ARB
Classes | Namespaces | Macros | Typedefs | Enumerations | Functions | Variables
ed4_class.hxx File Reference
#include <aw_font_group.hxx>
#include <pos_range.h>
#include <stringize.h>
#include <arb_error.h>
#include "ed4_defs.hxx"
#include "ed4_search.hxx"
#include <list>
#include <attributes.h>
#include <BI_basepos.hxx>
#include <downcast.h>
#include "chartable.h"
Include dependency graph for ed4_class.hxx:
This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes

class  ED4_list< T >
 
class  ED4_list_elem< T >
 
class  ED4_objspec
 
class  ED4_folding_line
 
struct  ED4_scroll_links
 
class  ED4_foldable
 
class  ED4_scrolled_rectangle
 
class  ED4_base_position
 
struct  ED4_TerminalPredicate
 
class  ED4_WinContextFree
 
class  ED4_cursor
 
class  ED4_window
 
class  ED4_container
 
class  ED4_species_pointer
 
class  ED4_cb_list< BASE, BASECB >
 
class  ED4_base
 
class  ED4_manager
 
class  ED4_terminal
 
class  ED4_reference_terminals
 
class  ED4_WinContext
 
class  ED4_root
 
struct  ED4_LocalWinContext
 
class  ED4_MostRecentWinContext
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
struct  ED4_device_manager
 
struct  ED4_area_manager
 
class  ED4_multi_species_manager
 
class  ED4_abstract_group_manager
 
struct  ED4_group_manager
 
class  ED4_remap
 
class  ED4_root_group_manager
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
struct  ED4_multi_sequence_manager
 
struct  ED4_sequence_manager
 
struct  ED4_multi_name_manager
 
struct  ED4_name_manager
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
struct  ED4_bracket_terminal
 
struct  ED4_text_terminal
 
class  ED4_abstract_sequence_terminal
 
class  ED4_orf_terminal
 
class  ED4_sequence_terminal
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
class  ED4_consensus_sequence_terminal
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 
class  ED4_line_terminal
 
class  FINAL_TYPE< SEQTYPE >
 xml element More...
 

Namespaces

 EDB_root_bact
 

Macros

#define e4_assert(bed)   arb_assert(bed)
 
#define DECLARE_DUMP_FOR_ROOTCLASS(self)
 
#define DECLARE_DUMP_FOR_BASECLASS(self, mybase)
 
#define DECLARE_DUMP_FOR_MIDCLASS(self, mybase)
 
#define DECLARE_DUMP_FOR_LEAFCLASS(mybase)
 
#define ed4_beep()   do { fputc(char(7), stdout); fflush(stdout); } while (0)
 
#define SPECIFIED_OBJECT_TYPES   23
 
#define E4B_DECL_CASTOP_helper(Class, toName)
 
#define E4B_AVOID_CAST__helper(Class, toName, isName)
 
#define E4B_IMPL_CASTOP_helper(Class, toName, isName)
 
#define E4B_DECL_CASTOP(name)   E4B_DECL_CASTOP_helper(concatenate(ED4_,name), concatenate(to_,name))
 
#define E4B_AVOID_UNNEEDED_CASTS(name)   E4B_AVOID_CAST__helper(concatenate(ED4_,name), concatenate(to_,name), concatenate(is_,name))
 
#define E4B_IMPL_CASTOP(name)   E4B_IMPL_CASTOP_helper(concatenate(ED4_,name), concatenate(to_,name), concatenate(is_,name))
 

Typedefs

typedef ED4_list< ED4_base > ED4_base_list
 
typedef ED4_list_elem< ED4_base > ED4_base_list_elem
 
typedef ED4_list
< ED4_highlighted_entry > 		ED4_highlighted_list
 
typedef ED4_list_elem
< ED4_highlighted_entry > 		ED4_highlighted_elem
 

Enumerations

enum  PositionType { ED4_POS_SEQUENCE, ED4_POS_ECOLI, ED4_POS_BASE }
 
enum  ED4_CursorType {
  ED4_RIGHT_ORIENTED_CURSOR, ED4_RIGHT_ORIENTED_CURSOR_THIN, ED4_TRADITIONAL_CURSOR, ED4_TRADITIONAL_CURSOR_BOTTOM,
  ED4_TRADITIONAL_CURSOR_CONNECTED, ED4_FUCKING_BIG_CURSOR, ED4_CURSOR_TYPES
}
 
enum  ED4_species_type { ED4_SP_NONE, ED4_SP_SPECIES, ED4_SP_SAI, ED4_SP_CONSENSUS }
 
enum  ED4_species_mode { ED4_SM_MOVE, ED4_SM_KILL, ED4_SM_MARK, ED4_SM_INFO }
 
enum  LoadableSaiState { LSAI_UNUSED, LSAI_UPTODATE, LSAI_OUTDATED }
 
enum  ED4_remap_mode {
  ED4_RM_NONE, ED4_RM_SHOW_ABOVE, ED4_RM_MAX_ALIGN, ED4_RM_MAX_EDIT,
  ED4_RM_DYNAMIC_GAPS, ED4_RM_MODES
}
 
enum  SpeciesCreationMode { CREATE_NEW_SPECIES, CREATE_FROM_CONSENSUS, COPY_SPECIES }
 

Functions

void EDB_root_bact::calc_no_of_all (const char *string_to_scan, long *group, long *species)
 
ED4_returncode EDB_root_bact::fill_species (ED4_multi_species_manager *multi_species_manager, ED4_reference_terminals &refterms, const char *str, int *index, int group_depth, arb_progress *progress)
 
ED4_returncode EDB_root_bact::fill_data (ED4_multi_species_manager *multi_species_manager, ED4_reference_terminals &refterms, char *str, int group_depth, ED4_datamode datamode)
 
ED4_returncode EDB_root_bact::search_sequence_data_rek (ED4_multi_sequence_manager *multi_sequence_manager, ED4_reference_terminals &refterms, GBDATA *gb_ali_xxx, int count_too, ED4_index *max_sequence_terminal_length, bool isSAI)
 
void EDB_root_bact::scan_string (ED4_multi_species_manager *parent, ED4_reference_terminals &refterms, const char *str, int *index, arb_progress &progress)
 
void EDB_root_bact::save_current_config (char *confname)
 
 DECLARE_CBTYPE_FVV_AND_BUILDERS (ED4_managerCallback, void, ED4_manager *)
 
 DECLARE_CBTYPE_FVV_AND_BUILDERS (ED4_species_managerCallback, void, ED4_species_manager *)
 
 DECLARE_CBTYPE_FVV_AND_BUILDERS (ED4_route_cb, ARB_ERROR, ED4_base *)
 
 MARK_NONFINAL_FUNCTION (ED4_base, bool, set_dynamic_size,(), false)
 
 DECLARE_CBTYPE_FVV_AND_BUILDERS (ED4_basePredicate, bool, ED4_base *)
 
 MARK_NONFINAL_METHOD (ED4_manager, update_requested_children,())
 
 MARK_NONFINAL_METHOD (ED4_manager, delete_requested_children,())
 
 MARK_NONFINAL_METHOD (ED4_terminal, Show,(bool, bool))
 
AW_device * current_device ()
 
ED4_window * current_ed4w ()
 
AW_window * current_aww ()
 
ED4_cursor & current_cursor ()
 
 MARK_NONFINAL_CLASS (ED4_sequence_terminal)
 
 MARK_NONFINAL_FUNCTION (ED4_sequence_terminal, int, get_length,() const, 0)
 
 MARK_NONFINAL_FUNCTION (ED4_sequence_terminal, char *, get_sequence_copy,(int *) const, NULp)
 
 E4B_IMPL_CASTOP (area_manager)
 
 E4B_IMPL_CASTOP (abstract_group_manager)
 
 E4B_IMPL_CASTOP (bracket_terminal)
 
 E4B_IMPL_CASTOP (columnStat_terminal)
 
 E4B_IMPL_CASTOP (consensus_sequence_terminal)
 
 E4B_IMPL_CASTOP (device_manager)
 
 E4B_IMPL_CASTOP (group_manager)
 
 E4B_IMPL_CASTOP (line_terminal)
 
 E4B_IMPL_CASTOP (manager)
 
 E4B_IMPL_CASTOP (multi_name_manager)
 
 E4B_IMPL_CASTOP (multi_sequence_manager)
 
 E4B_IMPL_CASTOP (multi_species_manager)
 
