#include "NT_local.h"
#include <RangeList.h>
#include <arbdbt.h>
#include <insdel.h>
#include <aw_window.hxx>
#include <aw_root.hxx>
#include <aw_awars.hxx>
#include <aw_msg.hxx>
#include <awt_sel_boxes.hxx>
#include <arb_defs.h>
#include <awt_config_manager.hxx>

Include dependency graph for NT_ins_col.cxx:

Classes
class	StaticData

Macros
#define	AWAR_INSDEL "insdel/"

#define	TMP_AWAR_INSDEL "tmp/" AWAR_INSDEL

#define	AWAR_INSDEL_AMOUNT AWAR_INSDEL "nchar"

#define	AWAR_INSDEL_DELETABLE AWAR_INSDEL "characters"

#define	AWAR_INSDEL_RANGE AWAR_INSDEL "range"

#define	AWAR_INSDEL_SAI AWAR_INSDEL "sainame"

#define	AWAR_INSDEL_CONTAINS AWAR_INSDEL "contain"

#define	AWAR_INSDEL_SAI_CHARS AWAR_INSDEL "saichars"

#define	AWAR_INSDEL_AFFECTED TMP_AWAR_INSDEL "affected"

#define	AWAR_INSDEL_WHAT TMP_AWAR_INSDEL "what"

#define	AWAR_INSDEL_DIRECTION AWAR_INSDEL "direction"

Enumerations
enum	SaiContains { DOESNT_CONTAIN, CONTAINS }

enum	InsdelMode { INSERT, DELETE }

Functions
static void	cleanup_when_closing (AW_window *)

static int	columns_of (const RangeList &ranges)

static void	range_count_update_cb (AW_root *root)

static void	range_changed_cb (AW_root *root)

static GB_ERROR	update_RangeList (AW_root root, GBDATA gb_main)

static void	update_RangeList_cb (AW_root *root)

void	create_insertDeleteColumn_variables (AW_root *root, AW_default props)

static void	insdel_event (AW_window *aws, InsdelMode mode)

static void	insdel_sai_event (AW_window *aws, InsdelMode mode)

AW_window *	create_insertDeleteColumn_window (AW_root *root)

AW_window *	create_insertDeleteBySAI_window (AW_root root, GBDATA gb_main)

Variables
static StaticData	SELECTED

static AWT_config_mapping_def	insdel_by_SAI_config_def []

static AWT_predefined_config	insdel_by_SAI_predef_config []

Macro Definition Documentation

#define AWAR_INSDEL "insdel/"

Definition at line 24 of file NT_ins_col.cxx.

#define TMP_AWAR_INSDEL "tmp/" AWAR_INSDEL

Definition at line 25 of file NT_ins_col.cxx.

#define AWAR_INSDEL_AMOUNT AWAR_INSDEL "nchar"

Definition at line 27 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), create_insertDeleteColumn_window(), insdel_event(), and insdel_sai_event().

#define AWAR_INSDEL_DELETABLE AWAR_INSDEL "characters"

Definition at line 28 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), create_insertDeleteColumn_window(), insdel_event(), and insdel_sai_event().

#define AWAR_INSDEL_RANGE AWAR_INSDEL "range"

Definition at line 29 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), insdel_sai_event(), range_changed_cb(), and range_count_update_cb().

#define AWAR_INSDEL_SAI AWAR_INSDEL "sainame"

Definition at line 30 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), and update_RangeList().

#define AWAR_INSDEL_CONTAINS AWAR_INSDEL "contain"

Definition at line 31 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), and update_RangeList().

#define AWAR_INSDEL_SAI_CHARS AWAR_INSDEL "saichars"

Definition at line 32 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), and update_RangeList().

#define AWAR_INSDEL_AFFECTED TMP_AWAR_INSDEL "affected"

Definition at line 33 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), and range_count_update_cb().

#define AWAR_INSDEL_WHAT TMP_AWAR_INSDEL "what"

Definition at line 34 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), and range_changed_cb().

#define AWAR_INSDEL_DIRECTION AWAR_INSDEL "direction"

Definition at line 35 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window(), create_insertDeleteColumn_variables(), and insdel_sai_event().

Enumeration Type Documentation

enum SaiContains

Enumerator
DOESNT_CONTAIN
CONTAINS

Definition at line 37 of file NT_ins_col.cxx.

enum InsdelMode

Enumerator
INSERT
DELETE

Definition at line 38 of file NT_ins_col.cxx.

Function Documentation

static void cleanup_when_closing ( AW_window * )

static

Definition at line 63 of file NT_ins_col.cxx.

Referenced by create_insertDeleteBySAI_window().

static int columns_of ( const RangeList & ranges )

static

Definition at line 67 of file NT_ins_col.cxx.

References RangeList::begin(), and RangeList::end().

Referenced by range_count_update_cb().

static void range_count_update_cb ( AW_root * root )

static

Definition at line 75 of file NT_ins_col.cxx.

References AW_root::awar(), AWAR_INSDEL_AFFECTED, AWAR_INSDEL_RANGE, columns_of(), StaticData::get_ranges(), RANGES, AW_awar::read_int(), SINGLE_COLUMNS, RangeList::size(), and AW_awar::write_int().

Referenced by range_changed_cb(), and update_RangeList().

static void range_changed_cb ( AW_root * root )

static

Definition at line 85 of file NT_ins_col.cxx.

References AW_root::awar(), AWAR_INSDEL_RANGE, AWAR_INSDEL_WHAT, NULp, range_count_update_cb(), RANGES, AW_awar::read_int(), SINGLE_COLUMNS, and AW_awar::write_string().

