ARB
Classes | Macros | Enumerations | Functions | Variables
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  streamSource { FROM_PIPE, FROM_FILE }
 

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_windowcreate_insertDeleteColumn_window (AW_root *root)
 
AW_windowcreate_insertDeleteBySAI_window (AW_root *root, GBDATA *gb_main)
 
AW_windowcreate_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_windowcreate_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_windowNT_create_save_quick_as_window (AW_root *aw_root, const char *base_name)
 
static void NT_database_optimization (AW_window *aww)
 
static AW_windowNT_create_database_optimization_window (AW_root *aw_root)
 
static AW_windowNT_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 charstream2str (streamSource source, const char *commandOrFile)
 
void removeTrailingNewlines (char *str)
 
void append_named_value (GBS_strstruct *out, const char *prefix, const char *value)
 
void append_command_output (GBS_strstruct *out, const char *prefix, const char *command)
 
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_windowcreate_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)
 
TreeNodeNT_get_tree_root_of_canvas (TREE_canvas *ntw)
 
static ARB_ERROR mark_referred_species (GBDATA *gb_main, const DBItemSet &referred)
 
static AW_windowcreate_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_windowNT_create_merge_from_window (AW_root *awr)
 
static AW_windowNT_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_canvasNT_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_windowpopup_new_main_window (AW_root *awr, int clone, TREE_canvas **result_ntw)
 
TREE_canvasNT_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 70 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 71 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"
#define AWAR_NTREE_TITLE_MODE   "tmp/title_mode"

Definition at line 73 of file NT_extern.cxx.

Referenced by nt_create_all_awars().

#define AWAR_DB_TYPE   AWAR_DBBASE "/type"

Definition at line 405 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 406 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"
#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

Enumerator
FROM_PIPE 
FROM_FILE 

Definition at line 563 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 1247 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(), and temp_minmax_changed_cb().

Referenced by nt_create_all_awars().

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
static void export_nds_cb ( AW_window aww,
bool  do_print 
)
static
static AW_window* create_nds_export_window ( AW_root root)
static
static void create_export_nds_awars ( AW_root awr,
AW_default  def 
)
static
static void selectedSpeciesChanged_cb ( AW_root awr)
static
static void expert_mode_changed_cb ( AW_root aw_root)
static
static void NT_toggle_expert_mode ( AW_window aww)
static
static void NT_toggle_focus_policy ( AW_window aww)
static
static void nt_create_all_awars ( AW_root awr)
static

Definition at line 180 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_nds_vars(), 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, 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
static void nt_run ( const char command)
static

Definition at line 321 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 331 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 337 of file NT_extern.cxx.

References nt_run().

Referenced by NT_exit(), and NT_restart().

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
static void NT_save_quick_cb ( AW_window aww)
static
static void NT_save_quick_as_cb ( AW_window aww)
static
static void NT_save_as_cb ( AW_window aww)
static
static AW_window* NT_create_save_quick_as_window ( AW_root aw_root,
const char base_name 
)
static
static void NT_database_optimization ( AW_window aww)
static
static AW_window* NT_create_database_optimization_window ( AW_root aw_root)
static
static AW_window* NT_create_save_as ( AW_root aw_root,
const char base_name 
)
static
static void NT_undo_cb ( AW_window ,
GB_UNDO_TYPE  undo_type,
TREE_canvas ntw 
)
static
static char* stream2str ( streamSource  source,
const char commandOrFile 
)
static
void removeTrailingNewlines ( char str)
inline

Definition at line 596 of file NT_extern.cxx.

Referenced by append_command_output().

void append_named_value ( GBS_strstruct out,
const char prefix,
const char value 
)
inline

Definition at line 601 of file NT_extern.cxx.

References GBS_global_string(), and GBS_strcat().

Referenced by append_command_output().

void append_command_output ( GBS_strstruct out,
const char prefix,
const char command 
)
inline

Definition at line 604 of file NT_extern.cxx.

References append_named_value(), FROM_PIPE, removeTrailingNewlines(), and stream2str().

static void NT_infomode_cb ( UNFIXED  ,
TREE_canvas canvas,
AWT_COMMAND_MODE  mode 
)
static
static void NT_mark_duplicates ( UNFIXED  ,
TREE_canvas ntw 
)
static
static void NT_justify_branch_lenghs ( UNFIXED  ,
TREE_canvas ntw 
)
static
static void relink_pseudo_species_to_organisms ( GBDATA *&  ref_gb_node,
char *&  ref_name,
GB_HASH organism_hash 
)
static
static void NT_pseudo_species_to_organism ( AW_window ,
TREE_canvas ntw 
)
static
static void NT_open_mask_window ( AW_window aww,
int  id,
GBDATA gb_main 
)
static
static void NT_create_mask_submenu ( AW_window_menu_modes awm)
static
static AW_window* create_colorize_species_window ( AW_root aw_root)
static
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 731 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
TreeNode* NT_get_tree_root_of_canvas ( TREE_canvas ntw)
static ARB_ERROR mark_referred_species ( GBDATA gb_main,
const DBItemSet referred 
)
static

Definition at line 836 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
static void merge_from_to ( AW_root awr,
const char db_awar_name,
bool  merge_to 
)
static
static void merge_from_cb ( AW_window aww,
AW_CL  cl_awarNamePtr 
)
static

Definition at line 873 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 874 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 876 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 884 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
static void canvas_tree_awar_changed_cb ( AW_awar ,
bool  ,
TREE_canvas ntw 
)
static
TREE_canvas* NT_get_canvas_by_index ( int  idx)

return canvas with index 'idx' [0...MAX_NT_WINDOWS-1]

Definition at line 945 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 
)
void NT_deselect_group ( AW_root awr)

Definition at line 988 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
static void group_awar_changed_cb ( AW_root awr)
static
static AW_window* popup_new_main_window ( AW_root awr,
int  clone,
TREE_canvas **  result_ntw 
)
static

create ARB_NTREE main window

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

Definition at line 1078 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_create_namesadmin_window(), AW_help_entry_pressed(), AW_init_color_group_defaults(), AW_insert_common_property_menu_entries(), AW_POPDOWN(), 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_nds_window(), 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, 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_startEditorOnOldConfiguration_window(), NT_create_syncScroll_window(), NT_create_trackAliChanges_window(), NT_createConcatenationWindow(), NT_createMergeSimilarSpeciesWindow(), NT_delete_mark_all_cb(), NT_deleteValidNames(), 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)

Variable Documentation

nt_item_type_species_selector item_type_species
static

Definition at line 716 of file NT_extern.cxx.

Referenced by NT_open_mask_window().

bool track_group_selection_by_canvas = true
static

Definition at line 992 of file NT_extern.cxx.