#include "tree_position.h"
#include "ad_trees.h"
#include "NT_tree_cmp.h"
#include <CT_ctree.hxx>
#include <TreeAdmin.h>
#include <TreeRead.h>
#include <TreeWrite.h>
#include <TreeCallbacks.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_modules.hxx>
#include <awt_TreeAwars.hxx>
#include <aw_awars.hxx>
#include <aw_edit.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <aw_select.hxx>
#include <arb_strbuf.h>
#include <arb_file.h>
#include <arb_diff.h>
#include <arb_defs.h>
#include <cctype>
#include <awt_config_manager.hxx>

Include dependency graph for ad_trees.cxx:

Classes
class	CombinedPosInfo

class	SortByTopo

Macros
#define	AWAR_TREE_SAV "ad_tree/"

#define	AWAR_TREE_TMP "tmp/ad_tree/"

#define	AWAR_TREE_SECURITY AWAR_TREE_TMP "tree_security"

#define	AWAR_TREE_REM AWAR_TREE_TMP "tree_rem"

#define	AWAR_TREE_IMPORT AWAR_TREE_TMP "import_tree"

#define	AWAR_GROUPXFER_SAV AWAR_TREE_SAV "groupxfer/"

#define	AWAR_GROUPXFER_SOURCE AWAR_GROUPXFER_SAV "restrict"

#define	AWAR_GROUPXFER_OVERWRITE_MODE AWAR_GROUPXFER_SAV "overwrite"

#define	AWAR_GROUPXFER_INGROUP_ABS AWAR_GROUPXFER_SAV "ingroup/abs"

#define	AWAR_GROUPXFER_INGROUP_REL AWAR_GROUPXFER_SAV "ingroup/rel"

#define	AWAR_GROUPXFER_INGROUP_LIM AWAR_GROUPXFER_SAV "ingroup/lim"

#define	AWAR_GROUPXFER_OUTGROUP_ABS AWAR_GROUPXFER_SAV "outgroup/abs"

#define	AWAR_GROUPXFER_OUTGROUP_REL AWAR_GROUPXFER_SAV "outgroup/rel"

#define	AWAR_GROUPXFER_OUTGROUP_LIM AWAR_GROUPXFER_SAV "outgroup/lim"

#define	AWAR_GROUPXFER_UNKNOWN_ABS AWAR_GROUPXFER_SAV "unknown"

#define	AWAR_GROUPXFER_KEELING AWAR_GROUPXFER_SAV "keeling"

#define	AWAR_GROUPXFER_ACI AWAR_GROUPXFER_SAV "aci"

#define	AWAR_TREE_EXPORT_FILEBASE AWAR_TREE_TMP "export_tree"

#define	AWAR_TREE_EXPORT_FILTER AWAR_TREE_EXPORT_FILEBASE "/filter"

#define	AWAR_TREE_EXPORT_NAME AWAR_TREE_EXPORT_FILEBASE "/file_name"

#define	AWAR_TREE_EXPORT_SAV AWAR_TREE_SAV "export_tree/"

#define	AWAR_TREE_EXPORT_FORMAT AWAR_TREE_EXPORT_SAV "format"

#define	AWAR_TREE_EXPORT_NDS AWAR_TREE_EXPORT_SAV "NDS"

#define	AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS AWAR_TREE_EXPORT_SAV "bootstraps"

#define	AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS AWAR_TREE_EXPORT_SAV "branchlens"

#define	AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES AWAR_TREE_EXPORT_SAV "groupnames"

#define	AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS AWAR_TREE_EXPORT_SAV "hide_folded"

#define	AWAR_TREE_EXPORT_QUOTEMODE AWAR_TREE_EXPORT_SAV "quote_mode"

#define	AWAR_TREE_EXPORT_NON_ASCII AWAR_TREE_EXPORT_SAV "non_ASCII"

#define	AWAR_TREE_EXPORT_REPLACE AWAR_TREE_EXPORT_SAV "replace"

#define	AWAR_TREE_CONSENSE_TMP AWAR_TREE_TMP "consense/"

#define	AWAR_TREE_CONSENSE_SAV AWAR_TREE_SAV "consense/"

#define	AWAR_TREE_CONSENSE_TREE AWAR_TREE_CONSENSE_SAV "tree"

#define	AWAR_TREE_CONSENSE_SELECTED AWAR_TREE_CONSENSE_TMP "selected"

#define	AWAR_MFURC "tree/multifurc/"

