DI_matr.cxx File Reference

#include "di_protdist.hxx"
#include "di_clusters.hxx"
#include "di_view_matrix.hxx"
#include "di_awars.hxx"
#include <neighbourjoin.hxx>
#include <AP_filter.hxx>
#include <CT_ctree.hxx>
#include <ColumnStat.hxx>
#include <awt.hxx>
#include <awt_sel_boxes.hxx>
#include <awt_filter.hxx>
#include <aw_preset.hxx>
#include <aw_awars.hxx>
#include <aw_file.hxx>
#include <aw_msg.hxx>
#include <aw_root.hxx>
#include <gui_aliview.hxx>
#include <climits>
#include <ctime>
#include <cmath>
#include <arb_sort.h>
#include <arb_global_defs.h>
#include <macros.hxx>
#include <ad_cb.h>
#include <awt_TreeAwars.hxx>
#include <arb_defs.h>

Include dependency graph for DI_matr.cxx:

Go to the source code of this file.

Classes
class	BoundWindowCallback
struct	RecalcNeeded
struct	TreeOrderedSpecies

Macros
#define	AWAR_DIST_BOOTSTRAP_COUNT   AWAR_DIST_PREFIX "bootstrap/count"
#define	AWAR_DIST_CANCEL_CHARS   AWAR_DIST_PREFIX "cancel/chars"
#define	AWAR_DIST_MATRIX_AUTO_RECALC   AWAR_DIST_PREFIX "recalc"
#define	AWAR_DIST_COLUMN_STAT_NAME   AWAR_DIST_COLUMN_STAT_PREFIX "name"
#define	AWAR_DIST_TREE_SORT_NAME   "tmp/" AWAR_DIST_TREE_PREFIX "sort_tree_name"
#define	AWAR_DIST_TREE_COMP_NAME   "tmp/" AWAR_DIST_TREE_PREFIX "compr_tree_name"
#define	AWAR_DIST_TREE_STD_NAME   AWAR_DIST_TREE_PREFIX "tree_name"
#define	AWAR_DIST_MATRIX_AUTO_CALC_TREE   AWAR_DIST_TREE_PREFIX "autocalc"
#define	AWAR_DIST_SAVE_MATRIX_TYPE   AWAR_DIST_SAVE_MATRIX_BASE "/type"
#define	AWAR_DIST_SAVE_MATRIX_FILENAME   AWAR_DIST_SAVE_MATRIX_BASE "/file_name"

Typedefs
typedef std::map< const char *, TreeNode *, charpLess >	NamedNodes

Functions
static AP_matrix *	get_user_matrix ()
static void	matrix_changed_cb ()
static unsigned	update_cb (AW_root *aw_root)
void	add_update_cb ()
void	matrix_needs_recalc_cb ()
void	tree_needs_recalc_cb ()
void	compressed_matrix_needs_recalc_cb ()
static void	auto_calc_changed_cb (AW_root *aw_root)
static AW_window *	create_dna_matrix_window (AW_root *aw_root)
static void	selected_tree_changed_cb ()
GB_ERROR	DI_create_matrix_variables (AW_root *aw_root, AW_default def, AW_default db)
static int	TreeOrderedSpecies_cmp (const void *p1, const void *p2, void *)
static size_t	get_load_count (LoadWhat what, GBDATA *gb_main, GBDATA **species_list)
GB_ERROR	link_to_tree (NamedNodes &named, TreeNode *node)
static TreeNode *	findNode (TreeNode *node, const char *name)
static GB_ERROR	init (NamedNodes &node, TreeNode *tree, const DI_ENTRY *const *const entries, size_t nentries)
LoadWhat	whatToLoad ()
static __ATTR__USERESULT GB_ERROR	di_calculate_matrix (AW_root *aw_root, const WeightedFilter *weighted_filter, bool bootstrap_flag, bool show_warnings, bool *aborted_flag)
static void	di_mark_by_distance (AW_window *aww, WeightedFilter *weighted_filter)
static GB_ERROR	di_recalc_matrix ()
static void	di_view_matrix_cb (AW_window *aww, save_matrix_params *sparam)
static void	di_save_matrix_cb (AW_window *aww)
AW_window *	DI_create_save_matrix_window (AW_root *aw_root, save_matrix_params *save_params)
static AW_window *	awt_create_select_cancel_window (AW_root *aw_root)
	STATIC_ASSERT (ARRAY_ELEMS(enum_trans_to_string)==DI_TRANSFORMATION_COUNT)
static void	di_calculate_tree_cb (AW_window *aww, WeightedFilter *weighted_filter, bool bootstrap_flag)
static void	di_autodetect_callback (AW_window *aww, GBDATA *gb_main)
static __ATTR__NORETURN void	di_exit (AW_window *aww, GBDATA *gb_main)
static void	di_calculate_full_matrix_cb (AW_window *aww, const WeightedFilter *weighted_filter)
static void	di_calculate_compressed_matrix_cb (AW_window *aww, WeightedFilter *weighted_filter)
static void	di_define_sort_tree_name_cb (AW_window *aww)
static void	di_define_compression_tree_name_cb (AW_window *aww)
static void	di_define_save_tree_name_cb (AW_window *aww)
AW_window *	DI_create_matrix_window (AW_root *aw_root, GBDATA *gb_main)

