FINAL_TYPE< SEQTYPE > Member List

This is the complete list of members for FINAL_TYPE< SEQTYPE >, including all inherited members.

_callback	AW_window
_create_option_entry(AW_VARIABLE_TYPE type, const char *name, const char *mnemonic, const char *name_of_color)	AW_window
_d_callback	AW_window
_get_area_size(AW_area area, AW_screen_area *square)	AW_window
_set_activate_callback(void *widget)	AW_window
acceptCurrentState(Level frame_level)	FINAL_TYPE< SEQTYPE >
accession	FINAL_TYPE< SEQTYPE >
acs	FINAL_TYPE< SEQTYPE >
activate()	AW_window	inline
activate_plugin(const string &plugin_id) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
activate_plugin_impl(const string &plugin_id)	FINAL_TYPE< SEQTYPE >
active() const	ItemShader	inline
active_plugin	ItemShader	protected
active_plugin_name() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
add(const char *pName, const char *pFullName, const char *pMatchPart, const char *pResult, const ArbProbeMatchWeighting &rMatchWeighting)	FINAL_TYPE< SEQTYPE >
add_attribute(const std::string &name_, const std::string &content_)	FINAL_TYPE< SEQTYPE >
add_attribute(const std::string &name_, int value)	FINAL_TYPE< SEQTYPE >
add_attribute(const std::string &name_, const std::string &content_)	FINAL_TYPE< SEQTYPE >	inline
add_awar_callbacks(AW_root *root, const RootCallback &cb) const	awt_item_type_selector
add_awarItem_callbacks()	awt_mask_awar_item	protected
add_db_callbacks()	awt_linked_to_item	protectedvirtual
add_delete_callback(const ED4_managerCallback &cb)	ED4_manager	inline
add_handler(awt_mask_item_ptr handler)	FINAL_TYPE< SEQTYPE >	inline
add_help(const char *help_file)	FINAL_TYPE< SEQTYPE >
add_remark(const char *rem)	FINAL_TYPE< SEQTYPE >	inline
add_remark(const char *key, const char *Str)	FINAL_TYPE< SEQTYPE >	inline
add_remarks_from(const GenBank &gbk)	FINAL_TYPE< SEQTYPE >
add_sequence_changed_cb(const ED4_species_managerCallback &cb)	FINAL_TYPE< SEQTYPE >	inline
add_son(XML_Node *son_, bool son_is_tag) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
addComment(const char *pComment)	FINAL_TYPE< SEQTYPE >
addOperator(const char *from, SaiOperatorPtr to)	FINAL_TYPE< SEQTYPE >
addSequence(GBDATA *gbspec) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
addSequence(GBDATA *gbspec) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
addTranslation(const char *from, char to)	FINAL_TYPE< SEQTYPE >
ED4_terminal::adjust_clipping_rectangle()	ED4_base
ED4_text_terminal::adjust_clipping_rectangle()	ED4_base
ED4_manager::adjust_clipping_rectangle()	ED4_base
AliData(size_t size_)	AliData	inline
AliFormatCommand(size_t wanted_len_)	FINAL_TYPE< SEQTYPE >	inline
AlignedSequenceLoader(class GBDATA *gb_main)	FINAL_TYPE< SEQTYPE >
alloc_named_data_color(int colnum, const char *colorname)	AW_window
allocated_index(int i) const	CharPtrArray	inlineprotected
AW_device::allow_bottom_font_overlap() const	AW_clipable	inline
AW_simple_device::allow_bottom_font_overlap() const	AW_clipable	inline
allow_delete_window(bool allow_close)	AW_window
AW_device::allow_left_font_overlap() const	AW_clipable	inline
AW_simple_device::allow_left_font_overlap() const	AW_clipable	inline
AW_device::allow_right_font_overlap() const	AW_clipable	inline
AW_simple_device::allow_right_font_overlap() const	AW_clipable	inline
AW_device::allow_top_font_overlap() const	AW_clipable	inline
AW_simple_device::allow_top_font_overlap() const	AW_clipable	inline
analyse_distances()	AP_tree
Analyser(class GBDATA *gb_main)	FINAL_TYPE< SEQTYPE >
TreeNode::ancestor_common_with(const TreeNode *other) const	TreeNode
TreeNode::ancestor_common_with(TreeNode *other)	TreeNode	inline
AP_tree::ancestor_common_with(const TreeNode *other) const	TreeNode
AP_tree::ancestor_common_with(TreeNode *other)	TreeNode	inline
ARB_countedTree::ancestor_common_with(const TreeNode *other) const	TreeNode
ARB_countedTree::ancestor_common_with(TreeNode *other)	TreeNode	inline
TreeNode::announce_tree_constructed()	TreeNode	inline
AP_tree::announce_tree_constructed()	TreeNode	inline
ARB_countedTree::announce_tree_constructed()	TreeNode	inline
AP_combinableSeq(const AliView *aliview)	AP_combinableSeq	inline
AP_main::destroyNode(AP_tree_nlen *node)	FINAL_TYPE< SEQTYPE >	friend
AP_pars_root(AliView *aliView, AP_sequence *seq_proto, bool add_delete_callbacks, const group_scaling *scaling)	FINAL_TYPE< SEQTYPE >	inline
AP_sequence(const AliView *aliview)	AP_sequence
AP_sequence_parsimony(const AliView *aliview)	FINAL_TYPE< SEQTYPE >
AP_sequence_protein(const AliView *aliview)	FINAL_TYPE< SEQTYPE >
AP_tree(AP_tree_root *troot)	AP_tree	inlineexplicit
AP_tree_edge class	FINAL_TYPE< SEQTYPE >	friend
AP_tree_nlen(AP_pars_root *troot)	FINAL_TYPE< SEQTYPE >	inlineexplicit
AP_tree_root(AliView *aliView, AP_sequence *seq_proto, bool add_delete_callbacks, const group_scaling *scaling)	AP_tree_root
append(ParagraphTree *new_brother)	FINAL_TYPE< SEQTYPE >	inline
append_member(ED4_base *new_member)	ED4_container
append_to(XML_Attribute *queue)	FINAL_TYPE< SEQTYPE >
ApplicationBGColor	FINAL_TYPE< SEQTYPE >
apply(AliDataPtr to, GB_ERROR &error) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
apply(const SaiCalcEnv &calcEnv) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
apply(const SaiCalcEnv &calcEnv) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
TreeNode::apply_aci_to_remarks(const char *aci, const GBL_call_env &callEnv)	TreeNode
AP_tree::apply_aci_to_remarks(const char *aci, const GBL_call_env &callEnv)	TreeNode
ARB_countedTree::apply_aci_to_remarks(const char *aci, const GBL_call_env &callEnv)	TreeNode
apply_zoom_settings_for_treetype(AWT_canvas *ntw)	AWT_graphic_tree
ARB_countedTree(ARB_seqtree_root *tree_root_)	ARB_countedTree	inlineexplicit
AP_tree::ARB_seqtree(ARB_seqtree_root *root)	ARB_seqtree	inline
ARB_countedTree::ARB_seqtree(ARB_seqtree_root *root)	ARB_seqtree	inline
AP_tree_root::ARB_seqtree_root(AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks)	ARB_seqtree_root
ARB_seqtree_root::ARB_seqtree_root(AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks)	ARB_seqtree_root
ArbMatchResultSet()	FINAL_TYPE< SEQTYPE >
ArbMatchResultSet(const ArbProbe *pProbe)	FINAL_TYPE< SEQTYPE >
ArbMatchResultSet(const ArbMatchResultSet &rCopy)	FINAL_TYPE< SEQTYPE >
ArbRefCount()	ArbRefCount	inline
ArbRefCount(const ArbRefCount &)	ArbRefCount	inline
ArbWriter(string ta, string f, int c)	FINAL_TYPE< SEQTYPE >	inline
AW_device::arc(int gc, AW::FillStyle filled, AW_pos x0, AW_pos y0, AW_pos xradius, AW_pos yradius, int start_degrees, int arc_degrees, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::arc(int gc, AW::FillStyle filled, const AW::Position &pos, const AW::Vector &radius, int start_degrees, int arc_degrees, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::arc(int gc, AW::FillStyle filled, AW_pos x0, AW_pos y0, AW_pos xradius, AW_pos yradius, int start_degrees, int arc_degrees, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::arc(int gc, AW::FillStyle filled, const AW::Position &pos, const AW::Vector &radius, int start_degrees, int arc_degrees, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
ArgCommand(const char *cmd, ArgFun fun_, CallMode emode_=STANDARD_CALL)	FINAL_TYPE< SEQTYPE >	inline
assign(int npos_, const AW::Position *pos_, int distance_, const AW_pos &nearest_rel_pos_, const AW_click_cd *click_cd_)	FINAL_TYPE< SEQTYPE >	inline
AW_clicked_element::assign(int distance_, const AW_pos &nearest_rel_pos_, const AW_click_cd *click_cd_)	AW_clicked_element	inlineprotected
AW_window::at(int x, int y)	AW_window
AW_window::at(const char *id)	AW_window
at_attach(int x, int y)	AW_window
at_attach_to(bool attach_x, bool attach_y, int xoff, int yoff)	AW_window
at_ifdef(const char *id)	AW_window
at_newline()	AW_window
TreeNode::at_root() const	TreeNode	inlineprotected
AP_tree::at_root() const	TreeNode	inlineprotected
ARB_countedTree::at_root() const	TreeNode	inlineprotected
at_shift(int x, int y)	AW_window
at_unattach()	AW_window
at_x(int x)	AW_window
at_y(int y)	AW_window
atcc	FINAL_TYPE< SEQTYPE >
attach_warning(const string &message) const	MessageAttachable	inline
attached_message(const string &message) const	MessageAttachable	inline
author	FINAL_TYPE< SEQTYPE >
auto_increment(int dx, int dy)	AW_window
auto_space(int xspace, int yspace)	AW_window
auto_subtitles(const char *prefix) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
auto_unfold(AP_tree *want_visible)	AWT_graphic_tree
AW_clicked_element()	AW_clicked_element	inlineprotected
AW_clicked_polygon()	FINAL_TYPE< SEQTYPE >	inline
AW_clicked_polygon(const AW_clicked_polygon &other)	FINAL_TYPE< SEQTYPE >	inline
AW_device::AW_clipable(const AW_screen_area &screen)	AW_clipable	inline
AW_simple_device::AW_clipable(const AW_screen_area &screen)	AW_clipable	inline
AW_device::AW_device(class AW_common *common_)	AW_device	inline
AW_simple_device::AW_device(class AW_common *common_)	AW_device	inline
AW_device_click(AW_common *common_)	FINAL_TYPE< SEQTYPE >