#define	AWAR_MFURC_CONSIDER_BOOTSTRAP AWAR_MFURC "use_bs"

#define	AWAR_MFURC_CONSIDER_LENGTH AWAR_MFURC "use_len"

#define	AWAR_MFURC_CONSIDER_TERMINALS AWAR_MFURC "terminals"

#define	AWAR_MFURC_LENGTH_LIMIT AWAR_MFURC "len"

#define	AWAR_MFURC_BOOTSTRAP_LIMIT AWAR_MFURC "bs"

Enumerations
enum	ExportTreeType { AD_TREE_EXPORT_FORMAT_NEWICK, AD_TREE_EXPORT_FORMAT_XML, AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY }

enum	ExportNodeType { AD_TREE_EXPORT_NODE_SPECIES_NAME, AD_TREE_EXPORT_NODE_NDS, AD_TREE_EXPORT_NODE_NDS_TRUNCATED }

Functions
static void	tree_vars_callback (AW_root *aw_root)

static void	update_default_treename_cb (AW_root *aw_root)

static void	ad_tree_set_security (AW_root *aw_root)

static void	update_filter_cb (AW_root *root)

void	create_trees_var (AW_root *aw_root, AW_default aw_def)

static void	tree_save_cb (AW_window *aww)

static AW_window *	create_tree_export_window (AW_root *root)

static char *	readXmlTree (char *fname)

static void	tree_load_cb (AW_window *aww)

static AW_window *	create_tree_import_window (AW_root *root)

static void	ad_move_tree_info (AW_window *aww, bool transferGroups)

static void	swap_source_dest_cb (AW_window *aww)

static void	copy_tree_awar_cb (UNFIXED, AW_awar aw_source, AW_awar aw_dest)

void	NT_create_twoTreeSelection (AW_window *aws)

static AW_window_simple *	create_select_other_tree_window (AW_root root, const char winId, const char winTitle, const char helpFile, AW_awar *awar_displayed_tree)

AW_window *	NT_create_compareTopologies_window (AW_root *root)

AW_window *	NT_create_moveGroupInfo_window (AW_root *root)

static void	reorder_trees_cb (AW_window *aww, awt_reorder_mode dest)

void	popup_tree_admin_window (AW_window *awp)

static void	create_consense_tree_cb (AW_window aww, AW_selection selected_trees)

static void	use_selected_as_target_cb (AW_window *aww)

AW_window *	NT_create_consense_window (AW_root *aw_root)

static GB_ERROR	sort_tree_by_other_tree (GBDATA gb_main, TreeNode tree, const char *other_tree)

static bool	sort_dtree_by_other_tree_cb (TreeNode *tree, GB_ERROR &error)

static void	sort_tree_by_other_tree_cb (UNFIXED, TREE_canvas *ntw)

AW_window *	NT_create_sort_tree_by_other_tree_window (AW_root aw_root, TREE_canvas ntw)

void	NT_create_multifurcate_tree_awars (AW_root *aw_root, AW_default props)

static void	multifurcation_cb (UNFIXED, TREE_canvas *ntw)

AW_window *	NT_create_multifurcate_tree_window (AW_root aw_root, TREE_canvas ntw)

Variables
static AWT_config_mapping_def	tree_export_config_mapping []

static AWT_config_mapping_def	moveGroupInfo_mapping []

static AWT_predefined_config	moveGroupInfo_predef []

Macro Definition Documentation

#define AWAR_TREE_SAV "ad_tree/"

Definition at line 41 of file ad_trees.cxx.

#define AWAR_TREE_TMP "tmp/ad_tree/"

Definition at line 42 of file ad_trees.cxx.

#define AWAR_TREE_SECURITY AWAR_TREE_TMP "tree_security"

Definition at line 44 of file ad_trees.cxx.

Referenced by ad_tree_set_security(), create_trees_var(), popup_tree_admin_window(), and tree_vars_callback().

#define AWAR_TREE_REM AWAR_TREE_TMP "tree_rem"

Definition at line 45 of file ad_trees.cxx.

Referenced by create_trees_var(), popup_tree_admin_window(), and tree_vars_callback().

#define AWAR_TREE_IMPORT AWAR_TREE_TMP "import_tree"

Definition at line 46 of file ad_trees.cxx.

Referenced by create_tree_import_window(), create_trees_var(), tree_load_cb(), and update_default_treename_cb().

#define AWAR_GROUPXFER_SAV AWAR_TREE_SAV "groupxfer/"

Definition at line 48 of file ad_trees.cxx.