Variables
DI_GLOBAL_MATRIX	GLOBAL_MATRIX
static MatrixDisplay *	matrixDisplay = NULp
static AP_userdef_matrix	userdef_DNA_matrix (AP_MAX, AWAR_DIST_MATRIX_DNA_BASE)
static SmartPtr < BoundWindowCallback >	recalculate_matrix_cb
static SmartPtr < BoundWindowCallback >	recalculate_tree_cb
static GB_ERROR	last_matrix_calculation_error = NULp
static RecalcNeeded	need_recalc
CONSTEXPR unsigned	UPDATE_DELAY = 200
static const char *	enum_trans_to_string []

Macro Definition Documentation

#define AWAR_DIST_BOOTSTRAP_COUNT   AWAR_DIST_PREFIX "bootstrap/count"

Definition at line 47 of file DI_matr.cxx.

Referenced by di_calculate_tree_cb(), DI_create_matrix_variables(), and DI_create_matrix_window().

#define AWAR_DIST_CANCEL_CHARS   AWAR_DIST_PREFIX "cancel/chars"

Definition at line 48 of file DI_matr.cxx.

Referenced by awt_create_select_cancel_window(), di_calculate_matrix(), DI_create_matrix_variables(), DI_create_matrix_window(), and di_mark_by_distance().

#define AWAR_DIST_MATRIX_AUTO_RECALC   AWAR_DIST_PREFIX "recalc"

Definition at line 49 of file DI_matr.cxx.

Referenced by auto_calc_changed_cb(), DI_create_matrix_variables(), DI_create_matrix_window(), and update_cb().

#define AWAR_DIST_COLUMN_STAT_NAME   AWAR_DIST_COLUMN_STAT_PREFIX "name"

Definition at line 51 of file DI_matr.cxx.

Referenced by DI_create_matrix_window().

#define AWAR_DIST_TREE_SORT_NAME   "tmp/" AWAR_DIST_TREE_PREFIX "sort_tree_name"

Definition at line 53 of file DI_matr.cxx.

Referenced by di_autodetect_callback(), di_calculate_matrix(), DI_create_matrix_variables(), DI_create_matrix_window(), and di_define_sort_tree_name_cb().

#define AWAR_DIST_TREE_COMP_NAME   "tmp/" AWAR_DIST_TREE_PREFIX "compr_tree_name"

Definition at line 54 of file DI_matr.cxx.

Referenced by di_calculate_compressed_matrix_cb(), DI_create_matrix_variables(), DI_create_matrix_window(), and di_define_compression_tree_name_cb().

#define AWAR_DIST_TREE_STD_NAME   AWAR_DIST_TREE_PREFIX "tree_name"

Definition at line 55 of file DI_matr.cxx.

Referenced by di_calculate_tree_cb(), DI_create_matrix_variables(), DI_create_matrix_window(), and di_define_save_tree_name_cb().

#define AWAR_DIST_MATRIX_AUTO_CALC_TREE   AWAR_DIST_TREE_PREFIX "autocalc"

Definition at line 56 of file DI_matr.cxx.

Referenced by auto_calc_changed_cb(), DI_create_matrix_variables(), DI_create_matrix_window(), and update_cb().