Referenced by create_insertDeleteColumn_variables().

static GB_ERROR update_RangeList	(	AW_root *	root,
		GBDATA *	gb_main
	)

static

Definition at line 96 of file NT_ins_col.cxx.

References AW_root::awar(), AWAR_INSDEL_CONTAINS, AWAR_INSDEL_SAI, AWAR_INSDEL_SAI_CHARS, build_RangeList_from_string(), chars, contains(), DOESNT_CONTAIN, error(), GB_await_error(), GB_have_error(), GB_read_char_pntr(), GBS_global_string(), GBT_expect_SAI(), GBT_find_sequence(), StaticData::get_ali(), NULp, range_count_update_cb(), AW_awar::read_char_pntr(), AW_awar::read_int(), StaticData::set_ranges(), ta, and StaticData::track_ali().

Referenced by create_insertDeleteColumn_variables(), and update_RangeList_cb().

static void update_RangeList_cb ( AW_root * root )

static

Definition at line 131 of file NT_ins_col.cxx.

References aw_message_if(), NT_global::gb_main, GLOBAL, and update_RangeList().

Referenced by create_insertDeleteColumn_variables().

void create_insertDeleteColumn_variables	(	AW_root *	root,
		AW_default	props
	)

Definition at line 135 of file NT_ins_col.cxx.

References AW_awar::add_callback(), AWAR_CURSOR_POSITION, AWAR_INSDEL_AFFECTED, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_CONTAINS, AWAR_INSDEL_DELETABLE, AWAR_INSDEL_DIRECTION, AWAR_INSDEL_RANGE, AWAR_INSDEL_SAI, AWAR_INSDEL_SAI_CHARS, AWAR_INSDEL_WHAT, AW_root::awar_int(), AW_root::awar_string(), BEHIND, DOESNT_CONTAIN, NT_global::gb_main, GLOBAL, info2bio(), range_changed_cb(), RANGES, AW_awar::set_minmax(), update_RangeList(), and update_RangeList_cb().

Referenced by nt_create_all_awars().

static void insdel_event	(	AW_window *	aws,
		InsdelMode	mode
	)

static

Definition at line 153 of file NT_ins_col.cxx.

References ARB_insdel_columns(), aw_message(), AW_root::awar(), AWAR_CURSOR_POSITION, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_DELETABLE, bio2info(), DELETE, error(), GB_begin_transaction(), GB_end_transaction_show_error(), gb_main, NT_global::gb_main, GBT_check_data(), StaticData::get_ali(), AW_window::get_root(), GLOBAL, NULp, AW_awar::read_char_pntr(), AW_awar::read_int(), and StaticData::track_ali().

Referenced by create_insertDeleteColumn_window().

static void insdel_sai_event	(	AW_window *	aws,
		InsdelMode	mode
	)

static

AW_window* create_insertDeleteColumn_window ( AW_root * root )

Definition at line 201 of file NT_ins_col.cxx.

References AW_POPDOWN(), AWAR_CURSOR_POSITION, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_DELETABLE, DELETE, insdel_event(), INSERT, makeHelpCallback(), and NULp.

Referenced by popup_new_main_window().

AW_window* create_insertDeleteBySAI_window	(	AW_root *	root,
		GBDATA *	gb_main
	)

Definition at line 268 of file NT_ins_col.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_INSDEL_AFFECTED, AWAR_INSDEL_AMOUNT, AWAR_INSDEL_CONTAINS, AWAR_INSDEL_DELETABLE, AWAR_INSDEL_DIRECTION, AWAR_INSDEL_RANGE, AWAR_INSDEL_SAI, AWAR_INSDEL_SAI_CHARS, AWAR_INSDEL_WHAT, awt_create_SAI_selection_button(), AWT_insert_config_manager(), BEHIND, cleanup_when_closing(), CONTAINS, DELETE, DOESNT_CONTAIN, INFRONTOF, insdel_sai_event(), INSERT, makeHelpCallback(), NULp, RANGES, and SINGLE_COLUMNS.

Referenced by popup_new_main_window().

Variable Documentation

StaticData SELECTED

static

Definition at line 61 of file NT_ins_col.cxx.

AWT_config_mapping_def insdel_by_SAI_config_def[]

static

Initial value:

= {
    { AWAR_INSDEL_RANGE,     "range" },
    { AWAR_INSDEL_SAI,       "sai" },
    { AWAR_INSDEL_CONTAINS,  "contain" },
    { AWAR_INSDEL_SAI_CHARS, "chars" },
    { AWAR_INSDEL_DELETABLE, "deletable" },
    { AWAR_INSDEL_AMOUNT,    "amount" },
    { AWAR_INSDEL_DIRECTION, "direction" },
    { NULp, NULp },
}

Definition at line 242 of file NT_ins_col.cxx.

AWT_predefined_config insdel_by_SAI_predef_config[]

static

Initial value:

= {
    {
        "*gaps_by_variability",
        "Use to insert 2 gaps next to all\ncolumns with high variability",
        "amount='2';chars='123';contain='1';direction='1';range='1';sai='POS_VAR_BY_PARSIMONY'",
    },
    {
        "*erase_columns_without_data",
        "selects all columns where \nMAX_FREQUENCY contains '='",
        "chars='=';contain='1';deletable='-.';range='1';sai='MAX_FREQUENCY'",
    },
    { NULp, NULp, NULp },
}

Definition at line 254 of file NT_ins_col.cxx.

Classes

Macros

Enumerations

Functions

Variables

Macro Definition Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation