic(), AW_window::insert_option(), AW_window::insert_sub_menu(), AWT_graphic_tree::install_group_changed_callback(), TREE_canvas_registry::instance(), launch_MapViewer_cb(), AW_window::local_id(), makeHelpCallback(), MAX_NT_WINDOWS, NDS_create_window(), NT_activate_configMarkers_display(), NT_alltree_remove_leafs(), NT_configure_treeShader(), NT_count_different_chars(), NT_create_alignment_admin_window(), NT_create_branch_analysis_window(), NT_create_colstat_2_gnuplot_window(), NT_create_compare_taxonomy_window(), NT_create_compareTopologies_window(), NT_create_consense_window(), NT_create_database_optimization_window(), NT_create_dna_2_pro_window(), NT_create_extendeds_window(), NT_create_mask_submenu(), NT_create_merge_from_window(), NT_create_merge_to_window(), NT_create_moveGroupInfo_window(), NT_create_multifurcate_tree_window(), NT_create_realign_dna_window(), NT_create_resort_window(), NT_create_sai_from_pfold(), NT_create_save_as(), NT_create_save_quick_as_window(), NT_create_searchManuallyNames_window(), NT_create_select_alignment_window(), NT_create_select_tree_window(), NT_create_sort_tree_by_other_tree_window(), NT_create_species_join_window(), NT_create_splitAlignment_window(), NT_create_startEditorOnOldConfiguration_window(), NT_create_syncroot_window(), NT_create_syncScroll_window(), NT_create_trackAliChanges_window(), NT_createConcatenationWindow(), NT_createMergeSimilarSpeciesWindow(), NT_delete_mark_all_cb(), NT_deleteValidNames(), NT_edit_bootstrap(), NT_exit(), NT_generate_tree(), NT_import_sequences(), NT_importValidNames(), NT_infomode_cb(), NT_insert_collapse_submenu(), NT_insert_mark_submenus(), NT_jump_cb(), NT_justify_branch_lenghs(), NT_mark_duplicates(), nt_mode_event(), NT_move_boot_branch(), NT_popup_configuration_admin(), NT_pseudo_species_to_organism(), NT_reload_tree_event(), NT_remove_bootstrap(), NT_remove_leafs(), NT_rerepair_DB(), NT_reset_branchlengths(), NT_reset_lzoom_cb(), NT_reset_pzoom_cb(), NT_resort_data_by_phylogeny(), NT_resort_tree_cb(), NT_save_quick_cb(), NT_scale_tree(), NT_select_bottom_tree(), NT_set_tree_style(), nt_start_2nd_arb(), NT_start_editor_on_tree(), NT_suggestValidNames(), NT_toggle_expert_mode(), NT_toggle_focus_policy(), NT_undo_cb(), NT_update_marked_counter(), NULp, popup_group_search_window(), DBUI::popup_species_info_window(), popup_tree_admin_window(), AW_awar::read_char_pntr(), TREE_canvas_registry::register_canvas(), SAI_popup_calculator_window(), AW_window::sep______________(), AW_window::set_bottom_area_height(), AW_window::set_info_area_height(), AWT_canvas::set_mode(), AWT_graphic_tree::set_tree_style(), AW_window::shadow_width(), RootAsWindowCallback::simple(), SQ_create_seq_quality_window(), STAT_create_chimera_check_window(), TREE_BUTTON_OVERSIZE, TREE_create_settings_window(), TREE_install_update_callbacks(), AW_awar::update(), update_main_window_title(), AW_window::update_option_menu(), AW_awar::write_string(), XCMD_ASYNC_WAIT_ON_ERROR, and XCMD_ASYNC_WAITKEY.

Referenced by NT_create_main_window().

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().

Variable Documentation

nt_item_type_species_selector item_type_species

static

Definition at line 749 of file NT_extern.cxx.

Referenced by NT_open_mask_window().

bool track_group_selection_by_canvas = true

static

Definition at line 1025 of file NT_extern.cxx.