#define AWAR_GROUPXFER_SOURCE AWAR_GROUPXFER_SAV "restrict"

Definition at line 50 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_OVERWRITE_MODE AWAR_GROUPXFER_SAV "overwrite"

Definition at line 51 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_INGROUP_ABS AWAR_GROUPXFER_SAV "ingroup/abs"

Definition at line 52 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_INGROUP_REL AWAR_GROUPXFER_SAV "ingroup/rel"

Definition at line 53 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_INGROUP_LIM AWAR_GROUPXFER_SAV "ingroup/lim"

Definition at line 54 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_OUTGROUP_ABS AWAR_GROUPXFER_SAV "outgroup/abs"

Definition at line 55 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_OUTGROUP_REL AWAR_GROUPXFER_SAV "outgroup/rel"

Definition at line 56 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_OUTGROUP_LIM AWAR_GROUPXFER_SAV "outgroup/lim"

Definition at line 57 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_UNKNOWN_ABS AWAR_GROUPXFER_SAV "unknown"

Definition at line 58 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_KEELING AWAR_GROUPXFER_SAV "keeling"

Definition at line 59 of file ad_trees.cxx.

Referenced by create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_GROUPXFER_ACI AWAR_GROUPXFER_SAV "aci"

Definition at line 60 of file ad_trees.cxx.

Referenced by ad_move_tree_info(), create_trees_var(), and NT_create_moveGroupInfo_window().

#define AWAR_TREE_EXPORT_FILEBASE AWAR_TREE_TMP "export_tree"

Definition at line 62 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_FILTER AWAR_TREE_EXPORT_FILEBASE "/filter"

Definition at line 63 of file ad_trees.cxx.

Referenced by tree_vars_callback(), and update_filter_cb().

#define AWAR_TREE_EXPORT_NAME AWAR_TREE_EXPORT_FILEBASE "/file_name"

Definition at line 64 of file ad_trees.cxx.

Referenced by tree_save_cb(), and tree_vars_callback().

#define AWAR_TREE_EXPORT_SAV AWAR_TREE_SAV "export_tree/"

Definition at line 66 of file ad_trees.cxx.

#define AWAR_TREE_EXPORT_FORMAT AWAR_TREE_EXPORT_SAV "format"

Definition at line 68 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), tree_save_cb(), and update_filter_cb().

#define AWAR_TREE_EXPORT_NDS AWAR_TREE_EXPORT_SAV "NDS"

Definition at line 69 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), tree_save_cb(), and update_filter_cb().

#define AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS AWAR_TREE_EXPORT_SAV "bootstraps"

Definition at line 70 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS AWAR_TREE_EXPORT_SAV "branchlens"

Definition at line 71 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES AWAR_TREE_EXPORT_SAV "groupnames"

Definition at line 72 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS AWAR_TREE_EXPORT_SAV "hide_folded"

Definition at line 73 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_QUOTEMODE AWAR_TREE_EXPORT_SAV "quote_mode"

Definition at line 74 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_NON_ASCII AWAR_TREE_EXPORT_SAV "non_ASCII"

Definition at line 75 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_EXPORT_REPLACE AWAR_TREE_EXPORT_SAV "replace"

Definition at line 76 of file ad_trees.cxx.

Referenced by create_tree_export_window(), create_trees_var(), and tree_save_cb().

#define AWAR_TREE_CONSENSE_TMP AWAR_TREE_TMP "consense/"

Definition at line 79 of file ad_trees.cxx.

#define AWAR_TREE_CONSENSE_SAV AWAR_TREE_SAV "consense/"

Definition at line 80 of file ad_trees.cxx.

#define AWAR_TREE_CONSENSE_TREE AWAR_TREE_CONSENSE_SAV "tree"

Definition at line 82 of file ad_trees.cxx.

Referenced by create_consense_tree_cb(), create_trees_var(), NT_create_consense_window(), and use_selected_as_target_cb().

#define AWAR_TREE_CONSENSE_SELECTED AWAR_TREE_CONSENSE_TMP "selected"

Definition at line 83 of file ad_trees.cxx.

Referenced by create_trees_var(), NT_create_consense_window(), and use_selected_as_target_cb().

#define AWAR_MFURC "tree/multifurc/"

Definition at line 1099 of file ad_trees.cxx.

#define AWAR_MFURC_CONSIDER_BOOTSTRAP AWAR_MFURC "use_bs"

Definition at line 1100 of file ad_trees.cxx.