AW_device_print(AW_common *common_)	FINAL_TYPE< SEQTYPE >	inline
AW_device_Xm(AW_common *commoni)	FINAL_TYPE< SEQTYPE >	inline
AW_repeated_question()	FINAL_TYPE< SEQTYPE >	inline
aw_root	FINAL_TYPE< SEQTYPE >
AW_simple_device(AW_common *common_)	AW_simple_device	inline
AW_device::AW_stylable(AW_common *common_)	AW_stylable	inline
AW_simple_device::AW_stylable(AW_common *common_)	AW_stylable	inline
AW_window()	AW_window
AW_window_simple()	FINAL_TYPE< SEQTYPE >
AW_device::AW_zoomable()	AW_zoomable	inline
AW_simple_device::AW_zoomable()	AW_zoomable	inline
awar() const	awt_mask_awar_item	inline
awar()	awt_mask_awar_item	inline
awar_changed() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
awar_changed() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
awar_name() const	awt_mask_awar_item	inline
AWT_graphic::AWT_graphic()	AWT_graphic	inline
AWT_graphic_parsimony::AWT_graphic()	AWT_graphic	inline
AWT_graphic_parsimony(ArbParsimony &parsimony_, GBDATA *gb_main_, AD_map_viewer_cb map_viewer_cb_)	AWT_graphic_parsimony
AWT_graphic_tree(AW_root *aw_root, GBDATA *gb_main, AD_map_viewer_cb map_viewer_cb)	AWT_graphic_tree
awt_input_mask(AW_root *awr, GBDATA *gb_main, const std::string &mask_name_, awt_item_type itemtype_, bool local, const awt_item_type_selector *sel_, bool test_edit_enabled)	FINAL_TYPE< SEQTYPE >	inline
awt_input_mask_descriptor(const char *title_, const char *maskname_, const char *itemtypename_, bool local, bool hidden_)	FINAL_TYPE< SEQTYPE >
awt_input_mask_descriptor(const awt_input_mask_descriptor &other)	FINAL_TYPE< SEQTYPE >
awt_item_type_selector(awt_item_type for_type)	awt_item_type_selector	inline
awt_linked_to_item()	awt_linked_to_item	inline
awt_marked_checkbox(awt_input_mask_global &global_, const std::string &label_)	FINAL_TYPE< SEQTYPE >	inline
awt_mask_awar_item(awt_input_mask_global &global_, const std::string &awar_base, const std::string &default_value, bool saved_with_properties)	awt_mask_awar_item
awt_viewport::awt_mask_item(awt_input_mask_global &global_)	awt_mask_item
awt_mask_item::awt_mask_item(awt_input_mask_global &global_)	awt_mask_item
awt_script(awt_input_mask_global &global_, const std::string &script_)	FINAL_TYPE< SEQTYPE >	inline
awt_script_viewport(awt_input_mask_global &global_, const awt_script *script_, const std::string &label_, long field_width_)	FINAL_TYPE< SEQTYPE >
awt_viewport(awt_input_mask_global &global_, const std::string &awar_base, const std::string &default_value, bool saved_with_properties, const std::string &label_)	awt_viewport	inline
awt_viewport(const awt_mask_awar_item &ref_item, const std::string &label_)	awt_viewport	inline
AwtiExportWriter(GBDATA *_gbmain, const char *_dbname, const char *eft, const char *out, int c)	FINAL_TYPE< SEQTYPE >	inline
backLine(const string &line)	LineReader	inline
BeginTexturizer()	FINAL_TYPE< SEQTYPE >
best_click(ClickPreference prefer=PREFER_NEARER)	FINAL_TYPE< SEQTYPE >
PS_BitSet::bias	PS_BitSet	protected
PS_BitMap::bias	PS_BitMap	protected
bind_to_species(GBDATA *gb_species)	AP_sequence
TreeNode::bootstrap2branchlen()	TreeNode
AP_tree::bootstrap2branchlen()	TreeNode
ARB_countedTree::bootstrap2branchlen()	TreeNode
AW_device::box(int gc, AW::FillStyle filled, const AW::Rectangle &rect, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::box(int gc, AW::FillStyle filled, const AW::Position &pos, const AW::Vector &size, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::box(int gc, AW::FillStyle filled, AW_pos x0, AW_pos y0, AW_pos width, AW_pos height, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::box(int gc, AW::FillStyle filled, const AW::Rectangle &rect, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::box(int gc, AW::FillStyle filled, const AW::Position &pos, const AW::Vector &size, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::box(int gc, AW::FillStyle filled, AW_pos x0, AW_pos y0, AW_pos width, AW_pos height, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::box_clip(AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_pos &x0out, AW_pos &y0out, AW_pos &x1out, AW_pos &y1out)	AW_clipable
AW_device::box_clip(const AW::Rectangle &rect, AW::Rectangle &clippedRect)	AW_clipable
AW_device::box_clip(int npos, const AW::Position *pos, int &nclippedPos, AW::Position *&clippedPos)	AW_clipable
AW_simple_device::box_clip(AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_pos &x0out, AW_pos &y0out, AW_pos &x1out, AW_pos &y1out)	AW_clipable
AW_simple_device::box_clip(const AW::Rectangle &rect, AW::Rectangle &clippedRect)	AW_clipable
AW_simple_device::box_clip(int npos, const AW::Position *pos, int &nclippedPos, AW::Position *&clippedPos)	AW_clipable
TreeNode::branchlen2bootstrap()	TreeNode
AP_tree::branchlen2bootstrap()	TreeNode
ARB_countedTree::branchlen2bootstrap()	TreeNode
BranchRotator(AW_device *device_, AP_tree *node_, const LineVector &clicked_branch_, const Position &mousepos, AWT_graphic_exports &exports_)	FINAL_TYPE< SEQTYPE >	inline
build_widget(AW_window *aws) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
build_widget(AW_window *aws) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
buildLeafList(AP_tree **&list, long &num)	AP_tree
buildParagraphTree(const Section &sec)	FINAL_TYPE< SEQTYPE >	inlinestatic
button_height(int height)	AW_window
button_length(int length)	AW_window
cache_is_flushed() const	MarkerDisplay	inline
cached_wbc	AP_sequence	mutableprotected
ED4_terminal::calc_bounding_box() FINAL_OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::calc_bounding_box() FINAL_OVERRIDE	ED4_terminal	virtual
ED4_manager::calc_bounding_box() FINAL_OVERRIDE	ED4_manager	virtual
TreeNode::calc_clade_level() const	TreeNode	inline
AP_tree::calc_clade_level() const	TreeNode	inline
ARB_countedTree::calc_clade_level() const	TreeNode	inline
ED4_terminal::calc_group_depth()	ED4_base
ED4_text_terminal::calc_group_depth()	ED4_base
ED4_manager::calc_group_depth()	ED4_base
ED4_terminal::calc_rel_coords(AW_pos *x, AW_pos *y)	ED4_base
ED4_text_terminal::calc_rel_coords(AW_pos *x, AW_pos *y)	ED4_base
ED4_manager::calc_rel_coords(AW_pos *x, AW_pos *y)	ED4_base
ED4_terminal::calc_world_coords(AW_pos *x, AW_pos *y) const	ED4_base	inline
ED4_terminal::calc_world_coords() const	ED4_base	inline
ED4_text_terminal::calc_world_coords(AW_pos *x, AW_pos *y) const	ED4_base	inline
ED4_text_terminal::calc_world_coords() const	ED4_base	inline
ED4_manager::calc_world_coords(AW_pos *x, AW_pos *y) const	ED4_base	inline
ED4_manager::calc_world_coords() const	ED4_base	inline
AP_tree::calcTreeInfo(ARB_tree_info &info)	ARB_seqtree
ARB_countedTree::calcTreeInfo(ARB_tree_info &info)	ARB_seqtree
calculate_helix_coordinates()	FINAL_TYPE< SEQTYPE >
calculate_helix_size()	FINAL_TYPE< SEQTYPE >
calculate_loop_coordinates()	FINAL_TYPE< SEQTYPE >
calculate_loop_size()	FINAL_TYPE< SEQTYPE >
calculate_scrollbars()	AW_window
calculate_segment_coordinates(const Position &start, const Position &end)	FINAL_TYPE< SEQTYPE >
calculate_segment_size()	FINAL_TYPE< SEQTYPE >
call(Interpreter &interpret) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
call(Interpreter &interpret) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
AW_window::callback(const WindowCallback &cb)	AW_window
AW_window::callback(const CreateWindowCallback &cwcb)	AW_window	inline
AW_window::callback(CreateWindowCallbackSimple cb)	AW_window	inline
AW_window::callback(WindowCallbackSimple cb)	AW_window	inline
calling_child_progress()	FINAL_TYPE< SEQTYPE >	inlinestatic
cantMoveNextTo(AP_tree *new_brother)	AP_tree
PS_BitSet::capacity	PS_BitSet	protected
PS_BitMap::capacity	PS_BitMap	protected
cd1() const	AW_clicked_element	inline
cd2() const	AW_clicked_element	inline
TreeRoot::change_root(TreeNode *old, TreeNode *newroot)	TreeRoot	virtual
AP_tree_root::change_root(TreeNode *old, TreeNode *newroot) FINAL_OVERRIDE	AP_tree_root	virtual
ED4_terminal::changed_by_database() OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::changed_by_database() OVERRIDE	ED4_terminal	virtual
ED4_manager::changed_by_database() OVERRIDE	ED4_manager	virtual
CharPtrArray()	CharPtrArray	inlineprotected
ED4_terminal::check_all()	ED4_base
ED4_text_terminal::check_all()	ED4_base
ED4_manager::check_all()	ED4_base
check_applicable_to(const Alignment &ali, size_t &resulting_ali_length) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
CHECK_DELETE enum value	AliData
check_delete_allowed(size_t start, size_t count) const	AliData	inline
check_dimension_change() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
check_for_DB_update(GBDATA *gb_main) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
check_in_bases(ED4_base *added_base)	ED4_manager
check_out_bases(ED4_base *subbed_base)	ED4_manager
check_update() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
checksum() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
checksum() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
child_progress(nestable *parent_, const char *title, SINT overall_count, const weightable &speed_)	FINAL_TYPE< SEQTYPE >	inline
child_updates_gauge(double child_gauge) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
AW_device::circle(int gc, AW::FillStyle filled, const AW::Position &center, const AW::Vector &radius, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::circle(int gc, AW::FillStyle filled, AW_pos x0, AW_pos y0, AW_pos xradius, AW_pos yradius, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::circle(int gc, AW::FillStyle filled, const AW::Rectangle &rect, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::circle(int gc, AW::FillStyle filled, const AW::Position &center, const AW::Vector &radius, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::circle(int gc, AW::FillStyle filled, AW_pos x0, AW_pos y0, AW_pos xradius, AW_pos yradius, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::circle(int gc, AW::FillStyle filled, const AW::Rectangle &rect, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
clear(AW_bitset filteri)	FINAL_TYPE< SEQTYPE >	virtual
ED4_manager::clear()	ED4_container
CharPtrArray::clear()	CharPtrArray	inline
ED4_terminal::clear_background(int color=0)	ED4_base
ED4_text_terminal::clear_background(int color=0)	ED4_base
ED4_manager::clear_background(int color=0)	ED4_base
clear_error() const	AliData	inline
clear_option_menu(AW_option_menu_struct *oms)	AW_window
clear_part(const AW::Rectangle &rect, AW_bitset filteri)	FINAL_TYPE< SEQTYPE >	virtual
AW_device::clear_part(AW_pos x, AW_pos y, AW_pos width, AW_pos height, AW_bitset filteri)	AW_device	inline
AW_simple_device::clear_part(AW_pos x, AW_pos y, AW_pos width, AW_pos height, AW_bitset filteri)	AW_device	inline
clear_refresh()	ED4_manager
clear_tags()	FINAL_TYPE< SEQTYPE >
clear_whole_background()	FINAL_TYPE< SEQTYPE >
AW_device::click_cd	AW_device	protected
AW_simple_device::click_cd	AW_device	protected
click_time	AW_window
ClickPreference enum name	FINAL_TYPE< SEQTYPE >
AW_device::clip(AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_pos &x0out, AW_pos &y0out, AW_pos &x1out, AW_pos &y1out)	AW_clipable
AW_device::clip(const AW::LineVector &line, AW::LineVector &clippedLine)	AW_clipable
AW_simple_device::clip(AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_pos &x0out, AW_pos &y0out, AW_pos &x1out, AW_pos &y1out)	AW_clipable
AW_simple_device::clip(const AW::LineVector &line, AW::LineVector &clippedLine)	AW_clipable
AW_device::clip_scale_stack	AW_device	protected
AW_simple_device::clip_scale_stack	AW_device	protected
clone(nestable *owner, SINT overall_count) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
clone() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
clone() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
clone() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
clone() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
close()	FINAL_TYPE< SEQTYPE >
close(FILE *out) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
close_sub_menu()	AW_window
ED4_terminal::clr_property(ED4_properties prop)	ED4_base	inline
ED4_text_terminal::clr_property(ED4_properties prop)	ED4_base	inline
ED4_manager::clr_property(ED4_properties prop)	ED4_base	inline
ClusterTree(ClusterTreeRoot *tree_root_)	FINAL_TYPE< SEQTYPE >	inlineexplicit
ClusterTreeRoot class	FINAL_TYPE< SEQTYPE >	friend
ClusterTreeRoot(AliView *aliview, AP_sequence *seqTemplate_, AP_FLOAT maxDistance_, size_t minClusterSize_)	FINAL_TYPE< SEQTYPE >
Cma(vector< string > &alph, int seq_number)	FINAL_TYPE< SEQTYPE >
cmp_combined(const AP_combinableSeq *other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
cmp_combined(const AP_combinableSeq *other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
cmp_data(size_t start, const AliData &other, size_t ostart, size_t count) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
cmp_whole_data(const AliData &other) const	AliData	inline
cmpPartWith(const void *mem, size_t start, size_t count) const	AliData	inline
color_table	AW_window
color_table_size	AW_window
colorize(GB_HASH *hashptr)	AP_tree
combine_count()	AP_combinableSeq	inlinestatic
combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights, char *mutation_per_site) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights, char *mutation_per_site=NULp) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
combinedEquals(const AP_combinableSeq *other) const	AP_combinableSeq	inline
commentList() const	FINAL_TYPE< SEQTYPE >	inline
comments	FINAL_TYPE< SEQTYPE >
COMPARE_WITH enum value	AliData
AW_device::completely_clipped() const	AW_clipable	inline
AW_simple_device::completely_clipped() const	AW_clipable	inline
AW_device::compoutcode(AW_pos xx, AW_pos yy) const	AW_clipable	inlineprotected
AW_simple_device::compoutcode(AW_pos xx, AW_pos yy) const	AW_clipable	inlineprotected
CompressionRoot class	FINAL_TYPE< SEQTYPE >	friend
CompressionTree(CompressionRoot *croot)	FINAL_TYPE< SEQTYPE >	inline
compute_mituples(MatrixXd mutualInformation)	FINAL_TYPE< SEQTYPE >
compute_tree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
compute_tree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
compute_tree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
compute_tree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
computeClusters(list< MITuple > mituples, size_t size, double threshold)	FINAL_TYPE< SEQTYPE >
computeMutualInformation(VecVecType &seq)	FINAL_TYPE< SEQTYPE >
computeMutualInformationP(VecVecType &seq)	FINAL_TYPE< SEQTYPE >
concat(AliDataPtr left, AliDataPtr right)	FINAL_TYPE< SEQTYPE >	friend
concrete_counter(nestable *owner, SINT overall_count)	FINAL_TYPE< SEQTYPE >	inline
ConfigMarkerDisplay(SmartPtr< ConstStrArray > config_, GBDATA *gb_main_)	FINAL_TYPE< SEQTYPE >	inline
configure_active_plugin(AW_root *awr)	FINAL_TYPE< SEQTYPE >	inline
configure_active_plugin_cb(AW_window *aww, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
configure_colors_cb(AW_window *aww)	FINAL_TYPE< SEQTYPE >	inline
configure_colors_cb(AW_window *aww, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
ED4_terminal::containing_species_manager() const	ED4_base	inline
ED4_text_terminal::containing_species_manager() const	ED4_base	inline
ED4_manager::containing_species_manager() const	ED4_base	inline
contains(ParagraphTree *that)	FINAL_TYPE< SEQTYPE >	inline
AP_tree::contains_marked_species()	ARB_seqtree
ARB_countedTree::contains_marked_species()	ARB_seqtree
Content() const	FINAL_TYPE< SEQTYPE >	inline
Content()	FINAL_TYPE< SEQTYPE >	inline
ConvertGCtoRGB(int gc)	FINAL_TYPE< SEQTYPE >
copy(const PS_BitMap_Fast *_other_bitmap)	FINAL_TYPE< SEQTYPE >
copy(const PS_BitMap_Counted *_other_bitmap)	FINAL_TYPE< SEQTYPE >
PS_BitMap::copy(const PS_BitMap *_other_bitmap)	PS_BitMap
copy_multi_rem(int &idx, int offset) const	FINAL_TYPE< SEQTYPE >	inline
COPY_TO enum value	AliData
copyPartTo(void *mem, size_t start, size_t count) const	AliData	inline
AliData::copyTo(void *mem) const	AliData	inline
LineReader::copyTo(FILE *out)	LineReader	inline
corresponding_sequence_terminal() const	FINAL_TYPE< SEQTYPE >	inline
corresponding_sequence_terminal() const	FINAL_TYPE< SEQTYPE >	inline
corresponding_species_name_terminal() const	FINAL_TYPE< SEQTYPE >	inline
costs(char *mutPerSite=NULp)	FINAL_TYPE< SEQTYPE >
TreeNode::count_clades() const	TreeNode
AP_tree::count_clades() const	TreeNode
ARB_countedTree::count_clades() const	TreeNode
count_leafs() const	AP_tree
countTextNodes()	FINAL_TYPE< SEQTYPE >	inline
create_autosize_button(const char *macro_name, AW_label label, const char *mnemonic=NULp, unsigned xtraSpace=1)	AW_window
create_button(const char *macro_name, AW_label label, const char *mnemonic=NULp, const char *color=NULp)	AW_window
create_child_progress(const char *title, SINT overall_count, const weightable &speed_) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
create_consensus(ED4_abstract_group_manager *upper_group_manager, arb_progress *progress)	ED4_manager
create_devices()	AW_window	protected
create_gap(size_t gapsize, const UnitPair &gapinfo) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
create_input_field(const char *awar_name, int columns=0)	AW_window
create_input_field_with_scaler(const char *awar_name, int textcolumns=4, int scaler_length=250, AW_ScalerType scalerType=AW_SCALER_LINEAR)	AW_window
create_inverse_toggle(const char *awar_name)	AW_window
create_invisible(int columns)	AW_window
create_menu(const char *name, const char *mnemonic, AW_active mask=AWM_ALL)	AW_window
create_mode(const char *pixmap, const char *help_text_, AW_active mask, const WindowCallback &cb)	AW_window
create_option_menu(const char *awar_name)	AW_window
create_selection_list(const char *awar_name, int columns, int rows)	AW_window
create_selection_list(const char *awar_name)	AW_window	inline
create_text_field(const char *awar_name, int columns=20, int rows=4)	AW_window
create_text_toggle(const char *var_name, const char *noText, const char *yesText, int buttonWidth=0)	AW_window
create_toggle(const char *awar_name)	AW_window