#define AWAR_DIST_SAVE_MATRIX_TYPE   AWAR_DIST_SAVE_MATRIX_BASE "/type"

Definition at line 58 of file DI_matr.cxx.

Referenced by DI_create_matrix_variables(), DI_create_save_matrix_window(), and di_save_matrix_cb().

#define AWAR_DIST_SAVE_MATRIX_FILENAME   AWAR_DIST_SAVE_MATRIX_BASE "/file_name"

Definition at line 59 of file DI_matr.cxx.

Referenced by di_save_matrix_cb().

Typedef Documentation

typedef std::map<const char*, TreeNode*, charpLess> NamedNodes

Definition at line 774 of file DI_matr.cxx.

Function Documentation

static AP_matrix* get_user_matrix ( )

static

Definition at line 68 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_MATRIX_DNA_ENABLED, AP_userdef_matrix::normize(), NULp, AW_awar::read_int(), AW_root::SINGLETON, AP_userdef_matrix::update_from_awars(), and userdef_DNA_matrix.

Referenced by di_calculate_matrix(), and di_mark_by_distance().

static void matrix_changed_cb ( )

static

Definition at line 94 of file DI_matr.cxx.

References MatrixDisplay::mark(), MatrixDisplay::NEED_SETUP, and MatrixDisplay::update_display().

Referenced by di_view_matrix_cb().

static unsigned update_cb ( AW_root *  aw_root )

static

Definition at line 132 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_MATRIX_AUTO_CALC_TREE, AWAR_DIST_MATRIX_AUTO_RECALC, di_assert, DI_GLOBAL_MATRIX::forget(), SmartPtr< T, C >::isSet(), RecalcNeeded::matrix, AW_awar::read_int(), RecalcNeeded::tree, and MatrixDisplay::willShow().

Referenced by add_update_cb(), and create_seq_color_awars().

void add_update_cb ( )

inline

Definition at line 113 of file DI_matr.cxx.

References AW_root::add_timed_callback(), AW_root::SINGLETON, update_cb(), and UPDATE_DELAY.

Referenced by matrix_needs_recalc_cb(), and tree_needs_recalc_cb().

void matrix_needs_recalc_cb ( )

inline

Definition at line 117 of file DI_matr.cxx.

References add_update_cb(), and RecalcNeeded::matrix.

Referenced by auto_calc_changed_cb(), compressed_matrix_needs_recalc_cb(), DI_create_matrix_variables(), and selected_tree_changed_cb().

void tree_needs_recalc_cb ( )

inline

Definition at line 121 of file DI_matr.cxx.

References add_update_cb(), and RecalcNeeded::tree.

Referenced by auto_calc_changed_cb(), di_calculate_compressed_matrix_cb(), di_calculate_full_matrix_cb(), and di_calculate_matrix().

void compressed_matrix_needs_recalc_cb ( )

inline

Definition at line 126 of file DI_matr.cxx.

References DI_MATRIX_COMPRESSED, DI_GLOBAL_MATRIX::has_type(), and matrix_needs_recalc_cb().

Referenced by DI_create_matrix_variables().

static void auto_calc_changed_cb ( AW_root *  aw_root )

static

Definition at line 164 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_MATRIX_AUTO_CALC_TREE, AWAR_DIST_MATRIX_AUTO_RECALC, DI_GLOBAL_MATRIX::exists(), matrix_needs_recalc_cb(), AW_awar::read_int(), and tree_needs_recalc_cb().

Referenced by DI_create_matrix_variables().

static AW_window* create_dna_matrix_window ( AW_root *  aw_root )

static

Definition at line 172 of file DI_matr.cxx.

References AW_window::auto_increment(), AW_POPDOWN(), AP_userdef_matrix::create_input_fields(), makeHelpCallback(), and userdef_DNA_matrix.

Referenced by DI_create_matrix_window().

static void selected_tree_changed_cb ( )

static

Definition at line 190 of file DI_matr.cxx.

References AWAR_DIST_CORR_TRANS, DI_TRANSFORMATION_FROM_TREE, matrix_needs_recalc_cb(), and AW_root::SINGLETON.

Referenced by DI_create_matrix_variables().

GB_ERROR DI_create_matrix_variables	(	AW_root *	aw_root,
		AW_default	def,
		AW_default	db
	)

Definition at line 196 of file DI_matr.cxx.

References AW_awar::add_callback(), AP_A, AP_C, AP_G, AP_GAP, AP_T, auto_calc_changed_cb(), AW_create_fileselection_awars(), AW_ROOT_DEFAULT, AW_root::awar(), AWAR_DIST_ALIGNMENT, AWAR_DIST_BOOTSTRAP_COUNT, AWAR_DIST_CANCEL_CHARS, AWAR_DIST_CORR_TRANS, AWAR_DIST_FILTER_ALIGNMENT, AWAR_DIST_FILTER_FILTER, AWAR_DIST_FILTER_NAME, AWAR_DIST_FILTER_SIMPLIFY, AWAR_DIST_MATRIX_AUTO_CALC_TREE, AWAR_DIST_MATRIX_AUTO_RECALC, AWAR_DIST_MATRIX_DNA_BASE, AWAR_DIST_MATRIX_DNA_ENABLED, AWAR_DIST_MAX_DIST, AWAR_DIST_MIN_DIST, AWAR_DIST_SAVE_MATRIX_BASE, AWAR_DIST_SAVE_MATRIX_TYPE, AWAR_DIST_TREE_COMP_NAME, AWAR_DIST_TREE_CURR_NAME, AWAR_DIST_TREE_SORT_NAME, AWAR_DIST_TREE_STD_NAME, AWAR_DIST_WHICH_SPECIES, AW_root::awar_float(), AW_root::awar_int(), AWAR_SPECIES_NAME, AW_root::awar_string(), AWAR_TREE, AWT_registerTreeAwarCallback(), compressed_matrix_needs_recalc_cb(), AP_userdef_matrix::create_awars(), DI_create_cluster_awars(), DI_TRANSFORMATION_COUNT, DI_TRANSFORMATION_SIMILARITY, GB_add_callback(), GB_await_error(), GB_CB_CHANGED, GB_FIND, GB_pop_transaction(), GB_push_transaction(), GB_search(), gb_species_data, GBT_get_default_alignment(), GBT_get_species_data(), AW_awar::map(), matrix_needs_recalc_cb(), NO_TREE_SELECTED, NULp, AW_awar::read_string(), selected_tree_changed_cb(), AP_userdef_matrix::set_descriptions(), AW_awar::set_minmax(), ta, userdef_DNA_matrix, and AW_awar::write_string().

Referenced by ARB_main().

static int TreeOrderedSpecies_cmp ( const void *  p1, const void *  p2, void *    )

static

Definition at line 383 of file DI_matr.cxx.

References TreeOrderedSpecies::order_index.

Referenced by MatrixOrder::applyTo().

static size_t get_load_count ( LoadWhat  what, GBDATA *  gb_main, GBDATA **  species_list  )

static

Definition at line 394 of file DI_matr.cxx.

References di_assert, DI_LOAD_ALL, DI_LOAD_LIST, DI_LOAD_MARKED, GBT_count_marked_species(), GBT_get_species_count(), and U.

Referenced by di_calculate_matrix(), di_calculate_tree_cb(), and DI_MATRIX::load().

GB_ERROR link_to_tree	(	NamedNodes &	named,
		TreeNode *	node
	)

Definition at line 776 of file DI_matr.cxx.

References error(), GBS_global_string(), TreeNode::is_leaf(), TreeNode::name, and NULp.

Referenced by init().

static TreeNode* findNode ( TreeNode *  node, const char *  name  )

static

Definition at line 798 of file DI_matr.cxx.

References TreeNode::is_leaf(), TreeNode::name, and NULp.

Referenced by init().

static GB_ERROR init ( NamedNodes &  node, TreeNode *  tree, const DI_ENTRY *const *const  entries, size_t  nentries  )

static

Definition at line 809 of file DI_matr.cxx.

References di_assert, error(), findNode(), GBS_global_string(), link_to_tree(), DI_ENTRY::name, and NULp.

Referenced by DI_MATRIX::extract_from_tree().

LoadWhat whatToLoad ( )

inline

Definition at line 882 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_WHICH_SPECIES, DI_LOAD_ALL, DI_LOAD_MARKED, AW_awar::read_char_pntr(), and AW_root::SINGLETON.

Referenced by di_autodetect_callback(), di_calculate_matrix(), and di_calculate_tree_cb().

static __ATTR__USERESULT GB_ERROR di_calculate_matrix ( AW_root *  aw_root, const WeightedFilter *  weighted_filter, bool  bootstrap_flag, bool  show_warnings, bool *  aborted_flag  )

static

Definition at line 887 of file DI_matr.cxx.

References arb_progress::aborted(), AW_root::awar(), AWAR_DIST_ALIGNMENT, AWAR_DIST_CANCEL_CHARS, AWAR_DIST_CORR_TRANS, AWAR_DIST_TREE_CURR_NAME, AWAR_DIST_TREE_SORT_NAME, DI_MATRIX::calculate(), DI_MATRIX::calculate_pro(), GB_transaction::close(), WeightedFilter::create_aliview(), di_assert, DI_MATRIX_FULL, DI_TRANSFORMATION_FROM_TREE, AP_filter::enable_bootstrap(), error(), DI_GLOBAL_MATRIX::exists(), DI_MATRIX::extract_from_tree(), DI_GLOBAL_MATRIX::forget(), GB_clear_error(), gb_main, GBT_get_alignment_len(), AliView::get_filter(), WeightedFilter::get_gb_main(), get_load_count(), get_user_matrix(), arb_progress::inc_and_check_user_abort(), DI_MATRIX::is_AA, SmartPtr< T, C >::isSet(), DI_MATRIX::load(), RecalcNeeded::matrix, DI_MATRIX::matrix_type, NULp, AW_awar::read_char_pntr(), AW_awar::read_int(), AW_awar::read_string(), DI_GLOBAL_MATRIX::replaceBy(), ta, tree_needs_recalc_cb(), triangular_number(), WEIGHTED, and whatToLoad().

Referenced by di_calculate_compressed_matrix_cb(), di_calculate_full_matrix_cb(), and di_calculate_tree_cb().

static void di_mark_by_distance ( AW_window *  aww, WeightedFilter *  weighted_filter  )

static

Definition at line 981 of file DI_matr.cxx.

References ASSERT_RESULT, aw_message(), AW_root::awar(), AWAR_DIST_ALIGNMENT, AWAR_DIST_CANCEL_CHARS, AWAR_DIST_CORR_TRANS, AWAR_DIST_MAX_DIST, AWAR_DIST_MIN_DIST, AWAR_SPECIES_NAME, DI_MATRIX::calculate(), DI_MATRIX::calculate_pro(), GB_transaction::close(), WeightedFilter::create_aliview(), di_assert, DI_LOAD_LIST, DI_MATRIX_FULL, arb_progress::done(), error(), DI_GLOBAL_MATRIX::exists(), gb_main, GB_write_flag(), GBS_global_string(), GBT_find_species(), GBT_first_species(), GBT_get_species_count(), GBT_next_species(), symmetric_matrix< T >::get(), WeightedFilter::get_gb_main(), AW_window::get_root(), get_user_matrix(), arb_progress::inc_and_check_user_abort(), DI_MATRIX::is_AA, DI_MATRIX::load(), DI_MATRIX::matrix, DI_MATRIX::matrix_type, DI_MATRIX::nentries, NULp, AW_awar::read_float(), AW_awar::read_int(), AW_awar::read_string(), DI_GLOBAL_MATRIX::swap(), and ta.

Referenced by DI_create_matrix_window().

static GB_ERROR di_recalc_matrix ( )

static

Definition at line 1080 of file DI_matr.cxx.

References di_assert, DI_GLOBAL_MATRIX::exists(), DI_GLOBAL_MATRIX::forget(), SmartPtr< T, C >::isSet(), last_matrix_calculation_error, RecalcNeeded::matrix, and NULp.

Referenced by di_save_matrix_cb(), and di_view_matrix_cb().

static void di_view_matrix_cb ( AW_window *  aww, save_matrix_params *  sparam  )

static

Definition at line 1091 of file DI_matr.cxx.

References DI_create_view_matrix_window(), di_recalc_matrix(), error(), WeightedFilter::get_gb_main(), AW_window::get_root(), MatrixDisplay::mark(), matrix_changed_cb(), matrixDisplay, MatrixDisplay::NEED_SETUP, NULp, DI_GLOBAL_MATRIX::set_changed_cb(), MatrixDisplay::update_display(), and save_matrix_params::weighted_filter.