Referenced by multifurcation_cb(), NT_create_multifurcate_tree_awars(), and NT_create_multifurcate_tree_window().

#define AWAR_MFURC_CONSIDER_LENGTH AWAR_MFURC "use_len"

Definition at line 1101 of file ad_trees.cxx.

Referenced by multifurcation_cb(), NT_create_multifurcate_tree_awars(), and NT_create_multifurcate_tree_window().

#define AWAR_MFURC_CONSIDER_TERMINALS AWAR_MFURC "terminals"

Definition at line 1102 of file ad_trees.cxx.

Referenced by multifurcation_cb(), NT_create_multifurcate_tree_awars(), and NT_create_multifurcate_tree_window().

#define AWAR_MFURC_LENGTH_LIMIT AWAR_MFURC "len"

Definition at line 1103 of file ad_trees.cxx.

Referenced by multifurcation_cb(), NT_create_multifurcate_tree_awars(), and NT_create_multifurcate_tree_window().

#define AWAR_MFURC_BOOTSTRAP_LIMIT AWAR_MFURC "bs"

Definition at line 1104 of file ad_trees.cxx.

Referenced by multifurcation_cb(), NT_create_multifurcate_tree_awars(), and NT_create_multifurcate_tree_window().

Enumeration Type Documentation

enum ExportTreeType

Enumerator
AD_TREE_EXPORT_FORMAT_NEWICK
AD_TREE_EXPORT_FORMAT_XML
AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY

Definition at line 166 of file ad_trees.cxx.

enum ExportNodeType

Enumerator
AD_TREE_EXPORT_NODE_SPECIES_NAME
AD_TREE_EXPORT_NODE_NDS
AD_TREE_EXPORT_NODE_NDS_TRUNCATED

Definition at line 172 of file ad_trees.cxx.

Function Documentation

static void tree_vars_callback ( AW_root * aw_root )

static

Definition at line 85 of file ad_trees.cxx.

References AW_root::awar(), AWAR_TREE_EXPORT_FILTER, AWAR_TREE_EXPORT_NAME, AWAR_TREE_NAME, AWAR_TREE_REM, AWAR_TREE_SECURITY, GB_FIND, GB_INT, NT_global::gb_main, GB_read_security_write(), GB_search(), GB_STRING, GBS_global_string(), GBS_string_eval(), GBT_find_tree(), GBT_readOrCreate_int(), GLOBAL, AW_awar::map(), AW_awar::read_string(), ta, AW_awar::unmap(), and AW_awar::write_string().

Referenced by create_trees_var().

static void update_default_treename_cb ( AW_root * aw_root )

static

Definition at line 123 of file ad_trees.cxx.

References AW_root::awar(), AWAR_TREE_IMPORT, NT_global::gb_main, GBS_string_eval(), GLOBAL, AW_awar::read_string(), ta, and AW_awar::write_string().

Referenced by create_trees_var().

static void ad_tree_set_security ( AW_root * aw_root )

static

Definition at line 144 of file ad_trees.cxx.

References aw_message_if(), AW_root::awar(), AWAR_TREE_NAME, AWAR_TREE_SECURITY, error(), NT_global::gb_main, GB_read_security_delete(), GB_write_security_delete(), GB_write_security_write(), GBT_find_tree(), GLOBAL, NULp, AW_awar::read_int(), AW_awar::read_string(), and ta.

Referenced by create_trees_var().

static void update_filter_cb ( AW_root * root )

static

Definition at line 178 of file ad_trees.cxx.

References AD_TREE_EXPORT_FORMAT_NEWICK, AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY, AD_TREE_EXPORT_FORMAT_XML, AD_TREE_EXPORT_NODE_NDS, AD_TREE_EXPORT_NODE_NDS_TRUNCATED, AD_TREE_EXPORT_NODE_SPECIES_NAME, AW_root::awar(), AWAR_TREE_EXPORT_FILTER, AWAR_TREE_EXPORT_FORMAT, AWAR_TREE_EXPORT_NDS, nt_assert, NULp, AW_awar::read_int(), and AW_awar::write_string().

Referenced by create_tree_export_window(), and create_trees_var().

void create_trees_var	(	AW_root *	aw_root,
		AW_default	aw_def
	)

Definition at line 202 of file ad_trees.cxx.

References AD_TREE_EXPORT_FORMAT_NEWICK, AD_TREE_EXPORT_NODE_SPECIES_NAME, ad_tree_set_security(), AW_awar::add_callback(), AW_create_fileselection_awars(), AW_root::awar(), AW_root::awar_float(), AWAR_GROUP, AWAR_GROUPXFER_ACI, AWAR_GROUPXFER_INGROUP_ABS, AWAR_GROUPXFER_INGROUP_LIM, AWAR_GROUPXFER_INGROUP_REL, AWAR_GROUPXFER_KEELING, AWAR_GROUPXFER_OUTGROUP_ABS, AWAR_GROUPXFER_OUTGROUP_LIM, AWAR_GROUPXFER_OUTGROUP_REL, AWAR_GROUPXFER_OVERWRITE_MODE, AWAR_GROUPXFER_SOURCE, AWAR_GROUPXFER_UNKNOWN_ABS, AW_root::awar_int(), AW_root::awar_pointer(), AW_root::awar_string(), AWAR_TREE, AWAR_TREE_CONSENSE_SELECTED, AWAR_TREE_CONSENSE_TREE, AWAR_TREE_EXPORT_FILEBASE, AWAR_TREE_EXPORT_FORMAT, AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS, AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS, AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS, AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES, AWAR_TREE_EXPORT_NDS, AWAR_TREE_EXPORT_NON_ASCII, AWAR_TREE_EXPORT_QUOTEMODE, AWAR_TREE_EXPORT_REPLACE, AWAR_TREE_IMPORT, AWAR_TREE_NAME, AWAR_TREE_REM, AWAR_TREE_SECURITY, AWT_registerTreeAwarSimple(), TreeAdmin::create_awars(), LABEL_SINGLE_QUOTES, AW_awar::map(), NULp, REMOVE_EXISTING_GROUPS, AW_awar::set_srt(), SRT_AUTOCORRECT_TREENAME, tree_vars_callback(), update_default_treename_cb(), update_filter_cb(), and XFER_ALL_GROUPS.

Referenced by nt_create_all_awars().

static void tree_save_cb ( AW_window * aww )

static

Definition at line 256 of file ad_trees.cxx.

References AD_TREE_EXPORT_FORMAT_NEWICK, AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY, AD_TREE_EXPORT_FORMAT_XML, AD_TREE_EXPORT_NODE_NDS, AD_TREE_EXPORT_NODE_NDS_TRUNCATED, AD_TREE_EXPORT_NODE_SPECIES_NAME, AW_refresh_fileselection(), AW_root::awar(), AWAR_DB_NAME, AWAR_TREE_EXPORT_FILEBASE, AWAR_TREE_EXPORT_FORMAT, AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS, AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS, AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS, AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES, AWAR_TREE_EXPORT_NAME, AWAR_TREE_EXPORT_NDS, AWAR_TREE_EXPORT_NON_ASCII, AWAR_TREE_EXPORT_QUOTEMODE, AWAR_TREE_EXPORT_REPLACE, AWAR_TREE_NAME, error(), NT_global::gb_main, AW_window::get_root(), GLOBAL, AW_window::hide_or_notify(), LABEL_ACCEPT_NON_ASCII, LABEL_FORCE_REPLACE, NDS_OUTPUT_LEAFTEXT, NDS_OUTPUT_LEAFTEXT_UNLIMITED, NULp, AW_awar::read_int(), AW_awar::read_string(), TREE_write_Newick(), and TREE_write_XML().

Referenced by create_tree_export_window().

static AW_window* create_tree_export_window ( AW_root * root )

static

Definition at line 325 of file ad_trees.cxx.

References AD_TREE_EXPORT_FORMAT_NEWICK, AD_TREE_EXPORT_FORMAT_NEWICK_PRETTY, AD_TREE_EXPORT_FORMAT_XML, AD_TREE_EXPORT_NODE_NDS, AD_TREE_EXPORT_NODE_NDS_TRUNCATED, AD_TREE_EXPORT_NODE_SPECIES_NAME, AW_create_standard_fileselection(), AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_TREE_EXPORT_FILEBASE, AWAR_TREE_EXPORT_FORMAT, AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS, AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS, AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS, AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES, AWAR_TREE_EXPORT_NDS, AWAR_TREE_EXPORT_NON_ASCII, AWAR_TREE_EXPORT_QUOTEMODE, AWAR_TREE_EXPORT_REPLACE, AWT_insert_config_manager(), LABEL_DISALLOW_QUOTES, LABEL_DOUBLE_QUOTES, LABEL_FORCE_QUOTES, LABEL_SINGLE_QUOTES, AW_window::load_xfig(), makeHelpCallback(), tree_save_cb(), and update_filter_cb().

Referenced by popup_tree_admin_window().

static char* readXmlTree ( char * fname )

static

Definition at line 386 of file ad_trees.cxx.

References ARB_strdup(), GBS_strstruct::cat(), command, GB_getenvARBHOME(), GB_xcmd(), GBS_global_string_copy(), GBS_strstruct::get_data(), NULp, GBS_strstruct::put(), and XCMD_SYNC_WAIT_ON_ERROR.

Referenced by tree_load_cb().

static void tree_load_cb ( AW_window * aww )

static

Definition at line 427 of file ad_trees.cxx.

References AW_root::awar(), AWAR_TREE, AWAR_TREE_IMPORT, error(), NT_global::gb_main, GB_unlink_or_warn(), AW_window::get_root(), GLOBAL, AW_window::hide_or_notify(), NULp, AW_awar::read_string(), readXmlTree(), TREE_load_to_db(), and AW_awar::write_string().

Referenced by create_tree_import_window().

static AW_window* create_tree_import_window ( AW_root * root )

static

Definition at line 457 of file ad_trees.cxx.

References AW_create_standard_fileselection(), AW_POPDOWN(), AWAR_TREE_IMPORT, AW_window::load_xfig(), makeHelpCallback(), and tree_load_cb().

Referenced by popup_tree_admin_window().

static void ad_move_tree_info	(	AW_window *	aww,
		bool	transferGroups
	)

static

Definition at line 491 of file ad_trees.cxx.

References AW_edit(), aw_message(), aw_message_if(), AW_root::awar(), AWAR_GROUPXFER_ACI, AWAR_GROUPXFER_INGROUP_ABS, AWAR_GROUPXFER_INGROUP_LIM, AWAR_GROUPXFER_INGROUP_REL, AWAR_GROUPXFER_OUTGROUP_ABS, AWAR_GROUPXFER_OUTGROUP_LIM, AWAR_GROUPXFER_OUTGROUP_REL, AWAR_GROUPXFER_OVERWRITE_MODE, AWAR_GROUPXFER_SOURCE, AWAR_GROUPXFER_UNKNOWN_ABS, COMPARE_TOPOLOGY, TreeAdmin::dest_tree_awar(), error(), GB_await_error(), GB_create_tempfile(), NT_global::gb_main, GB_remove_on_exit(), GB_unique_filename(), GBS_global_string(), AW_window::get_root(), GLOBAL, NT_deselect_group(), NT_get_canvas_showing_tree(), NTREE_move_tree_info(), NULp, AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), GroupMatchScorer::setLimits(), GroupMatchScorer::setPerErrorPenalties(), GroupMatchScorer::setRelativePenalties(), TreeAdmin::source_tree_awar(), and XFER_ALL_GROUPS.

Referenced by NT_create_compareTopologies_window(), and NT_create_moveGroupInfo_window().

static void swap_source_dest_cb ( AW_window * aww )

static

Definition at line 557 of file ad_trees.cxx.

References TreeAdmin::dest_tree_awar(), AW_window::get_root(), AW_awar::read_char_pntr(), AW_awar::read_string(), s, TreeAdmin::source_tree_awar(), and AW_awar::write_string().

Referenced by NT_create_twoTreeSelection().

static void copy_tree_awar_cb	(	UNFIXED	,
		AW_awar *	aw_source,
		AW_awar *	aw_dest
	)

static

Definition at line 569 of file ad_trees.cxx.

References AW_awar::read_char_pntr(), and AW_awar::write_string().

Referenced by create_select_other_tree_window(), and NT_create_twoTreeSelection().

void NT_create_twoTreeSelection ( AW_window * aws )

static AW_window_simple* create_select_other_tree_window	(	AW_root *	root,
		const char *	winId,
		const char *	winTitle,
		const char *	helpFile,
		AW_awar *	awar_displayed_tree
	)

static

Definition at line 607 of file ad_trees.cxx.

References AW_POPDOWN(), AW_awar::awar_name, awt_create_TREE_selection_list(), copy_tree_awar_cb(), TreeAdmin::dest_tree_awar(), NT_global::gb_main, GLOBAL, and makeHelpCallback().

Referenced by NT_create_sort_tree_by_other_tree_window().

AW_window* NT_create_compareTopologies_window ( AW_root * root )

Definition at line 636 of file ad_trees.cxx.

References ad_move_tree_info(), AW_POPDOWN(), AW_window::load_xfig(), makeHelpCallback(), and NT_create_twoTreeSelection().