create_toggle(const char *awar_name, const char *nobitmap, const char *yesbitmap, int buttonWidth=0)	AW_window
create_toggle_field(const char *awar_name, AW_label label, AW_orientation orientation=AW_VERTICAL)	AW_window
create_toggle_field(const char *awar_name, AW_orientation orientation=AW_VERTICAL)	AW_window
create_user_geometry_awars(int posx, int posy, int width, int height)	AW_window
create_window_variables()	AW_window
ED4_terminal::curr_timestamp	ED4_terminal
ED4_text_terminal::curr_timestamp	ED4_terminal
current(AW_root *root, GBDATA *gb_main) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
d_callback(const WindowCallback &cb)	AW_window
data()	FINAL_TYPE< SEQTYPE >	inline
data() const	FINAL_TYPE< SEQTYPE >	inline
PS_BitSet::data	PS_BitSet	protected
PS_BitMap::data	PS_BitMap	protected
date	FINAL_TYPE< SEQTYPE >
datec	FINAL_TYPE< SEQTYPE >
dateu	FINAL_TYPE< SEQTYPE >
db_changed() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
db_changed() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
deactivate_plugin()	ItemShader	inline
DECLARE_ASSIGNMENT_OPERATOR(ArbMatchResultSet)	FINAL_TYPE< SEQTYPE >
DECLARE_ASSIGNMENT_OPERATOR(AW_clicked_polygon)	FINAL_TYPE< SEQTYPE >
ED4_terminal::DECLARE_DUMP_FOR_BASECLASS(ED4_terminal, ED4_base)	ED4_terminal
ED4_text_terminal::DECLARE_DUMP_FOR_BASECLASS(ED4_text_terminal, ED4_terminal)	ED4_text_terminal
ED4_text_terminal::ED4_terminal::DECLARE_DUMP_FOR_BASECLASS(ED4_terminal, ED4_base)	ED4_terminal
ED4_manager::DECLARE_DUMP_FOR_BASECLASS(ED4_manager, ED4_base)	ED4_manager
DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_manager)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_text_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal)	FINAL_TYPE< SEQTYPE >
DECLARE_DUMP_FOR_LEAFCLASS(ED4_terminal)	FINAL_TYPE< SEQTYPE >
ED4_terminal::DECLARE_DUMP_FOR_ROOTCLASS(ED4_base)	ED4_base
ED4_text_terminal::DECLARE_DUMP_FOR_ROOTCLASS(ED4_base)	ED4_base
ED4_manager::DECLARE_DUMP_FOR_ROOTCLASS(ED4_base)	ED4_base
deduceTranslations(class ConfigMapping &mapping) const	FINAL_TYPE< SEQTYPE >
DEFINE_DOWNCAST_ACCESSORS(ClusterTree, get_root_node, ARB_seqtree_root::get_root_node())	FINAL_TYPE< SEQTYPE >
TreeNode::DEFINE_READ_ACCESSORS(TreeNode *, get_father, father)	TreeNode
TreeNode::DEFINE_READ_ACCESSORS(TreeNode *, get_leftson, leftson)	TreeNode
TreeNode::DEFINE_READ_ACCESSORS(TreeNode *, get_rightson, rightson)	TreeNode
TreeRoot::DEFINE_READ_ACCESSORS(TreeNode *, get_root_node, rootNode)	TreeRoot
AP_tree::DEFINE_READ_ACCESSORS(TreeNode *, get_father, father)	TreeNode
AP_tree::DEFINE_READ_ACCESSORS(TreeNode *, get_leftson, leftson)	TreeNode
AP_tree::DEFINE_READ_ACCESSORS(TreeNode *, get_rightson, rightson)	TreeNode
AP_tree_root::DEFINE_READ_ACCESSORS(TreeNode *, get_root_node, rootNode)	TreeRoot
ARB_countedTree::DEFINE_READ_ACCESSORS(TreeNode *, get_father, father)	TreeNode
ARB_countedTree::DEFINE_READ_ACCESSORS(TreeNode *, get_leftson, leftson)	TreeNode
ARB_countedTree::DEFINE_READ_ACCESSORS(TreeNode *, get_rightson, rightson)	TreeNode
ARB_seqtree_root::DEFINE_READ_ACCESSORS(TreeNode *, get_root_node, rootNode)	TreeRoot
DEFINE_TREE_ACCESSORS(CompressionRoot, CompressionTree)	FINAL_TYPE< SEQTYPE >
DEFINE_TREE_ACCESSORS(ClusterTreeRoot, ClusterTree)	FINAL_TYPE< SEQTYPE >
DEFINE_TREE_ACCESSORS(AP_pars_root, AP_tree_nlen)	FINAL_TYPE< SEQTYPE >
AP_tree::DEFINE_TREE_ACCESSORS(AP_tree_root, AP_tree)	AP_tree
AP_tree::ARB_seqtree::DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_seqtree)	ARB_seqtree
ARB_countedTree::DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_countedTree)	ARB_countedTree
ARB_seqtree::DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_seqtree)	ARB_seqtree
DEFINE_TREE_RELATIVES_ACCESSORS(SizeAwareTree)	FINAL_TYPE< SEQTYPE >
DEFINE_TREE_RELATIVES_ACCESSORS(GroupTree)	FINAL_TYPE< SEQTYPE >
DEFINE_TREE_RELATIVES_ACCESSORS(GroupSearchTree)	FINAL_TYPE< SEQTYPE >
DEFINE_TREE_ROOT_ACCESSORS(GroupSearchRoot, GroupSearchTree)	FINAL_TYPE< SEQTYPE >
AP_tree_root::DEFINE_TREE_ROOT_ACCESSORS(AP_tree_root, AP_tree)	AP_tree_root
AP_tree_root::ARB_seqtree_root::DEFINE_TREE_ROOT_ACCESSORS(ARB_seqtree_root, ARB_seqtree)	ARB_seqtree_root
ARB_seqtree_root::DEFINE_TREE_ROOT_ACCESSORS(ARB_seqtree_root, ARB_seqtree)	ARB_seqtree_root
definition	FINAL_TYPE< SEQTYPE >
ED4_terminal::Delete() OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::Delete() OVERRIDE	ED4_terminal	virtual
ED4_manager::Delete() FINAL_OVERRIDE	ED4_manager	virtual
TreeRoot::delete_by_node()	TreeRoot	inline
AP_tree_root::delete_by_node()	TreeRoot	inline
ARB_seqtree_root::delete_by_node()	TreeRoot	inline
delete_pointer_2(SEC_helix_strand *strand)	FINAL_TYPE< SEQTYPE >	inline
delete_requested_by_child()	ED4_manager
ED4_terminal::delete_requested_children() OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::delete_requested_children() OVERRIDE	ED4_terminal	virtual
ED4_manager::delete_requested_children() OVERRIDE	ED4_manager	virtual
ED4_terminal::deleted	ED4_terminal
ED4_text_terminal::deleted	ED4_terminal
ED4_terminal::deleted_from_database() OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::deleted_from_database() OVERRIDE	ED4_text_terminal	virtual
ED4_manager::deleted_from_database() OVERRIDE	ED4_manager	virtual
description	FINAL_TYPE< SEQTYPE >
deselect_group()	AWT_graphic_tree	inline
TreeNode::destroy()	TreeNode	inlineprotected
TreeNode::destroy(TreeRoot *viaRoot)	TreeNode	inlineprotected
TreeNode::destroy(TreeNode *that)	TreeNode	inlinestatic
TreeNode::destroy(TreeNode *that, TreeRoot *root)	TreeNode	inlinestatic
AP_tree::destroy()	TreeNode	inlineprotected
AP_tree::destroy(TreeRoot *viaRoot)	TreeNode	inlineprotected
AP_tree::destroy(TreeNode *that)	TreeNode	inlinestatic
AP_tree::destroy(TreeNode *that, TreeRoot *root)	TreeNode	inlinestatic
ARB_countedTree::destroy()	TreeNode	inlineprotected
ARB_countedTree::destroy(TreeRoot *viaRoot)	TreeNode	inlineprotected
ARB_countedTree::destroy(TreeNode *that)	TreeNode	inlinestatic
ARB_countedTree::destroy(TreeNode *that, TreeRoot *root)	TreeNode	inlinestatic
destroyNode(TreeNode *node) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
destroyNode(TreeNode *node) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
destroyNode(TreeNode *node) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
destroyNode(TreeNode *node) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
detect_clusters(arb_progress &progress)	FINAL_TYPE< SEQTYPE >
detect_group_state(AP_tree *at, AWT_graphic_tree_group_state *state, AP_tree *skip_this_son)	AWT_graphic_tree
diamond(int gc, const AW::Position &pos, int pixel_radius)	AWT_graphic_tree
differs_from(const AliData &other) const	AliData	inline
dislocate_selected_group()	AWT_graphic_tree	inline
disp_device	FINAL_TYPE< SEQTYPE >	protected
DisplayBasePositions()	FINAL_TYPE< SEQTYPE >
displayGrid	FINAL_TYPE< SEQTYPE >
DisplayHelices()	FINAL_TYPE< SEQTYPE >
DisplayHelixBackBone()	FINAL_TYPE< SEQTYPE >
DisplayHelixMidPoints(Texture2D *cImages)	FINAL_TYPE< SEQTYPE >
DisplayHelixNumbers()	FINAL_TYPE< SEQTYPE >
DisplayMappedSpBasePositions()	FINAL_TYPE< SEQTYPE >
DisplayMappedSpInsertions()	FINAL_TYPE< SEQTYPE >
DisplayMolecule(Structure3D *cStr)	FINAL_TYPE< SEQTYPE >
DisplayMoleculeMask(int w, int h)	FINAL_TYPE< SEQTYPE >
DisplayMoleculeName(int w, int h, Structure3D *cStr)	FINAL_TYPE< SEQTYPE >
distribute_children()	ED4_manager
do_align()	FINAL_TYPE< SEQTYPE >
do_callbacks()	FINAL_TYPE< SEQTYPE >	inline
do_drag(const AW_clicked_element *drag_target, const Position &mousepos)	Dragged	inline
do_drop(const AW_clicked_element *drop_target, const Position &mousepos)	Dragged	inline
do_lazy_load() const	AP_sequence	protected
does_exist() const	AW_clicked_element	inline
DoHelixMapping()	FINAL_TYPE< SEQTYPE >
done() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
dr	FINAL_TYPE< SEQTYPE >
AWT_graphic::drag_gc	AWT_graphic	protected
AWT_graphic_parsimony::drag_gc	AWT_graphic	protected
AWT_graphic::drag_target_detection(bool detect)	AWT_graphic	inline
AWT_graphic_parsimony::drag_target_detection(bool detect)	AWT_graphic	inline
DragAction enum name	Dragged
Dragged(AWT_graphic_exports &exports_)	Dragged	inline
dragged	FINAL_TYPE< SEQTYPE >
DRAGGING enum value	Dragged
draw() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
draw() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
draw() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
draw() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
draw() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
ED4_terminal::draw_bb(int color)	ED4_base
ED4_text_terminal::draw_bb(int color)	ED4_base
ED4_manager::draw_bb(int color)	ED4_base
draw_branch_line(int gc, const AW::Position &root, const AW::Position &leaf, AW_bitset filter)	AWT_graphic_tree	inline
ED4_terminal::draw_drag_box(AW_pos x, AW_pos y, GB_CSTR text=NULp, int cursor_y=-1)	ED4_terminal
ED4_text_terminal::draw_drag_box(AW_pos x, AW_pos y, GB_CSTR text=NULp, int cursor_y=-1)	ED4_terminal
draw_drag_indicator(AW_device *IF_DEBUG(same_device), int drag_gc) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
Dragged::draw_drag_indicator(AW_device *device, int drag_gc) const =0	Dragged	pure virtual
draw_line(int x1, int y1, int x2, int y2, int width, bool resize)	AW_window
draw_text(int gc, const char *textBuffer, size_t textStart, size_t textLen, const AW::Position &pos)	FINAL_TYPE< SEQTYPE >
DrawBox(float x, float y, float width, float height)	FINAL_TYPE< SEQTYPE >
drawnSize() const	SEC_constrainted	inline
DROPPED enum value	Dragged
dump_at_position(const char *debug_label) const	AW_window
dup() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
dup() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
ED4_terminal::dynamic_prop	ED4_base
ED4_text_terminal::dynamic_prop	ED4_base
ED4_manager::dynamic_prop	ED4_base
E4B_AVOID_UNNEEDED_CASTS(tree_terminal)	FINAL_TYPE< SEQTYPE >
E4B_AVOID_UNNEEDED_CASTS(pure_text_terminal)	FINAL_TYPE< SEQTYPE >
ED4_text_terminal::E4B_AVOID_UNNEEDED_CASTS(text_terminal)	ED4_text_terminal
ED4_manager::E4B_AVOID_UNNEEDED_CASTS(manager)	ED4_manager
ED4_terminal::E4B_DECL_CASTOP(area_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(abstract_group_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(bracket_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(columnStat_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(consensus_sequence_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(device_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(group_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(line_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(multi_name_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(multi_sequence_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(multi_species_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(name_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(orf_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(pure_text_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(root_group_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(sequence_info_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(sequence_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(sequence_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(spacer_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(species_manager)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(species_name_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(text_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(flag_header_terminal)	ED4_base
ED4_terminal::E4B_DECL_CASTOP(flag_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(area_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(abstract_group_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(bracket_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(columnStat_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(consensus_sequence_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(device_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(group_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(line_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(multi_name_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(multi_sequence_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(multi_species_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(name_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(orf_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(pure_text_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(root_group_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(sequence_info_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(sequence_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(sequence_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(spacer_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(species_manager)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(species_name_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(text_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(flag_header_terminal)	ED4_base
ED4_text_terminal::E4B_DECL_CASTOP(flag_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(area_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(abstract_group_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(bracket_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(columnStat_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(consensus_sequence_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(device_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(group_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(line_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(multi_name_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(multi_sequence_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(multi_species_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(name_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(orf_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(pure_text_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(root_group_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(sequence_info_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(sequence_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(sequence_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(spacer_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(species_manager)	ED4_base
ED4_manager::E4B_DECL_CASTOP(species_name_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(text_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(flag_header_terminal)	ED4_base
ED4_manager::E4B_DECL_CASTOP(flag_terminal)	ED4_base
ED4_terminal::ED4_base(const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_base
ED4_text_terminal::ED4_base(const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_base
ED4_manager::ED4_base(const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_base
ED4_columnStat_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_container()	ED4_container
ED4_flag_header_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_flag_terminal(const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_main_manager(const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_manager(const ED4_objspec &spec_, const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_manager
ED4_pure_text_terminal(const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_sequence_info_terminal(const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_spacer_terminal(const char *id, bool shallDraw_, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_species_manager(ED4_species_type type_, const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_species_name_terminal(GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
ED4_terminal::ED4_terminal(const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_terminal
ED4_text_terminal::ED4_terminal(const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_terminal
ED4_text_terminal(const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)	ED4_text_terminal
ED4_tree_terminal(const char *id, AW_pos width, AW_pos height, ED4_manager *parent)	FINAL_TYPE< SEQTYPE >
edgeTo(const AP_tree_nlen *brother) const	FINAL_TYPE< SEQTYPE >
elem_index(int i) const	CharPtrArray	inlineprotected
AliData::elems() const	AliData	inline
CharPtrArray::elems	CharPtrArray	protected
Embl()	FINAL_TYPE< SEQTYPE >	inline
AliData::empty() const	AliData	inline
ED4_manager::empty() const	ED4_container	inline
CharPtrArray::empty() const	CharPtrArray	inline
empty_box(int gc, const AW::Position &pos, int pixel_width)	AWT_graphic_tree	inline
endAttachAbspos() const	FINAL_TYPE< SEQTYPE >	inline
endAttachPoint() const	FINAL_TYPE< SEQTYPE >	inline
endFullName() const	FINAL_TYPE< SEQTYPE >	inline
EndTexturizer()	FINAL_TYPE< SEQTYPE >
ensure_sequence_loaded() const	AP_sequence	inline
enumerateResults(ArbMatchResultPtrByDoubleMultiMap &rMap, int nMaxFullName)	FINAL_TYPE< SEQTYPE >
equals(const AliData &other) const	AliData	inline
erase()	FINAL_TYPE< SEQTYPE >	inline
erase_elems()	CharPtrArray	inlineprotected
AW_device::establish_default(int gc)	AW_stylable
AW_simple_device::establish_default(int gc)	AW_stylable
event	AW_window
ED4_terminal::event_sent_by_parent(AW_event *event, AW_window *aww) OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::event_sent_by_parent(AW_event *event, AW_window *aww) OVERRIDE	ED4_terminal	virtual
ED4_manager::event_sent_by_parent(AW_event *event, AW_window *aww) FINAL_OVERRIDE	ED4_manager	virtual
exchange(AP_tree_nlen *other)	FINAL_TYPE< SEQTYPE >
existing_index(ED4_index idx) const	ED4_container	inlineprotected
AWT_graphic::exports	AWT_graphic
AWT_graphic_parsimony::exports	AWT_graphic
ED4_terminal::extension	ED4_base
ED4_text_terminal::extension	ED4_base
ED4_manager::extension	ED4_base
fake_agt(ArbParsimony &parsimony_)	FINAL_TYPE< SEQTYPE >	inline
fast()	AW_device	virtual
fast_sync_changed_folding(AP_tree *parent_of_all_changes)	AWT_graphic_tree
XML_Node::father	XML_Node	protected
TreeNode::father	TreeNode
AP_tree::father	TreeNode
ARB_countedTree::father	TreeNode
fHelixSize	FINAL_TYPE< SEQTYPE >
AW_device::Fill_Style enum name	AW_device	protected
AW_simple_device::Fill_Style enum name	AW_device	protected
filled_box(int gc, const AW::Position &pos, int pixel_width)	AWT_graphic_tree	inline
AW_device::filter	AW_device	protected
AW_simple_device::filter	AW_device	protected
find_clusters()	FINAL_TYPE< SEQTYPE >
find_first_that(ED4_level level, const ED4_basePredicate &fulfills_predicate)	ED4_manager
TreeRoot::find_innermost_edge()	TreeRoot
AP_tree_root::find_innermost_edge()	TreeRoot
ARB_seqtree_root::find_innermost_edge()	TreeRoot
TreeNode::find_parent_clade() const	TreeNode	inline
TreeNode::find_parent_clade()	TreeNode	inline
AP_tree::find_parent_clade() const	TreeNode	inline
AP_tree::find_parent_clade()	TreeNode	inline
ARB_countedTree::find_parent_clade() const	TreeNode	inline
ARB_countedTree::find_parent_clade()	TreeNode	inline
TreeNode::find_parent_with_groupInfo(bool skipKeeledBrothers=false) const	TreeNode	inline
TreeNode::find_parent_with_groupInfo(bool skipKeeledBrothers=false)	TreeNode	inline
AP_tree::find_parent_with_groupInfo(bool skipKeeledBrothers=false) const	TreeNode	inline
AP_tree::find_parent_with_groupInfo(bool skipKeeledBrothers=false)	TreeNode	inline
ARB_countedTree::find_parent_with_groupInfo(bool skipKeeledBrothers=false) const	TreeNode	inline
ARB_countedTree::find_parent_with_groupInfo(bool skipKeeledBrothers=false)	TreeNode	inline
TreeNode::findLeafNamed(const char *wantedName)	TreeNode
AP_tree::findLeafNamed(const char *wantedName)	TreeNode
ARB_countedTree::findLeafNamed(const char *wantedName)	TreeNode
findMaximumWeight(double &dMaximumWeight) const	FINAL_TYPE< SEQTYPE >
finish() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
finish() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
first_range_gc	ItemShader	protected
firstListMember()	FINAL_TYPE< SEQTYPE >	inline
firstWithLessIndentThan(int wanted_indentation)	FINAL_TYPE< SEQTYPE >	inline
fixAngleBugs(int version)	FINAL_TYPE< SEQTYPE >
fixAngleBugs(int version)	FINAL_TYPE< SEQTYPE >
TreeNode::fixDeletedSon()	TreeNode
AP_tree::fixDeletedSon()	TreeNode
ARB_countedTree::fixDeletedSon()	TreeNode
fixInvalidHelixPositions(int maxHelixNumber)	FINAL_TYPE< SEQTYPE >	inline
TreeNode::fixKeeledOrientation()	TreeNode	inlineprotected
AP_tree::fixKeeledOrientation()	TreeNode	inlineprotected
ARB_countedTree::fixKeeledOrientation()	TreeNode	inlineprotected
ED4_terminal::flag	ED4_base
ED4_text_terminal::flag	ED4_base
ED4_manager::flag	ED4_base
flip()	FINAL_TYPE< SEQTYPE >
flush()	FINAL_TYPE< SEQTYPE >	virtual
flush_cache()	MarkerDisplay	inline
force_expose()	AW_window
AW_device::force_into_clipbox(const AW::Position &pos, AW::Position &forcedPos)	AW_clipable
AW_simple_device::force_into_clipbox(const AW::Position &pos, AW::Position &forcedPos)	AW_clipable
forget_auto_unfolded()	AWT_graphic_tree
TreeNode::forget_origin()	TreeNode	inline
AP_tree::forget_origin()	TreeNode	inline
ARB_countedTree::forget_origin()	TreeNode	inline
forget_sequence()	AP_sequence	inline
format() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
format() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
format() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
format_indentations()	FINAL_TYPE< SEQTYPE >
format_lists()	FINAL_TYPE< SEQTYPE >
free() const	ArbRefCount	inline
AW_device::FS_EMPTY enum value	AW_device	protected
AW_simple_device::FS_EMPTY enum value	AW_device	protected
AW_device::FS_GREY enum value	AW_device	protected
AW_simple_device::FS_GREY enum value	AW_device	protected
AW_device::FS_SOLID enum value	AW_device	protected
AW_simple_device::FS_SOLID enum value	AW_device	protected
fSkeletonSize	FINAL_TYPE< SEQTYPE >
fullname() const	FINAL_TYPE< SEQTYPE >
G	FINAL_TYPE< SEQTYPE >
TreeNode::gb_node	TreeNode
AP_tree::gb_node	TreeNode
ARB_countedTree::gb_node	TreeNode
gb_struct	FINAL_TYPE< SEQTYPE >
gb_struct_ref	FINAL_TYPE< SEQTYPE >
gb_tree_gone	AP_tree_root
GenBank()	FINAL_TYPE< SEQTYPE >	inline
general_item_change() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
ED4_terminal::generate_configuration_string(GBS_strstruct &buffer)	ED4_base
ED4_text_terminal::generate_configuration_string(GBS_strstruct &buffer)	ED4_base
ED4_manager::generate_configuration_string(GBS_strstruct &buffer)	ED4_base
AW_device::generic_box(int gc, const AW::Rectangle &rect, AW_bitset filteri)	AW_device	protected
AW_simple_device::generic_box(int gc, const AW::Rectangle &rect, AW_bitset filteri)	AW_device	protected
AW_device::generic_circle(int gc, const AW::Position &center, const AW::Vector &radius, AW_bitset filteri)	AW_device	inlineprotected
AW_simple_device::generic_circle(int gc, const AW::Position &center, const AW::Vector &radius, AW_bitset filteri)	AW_device	inlineprotected
AW_device::generic_invisible(const AW::Position &pos, AW_bitset filteri)	AW_device	protected
AW_simple_device::generic_invisible(const AW::Position &pos, AW_bitset filteri)	AW_device	protected
AW_device::generic_polygon(int gc, int npos, const AW::Position *pos, AW_bitset filteri)	AW_device	protected
AW_simple_device::generic_polygon(int gc, int npos, const AW::Position *pos, AW_bitset filteri)	AW_device	protected
get(const long _row, const long _col) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
get(const long _row, const long _col) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
Get(const long _index) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
get_abs_angle() const	SEC_oriented	inline
AP_combinableSeq::get_aliview() const	AP_sequence	inline
AP_tree_root::get_aliview() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_aliview() const	ARB_seqtree_root	inline
get_alpha()	FINAL_TYPE< SEQTYPE >	inline
get_angle() const	AP_tree	inline
get_answer(const char *unique_id, const char *question, const char *buttons, const char *to_all, bool add_abort)	FINAL_TYPE< SEQTYPE >
ED4_terminal::get_area_level(ED4_multi_species_manager **multi_species_manager=NULp) const	ED4_base
ED4_text_terminal::get_area_level(ED4_multi_species_manager **multi_species_manager=NULp) const	ED4_base
ED4_manager::get_area_level(ED4_multi_species_manager **multi_species_manager=NULp) const	ED4_base
AW_device::get_area_size() const	AW_device
AW_simple_device::get_area_size() const	AW_device
get_at_position(int *x, int *y) const	AW_window
get_at_xposition() const	AW_window
get_at_yposition() const	AW_window
get_attach_point() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
AW_device::get_available_fontsizes(int gc, AW_font font_nr, int *available_sizes)	AW_stylable
AW_simple_device::get_available_fontsizes(int gc, AW_font font_nr, int *available_sizes)	AW_stylable
get_average_ingroup_distance() const	FINAL_TYPE< SEQTYPE >	inline
get_base_length()	FINAL_TYPE< SEQTYPE >	inline
get_bound_species_data() const	AP_sequence	inline
get_bounding_box() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
TreeNode::get_branchlength() const	TreeNode	inline
AP_tree::get_branchlength() const	TreeNode	inline
ARB_countedTree::get_branchlength() const	TreeNode	inline
TreeNode::get_branchlength_unrooted() const	TreeNode	inline
AP_tree::get_branchlength_unrooted() const	TreeNode	inline
ARB_countedTree::get_branchlength_unrooted() const	TreeNode	inline
TreeNode::get_brother()	TreeNode	inline
TreeNode::get_brother() const	TreeNode	inline
AP_tree::get_brother()	TreeNode	inline
AP_tree::get_brother() const	TreeNode	inline
ARB_countedTree::get_brother()	TreeNode	inline
ARB_countedTree::get_brother() const	TreeNode	inline
get_button_length() const	AW_window
get_center() const	FINAL_TYPE< SEQTYPE >	inline
get_circumference() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::get_click_cd() const	AW_device	inline
AW_simple_device::get_click_cd() const	AW_device	inline
get_click_device(AW_area area, int mousex, int mousey, int max_distance)	AW_window
AW_device::get_cliprect() const	AW_clipable	inline
AW_simple_device::get_cliprect() const	AW_clipable	inline
get_cluster_count() const	FINAL_TYPE< SEQTYPE >	inline
get_command_data()	AWT_graphic_tree	inlineprotected
get_common() const	FINAL_TYPE< SEQTYPE >	inline
AW_window::get_common(AW_area area)	AW_window
AW_device::get_common_screen(const AW_common *common_)	AW_device	protectedstatic
AW_simple_device::get_common_screen(const AW_common *common_)	AW_device	protectedstatic
get_competent_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)	ED4_manager
get_competent_clicked_child(AW_pos x, AW_pos y, ED4_properties relevant_prop)	ED4_manager
get_config() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
get_config() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
get_connecting_line(const AW_clicked_element &other) const	AW_clicked_element	inline
ED4_terminal::get_consensus_relevant_terminal() const	ED4_base
ED4_text_terminal::get_consensus_relevant_terminal() const	ED4_base
ED4_manager::get_consensus_relevant_terminal() const	ED4_base
get_cursor() const	AWT_graphic_tree	inline
get_date() const	FINAL_TYPE< SEQTYPE >	inline
get_defined_level(ED4_level lev) const	ED4_manager
SaiOperator::get_description() const	SaiOperator
ItemShader::get_description() const	ItemShader	inline
get_destination_loop()	FINAL_TYPE< SEQTYPE >	inline
get_device(AW_area area)	AW_window
get_displayed_text() const	FINAL_TYPE< SEQTYPE >
get_displayed_text() const	FINAL_TYPE< SEQTYPE >
get_distance() const	AW_clicked_element	inline
AWT_graphic::get_drag_gc() const	AWT_graphic	inline
AWT_graphic_parsimony::get_drag_gc() const	AWT_graphic	inline
get_enum_type() const	FINAL_TYPE< SEQTYPE >	inline
get_enumeration() const	FINAL_TYPE< SEQTYPE >	inline
get_error() const	FINAL_TYPE< SEQTYPE >	inline
get_error() const	FINAL_TYPE< SEQTYPE >	inline
get_error() const	FINAL_TYPE< SEQTYPE >	inline
get_event(AW_event *eventi) const	AW_window
get_exports()	Dragged	inlineprotected
AW_device::get_filter() const	AW_device	inline
AW_simple_device::get_filter() const	AW_device	inline
AP_combinableSeq::get_filter() const	AP_sequence	inline
AP_tree_root::get_filter() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_filter() const	ARB_seqtree_root	inline
get_first_field(GBDATA *gb_item) const	FINAL_TYPE< SEQTYPE >	inline
get_first_terminal(int start_index=0) const	ED4_manager
get_fixpoint() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
get_fixpoint() const	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_fixpoint() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_fixpoint_helix() const	FINAL_TYPE< SEQTYPE >	inline
get_fixpoint_strand() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::get_font_limits(int gc, char c) const	AW_stylable
AW_simple_device::get_font_limits(int gc, char c) const	AW_stylable
AW_device::get_font_overlap() const	AW_clipable	inline
AW_simple_device::get_font_overlap() const	AW_clipable	inline
AP_tree_root::get_gb_main() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_gb_main() const	ARB_seqtree_root	inline
AP_tree_root::get_gb_tree() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_gb_tree() const	ARB_seqtree_root	inline
get_gbmain() const	AWT_graphic_tree	inline
AW_device::get_grey_level(int gc)	AW_stylable
AW_simple_device::get_grey_level(int gc)	AW_stylable
get_group_cursor() const	AWT_graphic_tree	inline
TreeNode::get_group_name() const	TreeNode	inline
AP_tree::get_group_name() const	TreeNode	inline
ARB_countedTree::get_group_name() const	TreeNode	inline
get_group_scaling() const	AP_tree_root	inline
get_helix() const	FINAL_TYPE< SEQTYPE >	inline
get_helix()	FINAL_TYPE< SEQTYPE >	inline
get_id() const	FINAL_TYPE< SEQTYPE >	inline
get_internal_maskname() const	FINAL_TYPE< SEQTYPE >	inline
get_irs_tree_ruler_scale_factor() const	AWT_graphic_tree	inline
get_item_type() const	awt_item_type_selector	inline
get_itemtypename() const	FINAL_TYPE< SEQTYPE >	inline
get_label() const	awt_viewport	inline
get_last_terminal(int start_index=-1) const	ED4_manager
get_last_widget() const	AW_window
RefContainer< GenbankRef >::get_latest_ref() const	RefContainer< GenbankRef >	inline
RefContainer< GenbankRef >::get_latest_ref()	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::get_latest_ref() const	RefContainer< Emblref >	inline
RefContainer< Emblref >::get_latest_ref()	RefContainer< Emblref >	inline
get_leaf_count() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_leaf_count() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_leaf_count() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_leaf_count() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_leaf_count() const FINAL_OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_length() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_length() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_length() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
get_length() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_length() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_linewidth() const	AP_tree	inline
get_logical_root()	AWT_graphic_tree	inline
get_logical_root() const	AWT_graphic_tree	inline
get_loop() const	FINAL_TYPE< SEQTYPE >	inline
get_loop()	FINAL_TYPE< SEQTYPE >	inline
get_marked_count() const	FINAL_TYPE< SEQTYPE >	inline
get_marker_display()	AWT_graphic_tree	inline
get_marker_name(int markerIdx) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_maskname() const	FINAL_TYPE< SEQTYPE >	inline
get_maxDistance() const	FINAL_TYPE< SEQTYPE >	inline
get_min_bases() const	FINAL_TYPE< SEQTYPE >	inline
get_minClusterSize() const	FINAL_TYPE< SEQTYPE >	inline
get_name() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
ED4_terminal::get_name_of_species()	ED4_base
ED4_text_terminal::get_name_of_species()	ED4_base
ED4_manager::get_name_of_species()	ED4_base
get_name_terminal() const	FINAL_TYPE< SEQTYPE >	inline
get_NDS_Type() const	FINAL_TYPE< SEQTYPE >	inline
RefContainer< GenbankRef >::get_new_ref()	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::get_new_ref()	RefContainer< Emblref >	inline
get_next_segment() const	FINAL_TYPE< SEQTYPE >	inline
get_next_segment()	FINAL_TYPE< SEQTYPE >	inline
get_next_strand() const	FINAL_TYPE< SEQTYPE >	inline
get_next_strand()	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::get_next_terminal()	ED4_base
ED4_text_terminal::get_next_terminal()	ED4_base
ED4_manager::get_next_terminal()	ED4_base
AW_device::get_offset() const	AW_zoomable	inline
AW_simple_device::get_offset() const	AW_zoomable	inline
get_origin_loop() const	FINAL_TYPE< SEQTYPE >	inline
get_origin_loop()	FINAL_TYPE< SEQTYPE >	inline
get_other_strand() const	FINAL_TYPE< SEQTYPE >	inline
get_other_strand()	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::get_parent(ED4_level lev) const	ED4_base	inline
ED4_text_terminal::get_parent(ED4_level lev) const	ED4_base	inline
ED4_manager::get_parent(ED4_level lev) const	ED4_base	inline
get_parsimony()	AWT_graphic_parsimony	inline
get_polygon(int &posCount) const	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::get_prev_terminal()	ED4_base
ED4_text_terminal::get_prev_terminal()	ED4_base
ED4_manager::get_prev_terminal()	ED4_base
get_previous_segment()	FINAL_TYPE< SEQTYPE >
get_previous_strand()	FINAL_TYPE< SEQTYPE >
get_print_device(AW_area area)	AW_window
get_recalc_pos_atShow() const	AW_window
RefContainer< GenbankRef >::get_ref(int num) const	RefContainer< GenbankRef >	inline
RefContainer< GenbankRef >::get_ref(int num)	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::get_ref(int num) const	RefContainer< Emblref >	inline
RefContainer< Emblref >::get_ref(int num)	RefContainer< Emblref >	inline
RefContainer< GenbankRef >::get_refcount() const	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::get_refcount() const	RefContainer< Emblref >	inline
get_region() const	SEC_base_part	inline
get_region()	SEC_base_part	inline
get_rel_angle() const	SEC_oriented	inline
get_rel_pos() const	AW_clicked_element	inline
get_rem(int idx) const	FINAL_TYPE< SEQTYPE >	inline
get_rem_count() const	FINAL_TYPE< SEQTYPE >	inline
TreeNode::get_remark() const	TreeNode	inline
AP_tree::get_remark() const	TreeNode	inline
ARB_countedTree::get_remark() const	TreeNode	inline
TreeNode::get_remark_ptr() const	TreeNode	inline
AP_tree::get_remark_ptr() const	TreeNode	inline
ARB_countedTree::get_remark_ptr() const	TreeNode	inline
get_result() const	FINAL_TYPE< SEQTYPE >	inline
get_result_length() const	FINAL_TYPE< SEQTYPE >	inline
get_result_ref() const	FINAL_TYPE< SEQTYPE >	inline
get_root() const	FINAL_TYPE< SEQTYPE >	inline
get_root()	FINAL_TYPE< SEQTYPE >	inline
TreeNode::get_root_node() const	TreeNode	inline
TreeNode::get_root_node()	TreeNode	inline
AWT_graphic_parsimony::get_root_node()	AWT_graphic_parsimony	inline
AWT_graphic_parsimony::AWT_graphic_tree::get_root_node() const	AWT_graphic_tree	inline
AP_tree::get_root_node() const	TreeNode	inline
AP_tree::get_root_node()	TreeNode	inline
ARB_countedTree::get_root_node() const	TreeNode	inline
ARB_countedTree::get_root_node()	TreeNode	inline
get_rootside_helix() const	FINAL_TYPE< SEQTYPE >	inline
get_rootside_loop()	FINAL_TYPE< SEQTYPE >	inline
get_rootside_strand() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::get_rtransformed_cliprect() const	AW_device	inline
AW_simple_device::get_rtransformed_cliprect() const	AW_device	inline
AW_device::get_scale() const	AW_zoomable	inline
AW_simple_device::get_scale() const	AW_zoomable	inline
get_scrollarea_size(AW_screen_area *square)	AW_window
get_scrolled_picture_height() const	AW_window
get_scrolled_picture_width() const	AW_window
get_selected_group() const	AWT_graphic_tree	inline
get_self_awar() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_self_awar_content_length() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
AP_tree::get_seq()	ARB_seqtree	inline
AP_tree::get_seq() const	ARB_seqtree	inline
ARB_countedTree::get_seq()	ARB_seqtree	inline
ARB_countedTree::get_seq() const	ARB_seqtree	inline
AP_tree_root::get_seqTemplate() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_seqTemplate() const	ARB_seqtree_root	inline
