#include "PerfMeter.h"
#include "pars_main.hxx"
#include "pars_klprops.hxx"
#include "pars_awars.h"
#include "ap_tree_nlen.hxx"
#include "ap_main.hxx"
#include <ColumnStat.hxx>
#include <gui_aliview.hxx>
#include <macros.hxx>
#include <nds.h>
#include <TreeCallbacks.hxx>
#include <aw_awars.hxx>
#include <aw_preset.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <awt.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_filter.hxx>
#include <awt_config_manager.hxx>
#include <arb_progress.h>
#include <arb_misc.h>
#include <arb_defs.h>
#include <arb_global_defs.h>
#include <ad_cb.h>
#include <list>
#include <map>
#include <mod_rlimit.h>

Include dependency graph for PARS_main.cxx:

Classes
class	InsertData

class	AP_subtree

struct	EdgeBetween

struct	BestEdge

struct	NodeInsertOrder

class	PartialSequence

class	LowDataCheck

Macros
#define	AWAR_COLUMNSTAT_BASE "tmp/pars/colstat"

#define	AWAR_COLUMNSTAT_NAME AWAR_COLUMNSTAT_BASE "/name"

#define	AWT_TREE_PARS(ntw) DOWNCAST(AWT_graphic_parsimony*, (ntw)->gfx)

Typedefs
typedef vector< AP_tree_nlen * >	InsertedSpecies

typedef InsertedSpecies::const_iterator	InsertSpeciesIterator

Enumerations
enum	AddWhat { NT_ADD_MARKED, NT_ADD_SELECTED }

Functions
AWT_graphic_parsimony *	global_tree ()

AP_pars_root *	global_tree_root ()

static void	set_keep_ghostnodes ()

static void	delete_kept_ghostnodes ()

static __ATTR__NORETURN void	pars_exit (AW_window *aww)

static void	AP_user_push_cb (AW_window *aww)

static void	AP_user_pop_cb (AW_window aww, TREE_canvas ntw)

static int	sort_sequences_by_length (const char , long leaf0_ptr, const char , long leaf1_ptr)

static long	transform_gbd_to_leaf (const char key, long val, void )

static long	toInserted (const char , long val, void cd_toInsert)

int	maxAllowedInsertions (int inTree)

int	calcInsertNow (int toInsert, int inTree)

static long	calc_steps (int toInsert, int inTree)

static void	insert_species_into_tree (const InsertSpeciesIterator begin, const InsertSpeciesIterator end, arb_progress &progress)

static void	insert_all_species_into_tree (GB_HASH *&hash)

static void	nt_add (AWT_graphic_parsimony *agt, AddWhat what, bool quick)

static GB_ERROR	nt_best_partial_match_rec (list< PartialSequence > &partial, const AP_tree_nlen *tree)

static void	count_partial_and_full (const AP_tree_nlen at, int partial, int full, int zombies, int default_value, bool define_if_undef)

static const AP_tree_nlen *	find_least_deep_leaf (const AP_tree_nlen at, int depth, int min_depth)

AP_tree_nlen *	find_least_deep_leaf (AP_tree_nlen at, int depth, int min_depth)

static void	push_partial (const char , long val, void cd_partial)

static void	nt_add_partial (AWT_graphic_parsimony *agt)

static void	NT_add_partial_and_update (UNFIXED, TREE_canvas *ntw)

static void	nt_add_and_update (AWT_canvas *ntw, AddWhat what, bool quick)

static void	NT_add_and_NNI (UNFIXED, TREE_canvas *ntw, AddWhat what)

static void	NT_add_quick (UNFIXED, TREE_canvas *ntw, AddWhat what)

static void	nt_reAdd (AWT_graphic_parsimony *agt, AddWhat what, bool quick)

static void	nt_reAdd_and_update (AWT_canvas *ntw, AddWhat what, bool quick)

static void	NT_reAdd_and_NNI (UNFIXED, TREE_canvas *ntw, AddWhat what)