Referenced by popup_new_main_window().

AW_window* NT_create_moveGroupInfo_window ( AW_root * root )

static void reorder_trees_cb	(	AW_window *	aww,
		awt_reorder_mode	dest
	)

static

Definition at line 747 of file ad_trees.cxx.

References ARM_BOTTOM, ARM_DOWN, ARM_TOP, ARM_UP, aw_message(), AW_root::awar(), AWAR_TREE_NAME, error(), FALLTHROUGH, GB_entry(), NT_global::gb_main, GBT_BEHIND, GBT_find_bottom_tree(), GBT_find_top_tree(), GBT_get_tree_data(), GBT_INFRONTOF, GBT_move_tree(), GBT_tree_behind(), GBT_tree_infrontof(), AW_window::get_root(), GLOBAL, NULp, AW_awar::read_string(), and ta.

Referenced by popup_tree_admin_window().

void popup_tree_admin_window ( AW_window * awp )

static void create_consense_tree_cb	(	AW_window *	aww,
		AW_selection *	selected_trees
	)

static

static void use_selected_as_target_cb ( AW_window * aww )

static

Definition at line 943 of file ad_trees.cxx.

References AW_root::awar(), AWAR_TREE_CONSENSE_SELECTED, AWAR_TREE_CONSENSE_TREE, AW_window::get_root(), AW_awar::read_char_pntr(), and AW_awar::write_string().

Referenced by NT_create_consense_window().

AW_window* NT_create_consense_window ( AW_root * aw_root )

Definition at line 948 of file ad_trees.cxx.

References AW_POPDOWN(), AWAR_TREE_CONSENSE_SELECTED, AWAR_TREE_CONSENSE_TREE, awt_create_subset_selection_list(), awt_create_TREE_selection_list(), create_consense_tree_cb(), NT_global::gb_main, AW_selection::get_sellist(), GLOBAL, makeHelpCallback(), NULp, and use_selected_as_target_cb().

Referenced by popup_new_main_window().

static GB_ERROR sort_tree_by_other_tree	(	GBDATA *	gb_main,
		TreeNode *	tree,
		const char *	other_tree
	)

static

Definition at line 1062 of file ad_trees.cxx.

References destroy(), error(), GB_await_error(), GBT_read_tree(), NULp, SortByTopo::reorder_subtree(), and ta.

Referenced by sort_dtree_by_other_tree_cb().

static bool sort_dtree_by_other_tree_cb	(	TreeNode *	tree,
		GB_ERROR &	error
	)

static

Definition at line 1076 of file ad_trees.cxx.

References TreeAdmin::dest_tree_awar(), error(), NT_global::gb_main, GLOBAL, AW_awar::read_char_pntr(), AW_root::SINGLETON, and sort_tree_by_other_tree().

Referenced by sort_tree_by_other_tree_cb().

static void sort_tree_by_other_tree_cb	(	UNFIXED	,
		TREE_canvas *	ntw
	)

static

Definition at line 1082 of file ad_trees.cxx.

References aw_message_if(), error(), NT_with_displayed_tree_do(), and sort_dtree_by_other_tree_cb().

Referenced by NT_create_sort_tree_by_other_tree_window().

AW_window* NT_create_sort_tree_by_other_tree_window	(	AW_root *	aw_root,
		TREE_canvas *	ntw
	)

Definition at line 1087 of file ad_trees.cxx.

References AWT_canvas::aww, create_select_other_tree_window(), TREE_canvas::get_awar_tree(), AW_window::local_id(), and sort_tree_by_other_tree_cb().

Referenced by popup_new_main_window().

void NT_create_multifurcate_tree_awars	(	AW_root *	aw_root,
		AW_default	props
	)

Definition at line 1106 of file ad_trees.cxx.

References AW_root::awar_float(), AW_root::awar_int(), AWAR_MFURC_BOOTSTRAP_LIMIT, AWAR_MFURC_CONSIDER_BOOTSTRAP, AWAR_MFURC_CONSIDER_LENGTH, AWAR_MFURC_CONSIDER_TERMINALS, and AWAR_MFURC_LENGTH_LIMIT.

Referenced by nt_create_all_awars().

static void multifurcation_cb	(	UNFIXED	,
		TREE_canvas *	ntw
	)

static

Definition at line 1113 of file ad_trees.cxx.