Referenced by DI_create_matrix_window().

static void di_save_matrix_cb ( AW_window *  aww )

static

Definition at line 1108 of file DI_matr.cxx.

References AW_refresh_fileselection(), AW_root::awar(), AWAR_DIST_SAVE_MATRIX_BASE, AWAR_DIST_SAVE_MATRIX_FILENAME, AWAR_DIST_SAVE_MATRIX_TYPE, di_recalc_matrix(), error(), DI_GLOBAL_MATRIX::get(), AW_window::get_root(), AW_window::hide_or_notify(), AW_awar::read_int(), AW_awar::read_string(), DI_MATRIX::save(), and type.

Referenced by DI_create_save_matrix_window().

AW_window* DI_create_save_matrix_window	(	AW_root *	aw_root,
		save_matrix_params *	save_params
	)

Definition at line 1122 of file DI_matr.cxx.

References AW_create_standard_fileselection(), AW_POPDOWN(), save_matrix_params::awar_base, AWAR_DIST_SAVE_MATRIX_TYPE, di_save_matrix_cb(), DI_SAVE_PHYLIP_COMP, DI_SAVE_READABLE, DI_SAVE_TABBED, makeHelpCallback(), and NULp.

Referenced by DI_create_matrix_window(), and DI_create_view_matrix_window().

static AW_window* awt_create_select_cancel_window ( AW_root *  aw_root )

static

Definition at line 1157 of file DI_matr.cxx.

References AW_POPDOWN(), AWAR_DIST_CANCEL_CHARS, and AW_window::load_xfig().

Referenced by DI_create_matrix_window().

STATIC_ASSERT

(

ARRAY_ELEMS(enum_trans_to_string)

= =DI_TRANSFORMATION_COUNT

)

static void di_calculate_tree_cb ( AW_window *  aww, WeightedFilter *  weighted_filter, bool  bootstrap_flag  )

static

Definition at line 1194 of file DI_matr.cxx.

References ARB_strdup(), arb_progress::auto_subtitles(), aw_message(), AW_root::awar(), AWAR_DIST_BOOTSTRAP_COUNT, AWAR_DIST_CORR_TRANS, AWAR_DIST_TREE_CURR_NAME, AWAR_DIST_TREE_STD_NAME, AWAR_TREE_REFRESH, AWT_get_combined_filter_name(), destroy(), di_assert, di_calculate_matrix(), DI_TRANSFORMATION_FROM_TREE, arb_progress::done(), DI_MATRIX::entries, error(), arb_progress::error_if_aborted(), DI_GLOBAL_MATRIX::exists(), arb_progress::force_update(), DI_GLOBAL_MATRIX::forget(), GB_begin_transaction(), GB_end_transaction(), gb_main, GBS_global_string(), GBT_check_tree_name(), GBT_is_invalid(), GBT_log_to_named_trees_remark(), GBT_write_tree(), GBT_write_tree_remark(), DI_GLOBAL_MATRIX::get(), ConsensusTree::get_consensus_tree(), WeightedFilter::get_gb_main(), get_load_count(), AW_window::get_root(), arb_progress::inc(), ConsensusTree::insert_tree_weighted(), SmartPtr< T, C >::isNull(), SmartPtr< T, C >::isSet(), RecalcNeeded::matrix, DI_MATRIX::matrix, DI_ENTRY::name, names, neighbourjoining(), DI_MATRIX::nentries, NULp, AW_awar::read_char_pntr(), AW_awar::read_int(), AW_awar::read_string(), DI_GLOBAL_MATRIX::set_changed_cb(), SmartPtr< T, C >::setNull(), symmetric_matrix< T >::size(), sum_of_triangular_numbers(), AW_awar::touch(), RecalcNeeded::tree, triangular_number(), UNCOVERED, WEIGHTED, and whatToLoad().

Referenced by DI_create_matrix_window().

static void di_autodetect_callback ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 1436 of file DI_matr.cxx.

References aw_message(), AW_root::awar(), AWAR_DIST_ALIGNMENT, AWAR_DIST_CORR_TRANS, AWAR_DIST_FILTER_FILTER, AWAR_DIST_TREE_SORT_NAME, DI_MATRIX::detect_transformation(), error(), DI_GLOBAL_MATRIX::forget(), GB_clear_error(), GB_pop_transaction(), GB_push_transaction(), GBT_get_alignment_len(), AW_window::get_root(), AP_filter::is_invalid(), DI_MATRIX::load(), NULp, AW_awar::read_char_pntr(), AW_awar::read_string(), arb_progress::subtitle(), whatToLoad(), and AW_awar::write_int().

Referenced by DI_create_matrix_window().

static __ATTR__NORETURN void di_exit ( AW_window *  aww, GBDATA *  gb_main  )

static

Definition at line 1521 of file DI_matr.cxx.

References EXIT_SUCCESS, GB_close(), AW_window::get_root(), NULp, DI_GLOBAL_MATRIX::set_changed_cb(), shutdown_macro_recording(), and AW_root::unlink_awars_from_DB().

Referenced by DI_create_matrix_window().

static void di_calculate_full_matrix_cb ( AW_window *  aww, const WeightedFilter *  weighted_filter  )

static

Definition at line 1532 of file DI_matr.cxx.

References aw_message_if(), di_calculate_matrix(), DI_MATRIX_FULL, error(), DI_GLOBAL_MATRIX::forget_if_not_has_type(), AW_window::get_root(), last_matrix_calculation_error, NULp, and tree_needs_recalc_cb().

Referenced by DI_create_matrix_window().

static void di_calculate_compressed_matrix_cb ( AW_window *  aww, WeightedFilter *  weighted_filter  )

static

Definition at line 1542 of file DI_matr.cxx.

References aw_message_if(), AW_root::awar(), AWAR_DIST_TREE_COMP_NAME, DI_MATRIX::compress(), destroy(), di_calculate_matrix(), error(), DI_GLOBAL_MATRIX::exists(), DI_GLOBAL_MATRIX::forget(), GB_await_error(), gb_main, GBT_read_tree(), DI_GLOBAL_MATRIX::get(), WeightedFilter::get_gb_main(), AW_window::get_root(), last_matrix_calculation_error, MatrixDisplay::mark(), MatrixDisplay::NEED_SETUP, NULp, AW_awar::read_string(), ta, tree_needs_recalc_cb(), UNCOVERED, and MatrixDisplay::update_display().

Referenced by DI_create_matrix_window().

static void di_define_sort_tree_name_cb ( AW_window *  aww )

static

Definition at line 1584 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_TREE_CURR_NAME, AWAR_DIST_TREE_SORT_NAME, AW_window::get_root(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by DI_create_matrix_window().

static void di_define_compression_tree_name_cb ( AW_window *  aww )

static

Definition at line 1590 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_TREE_COMP_NAME, AWAR_DIST_TREE_CURR_NAME, AW_window::get_root(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by DI_create_matrix_window().

static void di_define_save_tree_name_cb ( AW_window *  aww )

static

Definition at line 1597 of file DI_matr.cxx.

References AW_root::awar(), AWAR_DIST_TREE_CURR_NAME, AWAR_DIST_TREE_STD_NAME, AW_window::get_root(), AW_awar::read_string(), and AW_awar::write_string().

Referenced by DI_create_matrix_window().

AW_window* DI_create_matrix_window	(	AW_root *	aw_root,
		GBDATA *	gb_main
	)

Definition at line 1605 of file DI_matr.cxx.