static void	NT_reAdd_quick (UNFIXED, TREE_canvas *ntw, AddWhat what)

static void	calc_branchlengths_and_reorder (AWT_graphic_parsimony *agt)

static void	NT_calc_branchlengths_reorder_and_update (AW_window , TREE_canvas ntw)

static void	NT_bootstrap (AW_window , TREE_canvas ntw, bool limit_only)

static void	optimizeTree (AWT_graphic_parsimony *agt, const KL_Settings &settings)

static void	NT_optimize (AW_window , TREE_canvas ntw)

static void	recursiveNNI (AWT_graphic_parsimony *agt, EdgeSpec whichEdges)

static void	NT_recursiveNNI (AW_window , TREE_canvas ntw)

static int	calculate_default_random_repeat (long leafs)

static void	update_random_repeat (AW_root awr, AWT_graphic_parsimony agt)

static void	mixtree_and_calclengths (AWT_graphic_parsimony *agt, int repeat, int percent, EdgeSpec whichEdges)

static void	randomMixTree (AW_window aww, TREE_canvas ntw)

static AW_window *	createOptimizeWindow (AW_root aw_root, TREE_canvas ntw)

static GB_ERROR	pars_check_size (AW_root awr, GB_ERROR &warning, const adfiltercbstruct filterDef)

static void	pars_reset_optimal_parsimony (AW_window *aww)

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

static void	pars_start_cb (AW_window aw_parent, WeightedFilter wfilt, const PARS_commands *cmds)

static AW_window *	create_pars_init_window (AW_root awr, const PARS_commands cmds)

static void	create_optimize_vars (AW_root *aw_root, AW_default props)

static void	pars_create_all_awars (AW_root awr, AW_default aw_def, GBDATA gb_main)

void	PARS_map_viewer (GBDATA *gb_species, AD_MAP_VIEWER_TYPE vtype)

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

Variables
static ArbParsimony *	GLOBAL_PARS = NULp

AP_main *	ap_main

static AWT_config_mapping_def	optimizer_config_mapping []

static AWT_predefined_config	optimizer_predefined_configs []

static AW_root *	AD_map_viewer_aw_root = NULp

Macro Definition Documentation

#define AWAR_COLUMNSTAT_BASE "tmp/pars/colstat"

Definition at line 54 of file PARS_main.cxx.

#define AWAR_COLUMNSTAT_NAME AWAR_COLUMNSTAT_BASE "/name"

Definition at line 55 of file PARS_main.cxx.

Referenced by create_pars_init_window().

#define AWT_TREE_PARS ( ntw ) DOWNCAST(AWT_graphic_parsimony*, (ntw)->gfx)

Definition at line 57 of file PARS_main.cxx.

Referenced by nt_add_and_update(), NT_add_partial_and_update(), NT_calc_branchlengths_reorder_and_update(), NT_optimize(), nt_reAdd_and_update(), NT_recursiveNNI(), pars_start_cb(), and randomMixTree().

Typedef Documentation

typedef vector<AP_tree_nlen*> InsertedSpecies

Definition at line 214 of file PARS_main.cxx.

typedef InsertedSpecies::const_iterator InsertSpeciesIterator

Definition at line 290 of file PARS_main.cxx.

Enumeration Type Documentation

enum AddWhat

Enumerator
NT_ADD_MARKED
NT_ADD_SELECTED

Definition at line 616 of file PARS_main.cxx.

Function Documentation

AWT_graphic_parsimony* global_tree ( )

inline

Definition at line 61 of file PARS_main.cxx.

References ArbParsimony::get_tree().

Referenced by delete_kept_ghostnodes(), global_tree_root(), and pars_start_cb().

AP_pars_root* global_tree_root ( )

inline

Definition at line 62 of file PARS_main.cxx.

References AWT_graphic_parsimony::get_tree_root(), and global_tree().

Referenced by pars_start_cb().

static void set_keep_ghostnodes ( )

static

Definition at line 73 of file PARS_main.cxx.

References ASSERT_NO_ERROR, GB_searchOrCreate_int(), GB_set_temporary(), AP_main::get_tree_root(), and ta.

Referenced by pars_start_cb().

static void delete_kept_ghostnodes ( )

static

Definition at line 82 of file PARS_main.cxx.

References aw_message(), error(), GB_delete(), GB_entry(), GB_get_root(), AP_main::get_graphic_tree(), AP_main::get_tree_root(), global_tree(), NULp, AWT_graphic_tree::save_to_DB(), and ta.

Referenced by pars_exit().

static __ATTR__NORETURN void pars_exit ( AW_window * aww )

static

Definition at line 102 of file PARS_main.cxx.

References AP_main::accept_all(), ap_main, delete_kept_ghostnodes(), EXIT_SUCCESS, AP_main::get_gb_main(), AW_window::get_root(), NULp, shutdown_macro_recording(), and AW_root::unlink_awars_from_DB().

Referenced by create_pars_init_window(), and pars_start_cb().

static void AP_user_push_cb ( AW_window * aww )

static

Definition at line 119 of file PARS_main.cxx.

References AW_root::awar(), AWAR_STACKPOINTER, AW_window::get_root(), AP_main::get_user_push_counter(), AP_main::remember_user_state(), and AW_awar::write_int().

Referenced by AP_user_pop_cb(), and pars_start_cb().

static void AP_user_pop_cb	(	AW_window *	aww,
		TREE_canvas *	ntw
	)

static

Definition at line 124 of file PARS_main.cxx.

References AP_user_push_cb(), aw_message(), AW_root::awar(), AWAR_STACKPOINTER, AW_window::get_root(), AP_main::get_user_push_counter(), AWT_canvas::request_save(), AP_main::revert_user_state(), and AW_awar::write_int().

Referenced by pars_start_cb().

static int sort_sequences_by_length	(	const char *	,
		long	leaf0_ptr,
		const char *	,
		long	leaf1_ptr
	)

static

Definition at line 165 of file PARS_main.cxx.

References ap_assert, and cmp.

Referenced by insert_all_species_into_tree().

static long transform_gbd_to_leaf	(	const char *	key,
		long	val,
		void *
	)

static

Definition at line 182 of file PARS_main.cxx.

References ARB_strdup(), destroy(), DOWNCAST, error(), GBS_global_string(), GBT_message(), AP_main::get_tree_root(), MIN_SEQUENCE_LENGTH, and NULp.

Referenced by nt_add().

static long toInserted	(	const char *	,
		long	val,
		void *	cd_toInsert
	)

static

Definition at line 216 of file PARS_main.cxx.

Referenced by insert_all_species_into_tree().

int maxAllowedInsertions ( int inTree )

inline

Definition at line 224 of file PARS_main.cxx.

Referenced by calcInsertNow(), and insert_all_species_into_tree().

int calcInsertNow	(	int	toInsert,
		int	inTree
	)

inline

Definition at line 228 of file PARS_main.cxx.

References maxAllowedInsertions(), and min.

Referenced by calc_steps(), and insert_all_species_into_tree().

static long calc_steps	(	int	toInsert,
		int	inTree
	)

static

Definition at line 233 of file PARS_main.cxx.

References ap_assert, calcInsertNow(), leafs_2_edges(), and UNROOTED.

Referenced by insert_all_species_into_tree().

static void insert_species_into_tree	(	const InsertSpeciesIterator	begin,
		const InsertSpeciesIterator	end,
		arb_progress &	progress
	)

static

static void insert_all_species_into_tree ( GB_HASH *& hash )

static

Definition at line 541 of file PARS_main.cxx.

References ap_assert, ASSERT_VALID_TREE, calc_steps(), calcInsertNow(), GBS_free_hash(), GBS_hash_do_loop(), GBS_hash_do_sorted_loop(), GBS_hash_elements(), AP_main::get_tree_root(), insert_species_into_tree(), maxAllowedInsertions(), NULp, rootEdge(), rootNode(), AP_tree_edge::set_root(), sort_sequences_by_length(), and toInserted().

Referenced by nt_add().

static void nt_add	(	AWT_graphic_parsimony *	agt,
		AddWhat	what,
		bool	quick
	)

static

static GB_ERROR nt_best_partial_match_rec	(	list< PartialSequence > &	partial,
		const AP_tree_nlen *	tree
	)

static

Definition at line 862 of file PARS_main.cxx.

References error(), GB_await_error(), GBT_is_partial(), and NULp.

Referenced by nt_add_partial().

static void count_partial_and_full	(	const AP_tree_nlen *	at,
		int *	partial,
		int *	full,
		int *	zombies,
		int	default_value,
		bool	define_if_undef
	)

static

Definition at line 889 of file PARS_main.cxx.

References GBT_is_partial().

Referenced by nt_add_partial().

static const AP_tree_nlen* find_least_deep_leaf	(	const AP_tree_nlen *	at,
		int	depth,
		int *	min_depth
	)

static

Definition at line 906 of file PARS_main.cxx.

References NULp.

Referenced by find_least_deep_leaf(), and nt_add_partial().

AP_tree_nlen* find_least_deep_leaf	(	AP_tree_nlen *	at,
		int	depth,
		int *	min_depth
	)

inline

Definition at line 924 of file PARS_main.cxx.

References find_least_deep_leaf().

static void push_partial	(	const char *	,
		long	val,
		void *	cd_partial
	)

static

Definition at line 928 of file PARS_main.cxx.

Referenced by nt_add_partial().

static void nt_add_partial ( AWT_graphic_parsimony * agt )

static

Definition at line 936 of file PARS_main.cxx.

References ap_assert, count_partial_and_full(), destroy(), error(), AWT_graphic::exports, father, find_least_deep_leaf(), GB_abort_transaction(), GB_await_error(), GB_begin_transaction(), GB_commit_transaction(), GB_INT, gb_main, GB_MIND_CASE, GBS_create_hash(), GBS_free_hash(), GBS_global_string(), GBS_hash_do_const_loop(), GBS_write_hash(), GBT_add_new_species_changekey(), GBT_find_sequence(), GBT_first_marked_species(), GBT_get_name_or_description(), GBT_get_species_count(), GBT_is_partial(), GBT_message(), GBT_next_marked_species(), AP_main::get_aliname(), POS_TREE1::get_father(), AWT_graphic_tree::get_gbmain(), nt_best_partial_match_rec(), NT_remove_species_in_tree_from_hash(), NULp, push_partial(), AWT_graphic_exports::request_save(), and rootNode().

Referenced by NT_add_partial_and_update().

static void NT_add_partial_and_update	(	UNFIXED	,
		TREE_canvas *	ntw
	)

static

Definition at line 1134 of file PARS_main.cxx.

References AWT_TREE_PARS, and nt_add_partial().

Referenced by pars_start_cb().

static void nt_add_and_update	(	AWT_canvas *	ntw,
		AddWhat	what,
		bool	quick
	)

static

Definition at line 1142 of file PARS_main.cxx.

References AWT_TREE_PARS, and nt_add().

Referenced by NT_add_and_NNI(), and NT_add_quick().

static void NT_add_and_NNI	(	UNFIXED	,
		TREE_canvas *	ntw,
		AddWhat	what
	)

static

Definition at line 1147 of file PARS_main.cxx.

References nt_add_and_update().

Referenced by pars_start_cb().

static void NT_add_quick	(	UNFIXED	,
		TREE_canvas *	ntw,
		AddWhat	what
	)

static

Definition at line 1148 of file PARS_main.cxx.

References nt_add_and_update().

Referenced by pars_start_cb().

static void nt_reAdd	(	AWT_graphic_parsimony *	agt,
		AddWhat	what,
		bool	quick
	)

static

Definition at line 1153 of file PARS_main.cxx.

References ap_assert, AWT_REMOVE_MARKED, AWT_graphic_parsimony::get_root_node(), AWT_graphic_parsimony::get_tree_root(), nt_add(), and NT_ADD_MARKED.

Referenced by nt_reAdd_and_update().

static void nt_reAdd_and_update	(	AWT_canvas *	ntw,
		AddWhat	what,
		bool	quick
	)

static

Definition at line 1161 of file PARS_main.cxx.

References AWT_TREE_PARS, and nt_reAdd().

Referenced by NT_reAdd_and_NNI(), and NT_reAdd_quick().

static void NT_reAdd_and_NNI	(	UNFIXED	,
		TREE_canvas *	ntw,
		AddWhat	what
	)

static

Definition at line 1166 of file PARS_main.cxx.

References nt_reAdd_and_update().

Referenced by pars_start_cb().

static void NT_reAdd_quick	(	UNFIXED	,
		TREE_canvas *	ntw,
		AddWhat	what
	)

static

Definition at line 1167 of file PARS_main.cxx.

References nt_reAdd_and_update().

Referenced by pars_start_cb().

static void calc_branchlengths_and_reorder ( AWT_graphic_parsimony * agt )

static

Definition at line 1171 of file PARS_main.cxx.

References BIG_BRANCHES_TO_TOP, AWT_graphic_tree::reorderTree(), and rootEdge().

Referenced by NT_calc_branchlengths_reorder_and_update(), optimizeTree(), and recursiveNNI().

static void NT_calc_branchlengths_reorder_and_update	(	AW_window *	,
		TREE_canvas *	ntw
	)

static

Definition at line 1177 of file PARS_main.cxx.

References AWT_TREE_PARS, and calc_branchlengths_and_reorder().

Referenced by pars_start_cb().

static void NT_bootstrap	(	AW_window *	,
		TREE_canvas *	ntw,
		bool	limit_only
	)

static

Definition at line 1182 of file PARS_main.cxx.

References ANY_EDGE, AP_BL_BL_ONLY, AP_BL_BOOTSTRAP_ESTIMATE, AP_BL_BOOTSTRAP_LIMIT, AWT_TREE, BIG_BRANCHES_TO_TOP, AWT_graphic_tree::get_root_node(), NULp, AWT_graphic_tree::reorderTree(), rootEdge(), and AWT_graphic_tree::set_logical_root_to().

Referenced by pars_start_cb().

static void optimizeTree	(	AWT_graphic_parsimony *	agt,
		const KL_Settings &	settings
	)

static

Definition at line 1193 of file PARS_main.cxx.

References ASSERT_VALID_TREE, calc_branchlengths_and_reorder(), AWT_graphic_parsimony::get_parsimony(), ArbParsimony::optimize_tree(), and rootNode().

Referenced by NT_optimize().

static void NT_optimize	(	AW_window *	,
		TREE_canvas *	ntw
	)

static

Definition at line 1199 of file PARS_main.cxx.

References AWT_canvas::awr, AWT_TREE_PARS, and optimizeTree().

Referenced by createOptimizeWindow().

static void recursiveNNI	(	AWT_graphic_parsimony *	agt,
		EdgeSpec	whichEdges
	)

static

Definition at line 1204 of file PARS_main.cxx.

References arb_progress::aborted(), AP_BL_NNI_ONLY, calc_branchlengths_and_reorder(), GBS_global_string(), NULp, rootEdge(), rootNode(), and arb_progress::subtitle().

Referenced by NT_recursiveNNI().

static void NT_recursiveNNI	(	AW_window *	,
		TREE_canvas *	ntw
	)

static

Definition at line 1223 of file PARS_main.cxx.

References AWT_canvas::awr, AWT_TREE_PARS, recursiveNNI(), and KL_Settings::whichEdges.

Referenced by createOptimizeWindow().

static int calculate_default_random_repeat ( long leafs )

static

Definition at line 1229 of file PARS_main.cxx.

Referenced by update_random_repeat().

static void update_random_repeat	(	AW_root *	awr,
		AWT_graphic_parsimony *	agt
	)

static

Definition at line 1236 of file PARS_main.cxx.