References AW_root::awar(), AWAR_MFURC_BOOTSTRAP_LIMIT, AWAR_MFURC_CONSIDER_BOOTSTRAP, AWAR_MFURC_CONSIDER_LENGTH, AWAR_MFURC_CONSIDER_TERMINALS, AWAR_MFURC_LENGTH_LIMIT, AWT_canvas::aww, AW_window::get_root(), NT_multifurcate_tree(), AW_awar::read_float(), and AW_awar::read_int().

Referenced by NT_create_multifurcate_tree_window().

AW_window* NT_create_multifurcate_tree_window	(	AW_root *	aw_root,
		TREE_canvas *	ntw
	)

Definition at line 1125 of file ad_trees.cxx.

References AW_window::at(), AW_POPDOWN(), AWAR_MFURC_BOOTSTRAP_LIMIT, AWAR_MFURC_CONSIDER_BOOTSTRAP, AWAR_MFURC_CONSIDER_LENGTH, AWAR_MFURC_CONSIDER_TERMINALS, AWAR_MFURC_LENGTH_LIMIT, AWT_canvas::aww, AW_window::local_id(), makeHelpCallback(), and multifurcation_cb().

Referenced by popup_new_main_window().

Variable Documentation

AWT_config_mapping_def tree_export_config_mapping[]

static

Initial value:

= {
    { AWAR_TREE_EXPORT_FORMAT,             "format" },
    { AWAR_TREE_EXPORT_NDS,                "nodetype" },
    { AWAR_TREE_EXPORT_INCLUDE_BRANCHLENS, "lengths" },
    { AWAR_TREE_EXPORT_INCLUDE_BOOTSTRAPS, "bootstraps" },
    { AWAR_TREE_EXPORT_INCLUDE_GROUPNAMES, "groupnames" },
    { AWAR_TREE_EXPORT_HIDE_FOLDED_GROUPS, "hidefolded" },
    { AWAR_TREE_EXPORT_QUOTEMODE,          "quotemode" },
    { AWAR_TREE_EXPORT_NON_ASCII,          "nonASCII" },
    { AWAR_TREE_EXPORT_REPLACE,            "replacechars" },
    { NULp, NULp }
}

Definition at line 311 of file ad_trees.cxx.

AWT_config_mapping_def moveGroupInfo_mapping[]

static

Initial value:

= {
    { AWAR_GROUPXFER_INGROUP_ABS,    "ingroup_abs" },
    { AWAR_GROUPXFER_INGROUP_REL,    "ingroup_rel" },
    { AWAR_GROUPXFER_OUTGROUP_ABS,   "outgroup_abs" },
    { AWAR_GROUPXFER_OUTGROUP_REL,   "outgroup_rel" },
    { AWAR_GROUPXFER_UNKNOWN_ABS,    "unknown_abs" },
    { AWAR_GROUPXFER_KEELING,        "keeling" },
    { AWAR_GROUPXFER_INGROUP_LIM,    "ingroup_lim" },
    { AWAR_GROUPXFER_OUTGROUP_LIM,   "outgroup_lim" },
    { AWAR_GROUPXFER_SOURCE,         "sourceGroups" },
    { AWAR_GROUPXFER_OVERWRITE_MODE, "overwriteGroups" },
    { AWAR_GROUPXFER_ACI,            "aci" },
    { NULp, NULp },
}

Definition at line 658 of file ad_trees.cxx.

AWT_predefined_config moveGroupInfo_predef[]

static

Initial value:

= {
    { "*only_perfect_groups", "Only copy perfectly matching groups with\n * 100% ingroup ratio and\n * 0% outgroup ratio", "ingroup_lim='100';outgroup_lim='0'" },
    { "*maximize_ingroup_ratio", "Maximize ingroup ratio \n   over outgroup ratio.\n(Note: diff of factor 10 is maybe too strong)", "ingroup_abs='0';ingroup_rel='100';outgroup_abs='0';outgroup_rel='10'" },
    { "*minimize_outgroup_ratio", "Minimize outgroup ratio \n     over ingroup ratio.\n(Note: diff of factor 10 is maybe too strong)", "ingroup_abs='0';ingroup_rel='10';outgroup_abs='0';outgroup_rel='100'" },
    { "*report2name", "custom target group name:\n * add prefix \"XFRD_\" (allows to distinguish newly transferred from existing groups)\n * add suffix reporting penalty", "aci='\"XFRD_\";groupname;\" {penalty = \";penalty;\"}\"'" },
    { NULp, NULp, NULp },
}

Definition at line 678 of file ad_trees.cxx.

Classes

Macros

Enumerations

Functions

Variables

Macro Definition Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation