di_matr.hxx File Reference

#include <AP_pro_a_nucs.hxx>
#include <AP_Tree.hxx>
#include <AP_matrix.hxx>
#include <AP_seq_dna.hxx>
#include <AP_seq_simple_pro.hxx>
#include <string>

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Classes
class	DI_ENTRY
class	MatrixOrder
class	DI_MATRIX
class	DI_GLOBAL_MATRIX
struct	save_matrix_params

Macros
#define	di_assert(cond)   arb_assert(cond)
#define	AWAR_DIST_PREFIX   "dist/"
#define	AWAR_DIST_CORR_TRANS   AWAR_DIST_PREFIX "correction/trans"
#define	AWAR_DIST_SAVE_MATRIX_BASE   "tmp/" AWAR_DIST_PREFIX "save_matrix"
#define	AWAR_DIST_DIST_PREFIX   AWAR_DIST_PREFIX "dist/"
#define	AWAR_DIST_MIN_DIST   AWAR_DIST_DIST_PREFIX "lower"
#define	AWAR_DIST_MAX_DIST   AWAR_DIST_DIST_PREFIX "upper"

Typedefs
typedef void(*	DI_MATRIX_CB )()

Enumerations
enum	DI_TRANSFORMATION {   DI_TRANSFORMATION_NONE, DI_TRANSFORMATION_SIMILARITY, DI_TRANSFORMATION_JUKES_CANTOR, DI_TRANSFORMATION_FELSENSTEIN,   DI_TRANSFORMATION_PAM, DI_TRANSFORMATION_CATEGORIES_HALL, DI_TRANSFORMATION_CATEGORIES_BARKER, DI_TRANSFORMATION_CATEGORIES_CHEMICAL,   DI_TRANSFORMATION_KIMURA, DI_TRANSFORMATION_OLSEN, DI_TRANSFORMATION_FELSENSTEIN_VOIGT, DI_TRANSFORMATION_OLSEN_VOIGT,   DI_TRANSFORMATION_ML, DI_TRANSFORMATION_FROM_TREE, DI_TRANSFORMATION_COUNT, DI_TRANSFORMATION_NONE_DETECTED }
enum	DI_MATRIX_TYPE { DI_MATRIX_FULL, DI_MATRIX_COMPRESSED }
enum	DI_SAVE_TYPE { DI_SAVE_PHYLIP_COMP, DI_SAVE_READABLE, DI_SAVE_TABBED }
enum	LoadWhat { DI_LOAD_ALL, DI_LOAD_MARKED, DI_LOAD_LIST }

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

Variables
DI_GLOBAL_MATRIX	GLOBAL_MATRIX

Macro Definition Documentation

#define di_assert

(

cond

)

arb_assert(cond)

Definition at line 33 of file di_matr.hxx.

#define AWAR_DIST_PREFIX   "dist/"

Definition at line 35 of file di_matr.hxx.

#define AWAR_DIST_CORR_TRANS   AWAR_DIST_PREFIX "correction/trans"

Definition at line 36 of file di_matr.hxx.

Referenced by di_autodetect_callback(), di_calculate_matrix(), di_calculate_tree_cb(), DI_create_matrix_variables(), DI_create_matrix_window(), di_mark_by_distance(), and selected_tree_changed_cb().

#define AWAR_DIST_SAVE_MATRIX_BASE   "tmp/" AWAR_DIST_PREFIX "save_matrix"

Definition at line 37 of file di_matr.hxx.

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

#define AWAR_DIST_DIST_PREFIX   AWAR_DIST_PREFIX "dist/"

Definition at line 39 of file di_matr.hxx.

#define AWAR_DIST_MIN_DIST   AWAR_DIST_DIST_PREFIX "lower"

Definition at line 40 of file di_matr.hxx.

Referenced by di_bind_dist_awars(), DI_create_matrix_variables(), DI_create_matrix_window(), DI_create_view_matrix_window(), di_mark_by_distance(), di_view_set_distances(), di_view_set_max_dist(), and input_cb().

#define AWAR_DIST_MAX_DIST   AWAR_DIST_DIST_PREFIX "upper"

Definition at line 41 of file di_matr.hxx.

Referenced by di_bind_dist_awars(), DI_create_matrix_variables(), DI_create_matrix_window(), DI_create_view_matrix_window(), di_mark_by_distance(), di_view_set_distances(), di_view_set_max_dist(), and input_cb().

Typedef Documentation

typedef void(* DI_MATRIX_CB)()

Definition at line 134 of file di_matr.hxx.

Enumeration Type Documentation

enum DI_TRANSFORMATION

Enumerator
DI_TRANSFORMATION_NONE
DI_TRANSFORMATION_SIMILARITY
DI_TRANSFORMATION_JUKES_CANTOR
DI_TRANSFORMATION_FELSENSTEIN
DI_TRANSFORMATION_PAM
DI_TRANSFORMATION_CATEGORIES_HALL
DI_TRANSFORMATION_CATEGORIES_BARKER
DI_TRANSFORMATION_CATEGORIES_CHEMICAL
DI_TRANSFORMATION_KIMURA
DI_TRANSFORMATION_OLSEN
DI_TRANSFORMATION_FELSENSTEIN_VOIGT
DI_TRANSFORMATION_OLSEN_VOIGT
DI_TRANSFORMATION_ML
DI_TRANSFORMATION_FROM_TREE
DI_TRANSFORMATION_COUNT
DI_TRANSFORMATION_NONE_DETECTED

Definition at line 43 of file di_matr.hxx.

enum DI_MATRIX_TYPE

Enumerator
DI_MATRIX_FULL
DI_MATRIX_COMPRESSED

Definition at line 68 of file di_matr.hxx.

enum DI_SAVE_TYPE

Enumerator
DI_SAVE_PHYLIP_COMP
DI_SAVE_READABLE
DI_SAVE_TABBED

Definition at line 93 of file di_matr.hxx.

enum LoadWhat

Enumerator
DI_LOAD_ALL
DI_LOAD_MARKED
DI_LOAD_LIST

Definition at line 99 of file di_matr.hxx.

Function Documentation

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().

Variable Documentation

DI_GLOBAL_MATRIX GLOBAL_MATRIX

Definition at line 63 of file DI_matr.cxx.

Referenced by MatrixDisplay::get_matrix().