References AW_root::awar(), AWAR_RAND_REPEAT, calculate_default_random_repeat(), AWT_graphic_parsimony::get_root_node(), and AW_awar::write_int().

Referenced by pars_start_cb().

static void mixtree_and_calclengths	(	AWT_graphic_parsimony *	agt,
		int	repeat,
		int	percent,
		EdgeSpec	whichEdges
	)

static

Definition at line 1242 of file PARS_main.cxx.

References AWT_graphic::exports, AWT_graphic_exports::request_save(), rootEdge(), arb_progress::subtitle(), and WEIGHTED.

Referenced by randomMixTree().

static void randomMixTree	(	AW_window *	aww,
		TREE_canvas *	ntw
	)

static

Definition at line 1258 of file PARS_main.cxx.

References AW_root::awar(), AWAR_RAND_PERCENT, AWAR_RAND_REPEAT, AWT_TREE_PARS, BIG_BRANCHES_TO_TOP, AW_window::get_root(), mixtree_and_calclengths(), AW_awar::read_int(), rootNode(), TreeNode::set_root(), ARB_edge::son(), and KL_Settings::whichEdges.

Referenced by createOptimizeWindow().

static AW_window* createOptimizeWindow	(	AW_root *	aw_root,
		TREE_canvas *	ntw
	)

static

Definition at line 1310 of file PARS_main.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_OPTI_MARKED_ONLY, AWAR_OPTI_SKIP_FOLDED, AWAR_RAND_PERCENT, AWAR_RAND_REPEAT, AWT_insert_config_manager(), create_kernighan_properties_window(), AW_window::load_xfig(), makeHelpCallback(), NT_optimize(), NT_recursiveNNI(), NULp, and randomMixTree().

Referenced by pars_start_cb().

static GB_ERROR pars_check_size	(	AW_root *	awr,
		GB_ERROR &	warning,
		const adfiltercbstruct *	filterDef
	)

static

Definition at line 1427 of file PARS_main.cxx.

References ap_assert, AW_root::awar(), AWAR_ALIGNMENT, AWAR_TREE, adfiltercbstruct::def_filter, error(), GB_clear_error(), GB_get_usable_memory(), GB_have_error(), GBS_global_string(), GBS_readable_size(), GBT_get_alignment_len(), GBT_size_of_tree(), AP_main::get_gb_main(), NULp, and AW_awar::read_string().

Referenced by pars_start_cb().

static void pars_reset_optimal_parsimony ( AW_window * aww )

static

Definition at line 1473 of file PARS_main.cxx.

References AW_root::awar(), AWAR_BEST_PARSIMONY, AWAR_PARSIMONY, AW_window::get_root(), AW_awar::read_int(), and AW_awar::write_int().

Referenced by pars_start_cb().

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

static

Definition at line 1506 of file PARS_main.cxx.

References AWT_trigger_remote_action(), AWT_canvas::gb_main, nt_mode_event(), and NULp.

Referenced by pars_start_cb().

static void pars_start_cb	(	AW_window *	aw_parent,
		WeightedFilter *	wfilt,
		const PARS_commands *	cmds
	)

static

Definition at line 1511 of file PARS_main.cxx.

References PARS_commands::add_marked, PARS_commands::add_selected, AP_JUMP_BY_BUTTON, AP_LIST_SIMPLE, AP_TREE_NORMAL, AP_TREE_RADIAL, AP_user_pop_cb(), AP_user_push_cb(), AW_window::at(), AW_window::at_newline(), AW_window::at_x(), AW_window::auto_space(), aw_ask_sure(), AW_AT_MAXSIZE, AW_create_gc_window(), AW_insert_common_property_menu_entries(), aw_message(), aw_popup_exit(), AW_preset_window(), AW_save_properties(), AW_root::awar(), AWAR_ALIGNMENT, AWAR_BEST_PARSIMONY, AWAR_FOOTER, AWAR_FOOTER_MAX_LEN, AWAR_PARSIMONY, AWAR_STACKPOINTER, AWAR_TREE, AWM_ALL, AWT_KEEP_MARKED, AWT_MODE_EMPTY, AWT_MODE_GROUP, AWT_MODE_INFO, AWT_MODE_KERNINGHAN, AWT_MODE_LZOOM, AWT_MODE_MARK, AWT_MODE_MOVE, AWT_MODE_NNI, AWT_MODE_OPTIMIZE, AWT_MODE_SELECT, AWT_MODE_SETROOT, AWT_MODE_SWAP, AWT_MODE_ZOOM, AWT_popup_print_window(), AWT_popup_tree_export_window(), AWT_REMOVE_MARKED, AWT_REMOVE_NO_SEQUENCE, AWT_REMOVE_ZOMBIES, AWT_TREE_PARS, BIG_BRANCHES_TO_TOP, AW_window::button_length(), PARS_commands::calc_bootstrap, PARS_commands::calc_branch_lengths, AW_window::callback(), AW_window::close_sub_menu(), LowDataCheck::count(), AW_window::create_button(), create_kernighan_properties_window(), AW_window::create_menu(), AW_window::create_mode(), createOptimizeWindow(), error(), GB_begin_transaction(), GB_commit_transaction(), GB_end_transaction(), gb_main, AWT_canvas::gb_main, GBS_global_string(), GBS_global_string_copy(), GBT_set_startup_alignment(), AWT_canvas::gc_manager, ArbParsimony::generate_tree(), WeightedFilter::get_adfiltercbstruct(), AW_window::get_at_position(), AW_window::get_at_yposition(), AP_main::get_gb_main(), LowDataCheck::get_inner(), LowDataCheck::get_leafs(), AW_window::get_root(), AWT_graphic_tree::get_tree_style(), AW_window::get_window_id(), global_tree(), global_tree_root(), AW_window::help_text(), AW_window::hide(), AW_window_menu_modes::init(), AP_tree_edge::initialize(), AW_window::insert_help_topic(), insert_macro_menu_entry(), AW_window::insert_menu_topic(), AW_window::insert_sub_menu(), AW_window::label(), AW_window::label_length(), AW_at_storage::make(), makeHelpCallback(), MIN_SEQUENCE_LENGTH, NDS_create_window(), NT_add_and_NNI(), NT_ADD_MARKED, NT_add_partial_and_update(), NT_add_quick(), NT_ADD_SELECTED, NT_bootstrap(), NT_calc_branchlengths_reorder_and_update(), NT_insert_collapse_submenu(), NT_insert_mark_submenus(), NT_jump_cb(), nt_mode_event(), NT_reAdd_and_NNI(), NT_reAdd_quick(), NT_reload_tree_event(), NT_remove_bootstrap(), NT_remove_leafs(), NT_reset_lzoom_cb(), NT_reset_pzoom_cb(), NT_resort_tree_cb(), NT_set_tree_style(), NULp, pars_check_size(), pars_exit(), PARS_infomode_cb(), pars_reset_optimal_parsimony(), PARS_tree_init(), PARS_commands::quit, AW_awar::read_char_pntr(), AW_window::restore_at_from(), rootNode(), AW_window::sep______________(), AW_window::set_bottom_area_height(), AW_window::set_info_area_height(), set_keep_ghostnodes(), AWT_graphic_tree::set_tree_style(), AW_window::shadow_width(), AW_window::show(), stringize_pscan, arb_progress::subtitle(), ta, TREE_create_settings_window(), TREE_install_update_callbacks(), TREEDISP_STACKSIZE, update_random_repeat(), and warning().

Referenced by create_pars_init_window().

static AW_window* create_pars_init_window	(	AW_root *	awr,
		const PARS_commands *	cmds
	)

static

Definition at line 1822 of file PARS_main.cxx.