 E4B_IMPL_CASTOP (name_manager)
 
 E4B_IMPL_CASTOP (orf_terminal)
 
 E4B_IMPL_CASTOP (pure_text_terminal)
 
 E4B_IMPL_CASTOP (root_group_manager)
 
 E4B_IMPL_CASTOP (sequence_info_terminal)
 
 E4B_IMPL_CASTOP (sequence_manager)
 
 E4B_IMPL_CASTOP (sequence_terminal)
 
 E4B_IMPL_CASTOP (spacer_terminal)
 
 E4B_IMPL_CASTOP (species_manager)
 
 E4B_IMPL_CASTOP (species_name_terminal)
 
 E4B_IMPL_CASTOP (terminal)
 
 E4B_IMPL_CASTOP (text_terminal)
 
 E4B_IMPL_CASTOP (flag_header_terminal)
 
 E4B_IMPL_CASTOP (flag_terminal)
 
CONSTEXPR_INLINE bool valid (SpeciesCreationMode m)
 
ED4_group_manager * ED4_build_group_manager_start (ED4_manager *group_parent, GB_CSTR group_name, int group_depth, bool is_folded, ED4_reference_terminals &refterms, ED4_multi_species_manager *&multi_species_manager)
 
void ED4_build_group_manager_end (ED4_multi_species_manager *multi_species_manager)
 
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)
 
ED4_species_name_terminal * ED4_find_species_or_SAI_name_terminal (const char *species_name)
 
ED4_multi_species_manager * ED4_find_MoreSequences_manager ()
 
void ED4_new_editor_window (AW_window *aww)
 
void ED4_with_all_edit_windows (void(*cb)(ED4_window *))
 
void ED4_resize_all_extensions ()
 
void ED4_calc_terminal_extentions ()
 
void ED4_input_cb (AW_window *aww)
 
void ED4_remote_event (AW_event *faked_event)
 
void ED4_motion_cb (AW_window *aww)
 
void ED4_vertical_change_cb (AW_window *aww)
 
void ED4_horizontal_change_cb (AW_window *aww)
 
void ED4_scrollbar_change_cb (AW_window *aww)
 
void ED4_trigger_instant_refresh ()
 
void ED4_request_relayout ()
 
void ED4_request_full_refresh ()
 
void ED4_request_full_instant_refresh ()
 
void ED4_store_curpos (AW_window *aww)
 
void ED4_restore_curpos (AW_window *aww)
 
void ED4_clear_stored_curpos ()
 
void ED4_helix_jump_opposite (AW_window *aww)
 
void ED4_jump_to_cursor_position (AW_window *aww, const char *awar_name, PositionType posType)
 
void ED4_remote_set_cursor_cb (AW_root *awr)
 
void ED4_change_cursor (AW_window *aww)
 
void ED4_set_iupac (AW_window *aww, const char *awar_name)
 
void ED4_set_helixnr (AW_window *aww, const char *awar_name)
 
void ed4_changesecurity (AW_root *root)
 
void ed4_change_edit_mode (AW_root *root)
 
void ED4_jump_to_current_species (AW_window *)
 
void ED4_get_and_jump_to_current (AW_window *)
 
void ED4_get_and_jump_to_species (GB_CSTR species_name)
 
void ED4_get_marked_from_menu (AW_window *)
 
void ED4_selected_species_changed_cb (AW_root *aw_root)
 
AW_window * ED4_create_loadSAI_window (AW_root *awr)
 
void ED4_get_and_jump_to_selected_SAI (AW_window *aww)
 
void ED4_selected_SAI_changed_cb (AW_root *aw_root)
 
void ED4_init_notFoundMessage ()
 
void ED4_finish_and_show_notFoundMessage ()
 
const AlignDataAccess * ED4_get_aligner_data_access ()
 
void ED4_popup_gc_window (AW_window *awp, AW_gc_manager *gcman)
 
void ED4_no_dangerous_modes ()
 
void group_species_cb (AW_window *aww, bool use_fields)
 
AW_window * ED4_create_group_species_by_field_window (AW_root *aw_root)
 
AW_window * ED4_create_loadConfiguration_window (AW_root *awr)
 
void ED4_reloadConfiguration (AW_window *aww)
 
void ED4_saveConfiguration (AW_window *aww, bool hide_aww)
 
AW_window * ED4_create_saveConfigurationAs_window (AW_root *awr)
 
ARB_ERROR rebuild_consensus (ED4_base *object)
 
void ED4_create_consensus_awars (AW_root *aw_root)
 
AW_window * ED4_create_consensus_definition_window (AW_root *root)
 
void ED4_consensus_definition_changed (AW_root *)
 
void ED4_consensus_display_changed (AW_root *root)
 
AW_window * ED4_create_editor_options_window (AW_root *root)
 
void ED4_compression_toggle_changed_cb (AW_root *root, bool hideChanged)
 
void ED4_compression_changed_cb (AW_root *awr)
 
void ED4_alignment_length_changed (GBDATA *gb_alignment_len, GB_CB_TYPE gbtype)
 
AW_window * ED4_create_new_seq_window (AW_root *root, SpeciesCreationMode creation_mode)
 
void ED4_quit_editor (AW_window *aww)
 
void ED4_exit () __ATTR__NORETURN
 

Variables

ST_ML * st_ml
 

Macro Definition Documentation

#define e4_assert (   bed)    arb_assert(bed)

Definition at line 14 of file ed4_class.hxx.

Referenced by add_area_for_gde(), ED4_SearchResults::addSearchPosition(), ED4_remap::adjacent_screen_positions(), ED4_multi_species_manager::all_are_selected(), ED4_objspec::allowed_to_contain(), ED4_objspec::announce_added(), ED4_base_position::announce_deletion(), ED4_container::append_member(), ARB_main(), awarname(), ED4_SearchResults::buildColorString(), ED4_scrolled_rectangle::calc_bottomRight_folding_dimensions(), SpeciesFlags::calculate_header_dimensions(), call_edit(), ED4_base::changed_by_database(), ED4_terminal::changed_by_database(), ED4_manager::check_in_bases(), ED4_manager::check_out_bases(), ED4_window::check_valid_scrollbar_values(), ED4_manager::clear_refresh(), colorDefTabNameChanged_callback(), ED4_remap::compile(), ED4_window::completely_shows(), ED4_manager::create_consensus(), ED4_root::create_hierarchy(), create_new_species(), create_seq_color_awars(), createGroupFromSelected(), ED4_reference::data_changed_cb(), ED4_foldable::delete_folding_line(), ED4_manager::delete_requested_children(), ED4_terminal::delete_requested_children(), ED4_multi_species_manager::delete_requested_children(), ED4_manager::deleted_from_database(), ED4_multi_species_manager::deselect_all_species_and_SAI(), do_sth_with_species(), dot_missing_bases(), ED4_CursorShape::draw(), ED4_bracket_terminal::draw(), ED4_text_terminal::draw(), ED4_alignment_length_changed(), ED4_base::ED4_base(), ED4_compression_toggle_changed_cb(), ed4_create_all_awars(), ED4_create_faligner_window(), ED4_create_new_seq_window(), ED4_CursorShape::ED4_CursorShape(), ED4_encodeSearchDescriptor(), ED4_get_and_jump_to_species(), ED4_get_NDS_text(), ED4_getSaiColorString(), ED4_jump_to_cursor_position(), ED4_list_elem< T >::ED4_list_elem(), ED4_mark_matching_species(), ED4_menu_highlight(), ED4_objspec::ED4_objspec(), ED4_perform_block_operation(), ED4_popup_detect_bad_alignment_window(), ED4_popup_dot_missing_bases_window(), ED4_SearchPosition::ED4_SearchPosition(), ED4_set_iupac(), ED4_setColumnblockCorner(), ED4_Edit_String::edit(), ED4_terminal::event_sent_by_parent(), executeKeystroke(), EDB_root_bact::fill_data(), EDB_root_bact::fill_species(), SearchTreeNode::findMatches(), ED4_base::generate_configuration_string(), ED4_root::generate_window(), ED4_objspec::get_allowed_descendants(), ED4_CursorShape::get_bounding_box(), ED4_block::get_colblock_range(), ED4_base::get_consensus_relevant_terminal(), ED4_manager::get_defined_level(), ED4_SearchResults::get_first_at(), ED4_window::get_matching_ed4w(), SpeciesFlags::get_min_flag_distance(), ED4_root::get_most_recently_used_window(), ED4_multi_species_manager::get_no_of_selected_species(), ED4_multi_species_manager::get_no_of_species(), ED4_objspec_registry::get_object_spec_at_index(), SpeciesFlags::get_pixel_width(), ED4_objspec::get_possible_descendants(), ED4_SearchResults::get_shown_at(), get_upper_lower_cursor_pos(), SpeciesFlag::get_width(), ED4_scrolled_rectangle::get_window_rect(), ED4_scrolled_rectangle::get_world_rect(), SpeciesFlag::get_xpos(), getClrDefAwar(), group_species(), ED4_manager::handle_move(), ED4_objspec_registry::init_object_specs(), ED4_objspec::init_object_specs(), ED4_container::insert_member(), SearchTreeNode::insert_unified_pattern(), ED4_folding_line::insertAs(), SpeciesFlags::instance(), ED4_multi_species_manager::invert_selection_of_all_species(), ED4_base::is_abstract_group_manager(), ED4_base::is_area_manager(), ED4_base::is_bracket_terminal(), ED4_base::is_columnStat_terminal(), ED4_cursor::is_completely_visible(), ED4_base::is_device_manager(), ED4_base::is_flag_header_terminal(), ED4_base::is_flag_terminal(), ED4_base::is_group_manager(), ED4_cursor::is_hidden_inside_group(), ED4_base::is_line_terminal(), ED4_scrolled_rectangle::is_linked(), ED4_base::is_manager(), ED4_base::is_multi_name_manager(), ED4_base::is_multi_sequence_manager(), ED4_base::is_multi_species_manager(), ED4_base::is_name_manager(), is_named(), ED4_base::is_orf_terminal(), ED4_cursor::is_partly_visible(), ED4_base::is_pure_text_terminal(), ED4_base::is_root_group_manager(), ED4_base::is_sequence_info_terminal(), ED4_base::is_sequence_manager(), ED4_base::is_sequence_terminal(), ED4_base::is_spacer_terminal(), ED4_base::is_species_manager(), ED4_base::is_species_name_terminal(), ED4_base::is_terminal(), ED4_base::is_text_terminal(), ED4_cursor::jump_base_pos(), ED4_cursor::jump_screen_pos(), ED4_cursor::jump_sequence_pos(), level2index(), ED4_scrolled_rectangle::link(), ED4_multi_species_manager::marked_species_select(), ED4_container::member(), ED4_cursor::move_cursor(), ED4_container::move_member(), CursorPos::moveToEnd(), ED4_window::partly_shows(), SpeciesFlag::prepare_itemfield(), propertyName(), PV_WriteTranslatedSequenceToDB(), range_contained_in(), ranges_overlap(), ED4_manager::refresh_requested_by_child(), ED4_objspec_registry::register_objspec(), ED4_container::remove_member(), ED4_window::reset_all_for_new_config(), ED4_base::resize_dynamic(), ED4_base::resize_requested_by_link(), ED4_root_group_manager::resize_requested_children(), ED4_terminal::resolve_pointer_to_char_pntr(), ED4_remap::screen_to_sequence(), ED4_SearchResults::search(), EDB_root_bact::search_sequence_data_rek(), ED4_manager::search_spec_child_rek(), ED4_container::search_target_species(), SearchTree::SearchTree(), SearchTreeNode::SearchTreeNode(), ED4_multi_species_manager::selected_species_mark(), sequence_changed_cb(), ED4_remap::sequence_to_screen(), ED4_remap::sequence_to_screen_PLAIN(), set_diff_reference(), SearchTreeNode::set_mismatches(), ED4_window::set_scrolled_rectangle(), settingName(), ED4_manager::Show(), ED4_terminal::Show(), ED4_cursor::ShowCursor(), ED4_remap::shown_sequence_to_screen(), ED4_root::special_window_refresh(), SpeciesFlag::SpeciesFlag(), stat2display(), TranslateGeneToAminoAcidSequence(), ED4_base::unlink_from_parent(), ED4_manager::update_bases(), ED4_manager::update_bases_and_rebuild_consensi(), ED4_multi_species_manager::update_group_id(), ED4_manager::update_requested_children(), ED4_multi_species_manager::update_requested_children(), ED4_window::update_scrolled_rectangle(), ED4_foldable::win_to_world_coords(), ED4_foldable::world_to_win_coords(), ED4_terminal::write_sequence(), ED4_base::~ED4_base(), ED4_cb_list< ED4_species_manager, ED4_species_managerCallback >::~ED4_cb_list(), ED4_consensus_sequence_terminal::~ED4_consensus_sequence_terminal(), ED4_container::~ED4_container(), and ED4_species_pointer::~ED4_species_pointer().

#define DECLARE_DUMP_FOR_ROOTCLASS (   self)

Definition at line 93 of file ed4_class.hxx.

#define DECLARE_DUMP_FOR_BASECLASS (   self,
  mybase 
)

Definition at line 94 of file ed4_class.hxx.

#define DECLARE_DUMP_FOR_MIDCLASS (   self,
  mybase 
)

Definition at line 95 of file ed4_class.hxx.

#define DECLARE_DUMP_FOR_LEAFCLASS (   mybase)

Definition at line 96 of file ed4_class.hxx.

#define ed4_beep ( )    do { fputc(char(7), stdout); fflush(stdout); } while (0)

Definition at line 107 of file ed4_class.hxx.

#define SPECIFIED_OBJECT_TYPES   23

Definition at line 211 of file ed4_class.hxx.

Referenced by ED4_objspec_registry::get_object_spec_at_index(), ED4_objspec_registry::has_manager_that_may_contain(), ED4_objspec_registry::init_object_specs(), ED4_objspec::recalc_descendants(), and ED4_objspec_registry::register_objspec().

#define E4B_DECL_CASTOP_helper (   Class,
  toName 
)
Value:
inline const Class *toName() const; \
inline Class *toName();

Definition at line 1114 of file ed4_class.hxx.

#define E4B_AVOID_CAST__helper (   Class,
  toName,
  isName 
)
Value:
const Class *toName() const; \
Class *toName(); \
int isName() const;

Definition at line 1118 of file ed4_class.hxx.

#define E4B_IMPL_CASTOP_helper (   Class,
  toName,
  isName 
)
Value:
const Class *ED4_base::toName() const { \
e4_assert(isName()); \
return DOWNCAST(const Class*, this); \
} \
Class *ED4_base::toName() { \
return const_cast<Class*>(const_cast<const ED4_base*>(this)->toName()); \
}
ED4_base
Definition: ed4_class.hxx:893
e4_assert
#define e4_assert(bed)
Definition: ed4_class.hxx:14
DOWNCAST
#define DOWNCAST(totype, expr)
Definition: downcast.h:141

Definition at line 1123 of file ed4_class.hxx.

#define E4B_DECL_CASTOP (   name)    E4B_DECL_CASTOP_helper(concatenate(ED4_,name), concatenate(to_,name))

Definition at line 1132 of file ed4_class.hxx.

#define E4B_AVOID_UNNEEDED_CASTS (   name)    E4B_AVOID_CAST__helper(concatenate(ED4_,name), concatenate(to_,name), concatenate(is_,name))

Definition at line 1133 of file ed4_class.hxx.

#define E4B_IMPL_CASTOP (   name)    E4B_IMPL_CASTOP_helper(concatenate(ED4_,name), concatenate(to_,name), concatenate(is_,name))

Definition at line 1134 of file ed4_class.hxx.

Typedef Documentation

typedef ED4_list<ED4_base> ED4_base_list

Definition at line 168 of file ed4_class.hxx.

typedef ED4_list_elem<ED4_base> ED4_base_list_elem

Definition at line 171 of file ed4_class.hxx.

typedef ED4_list<ED4_highlighted_entry> ED4_highlighted_list

Definition at line 173 of file ed4_class.hxx.

typedef ED4_list_elem<ED4_highlighted_entry> ED4_highlighted_elem

Definition at line 174 of file ed4_class.hxx.

Enumeration Type Documentation

enum PositionType
Enumerator
ED4_POS_SEQUENCE 
ED4_POS_ECOLI 
ED4_POS_BASE 

Definition at line 109 of file ed4_class.hxx.

enum ED4_CursorType
Enumerator
ED4_RIGHT_ORIENTED_CURSOR 
ED4_RIGHT_ORIENTED_CURSOR_THIN 
ED4_TRADITIONAL_CURSOR 
ED4_TRADITIONAL_CURSOR_BOTTOM 
ED4_TRADITIONAL_CURSOR_CONNECTED 
ED4_FUCKING_BIG_CURSOR 
ED4_CURSOR_TYPES 

Definition at line 602 of file ed4_class.hxx.

enum ED4_species_type
Enumerator
ED4_SP_NONE 
ED4_SP_SPECIES 
ED4_SP_SAI 
ED4_SP_CONSENSUS 

Definition at line 886 of file ed4_class.hxx.

enum ED4_species_mode
Enumerator
ED4_SM_MOVE 
ED4_SM_KILL 
ED4_SM_MARK 
ED4_SM_INFO 

Definition at line 1340 of file ed4_class.hxx.

enum LoadableSaiState
Enumerator
LSAI_UNUSED 
LSAI_UPTODATE 
LSAI_OUTDATED 

Definition at line 1402 of file ed4_class.hxx.

enum ED4_remap_mode
Enumerator
ED4_RM_NONE 
ED4_RM_SHOW_ABOVE 
ED4_RM_MAX_ALIGN 
ED4_RM_MAX_EDIT 
ED4_RM_DYNAMIC_GAPS 
ED4_RM_MODES 

Definition at line 1673 of file ed4_class.hxx.

enum SpeciesCreationMode
Enumerator
CREATE_NEW_SPECIES 
CREATE_FROM_CONSENSUS 
COPY_SPECIES 

Definition at line 2240 of file ed4_class.hxx.

Function Documentation

DECLARE_CBTYPE_FVV_AND_BUILDERS ( ED4_managerCallback  ,
void  ,
ED4_manager *   
)
DECLARE_CBTYPE_FVV_AND_BUILDERS ( ED4_species_managerCallback  ,
void  ,
ED4_species_manager *   
)
DECLARE_CBTYPE_FVV_AND_BUILDERS ( ED4_route_cb  ,
ARB_ERROR  ,
ED4_base *   
)
MARK_NONFINAL_FUNCTION ( ED4_base  ,
bool  ,
set_dynamic_size  ,
()  ,
false   
)
DECLARE_CBTYPE_FVV_AND_BUILDERS ( ED4_basePredicate  ,
bool  ,
ED4_base *   
)
MARK_NONFINAL_METHOD ( ED4_manager  ,
update_requested_children  ,
()   
)
MARK_NONFINAL_METHOD ( ED4_manager  ,
delete_requested_children  ,
()   
)
MARK_NONFINAL_METHOD ( ED4_terminal  ,
Show  ,
(bool, bool)   
)
AW_device* current_device ( )
inline

Definition at line 1397 of file ed4_class.hxx.

References ED4_WinContext::get_current_context(), and ED4_WinContext::get_device().

Referenced by ED4_base::adjust_clipping_rectangle(), ED4_abstract_sequence_terminal::calc_update_interval(), clear_and_update_rectangle(), ED4_base::clear_background(), ED4_bracket_terminal::draw(), ED4_text_terminal::draw(), ED4_line_terminal::draw(), ED4_base::draw_bb(), ED4_terminal::draw_drag_box(), ED4_expose_cb(), ED4_resize_cb(), ED4_set_clipping_rectangle(), ED4_root::get_area_rectangle(), get_max_slider_xpos(), get_max_slider_ypos(), move_and_update_rectangle(), ED4_root::recalc_font_group(), ED4_manager::Show(), and ED4_terminal::Show().

ED4_window* current_ed4w ( )
inline

Definition at line 1398 of file ed4_class.hxx.

References ED4_WinContext::get_current_context(), and ED4_WinContext::get_ed4w().

Referenced by ED4_base::adjust_clipping_rectangle(), ED4_abstract_sequence_terminal::calc_interval_displayed_in_rectangle(), ED4_abstract_sequence_terminal::calc_update_interval(), ED4_base::clear_background(), current_aww(), current_cursor(), ED4_bracket_terminal::draw(), ED4_text_terminal::draw(), ED4_line_terminal::draw(), ED4_base::draw_bb(), ED4_terminal::draw_drag_box(), ED4_expose_cb(), ED4_horizontal_change_cb(), ED4_input_cb(), ED4_jump_to_cursor_position(), ED4_motion_cb(), ED4_quit_editor(), ED4_resize_cb(), ED4_scrollbar_change_cb(), ED4_setColumnblockCorner(), ED4_vertical_change_cb(), ED4_terminal::event_sent_by_parent(), ED4_root::generate_window(), ED4_root::get_area_rectangle(), get_upper_lower_cursor_pos(), jump_to_next_helix_cb(), ED4_terminal::scroll_into_view(), scrollHalfPage(), searchParamsChanged(), and ED4_manager::Show().

AW_window* current_aww ( )
inline

Definition at line 1399 of file ed4_class.hxx.

References ED4_window::aww, and current_ed4w().

Referenced by ED4_quit_editor().

ED4_cursor& current_cursor ( )
inline

Definition at line 1400 of file ed4_class.hxx.

References current_ed4w(), and ED4_window::cursor.

Referenced by create_new_species(), detect_current_ref_terminal(), dot_missing_bases(), ED4_change_cursor(), ED4_helix_jump_opposite(), ED4_jump_to_cursor_position(), ED4_remote_set_cursor_cb(), ED4_restore_curpos(), ED4_search_cb(), ED4_set_helixnr(), ED4_set_iupac(), ED4_set_protection(), ED4_store_curpos(), ED4_toggle_detailed_column_stats(), ED4_undo_redo(), ED4_terminal::event_sent_by_parent(), executeKeystroke(), jump_to_corresponding_seq_terminal(), modsai_cb(), PV_ManageTerminals(), searchParamsChanged(), select_named_sequence_terminal(), toggle_cursor_group_folding(), and toggle_helix_for_SAI().

MARK_NONFINAL_CLASS ( ED4_sequence_terminal  )
MARK_NONFINAL_FUNCTION ( ED4_sequence_terminal  ,
int  ,
get_length  ,
()  const,
0   
)
MARK_NONFINAL_FUNCTION ( ED4_sequence_terminal  ,
char *  ,
get_sequence_copy  ,
(int *)  const,
NULp   
)
E4B_IMPL_CASTOP ( area_manager  )
E4B_IMPL_CASTOP ( abstract_group_manager  )
E4B_IMPL_CASTOP ( bracket_terminal  )
E4B_IMPL_CASTOP ( columnStat_terminal  )
E4B_IMPL_CASTOP ( consensus_sequence_terminal  )
E4B_IMPL_CASTOP ( device_manager  )
E4B_IMPL_CASTOP ( group_manager  )
E4B_IMPL_CASTOP ( line_terminal  )
E4B_IMPL_CASTOP ( manager  )
E4B_IMPL_CASTOP ( multi_name_manager  )
E4B_IMPL_CASTOP ( multi_sequence_manager  )
E4B_IMPL_CASTOP ( multi_species_manager  )
E4B_IMPL_CASTOP ( name_manager  )
E4B_IMPL_CASTOP ( orf_terminal  )
E4B_IMPL_CASTOP ( pure_text_terminal  )
E4B_IMPL_CASTOP ( root_group_manager  )
E4B_IMPL_CASTOP ( sequence_info_terminal  )
E4B_IMPL_CASTOP ( sequence_manager  )
E4B_IMPL_CASTOP ( sequence_terminal  )
E4B_IMPL_CASTOP ( spacer_terminal  )
E4B_IMPL_CASTOP ( species_manager  )
E4B_IMPL_CASTOP ( species_name_terminal  )
E4B_IMPL_CASTOP ( terminal  )
E4B_IMPL_CASTOP ( text_terminal  )
E4B_IMPL_CASTOP ( flag_header_terminal  )
E4B_IMPL_CASTOP ( flag_terminal  )
CONSTEXPR_INLINE bool valid ( SpeciesCreationMode  m)

Definition at line 2247 of file ed4_class.hxx.

References COPY_SPECIES, and CREATE_NEW_SPECIES.

Referenced by AP_main::all_available_reverts_will_produce_valid_trees(), Candidate::Candidate(), ED4_create_new_seq_window(), AP_subtree::edgeToSubtree(), parse_env_mem_definition(), AP_main::revert_will_produce_valid_tree(), and write_GBDATA().

ED4_group_manager* ED4_build_group_manager_start ( ED4_manager *  group_parent,
GB_CSTR  group_name,
int  group_depth,
bool  is_folded,
ED4_reference_terminals &  refterms,
ED4_multi_species_manager *&  multi_species_manager 
)

Definition at line 233 of file ED4_base.cxx.

References ED4_container::append_member(), BRACKET_WIDTH, ED4_counter, ED4_SP_CONSENSUS, MAXNAME_WIDTH, NAME_BUFFERSIZE, NULp, PROP_CURSOR_ALLOWED, PROP_DRAGABLE, PROP_IS_FOLDED, PROP_IS_HANDLE, PROP_MOVABLE, PROP_SELECTABLE, ED4_reference_terminals::sequence(), ED4_reference_terminals::sequence_info(), SEQUENCE_INFO_WIDTH, ED4_base::set_both_links(), ED4_base::set_links(), ED4_base::set_property(), SPACER_HEIGHT, and TERMINAL_HEIGHT.

Referenced by createGroupFromSelected(), and EDB_root_bact::scan_string().

void ED4_build_group_manager_end ( ED4_multi_species_manager *  multi_species_manager)

Definition at line 316 of file ED4_base.cxx.

References ED4_container::append_member(), ED4_counter, NAME_BUFFERSIZE, and SPACER_HEIGHT.

Referenced by createGroupFromSelected(), and EDB_root_bact::scan_string().

ED4_species_name_terminal* ED4_find_species_name_terminal ( const char *  species_name)

Definition at line 877 of file ED4_root.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), is_species_named(), LEV_SPECIES_NAME, NULp, and ED4_root::root_group_man.

Referenced by ED4_get_and_jump_to_species(), ED4_get_marked_from_menu(), ED4_jump_to_current_species(), get_group_consensus(), insert_new_species_terminal(), PV_AddOrfTerminalsToLoadedSpecies(), and PV_ManageTerminals().

ED4_species_name_terminal* ED4_find_SAI_name_terminal ( const char *  sai_name)

Definition at line 881 of file ED4_root.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), is_SAI_named(), LEV_SPECIES_NAME, NULp, and ED4_root::root_group_man.

Referenced by ED4_get_and_jump_to_selected_SAI(), filter_loadable_SAIs(), and insert_new_species_terminal().

ED4_species_name_terminal* ED4_find_species_or_SAI_name_terminal ( const char *  species_name)

Definition at line 873 of file ED4_root.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), is_species_named(), LEV_SPECIES_NAME, NULp, and ED4_root::root_group_man.

Referenced by select_named_sequence_terminal().

ED4_multi_species_manager* ED4_find_MoreSequences_manager ( )

Definition at line 560 of file ED4_cursor.cxx.

References ED4_ROOT, ED4_manager::find_first_that(), LEV_MULTI_SPECIES, multi_species_man_consensus_id_starts_with(), NULp, and ED4_root::root_group_man.

Referenced by ED4_get_marked_from_menu(), insert_new_species_terminal(), and ED4_terminal::kill_object().

void ED4_new_editor_window ( AW_window *  aww)

Definition at line 1313 of file ED4_no_class.cxx.

References ED4_window::aww, ED4_R_BREAK, ED4_ROOT, ED4_root::generate_window(), ED4_scroll_links::link_for_hor_slider, ED4_scroll_links::link_for_ver_slider, NULp, ED4_root::scroll_links, ED4_window::set_scrolled_rectangle(), AW_window::show(), and ED4_window::update_scrolled_rectangle().

Referenced by ED4_root::generate_window().

void ED4_with_all_edit_windows ( void(*)(ED4_window *)  cb)

Definition at line 263 of file ED4_main.cxx.

References cb, ED4_root::first_window, and win.

Referenced by ED4_edit_direction_changed().

void ED4_resize_all_extensions ( )

Definition at line 229 of file ED4_no_class.cxx.

References ED4_calc_terminal_extentions(), ED4_G_SEQUENCES, ED4_ROOT, ED4_base::extension, ED4_root::font_group, AW_font_group::get_width(), HEIGHT, ED4_root::main_manager, MAXINFO_WIDTH, MAXSEQUENCECHARACTERLENGTH, ED4_root::ref_terminals, ED4_root_group_manager::remap(), ED4_root::resize_all_requesting_childs(), ED4_root::root_group_man, ED4_reference_terminals::sequence(), ED4_reference_terminals::sequence_info(), ED4_remap::shown_sequence_to_screen(), ED4_extension::size, TERMINAL_HEIGHT, update_extension_size(), and WIDTH.

Referenced by ED4_compression_changed_cb(), ED4_request_relayout(), and gc_change_cb().

void ED4_calc_terminal_extentions ( )

Definition at line 87 of file ED4_no_class.cxx.

References AW_font_limits::ascent, ED4_root::aw_root, AW_root::awar(), BRACKET_WIDTH, calculate_group_folding(), SpeciesFlags::calculate_header_dimensions(), CHARACTEROFFSET, AW_font_limits::descent, ED4_AWAR_NDS_INFO_WIDTH, ED4_G_FLAG_INFO, ED4_G_SEQUENCES, ED4_G_STANDARD, ED4_get_NDS_width(), ED4_ROOT, ED4_root::first_window, FLAG_WIDTH, flags, folding, ED4_root::font_group, ED4_window::get_device(), AW_stylable::get_font_limits(), SpeciesFlags::get_header_length(), AW_font_limits::get_height(), AW_font_group::get_limits(), SpeciesFlags::get_pixel_width(), ED4_root::helix, ED4_root::helix_add_spacing, ED4_root::helix_spacing, INFO_TERM_TEXT_YOFFSET, AW_helix::is_enabled(), group_folding::max_unfolded, MAXINFO_WIDTH, MAXNAME_WIDTH, SpeciesFlags::mutable_instance(), ED4_root::protstruct, AW_awar::read_int(), ED4_root::recalc_font_group(), SEQ_TERM_TEXT_YOFFSET, ED4_root::terminal_add_spacing, TERMINAL_HEIGHT, and AW_font_limits::width.

Referenced by ED4_root::create_first_window(), and ED4_resize_all_extensions().

void ED4_input_cb ( AW_window *  aww)

Definition at line 539 of file ED4_no_class.cxx.

References AW_BUTTON_LEFT, AW_BUTTON_MIDDLE, AW_Keyboard_Press, AW_Keyboard_Release, AW_KEYMODE_ALT, AW_Mouse_Press, AW_Mouse_Release, ED4_root::aw_root, AW_WHEEL_DOWN, AW_WHEEL_UP, AW_event::button, AW_event::character, current_ed4w(), ED4_ROOT, ed4_scroll(), ED4_trigger_instant_refresh(), executeKeystroke(), ED4_root::font_group, AW_window::get_event(), ED4_root::get_gb_main(), AW_font_group::get_max_height(), AW_font_group::get_max_width(), KEY_PRESSED, KEY_RELEASED, AW_event::keycode, AW_event::keymodifier, ED4_root::main_manager, ED4_scroll_picture::old_x, ED4_scroll_picture::old_y, AW_root::peek_key_event(), ED4_scroll_picture::scroll, ED4_root::scroll_picture, ta, AW_event::type, ED4_foldable::win_to_world_coords(), AW_event::x, and AW_event::y.

Referenced by ED4_window::insert_window().

void ED4_remote_event ( AW_event *  faked_event)

Definition at line 534 of file ED4_no_class.cxx.

References executeKeystroke().

Referenced by ED4_host::forward_event().

void ED4_motion_cb ( AW_window *  aww)

Definition at line 747 of file ED4_no_class.cxx.

References AW_BUTTON_LEFT, AW_BUTTON_MIDDLE, AW_Mouse_Drag, AW_event::button, current_ed4w(), ED4_ROOT, ed4_scroll(), AW_window::get_event(), ED4_root::get_gb_main(), ED4_root::main_manager, ED4_scroll_picture::old_x, ED4_scroll_picture::old_y, ED4_scroll_picture::scroll, ED4_root::scroll_picture, ta, AW_event::type, ED4_foldable::win_to_world_coords(), AW_event::x, and AW_event::y.

Referenced by ED4_window::insert_window().

void ED4_vertical_change_cb ( AW_window *  aww)

Definition at line 653 of file ED4_no_class.cxx.

