ARB
Macros | Enumerations | Functions | Variables
ED4_root.cxx File Reference
#include "ed4_class.hxx"
#include "ed4_awars.hxx"
#include "ed4_tools.hxx"
#include "ed4_block.hxx"
#include "ed4_dots.hxx"
#include "ed4_nds.hxx"
#include "ed4_list.hxx"
#include "ed4_plugins.hxx"
#include "ed4_visualizeSAI.hxx"
#include "ed4_naligner.hxx"
#include "ed4_ProteinViewer.hxx"
#include "ed4_protein_2nd_structure.hxx"
#include "graph_aligner_gui.hxx"
#include "ed4_colStat.hxx"
#include "ed4_seq_colors.hxx"
#include "ed4_flags.hxx"
#include <ed4_extern.hxx>
#include <fast_aligner.hxx>
#include <AW_helix.hxx>
#include <gde.hxx>
#include <awt.hxx>
#include <awt_map_key.hxx>
#include <aw_awars.hxx>
#include <aw_preset.hxx>
#include <aw_msg.hxx>
#include <arb_progress.h>
#include <aw_root.hxx>
#include <aw_question.hxx>
#include <aw_advice.hxx>
#include <rootAsWin.h>
#include "../WINDOW/aw_status.hxx"
#include <arb_version.h>
#include <arb_file.h>
#include <arb_defs.h>
#include <arbdbt.h>
#include <ad_cb.h>
#include <macros.hxx>
#include <st_window.hxx>
#include <cctype>
#include <map>
Include dependency graph for ED4_root.cxx:

Go to the source code of this file.

Macros

#define INSERT_SEARCH_FIELDS(Short, label_prefix, prefix)
 

Enumerations

enum  MenuSelectType {
  ED4_MS_NONE, ED4_MS_ALL, ED4_MS_INVERT, ED4_MS_INVERT_GROUP,
  ED4_MS_UNMARK_ALL, ED4_MS_MARK_SELECTED, ED4_MS_UNMARK_SELECTED, ED4_MS_SELECT_MARKED,
  ED4_MS_DESELECT_MARKED, ED4_MS_TOGGLE_BLOCKTYPE
}
 

Functions

static ARB_ERROR request_terminal_refresh (ED4_base *base, ED4_level lev)
 
static ARB_ERROR request_sequence_refresh (ED4_base *base, bool consensi)
 
static ARB_ERROR change_char_table_length (ED4_base *base, int new_length)
 
void ED4_alignment_length_changed (GBDATA *gb_alignment_len, GB_CB_TYPE gbtype)
 
static ARB_ERROR force_group_update (ED4_base *base)
 
static void reload_helix_cb ()
 
static void reload_ecoli_cb ()
 
 DECLARE_CBTYPE_FVV_AND_BUILDERS (ED4_Species_Callback, ARB_ERROR, GBDATA *)
 
static ARB_ERROR do_sth_with_species (ED4_base *base, const ED4_Species_Callback *cb)
 
static ARB_ERROR ED4_with_all_loaded_species (const ED4_Species_Callback &cb)
 
static bool is_named (ED4_base *base, const char *wanted_name)
 
static bool is_species_named (ED4_base *base, const char *species_name)
 
static bool is_SAI_named (ED4_base *base, const char *sai_name)
 
ED4_species_name_terminal * ED4_find_species_or_SAI_name_terminal (const char *species_name)
 
ED4_species_name_terminal * ED4_find_species_name_terminal (const char *species_name)
 
ED4_species_name_terminal * ED4_find_SAI_name_terminal (const char *sai_name)
 
static charget_group_consensus (const char *species_name, PosRange range)
 
static bool get_selected_range (PosRange &range)
 
static GBDATAget_next_selected_species ()
 
static GBDATAget_first_selected_species (int *total_no_of_selected_species)
 
static ARB_ERROR ED4_delete_temp_entries (GBDATA *species, GB_CSTR alignment_name)
 
static void ED4_remove_faligner_entries ()
 
static void toggle_helix_for_SAI (AW_window *aww)
 
static void title_mode_changed (AW_root *aw_root, AW_window *aww)
 
static void ED4_undo_redo (AW_window *aww, GB_UNDO_TYPE undo_type)
 
static AW_windowED4_zoom_message_window (AW_root *root)
 
static charcat (char *toBuf, const char *s1, const char *s2)
 
static void insert_search_fields (AW_window_menu_modes *awmm, const char *label_prefix, const char *macro_prefix, const char *pattern_awar_name, const char *show_awar_name, int short_form, ED4_SearchPositionType type, ED4_window *ed4w)
 
static void ED4_set_protection (AW_window *aww, int wanted_protection)
 
static void ED4_menu_highlight (AW_window *aww, MenuSelectType select)
 
static void ED4_menu_perform_block_operation (AW_window *, ED4_blockoperation_type type)
 
static void modes_cb (AW_window *, ED4_species_mode smode)
 
void ED4_no_dangerous_modes ()
 
static charget_helix_string (GBDATA *gb_main, const char *alignment_name)
 
const AlignDataAccessED4_get_aligner_data_access ()
 
static AW_windowED4_create_faligner_window (AW_root *awr, const AlignDataAccess *data_access)
 
static const charpropertyName (GBDATA *gb_main, int mode)
 
static void ED4_save_properties (AW_window *aw, int mode)
 
void ED4_popup_gc_window (AW_window *awp, AW_gc_manager *gcman)
 
static void gc_change_cb (GcChange whatChanged)
 
chardetectProperties (GBDATA *gb_main)
 

Variables

static ED4_selected_elemcurr_aligner_elem = NULp
 

Macro Definition Documentation

#define INSERT_SEARCH_FIELDS (   Short,
  label_prefix,
  prefix 
)
Value:
#label_prefix, \
#prefix, \
ED4_AWAR_##prefix##_SEARCH_PATTERN, \
ED4_AWAR_##prefix##_SEARCH_SHOW, \
Short, \
ED4_##prefix##_PATTERN, \
)
static void insert_search_fields(AW_window_menu_modes *awmm, const char *label_prefix, const char *macro_prefix, const char *pattern_awar_name, const char *show_awar_name, int short_form, ED4_SearchPositionType type, ED4_window *ed4w)
Definition: ED4_root.cxx:1047
ED4_window * current_ed4w()
Definition: ed4_class.hxx:1397

Referenced by ED4_root::generate_window().

Enumeration Type Documentation

Enumerator
ED4_MS_NONE 
ED4_MS_ALL 
ED4_MS_INVERT 
ED4_MS_INVERT_GROUP 
ED4_MS_UNMARK_ALL 
ED4_MS_MARK_SELECTED 
ED4_MS_UNMARK_SELECTED 
ED4_MS_SELECT_MARKED 
ED4_MS_DESELECT_MARKED 
ED4_MS_TOGGLE_BLOCKTYPE 

Definition at line 1101 of file ED4_root.cxx.

Function Documentation

static ARB_ERROR request_terminal_refresh ( ED4_base base,
ED4_level  lev 
)
static
static ARB_ERROR request_sequence_refresh ( ED4_base base,
bool  consensi 
)
static
static ARB_ERROR change_char_table_length ( ED4_base base,
int  new_length 
)
static
void ED4_alignment_length_changed ( GBDATA gb_alignment_len,
GB_CB_TYPE  gbtype 
)
static ARB_ERROR force_group_update ( ED4_base base)
static

Definition at line 543 of file ED4_root.cxx.

References ED4_base::is_multi_species_manager(), and NULp.

Referenced by ED4_root::create_hierarchy().

static void reload_helix_cb ( )
static
static void reload_ecoli_cb ( )
static
DECLARE_CBTYPE_FVV_AND_BUILDERS ( ED4_Species_Callback  ,
ARB_ERROR  ,
GBDATA  
)
static ARB_ERROR do_sth_with_species ( ED4_base base,
const ED4_Species_Callback *  cb 
)
static
static ARB_ERROR ED4_with_all_loaded_species ( const ED4_Species_Callback &  cb)
static
static bool is_named ( ED4_base base,
const char wanted_name 
)
static

Definition at line 867 of file ED4_root.cxx.

References e4_assert, and GB_read_char_pntr().

Referenced by is_SAI_named(), and is_species_named().

static bool is_species_named ( ED4_base base,
const char species_name 
)
static
static bool is_SAI_named ( ED4_base base,
const char sai_name 
)
static

Definition at line 883 of file ED4_root.cxx.

References ED4_base::inside_SAI_manager(), and is_named().

Referenced by ED4_find_SAI_name_terminal().

ED4_species_name_terminal* ED4_find_species_or_SAI_name_terminal ( const char species_name)
ED4_species_name_terminal* ED4_find_species_name_terminal ( const char species_name)
ED4_species_name_terminal* ED4_find_SAI_name_terminal ( const char sai_name)
static char* get_group_consensus ( const char species_name,
PosRange  range 
)
static
static bool get_selected_range ( PosRange range)
static
static GBDATA* get_next_selected_species ( )
static
static GBDATA* get_first_selected_species ( int total_no_of_selected_species)
static
static ARB_ERROR ED4_delete_temp_entries ( GBDATA species,
GB_CSTR  alignment_name 
)
static

Definition at line 950 of file ED4_root.cxx.

References FastAligner_delete_temp_entries().

Referenced by ED4_remove_faligner_entries().

static void ED4_remove_faligner_entries ( )
static
static void toggle_helix_for_SAI ( AW_window aww)
static
static void title_mode_changed ( AW_root aw_root,
AW_window aww 
)
static
static void ED4_undo_redo ( AW_window aww,
GB_UNDO_TYPE  undo_type 
)
static
static AW_window* ED4_zoom_message_window ( AW_root root)
static
static char* cat ( char toBuf,
const char s1,
const char s2 
)
static

Definition at line 1037 of file ED4_root.cxx.

Referenced by insert_search_fields(), and mergeKnownFields().

static void insert_search_fields ( AW_window_menu_modes awmm,
const char label_prefix,
const char macro_prefix,
const char pattern_awar_name,
const char show_awar_name,
int  short_form,
ED4_SearchPositionType  type,
ED4_window ed4w 
)
static
static void ED4_set_protection ( AW_window aww,
int  wanted_protection 
)
static
static void ED4_menu_highlight ( AW_window aww,
MenuSelectType  select 
)
static
static void ED4_menu_perform_block_operation ( AW_window ,
ED4_blockoperation_type  type 
)
static

Definition at line 1193 of file ED4_root.cxx.

References ED4_perform_block_operation().

Referenced by ED4_root::generate_window().

static void modes_cb ( AW_window ,
ED4_species_mode  smode 
)
static
void ED4_no_dangerous_modes ( )
static char* get_helix_string ( GBDATA gb_main,
const char alignment_name 
)
static
const AlignDataAccess* ED4_get_aligner_data_access ( )
static AW_window* ED4_create_faligner_window ( AW_root awr,
const AlignDataAccess data_access 
)
static

Definition at line 1245 of file ED4_root.cxx.

References e4_assert, FastAligner_create_window(), and NULp.

Referenced by ED4_root::generate_window().

static const char* propertyName ( GBDATA gb_main,
int  mode 
)
static
static void ED4_save_properties ( AW_window aw,
int  mode 
)
static
void ED4_popup_gc_window ( AW_window awp,
AW_gc_manager gcman 
)
static void gc_change_cb ( GcChange  whatChanged)
static
char* detectProperties ( GBDATA gb_main)
inline

Variable Documentation

ED4_selected_elem* curr_aligner_elem = NULp
static

Definition at line 923 of file ED4_root.cxx.