ED4_detect_bad_ali.cxx File Reference

#include "ed4_detect_bad_ali.hxx"
#include "ed4_class.hxx"
#include <AW_helix.hxx>
#include <aw_awar_defs.hxx>
#include <aw_awar.hxx>
#include <aw_msg.hxx>
#include <aw_select.hxx>
#include <aw_root.hxx>
#include <arbdbt.h>
#include <arb_defs.h>
#include <string>
#include <map>
#include <vector>
#include <items.h>
#include <item_sel_list.h>

Include dependency graph for ED4_detect_bad_ali.cxx:

Go to the source code of this file.

Classes
class	HelixAlignmentQuality
class	BadPositionsOrder

Macros
#define	StrArray_FROM_HELIXLIST(varname, helixlist)   StrArray varname; parse_helix_list(varname, helixlist)
#define	AWAR_BADALI_BASE   "badali/"
#define	AWAR_BADALI_HELIXLIST   AWAR_BADALI_BASE "helixlist"
#define	AWAR_BADALI_SYMBOLS   AWAR_BADALI_BASE "symbols"
#define	AWAR_BADALI_TEMP   "tmp/" AWAR_BADALI_BASE
#define	AWAR_BADALI_SPECIES   AWAR_BADALI_TEMP "selected"
#define	AWAR_BADALI_FIELD   AWAR_BADALI_TEMP "field"

Typedefs
typedef map< string, long >	BadPositionsForSpecies
typedef const BadPositionsForSpecies	BadPositionsForSpeciesConst
typedef map< size_t, size_t >	PairedPositions
typedef vector< string >	StringVector

Enumerations
enum	JumpWhy { BY_SELECTION, BY_BUTTON }
enum	SelectedAwar { SELECTED_SPECIES, SELECTED_BAD_ALI }

Functions
static void	getSpeciesSortedByBadPositions (BadPositionsForSpeciesConst &bad_pos, StringVector &result)
static void	parse_helix_list (StrArray &result_helices, const char *helix_list)
void	ED4_create_detect_bad_alignment_awars (AW_root *aw_root, AW_default aw_def)
static ARB_ERROR	add_species_to_list_cb (ED4_base *base, StrArray *species)
static char *	create_list_of_loaded_species ()
static void	calc_and_update_alignment_errors_cb (AW_window *aww, AW_selection_list *sellst)
static void	jump_to_next_helix_cb (AW_window *, JumpWhy called)
static void	selected_changed_cb (AW_root *aw_root, SelectedAwar whatChanged)
void	ED4_popup_detect_bad_alignment_window (AW_window *editor_window, const WindowCallback *helixSettings_cb)

Variables
const long	NOT_CALCULATED = -1

Macro Definition Documentation

#define StrArray_FROM_HELIXLIST	(		varname,
			helixlist
	)		StrArray varname; parse_helix_list(varname, helixlist)

Definition at line 266 of file ED4_detect_bad_ali.cxx.

Referenced by calc_and_update_alignment_errors_cb(), and jump_to_next_helix_cb().

#define AWAR_BADALI_BASE   "badali/"

Definition at line 395 of file ED4_detect_bad_ali.cxx.

#define AWAR_BADALI_HELIXLIST   AWAR_BADALI_BASE "helixlist"

Definition at line 396 of file ED4_detect_bad_ali.cxx.

Referenced by calc_and_update_alignment_errors_cb(), ED4_create_detect_bad_alignment_awars(), ED4_popup_detect_bad_alignment_window(), and jump_to_next_helix_cb().

#define AWAR_BADALI_SYMBOLS   AWAR_BADALI_BASE "symbols"

Definition at line 397 of file ED4_detect_bad_ali.cxx.

Referenced by calc_and_update_alignment_errors_cb(), ED4_create_detect_bad_alignment_awars(), and ED4_popup_detect_bad_alignment_window().

#define AWAR_BADALI_TEMP   "tmp/" AWAR_BADALI_BASE

Definition at line 399 of file ED4_detect_bad_ali.cxx.

#define AWAR_BADALI_SPECIES   AWAR_BADALI_TEMP "selected"

Definition at line 400 of file ED4_detect_bad_ali.cxx.

Referenced by ED4_create_detect_bad_alignment_awars(), ED4_popup_detect_bad_alignment_window(), and selected_changed_cb().

#define AWAR_BADALI_FIELD   AWAR_BADALI_TEMP "field"

Definition at line 401 of file ED4_detect_bad_ali.cxx.

Referenced by calc_and_update_alignment_errors_cb(), ED4_create_detect_bad_alignment_awars(), and ED4_popup_detect_bad_alignment_window().

Typedef Documentation

typedef map<string, long> BadPositionsForSpecies

Definition at line 35 of file ED4_detect_bad_ali.cxx.

typedef const BadPositionsForSpecies BadPositionsForSpeciesConst

Definition at line 36 of file ED4_detect_bad_ali.cxx.

typedef map<size_t, size_t> PairedPositions

Definition at line 38 of file ED4_detect_bad_ali.cxx.

typedef vector<string> StringVector

Definition at line 223 of file ED4_detect_bad_ali.cxx.

Enumeration Type Documentation

enum JumpWhy

Enumerator
BY_SELECTION
BY_BUTTON

Definition at line 521 of file ED4_detect_bad_ali.cxx.

enum SelectedAwar

Enumerator
SELECTED_SPECIES
SELECTED_BAD_ALI

Definition at line 567 of file ED4_detect_bad_ali.cxx.