References ED4_window::coords, current_ed4w(), ED4_ROOT, ED4_root::get_gb_main(), get_max_slider_ypos(), ED4_window::scroll_rectangle(), AW_window::set_vertical_scrollbar_position(), AW_window::slider_pos_vertical, ED4_window::slider_pos_vertical, ta, ED4_window::update_window_coords(), win, ED4_coords::window_lower_clip_point, and ED4_coords::window_upper_clip_point.

Referenced by ed4_scroll(), and ED4_window::insert_window().

void ED4_horizontal_change_cb ( AW_window *  aww)

Definition at line 680 of file ED4_no_class.cxx.

References ED4_window::coords, current_ed4w(), ED4_ROOT, ED4_root::get_gb_main(), get_max_slider_xpos(), ED4_window::scroll_rectangle(), AW_window::set_horizontal_scrollbar_position(), AW_window::slider_pos_horizontal, ED4_window::slider_pos_horizontal, ta, ED4_window::update_window_coords(), win, ED4_coords::window_left_clip_point, and ED4_coords::window_right_clip_point.

Referenced by ed4_scroll(), ED4_window::insert_window(), ED4_cursor::jump_screen_pos(), and ED4_cursor::set_screen_relative_pos().

void ED4_scrollbar_change_cb ( AW_window *  aww)

Definition at line 707 of file ED4_no_class.cxx.

References ED4_window::coords, current_ed4w(), ED4_ROOT, ED4_root::get_gb_main(), get_max_slider_xpos(), get_max_slider_ypos(), ED4_window::scroll_rectangle(), AW_window::set_horizontal_scrollbar_position(), AW_window::set_vertical_scrollbar_position(), AW_window::slider_pos_horizontal, ED4_window::slider_pos_horizontal, AW_window::slider_pos_vertical, ED4_window::slider_pos_vertical, ta, ED4_window::update_window_coords(), win, ED4_coords::window_left_clip_point, ED4_coords::window_lower_clip_point, ED4_coords::window_right_clip_point, and ED4_coords::window_upper_clip_point.

Referenced by ED4_terminal::scroll_into_view().

void ED4_trigger_instant_refresh ( )

Definition at line 998 of file ED4_no_class.cxx.

References AW_root::add_timed_callback(), ED4_root::aw_root, ED4_ROOT, ED4_timer(), and fflush().

Referenced by ED4_get_aligner_data_access(), ED4_input_cb(), ED4_postcbcb(), ED4_request_full_instant_refresh(), ED4_request_relayout(), and ED4_terminal::event_sent_by_parent().

void ED4_request_relayout ( )

Definition at line 1013 of file ED4_no_class.cxx.

References ED4_resize_all_extensions(), ED4_ROOT, ED4_trigger_instant_refresh(), and ED4_root::main_manager.

Referenced by ED4_root::create_hierarchy(), ed4_create_all_awars(), ED4_popup_helix_or_pfold_window(), ED4_group_manager::fold(), ED4_manager::handle_move(), header_changed_cb(), NDS_changed(), and ED4_group_manager::unfold().

void ED4_request_full_refresh ( )

Definition at line 1005 of file ED4_no_class.cxx.

References ED4_ROOT, and ED4_root::main_manager.

Referenced by ED4_menu_highlight(), ED4_request_full_instant_refresh(), ED4_root::generate_window(), reload_ecoli_cb(), and reload_helix_cb().

void ED4_request_full_instant_refresh ( )

Definition at line 1008 of file ED4_no_class.cxx.

References ED4_request_full_refresh(), and ED4_trigger_instant_refresh().

Referenced by ED4_compression_changed_cb(), and gc_change_cb().

void ED4_store_curpos ( AW_window *  aww)

Definition at line 1597 of file ED4_cursor.cxx.

References aw_message(), current_cursor(), ED4_ROOT, ED4_root::get_gb_main(), ED4_cursor::get_sequence_pos(), ED4_cursor::owner_of_cursor, and ta.

Referenced by ED4_root::generate_window().

void ED4_restore_curpos ( AW_window *  aww)

Definition at line 1610 of file ED4_cursor.cxx.

References aw_message(), current_cursor(), ED4_JUMP_KEEP_VISIBLE, ED4_ROOT, ED4_root::get_gb_main(), CursorPos::get_head(), CursorPos::get_seq_pos(), CursorPos::get_terminal(), CursorPos::moveToEnd(), ED4_terminal::setCursorTo(), and ta.

Referenced by ED4_root::generate_window().

void ED4_clear_stored_curpos ( )

Definition at line 1625 of file ED4_cursor.cxx.

References CursorPos::clear().

Referenced by ED4_root::generate_window().

void ED4_helix_jump_opposite ( AW_window *  aww)

Definition at line 1633 of file ED4_cursor.cxx.

References aw_message(), current_cursor(), ED4_JUMP_KEEP_POSITION, ED4_ROOT, ED4_root::get_gb_main(), ED4_cursor::get_sequence_pos(), ED4_root::helix, BI_helix::is_pairpos(), ED4_cursor::jump_sequence_pos(), BI_helix::opposite_position(), ED4_cursor::owner_of_cursor, and ta.

Referenced by ED4_root::generate_window().

void ED4_jump_to_cursor_position ( AW_window *  aww,
const char *  awar_name,
PositionType  posType 
)

Definition at line 802 of file ED4_no_class.cxx.

References BasePosition::abs_2_rel(), aw_message(), AW_root::awar(), ED4_cursor::base2sequence_position(), bio2info(), current_cursor(), current_ed4w(), e4_assert, ED4_root::ecoli_ref, ED4_JUMP_CENTERED, ED4_POS_BASE, ED4_POS_ECOLI, ED4_POS_SEQUENCE, ED4_ROOT, error(), ED4_remap::get_max_screen_pos(), AW_window::get_root(), BasePosition::gotData(), ED4_cursor::jump_sequence_pos(), max, MAXSEQUENCECHARACTERLENGTH, NULp, AW_awar::read_int(), BasePosition::rel_2_abs(), ED4_root_group_manager::remap(), ED4_root::root_group_man, ED4_remap::screen_to_sequence(), and ED4_cursor::sequence2base_position().

Referenced by ED4_root::generate_window().

void ED4_remote_set_cursor_cb ( AW_root *  awr)

Definition at line 790 of file ED4_no_class.cxx.

References AW_root::awar(), AWAR_SET_CURSOR_POSITION, current_cursor(), ED4_JUMP_CENTERED, ED4_cursor::jump_sequence_pos(), AW_awar::read_int(), and AW_awar::write_int().

Referenced by ed4_bind_mainDB_awar_callbacks().

void ED4_change_cursor ( AW_window *  aww)

Definition at line 1655 of file ED4_cursor.cxx.

References ED4_cursor::changeType(), current_cursor(), ED4_CURSOR_TYPES, and ED4_cursor::getType().

Referenced by ED4_root::generate_window().

void ED4_set_iupac ( AW_window *  aww,
const char *  awar_name 
)

Definition at line 903 of file ED4_no_class.cxx.

References ED4_root::alignment_type, aw_message(), ED4_root::aw_root, AW_root::awar(), current_cursor(), e4_assert, ED4_ROOT, iupac::encode(), ED4_cursor::get_sequence_pos(), ED4_cursor::in_consensus_terminal(), ED4_cursor::owner_of_cursor, AW_awar::read_string(), ED4_terminal::resolve_pointer_to_string_copy(), seq, and ED4_terminal::write_sequence().

Referenced by ED4_root::generate_window().

void ED4_set_helixnr ( AW_window *  aww,
const char *  awar_name 
)

Definition at line 877 of file ED4_no_class.cxx.

References aw_message(), AW_root::awar(), current_cursor(), ED4_JUMP_CENTERED, ED4_ROOT, BI_helix::first_position(), GBS_global_string(), AW_window::get_root(), BI_helix::has_entries(), ED4_root::helix, ED4_cursor::jump_sequence_pos(), ED4_cursor::owner_of_cursor, and AW_awar::read_string().

Referenced by ED4_root::generate_window(), and jump_to_next_helix_cb().

void ed4_changesecurity ( AW_root *  root)

Definition at line 1279 of file ED4_no_class.cxx.

References AD_ALIGN, ED4_root::aw_root, AW_root::awar(), AWAR_EDIT_SECURITY_LEVEL, AWAR_EDIT_SECURITY_LEVEL_ALIGN, AWAR_EDIT_SECURITY_LEVEL_CHANGE, ED4_get_edit_mode(), ED4_ROOT, GB_change_my_security(), ED4_root::get_gb_main(), AW_awar::map(), NULp, and AW_awar::read_int().

Referenced by ed4_change_edit_mode(), and ed4_create_all_awars().

void ed4_change_edit_mode ( AW_root *  root)

Definition at line 1297 of file ED4_no_class.cxx.

References awar_edit_mode, ed4_changesecurity(), and ED4_get_edit_mode().

Referenced by ed4_create_all_awars().

void ED4_jump_to_current_species ( AW_window *  )

Definition at line 518 of file ED4_cursor.cxx.

References aw_message(), AWAR_SPECIES_NAME, ED4_find_species_name_terminal(), ED4_ROOT, gb_main, GBS_global_string(), GBT_read_string(), ED4_root::get_gb_main(), jump_to_corresponding_seq_terminal(), and ta.

Referenced by ED4_root::generate_window().

void ED4_get_and_jump_to_current ( AW_window *  )

Definition at line 672 of file ED4_cursor.cxx.

References aw_message(), AWAR_SPECIES_NAME, ED4_get_and_jump_to_species(), ED4_ROOT, GBT_read_string(), and ED4_root::get_gb_main().

Referenced by ED4_root::generate_window().

void ED4_get_and_jump_to_species ( GB_CSTR  species_name)

Definition at line 652 of file ED4_cursor.cxx.

References aw_message(), e4_assert, ED4_find_species_name_terminal(), ED4_ROOT, GBS_global_string(), ED4_root::get_gb_main(), insert_new_species_terminal(), jump_to_corresponding_seq_terminal(), and ta.

Referenced by create_new_species(), and ED4_get_and_jump_to_current().

void ED4_get_marked_from_menu ( AW_window *  )

Definition at line 683 of file ED4_cursor.cxx.

References ED4_root::alignment_type, aw_message(), buffer, BUFFERSIZE, ED4_base::calc_group_depth(), ED4_find_MoreSequences_manager(), ED4_find_species_name_terminal(), ED4_finish_and_show_notFoundMessage(), ED4_init_notFoundMessage(), ED4_ROOT, EDB_root_bact::fill_species(), GB_AT_DNA, gb_main, GB_read_string(), GB_read_string_count(), GBS_global_string(), GBT_count_marked_species(), GBT_find_sequence(), GBT_first_marked_species(), GBT_get_name_or_description(), GBT_next_marked_species(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), ED4_base::get_parent(), arb_progress::inc(), LEV_GROUP, ED4_root::main_manager, NULp, PV_AddOrfTerminalsToLoadedSpecies(), ED4_root::ref_terminals, ta, and ED4_abstract_group_manager::table().

Referenced by ED4_root::generate_window().

void ED4_selected_species_changed_cb ( AW_root *  aw_root)

Definition at line 499 of file ED4_cursor.cxx.

References allow_update_global_cursorpos, AWAR_SPECIES_NAME, ED4_ROOT, GBT_read_string(), ED4_root::get_gb_main(), and select_named_sequence_terminal().

Referenced by ed4_bind_mainDB_awar_callbacks().

AW_window* ED4_create_loadSAI_window ( AW_root *  awr)

Definition at line 1720 of file ED4_no_class.cxx.

References AW_POPDOWN(), AWAR_SAI_NAME, awt_create_SAI_selection_list(), ED4_get_and_jump_to_selected_SAI(), ED4_ROOT, filter_loadable_SAIs(), ED4_root::get_gb_main(), ED4_root::loadable_SAIs, LSAI_UPTODATE, makeHelpCallback(), and NULp.

Referenced by ED4_root::generate_window().

void ED4_get_and_jump_to_selected_SAI ( AW_window *  aww)

Definition at line 629 of file ED4_cursor.cxx.

References aw_message(), AW_root::awar(), AWAR_SAI_NAME, ED4_find_SAI_name_terminal(), ED4_ROOT, GBS_global_string(), ED4_root::get_gb_main(), AW_window::get_root(), insert_new_species_terminal(), jump_to_corresponding_seq_terminal(), AW_awar::read_char_pntr(), and ta.

Referenced by ED4_create_loadSAI_window().

void ED4_selected_SAI_changed_cb ( AW_root *  aw_root)

Definition at line 484 of file ED4_cursor.cxx.

References allow_update_global_cursorpos, AWAR_SAI_NAME, ED4_ROOT, GBT_read_string(), ED4_root::get_gb_main(), and select_named_sequence_terminal().

Referenced by ed4_bind_mainDB_awar_callbacks().

void ED4_init_notFoundMessage ( )

Definition at line 566 of file ED4_cursor.cxx.

References not_found_counter, and not_found_message.

Referenced by ED4_root::create_first_window(), ED4_get_marked_from_menu(), ED4_load_new_config(), and insert_new_species_terminal().

void ED4_finish_and_show_notFoundMessage ( )

Definition at line 570 of file ED4_cursor.cxx.

References aw_message(), GBS_global_string(), GBS_strstruct::get_data(), MAX_SHOWN_MISSING_SPECIES, not_found_counter, not_found_message, GBS_strstruct::nprintf(), and NULp.

Referenced by ED4_root::create_hierarchy(), ED4_get_marked_from_menu(), and insert_new_species_terminal().

const AlignDataAccess* ED4_get_aligner_data_access ( )

Definition at line 1214 of file ED4_root.cxx.

References SmartPtr< T, C >::content(), ED4_ROOT, ED4_trigger_instant_refresh(), ED4_root::get_alignment_name(), get_first_selected_species(), ED4_root::get_gb_main(), get_group_consensus(), get_helix_string(), get_next_selected_species(), get_selected_range(), and SmartPtr< T, C >::isNull().

Referenced by ED4_root::generate_window().

void ED4_popup_gc_window ( AW_window *  awp,
AW_gc_manager *  gcman 
)

Definition at line 1285 of file ED4_root.cxx.

References AW_window::activate(), AW_create_gc_window(), AW_window::get_root(), NULp, and win.

Referenced by create_editColorTranslationTable_window(), ED4_CreateProteinViewer_window(), and ED4_root::generate_window().

void ED4_no_dangerous_modes ( )

Definition at line 1193 of file ED4_root.cxx.

References ED4_ROOT, ED4_SM_KILL, ED4_SM_MOVE, modes_cb(), NULp, and ED4_root::species_mode.

Referenced by ED4_terminal::event_sent_by_parent().

void group_species_cb ( AW_window *  aww,
bool  use_fields 
)

Definition at line 1218 of file ED4_no_class.cxx.

References AW_window::activate(), ED4_root::aw_root, create_group_species_by_field_window(), ED4_ROOT, and group_species().

Referenced by ED4_root::generate_window().

AW_window* ED4_create_group_species_by_field_window ( AW_root *  aw_root)
AW_window* ED4_create_loadConfiguration_window ( AW_root *  awr)

Definition at line 1643 of file ED4_no_class.cxx.

References AW_POPDOWN(), AWAR_EDIT_CONFIGURATION, awt_create_CONFIG_selection_list(), ED4_ROOT, ED4_start_editor_on_configuration(), ED4_root::get_gb_main(), makeHelpCallback(), and NULp.

Referenced by ED4_root::generate_window().

void ED4_reloadConfiguration ( AW_window *  aww)

Definition at line 1639 of file ED4_no_class.cxx.

References ED4_start_editor_on_configuration().

Referenced by ED4_root::generate_window().

void ED4_saveConfiguration ( AW_window *  aww,
bool  hide_aww 
)

Definition at line 1670 of file ED4_no_class.cxx.

References AW_root::awar(), AWAR_EDIT_CONFIGURATION, AW_window::get_root(), AW_window::hide(), AW_awar::read_string(), and EDB_root_bact::save_current_config().

Referenced by ED4_create_saveConfigurationAs_window(), and ED4_root::generate_window().

AW_window* ED4_create_saveConfigurationAs_window ( AW_root *  awr)

Definition at line 1678 of file ED4_no_class.cxx.

References AW_POPDOWN(), AWAR_EDIT_CONFIGURATION, awt_create_CONFIG_selection_list(), ED4_ROOT, ED4_saveConfiguration(), ED4_root::get_gb_main(), makeHelpCallback(), and NULp.

Referenced by ED4_root::generate_window().

ARB_ERROR rebuild_consensus ( ED4_base *  object)

Definition at line 1302 of file ED4_no_class.cxx.

References ED4_base::is_consensus_manager(), LEV_SEQUENCE_STRING, NULp, and ED4_base::request_refresh().

Referenced by ED4_manager::rebuild_consensi().

void ED4_create_consensus_awars ( AW_root *  aw_root)

Definition at line 1623 of file ED4_no_class.cxx.

References AW_awar::add_callback(), AW_root::awar_int(), consensus_upper_lower_changed_cb(), ED4_AWAR_CONSENSUS_CONSIDBOUND, ED4_AWAR_CONSENSUS_COUNTGAPS, ED4_AWAR_CONSENSUS_GAPBOUND, ED4_AWAR_CONSENSUS_GROUP, ED4_AWAR_CONSENSUS_LOWER, ED4_AWAR_CONSENSUS_SHOW, ED4_AWAR_CONSENSUS_UPPER, ED4_consensus_definition_changed(), ED4_consensus_display_changed(), ED4_ROOT, ED4_root::get_gb_main(), AW_awar::set_minmax(), ta, and AW_awar::write_int().

Referenced by ed4_create_all_awars().

AW_window* ED4_create_consensus_definition_window ( AW_root *  root)

Definition at line 1541 of file ED4_no_class.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AW_SCALER_LINEAR, AWT_create_IUPAC_info_window(), AWT_insert_config_manager(), CONSENSUS_CONFIG_ID, ED4_AWAR_CONSENSUS_CONSIDBOUND, ED4_AWAR_CONSENSUS_COUNTGAPS, ED4_AWAR_CONSENSUS_GAPBOUND, ED4_AWAR_CONSENSUS_GROUP, ED4_AWAR_CONSENSUS_LOWER, ED4_AWAR_CONSENSUS_SHOW, ED4_AWAR_CONSENSUS_UPPER, makeHelpCallback(), and NULp.

Referenced by ED4_popup_dot_missing_bases_window(), and ED4_root::generate_window().

void ED4_consensus_definition_changed ( AW_root *  )

Definition at line 37 of file ED4_consensus.cxx.

References ED4_reference::data_changed_cb(), ED4_ROOT, LEV_SEQUENCE_STRING, NULp, ED4_root::reference, ED4_reference::reference_is_a_consensus(), ED4_root::request_refresh_for_consensus_terminals(), ED4_root::request_refresh_for_specific_terminals(), and ED4_root::reset_consensus_params().

Referenced by consensus_upper_lower_changed_cb(), and ED4_create_consensus_awars().

void ED4_consensus_display_changed ( AW_root *  root)

Definition at line 67 of file ED4_consensus.cxx.

References AW_root::awar(), ED4_AWAR_CONSENSUS_SHOW, ED4_ROOT, ARB_ERROR::expect_no_error(), AW_awar::read_int(), ED4_root::root_group_man, ED4_manager::route_down_hierarchy(), and toggle_consensus_display().

Referenced by ED4_create_consensus_awars().

AW_window* ED4_create_editor_options_window ( AW_root *  root)

Definition at line 1448 of file ED4_no_class.cxx.

References AW_POPDOWN(), AW_ROOT_DEFAULT, AW_SCALER_EXP_CENTER, AW_SCALER_LINEAR, AWAR_EDIT_HELIX_SPACING, AWAR_EDIT_TERMINAL_SPACING, AWT_insert_config_manager(), ED4_AWAR_ANNOUNCE_CHECKSUM_CHANGES, ED4_AWAR_COMPRESS_SEQUENCE_GAPS, ED4_AWAR_COMPRESS_SEQUENCE_HIDE, ED4_AWAR_COMPRESS_SEQUENCE_PERCENT, ED4_AWAR_DIGITS_AS_REPEAT, ED4_AWAR_FAST_CURSOR_JUMP, ED4_AWAR_GAP_CHARS, ED4_AWAR_SCROLL_MARGIN, ED4_AWAR_SCROLL_SPEED_X, ED4_AWAR_SCROLL_SPEED_Y, AW_window::load_xfig(), and makeHelpCallback().

Referenced by ED4_root::generate_window().

void ED4_compression_toggle_changed_cb ( AW_root *  root,
bool  hideChanged 
)

Definition at line 1392 of file ED4_no_class.cxx.

References AW_root::awar(), e4_assert, ED4_AWAR_COMPRESS_SEQUENCE_GAPS, ED4_AWAR_COMPRESS_SEQUENCE_HIDE, ED4_AWAR_COMPRESS_SEQUENCE_TYPE, ED4_RM_DYNAMIC_GAPS, ED4_RM_MAX_ALIGN, ED4_RM_NONE, ED4_RM_SHOW_ABOVE, AW_awar::read_int(), and AW_awar::write_int().

Referenced by ed4_create_all_awars().

void ED4_compression_changed_cb ( AW_root *  awr)

Definition at line 1363 of file ED4_no_class.cxx.

References AW_root::awar(), ED4_AWAR_COMPRESS_SEQUENCE_PERCENT, ED4_AWAR_COMPRESS_SEQUENCE_TYPE, ED4_JUMP_KEEP_POSITION, ED4_request_full_instant_refresh(), ED4_resize_all_extensions(), ED4_ROOT, ED4_root::first_window, ED4_root::get_gb_main(), ED4_cursor::jump_sequence_pos(), AW_awar::read_int(), ED4_root_group_manager::remap(), ED4_root::root_group_man, ED4_remap::set_mode(), ED4_cursor::set_screen_relative_pos(), ta, ED4_window::update_scrolled_rectangle(), win, and ED4_cursor::window().

Referenced by ed4_create_all_awars().

void ED4_alignment_length_changed ( GBDATA *  gb_alignment_len,
GB_CB_TYPE  gbtype 
)

Definition at line 456 of file ED4_root.cxx.

References ED4_root::alignment_type, aw_message_if(), change_char_table_length(), e4_assert, ED4_root::ecoli_ref, ED4_pfold_set_SAI(), ED4_ROOT, GB_AT_AA, GB_CB_CHANGED, gb_main, GB_read_int(), ED4_root::get_alignment_name(), ED4_root::get_gb_main(), ED4_root::helix, BI_helix::init(), BI_ecoli_ref::init(), ED4_root::main_manager, ED4_remap::mark_compile_needed_force(), MAXSEQUENCECHARACTERLENGTH, ED4_root::protstruct, ED4_root::protstruct_len, ED4_root_group_manager::remap(), and ED4_root::root_group_man.

Referenced by ED4_terminal::changed_by_database(), and ED4_root::init_alignment().

AW_window* ED4_create_new_seq_window ( AW_root *  root,
SpeciesCreationMode  creation_mode 
)

Definition at line 2203 of file ED4_no_class.cxx.

References AW_POPDOWN(), COPY_SPECIES, CREATE_FROM_CONSENSUS, create_new_species(), CREATE_NEW_SPECIES, e4_assert, ED4_AWAR_CREATE_FROM_CONS_ALL_UPPER, ED4_AWAR_CREATE_FROM_CONS_CREATE_POINTS, ED4_AWAR_CREATE_FROM_CONS_DATA_SOURCE, ED4_AWAR_CREATE_FROM_CONS_REPL_EQUAL, ED4_AWAR_CREATE_FROM_CONS_REPL_POINT, ED4_AWAR_SPECIES_TO_CREATE, NULp, and valid().

Referenced by ED4_root::generate_window().

void ED4_quit_editor ( AW_window *  aww)

Definition at line 962 of file ED4_no_class.cxx.

References current_aww(), current_ed4w(), ED4_exit(), ED4_ROOT, ED4_root::first_window, AW_window::hide(), and ED4_window::is_hidden.

Referenced by ED4_root::generate_window().

void ED4_exit ( )

Definition at line 933 of file ED4_no_class.cxx.

References ED4_root::aw_root, ED4_window::aww, ED4_window::cursor, ED4_window::delete_window(), ED4_ROOT, EXIT_SUCCESS, ED4_root::first_window, GB_close(), gb_main, ED4_root::get_gb_main(), AW_window::hide(), ED4_window::next, ED4_cursor::prepare_shutdown(), shutdown_macro_recording(), and AW_root::unlink_awars_from_DB().

Referenced by ARB_main(), ED4_root::create_hierarchy(), ED4_quit_editor(), and EDB_root_bact::fill_species().

Variable Documentation

ST_ML* st_ml

Referenced by st_ml_check_sequence_quality(), and STAT_destroy_ST_ML().

Generated by   doxygen 1.8.8