References AWAR_ALIGNMENT, AWAR_COLUMNSTAT_NAME, AWAR_FILTER_NAME, AWAR_TREE, AWM_ALL, AWM_EXP, awt_create_ALI_selection_list(), awt_create_select_filter_win(), awt_create_TREE_selection_list(), COLSTAT_create_selection_window(), gb_main, WeightedFilter::get_adfiltercbstruct(), WeightedFilter::get_column_stat(), AP_main::get_gb_main(), AW_window::load_xfig(), makeHelpCallback(), pars_exit(), and pars_start_cb().

Referenced by ARB_main().

static void create_optimize_vars	(	AW_root *	aw_root,
		AW_default	props
	)

static

static void pars_create_all_awars	(	AW_root *	awr,
		AW_default	aw_def,
		GBDATA *	gb_main
	)

static

void PARS_map_viewer	(	GBDATA *	gb_species,
		AD_MAP_VIEWER_TYPE	vtype
	)

Definition at line 1991 of file PARS_main.cxx.

References ADMVT_INFO, ADMVT_SELECT, AW_root::awar(), AWAR_SPECIES_NAME, GBT_get_name(), and AW_awar::write_string().

Referenced by ArbParsimony::generate_tree().

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

Variable Documentation

ArbParsimony* GLOBAL_PARS = NULp

static

Definition at line 59 of file PARS_main.cxx.

AP_main* ap_main

Definition at line 65 of file PARS_main.cxx.

Referenced by ArbParsimony::kernighan_optimize_tree(), AP_tree_edge::kl_rec(), PARSIMONY_testenv< SEQTYPE >::load_tree(), AP_tree_edge::nni_mutPerSite(), AP_tree_edge::nni_rec(), pars_exit(), PARS_tree_init(), PARSIMONY_testenv< SEQTYPE >::PARSIMONY_testenv(), push_all_upnode_sequences(), undefine_branchlengths(), update_undefined_leaf_branchlength(), and PARSIMONY_testenv< SEQTYPE >::~PARSIMONY_testenv().

AWT_config_mapping_def optimizer_config_mapping[]

static

Initial value:

= {
    { AWAR_OPTI_MARKED_ONLY, "marked_only" },
    { AWAR_OPTI_SKIP_FOLDED, "skip_folded" },
    
    { AWAR_RAND_PERCENT, "rand_percent" },
    { AWAR_KL_MAXDEPTH, "maxdepth" },
    { AWAR_KL_INCDEPTH, "incdepth" },
    { AWAR_KL_STATIC_ENABLED, "static" },
    { AWAR_KL_STATIC_DEPTH1,  "s_depth1" },
    { AWAR_KL_STATIC_DEPTH2,  "s_depth2" },
    { AWAR_KL_STATIC_DEPTH3,  "s_depth3" },
    { AWAR_KL_STATIC_DEPTH4,  "s_depth4" },
    { AWAR_KL_STATIC_DEPTH5,  "s_depth5" },
    { AWAR_KL_DYNAMIC_ENABLED, "dynamic" },
    { AWAR_KL_DYNAMIC_START,   "start" },
    { AWAR_KL_DYNAMIC_MAXX,    "maxx" },
    { AWAR_KL_DYNAMIC_MAXY,    "maxy" },
    { NULp, NULp }
}

Definition at line 1271 of file PARS_main.cxx.

AWT_predefined_config optimizer_predefined_configs[]

static

Initial value:

= {
    {
        "*minimum_static_reduction",
        "Sets paths allowed by static reduction to maximum\n(causing the minimal reduction)",
        "s_depth1='8';s_depth2='6';s_depth3='6';s_depth4='6';s_depth5='6';static='1'" 
    },
    {
        "*whole_tree_level8",
        "Level-8-optimization of whole tree\n(no path reduction)",
        "dynamic='0';incdepth='0';marked_only='0';maxdepth='8';skip_folded='0';static='0'"
    },
    { NULp, NULp, NULp }
}

Definition at line 1296 of file PARS_main.cxx.

AW_root* AD_map_viewer_aw_root = NULp

static

Definition at line 1989 of file PARS_main.cxx.

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