Function Documentation

static void getSpeciesSortedByBadPositions ( BadPositionsForSpeciesConst &  bad_pos, StringVector &  result  )

static

Definition at line 225 of file ED4_detect_bad_ali.cxx.

References long, and s.

Referenced by calc_and_update_alignment_errors_cb().

static void parse_helix_list ( StrArray &  result_helices, const char *  helix_list  )

static

Definition at line 236 of file ED4_detect_bad_ali.cxx.

References ConstStrArray::erase(), GBS_global_string_copy(), GBT_split_string(), CharPtrArray::size(), and swap().

void ED4_create_detect_bad_alignment_awars	(	AW_root *	aw_root,
		AW_default	aw_def
	)

Definition at line 403 of file ED4_detect_bad_ali.cxx.

References AWAR_BADALI_FIELD, AWAR_BADALI_HELIXLIST, AWAR_BADALI_SPECIES, AWAR_BADALI_SYMBOLS, AW_root::awar_string(), and AW_awar::set_srt().

Referenced by ed4_create_all_awars().

static ARB_ERROR add_species_to_list_cb ( ED4_base *  base, StrArray *  species  )

static

Definition at line 410 of file ED4_detect_bad_ali.cxx.

References error(), GB_read_as_string(), ED4_base::is_species_manager(), LEV_SPECIES_NAME, and NULp.

Referenced by create_list_of_loaded_species().

static char* create_list_of_loaded_species ( )

static

Definition at line 426 of file ED4_detect_bad_ali.cxx.

References add_species_to_list_cb(), aw_message_if(), ARB_ERROR::deliver(), ED4_ROOT, error(), GBT_join_strings(), ED4_root::get_gb_main(), ED4_root::root_group_man, ED4_manager::route_down_hierarchy(), and ta.

Referenced by calc_and_update_alignment_errors_cb().

static void calc_and_update_alignment_errors_cb ( AW_window *  aww, AW_selection_list *  sellst  )

static

Definition at line 434 of file ED4_detect_bad_ali.cxx.

References aw_message(), aw_message_if(), AW_root::awar(), AWAR_BADALI_FIELD, AWAR_BADALI_HELIXLIST, AWAR_BADALI_SYMBOLS, AW_selection_list::clear(), create_list_of_loaded_species(), ED4_ROOT, error(), FIF_ALLOW_NONE, GB_await_error(), GB_have_error(), gb_species_data, GB_write_lossless_int(), GBS_global_string(), GBT_find_species_rel_species_data(), GBT_get_species_data(), GBT_searchOrCreate_itemfield_according_to_changekey(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), AW_window::get_root(), getSpeciesSortedByBadPositions(), ED4_root::helix, AW_selection_list::insert(), AW_selection_list::insert_default(), NULp, prepare_and_get_selected_itemfield(), AW_awar::read_char_pntr(), AW_awar::read_string(), SPECIES_get_selector(), StrArray_FROM_HELIXLIST, ta, and AW_selection_list::update().

Referenced by ED4_popup_detect_bad_alignment_window().

static void jump_to_next_helix_cb ( AW_window *  , JumpWhy  called  )

static

Definition at line 523 of file ED4_detect_bad_ali.cxx.

References abs, aw_message(), AW_root::awar(), AWAR_BADALI_HELIXLIST, ED4_window::awar_path_for_helixNr, ED4_window::aww, BY_BUTTON, BY_SELECTION, current_ed4w(), ED4_set_helixnr(), GBS_global_string(), AW_window::get_root(), AW_awar::read_char_pntr(), StrArray_FROM_HELIXLIST, and win.

Referenced by ED4_popup_detect_bad_alignment_window(), and selected_changed_cb().

static void selected_changed_cb ( AW_root *  aw_root, SelectedAwar  whatChanged  )

static

Definition at line 569 of file ED4_detect_bad_ali.cxx.

References AW_root::awar(), AWAR_BADALI_SPECIES, AWAR_SPECIES_NAME, BY_SELECTION, jump_to_next_helix_cb(), NULp, AW_awar::read_char_pntr(), SELECTED_BAD_ALI, SELECTED_SPECIES, swap(), and AW_awar::write_string().

Referenced by ED4_popup_detect_bad_alignment_window().

void ED4_popup_detect_bad_alignment_window	(	AW_window *	editor_window,
		const WindowCallback *	helixSettings_cb
	)

Definition at line 592 of file ED4_detect_bad_ali.cxx.

References AW_awar::add_callback(), AW_POPDOWN(), AW_root::awar(), AWAR_BADALI_FIELD, AWAR_BADALI_HELIXLIST, AWAR_BADALI_SPECIES, AWAR_BADALI_SYMBOLS, AWAR_SPECIES_NAME, BY_BUTTON, calc_and_update_alignment_errors_cb(), create_itemfield_selection_button(), e4_assert, ED4_ROOT, FIELD_FILTER_INT_WRITEABLE, ED4_root::get_gb_main(), AW_window::get_root(), AW_selection_list::insert_default(), jump_to_next_helix_cb(), makeHelpCallback(), NULp, SELECTED_BAD_ALI, selected_changed_cb(), SELECTED_SPECIES, SF_ALLOW_NEW, SPECIES_get_selector(), and AW_selection_list::update().

Referenced by ED4_root::generate_window().

Variable Documentation

const long NOT_CALCULATED = -1

Definition at line 33 of file ED4_detect_bad_ali.cxx.