References ARB_in_expert_mode(), AW_window::at(), AW_insert_common_property_menu_entries(), AW_preset_window(), AW_save_properties(), AW_root::awar(), save_matrix_params::awar_base, AWAR_DIST_ALIGNMENT, AWAR_DIST_BOOTSTRAP_COUNT, AWAR_DIST_CANCEL_CHARS, AWAR_DIST_COLUMN_STAT_NAME, AWAR_DIST_CORR_TRANS, AWAR_DIST_FILTER_NAME, AWAR_DIST_MATRIX_AUTO_CALC_TREE, AWAR_DIST_MATRIX_AUTO_RECALC, AWAR_DIST_MATRIX_DNA_ENABLED, AWAR_DIST_MAX_DIST, AWAR_DIST_MIN_DIST, AWAR_DIST_SAVE_MATRIX_BASE, AWAR_DIST_TREE_COMP_NAME, AWAR_DIST_TREE_CURR_NAME, AWAR_DIST_TREE_SORT_NAME, AWAR_DIST_TREE_STD_NAME, AWAR_DIST_WHICH_SPECIES, AW_root::awar_string(), AWM_ALL, AWM_EXP, awt_create_ALI_selection_list(), awt_create_select_cancel_window(), awt_create_select_filter_win(), awt_create_TREE_selection_list(), AW_window::button_length(), AW_window::callback(), COLSTAT_create_selection_window(), AW_window::create_autosize_button(), AW_window::create_button(), create_dna_matrix_window(), AW_window::create_input_field(), AW_window::create_menu(), AW_window::create_option_menu(), AW_window::create_toggle(), di_autodetect_callback(), di_calculate_compressed_matrix_cb(), di_calculate_full_matrix_cb(), di_calculate_tree_cb(), DI_create_cluster_detection_window(), DI_create_save_matrix_window(), di_define_compression_tree_name_cb(), di_define_save_tree_name_cb(), di_define_sort_tree_name_cb(), di_exit(), di_mark_by_distance(), DI_TRANSFORMATION_CATEGORIES_BARKER, DI_TRANSFORMATION_CATEGORIES_CHEMICAL, DI_TRANSFORMATION_CATEGORIES_HALL, DI_TRANSFORMATION_FELSENSTEIN, DI_TRANSFORMATION_FELSENSTEIN_VOIGT, DI_TRANSFORMATION_FROM_TREE, DI_TRANSFORMATION_JUKES_CANTOR, DI_TRANSFORMATION_KIMURA, DI_TRANSFORMATION_NONE, DI_TRANSFORMATION_OLSEN, DI_TRANSFORMATION_OLSEN_VOIGT, DI_TRANSFORMATION_PAM, DI_TRANSFORMATION_SIMILARITY, di_view_matrix_cb(), GB_pop_transaction(), GB_push_transaction(), WeightedFilter::get_adfiltercbstruct(), WeightedFilter::get_column_stat(), AW_window::get_root(), AW_window_simple_menu::init(), AW_window::insert_default_option(), AW_window::insert_help_topic(), insert_macro_menu_entry(), AW_window::insert_menu_topic(), AW_window::insert_option(), AW_window::label(), AW_window::load_xfig(), makeHelpCallback(), AW_window::sens_mask(), AW_window::sep______________(), AW_window::update_option_menu(), save_matrix_params::weighted_filter, and AW_awar::write_int().

Referenced by ARB_main().

Variable Documentation

DI_GLOBAL_MATRIX GLOBAL_MATRIX

Definition at line 63 of file DI_matr.cxx.

Referenced by MatrixDisplay::get_matrix().

MatrixDisplay* matrixDisplay = NULp

static

Definition at line 65 of file DI_matr.cxx.

Referenced by di_view_matrix_cb().

AP_userdef_matrix userdef_DNA_matrix(AP_MAX, AWAR_DIST_MATRIX_DNA_BASE)

static

Referenced by create_dna_matrix_window(), DI_create_matrix_variables(), and get_user_matrix().

SmartPtr<BoundWindowCallback> recalculate_matrix_cb

static

Definition at line 89 of file DI_matr.cxx.

SmartPtr<BoundWindowCallback> recalculate_tree_cb

static

Definition at line 90 of file DI_matr.cxx.

GB_ERROR last_matrix_calculation_error = NULp

static

Definition at line 92 of file DI_matr.cxx.

Referenced by di_calculate_compressed_matrix_cb(), di_calculate_full_matrix_cb(), and di_recalc_matrix().

RecalcNeeded need_recalc

static

Definition at line 108 of file DI_matr.cxx.

CONSTEXPR unsigned UPDATE_DELAY = 200

Definition at line 110 of file DI_matr.cxx.

Referenced by add_update_cb().

const char* enum_trans_to_string[]

static

Initial value:

= {
    "none",
    "similarity",
    "jukes_cantor",
    "felsenstein",

    "pam",
    "hall",
    "barker",
    "chemical",

    "kimura",
    "olsen",
    "felsenstein voigt",
    "olsen voigt",
    "max ml",

    NULp, 
}

Definition at line 1172 of file DI_matr.cxx.