get_sequence() const	FINAL_TYPE< SEQTYPE >	inline
get_sequence() const	FINAL_TYPE< SEQTYPE >	inline
get_sequence_dists() const	FINAL_TYPE< SEQTYPE >	inline
get_sequence_length() const	AP_sequence	inline
get_size_device(AW_area area)	AW_window
get_species() const	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::get_species_pointer() const	ED4_base	inline
ED4_text_terminal::get_species_pointer() const	ED4_base	inline
ED4_manager::get_species_pointer() const	ED4_base	inline
ED4_terminal::get_species_type() const	ED4_base	inline
ED4_text_terminal::get_species_type() const	ED4_base	inline
ED4_manager::get_species_type() const	ED4_base	inline
get_state() const	FINAL_TYPE< SEQTYPE >	inline
get_states() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::get_string_size(int gc, long textlen) const	AW_stylable
AW_device::get_string_size(int gc, const SizedCstr &cstr) const	AW_stylable
AW_simple_device::get_string_size(int gc, long textlen) const	AW_stylable
AW_simple_device::get_string_size(int gc, const SizedCstr &cstr) const	AW_stylable
get_tagged_count() const	FINAL_TYPE< SEQTYPE >	inline
get_target_data(const QueryTarget &target, GB_ERROR &error) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
get_threshold()	FINAL_TYPE< SEQTYPE >	inlinestatic
get_title() const	FINAL_TYPE< SEQTYPE >	inline
get_top_middle_line_terminal() const	FINAL_TYPE< SEQTYPE >	inline
get_top_middle_spacer_terminal() const	FINAL_TYPE< SEQTYPE >	inline
AP_tree_root::get_tree_name() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_tree_name() const	ARB_seqtree_root	inline
TreeNode::get_tree_root() const	TreeNode	inline
AWT_graphic_parsimony::get_tree_root()	AWT_graphic_parsimony	inline
AP_tree::get_tree_root() const	TreeNode	inline
ARB_countedTree::get_tree_root() const	TreeNode	inline
get_tree_shader()	AP_tree	inlinestatic
get_tree_style() const	AWT_graphic_tree	inline
get_type() const	FINAL_TYPE< SEQTYPE >	inline
get_type() const	FINAL_TYPE< SEQTYPE >	inline
get_type() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::get_unscale() const	AW_zoomable	inline
AW_simple_device::get_unscale() const	AW_zoomable	inline
get_usequence() const	FINAL_TYPE< SEQTYPE >	inline
get_value() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
AP_combinableSeq::get_weights() const	AP_sequence	inline
AP_tree_root::get_weights() const	ARB_seqtree_root	inline
ARB_seqtree_root::get_weights() const	ARB_seqtree_root	inline
ED4_terminal::get_win_area(ED4_window *ed4w) const	ED4_base	inline
ED4_text_terminal::get_win_area(ED4_window *ed4w) const	ED4_base	inline
ED4_manager::get_win_area(ED4_window *ed4w) const	ED4_base	inline
get_window()	FINAL_TYPE< SEQTYPE >	inline
get_window_id() const	AW_window	inline
get_window_size(int &width, int &height)	AW_window
get_window_title() const	AW_window
get_zombie_count() const	FINAL_TYPE< SEQTYPE >	inline
get_zombies_and_duplicates(int &zomb, int &dups) const	AWT_graphic_tree	inline
getCapacity() const	PS_BitSet	inline
getClusters()	FINAL_TYPE< SEQTYPE >
getCma()	FINAL_TYPE< SEQTYPE >
GetColor(int gc)	FINAL_TYPE< SEQTYPE >
getConstRootNode()	FINAL_TYPE< SEQTYPE >	inline
getCountFor(const long _index)	FINAL_TYPE< SEQTYPE >	inline
getCountOfTrues() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
PS_BitSet::getCountOfTrues(const long _fill_index=-1)	PS_BitSet
getEntropy()	FINAL_TYPE< SEQTYPE >
getFalseIndices(IndexSet &_index_set, const long _fill_index)	PS_BitSet
getFalseIndicesFor(const long _index, PS_BitSet::IndexSet &_index_set) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
getFalseIndicesForRow(const long _row, PS_BitSet::IndexSet &_index_set)	FINAL_TYPE< SEQTYPE >
getFilename() const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
getIDForName(SpeciesID &_id, const string &_name)	FINAL_TYPE< SEQTYPE >	inline
getJointEntropy()	FINAL_TYPE< SEQTYPE >
getKeyPath() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
getLine(string &line)	LineReader	inline
getLineNumber() const	LineReader	inline
getLoader()	FINAL_TYPE< SEQTYPE >
getMaxID()	FINAL_TYPE< SEQTYPE >	inline
getMaxUsedIndex() const	PS_BitSet	inline
getMI()	FINAL_TYPE< SEQTYPE >
getMinID()	FINAL_TYPE< SEQTYPE >	inline
getMIp()	FINAL_TYPE< SEQTYPE >
getMsaLen()	FINAL_TYPE< SEQTYPE >
getName() const	FINAL_TYPE< SEQTYPE >	inline
getNameForID(const SpeciesID _id, string &_name)	FINAL_TYPE< SEQTYPE >	inline
getNextAbspos() const	SEC_base_part
getPositionMap()	FINAL_TYPE< SEQTYPE >
getRoot()	FINAL_TYPE< SEQTYPE >	inline
getRootNode()	FINAL_TYPE< SEQTYPE >	inline
getSAIname()	FINAL_TYPE< SEQTYPE >	inlinestatic
getSequenceCopy()	FINAL_TYPE< SEQTYPE >
getSequences()	FINAL_TYPE< SEQTYPE >
getSpeciesCount()	FINAL_TYPE< SEQTYPE >	inline
getTrueIndices(IndexSet &_index_set, const long _fill_index)	PS_BitSet
getTrueIndicesFor(const long _index, PS_BitSet::IndexSet &_index_set) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
getTrueIndicesForRow(const long _row, PS_BitSet::IndexSet &_index_set)	FINAL_TYPE< SEQTYPE >
getType() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
getType() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
GLRenderer()	FINAL_TYPE< SEQTYPE >
gone_tree_name	AP_tree_root
gr	AP_tree
group_rest_tree(AP_tree *at, CollapseMode mode, int color_group)	AWT_graphic_tree
group_tree(AP_tree *at, CollapseMode mode, int color_group)	AWT_graphic_tree
groupLabel(GBDATA *gb_main, GBDATA *gb_group, TreeNode *species, const char *tree_name) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
groupScale	AWT_graphic_tree	protected
GroupSearchRoot()	FINAL_TYPE< SEQTYPE >	inline
GroupSearchTree(GroupSearchRoot *root)	FINAL_TYPE< SEQTYPE >	inline
GroupTree(GroupTreeRoot *root)	FINAL_TYPE< SEQTYPE >	inlineexplicit
GroupTreeRoot class	FINAL_TYPE< SEQTYPE >	friend
GroupTreeRoot(AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks)	FINAL_TYPE< SEQTYPE >
handle_click(int markerIdx, AW_MouseButton button, AWT_graphic_exports &exports) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
handle_command(AW_device *device, AWT_graphic_event &event) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
handle_left_click(const AW::Position &click)	FINAL_TYPE< SEQTYPE >
handle_move(ED4_move_info *moveinfo)	ED4_manager
handleKey(AW_event_type event, AW_key_mod key_modifier, AW_key_code key_code, char key_char)	FINAL_TYPE< SEQTYPE >	protected
handleMouse(AW_device *device, AW_event_type event, int button, AWT_COMMAND_MODE cmd, const Position &world, SEC_base *elem, int abspos)	FINAL_TYPE< SEQTYPE >	protected
has_auto_subtitles() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
TreeRoot::has_bootstrap() const	TreeRoot	inline
AP_tree_root::has_bootstrap() const	TreeRoot	inline
ARB_seqtree_root::has_bootstrap() const	TreeRoot	inline
ED4_terminal::has_callback() const	ED4_base	inline
ED4_text_terminal::has_callback() const	ED4_base	inline
ED4_manager::has_callback() const	ED4_base	inline
has_correct_mark_flags() const	AP_tree
has_error() const	FINAL_TYPE< SEQTYPE >	inline
has_error() const	FINAL_TYPE< SEQTYPE >	inline
TreeNode::has_group_info() const	TreeNode	inline
AP_tree::has_group_info() const	TreeNode	inline
ARB_countedTree::has_group_info() const	TreeNode	inline
awt_viewport::has_name() const	awt_mask_item	inline
awt_mask_item::has_name() const	awt_mask_item	inline
TreeNode::has_no_remark() const	TreeNode	inline
AP_tree::has_no_remark() const	TreeNode	inline
ARB_countedTree::has_no_remark() const	TreeNode	inline
ED4_terminal::has_parent(ED4_manager *Parent)	ED4_base
ED4_text_terminal::has_parent(ED4_manager *Parent)	ED4_base
ED4_manager::has_parent(ED4_manager *Parent)	ED4_base
ED4_terminal::has_property(ED4_properties prop) const	ED4_base	inline
ED4_text_terminal::has_property(ED4_properties prop) const	ED4_base	inline
ED4_manager::has_property(ED4_properties prop) const	ED4_base	inline
RefContainer< GenbankRef >::has_refs() const	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::has_refs() const	RefContainer< Emblref >	inline
has_slice() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
TreeNode::has_valid_root_remarks() const	TreeNode
AP_tree::has_valid_root_remarks() const	TreeNode
ARB_countedTree::has_valid_root_remarks() const	TreeNode
hasLoop(SEC_loop *loop) const	FINAL_TYPE< SEQTYPE >	inline
hasName(const char *Name) const	AP_tree	inline
hasResults() const	FINAL_TYPE< SEQTYPE >	inline
AP_combinableSeq::hasSequence() const	AP_sequence	inline
AP_tree::hasSequence() const	ARB_seqtree	inline
ARB_countedTree::hasSequence() const	ARB_seqtree	inline
headline(const char *pHeadline, int nEndFullName)	FINAL_TYPE< SEQTYPE >	inline
headline() const	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::height_link	ED4_base
ED4_text_terminal::height_link	ED4_base
ED4_manager::height_link	ED4_base
help_text(const char *id)	AW_window
hide()	FINAL_TYPE< SEQTYPE >	inline
hide_children()	ED4_manager
hide_drag_indicator(AW_device *device, int drag_gc) const	Dragged	inline
hide_marker_display()	AWT_graphic_tree	inline
hide_or_notify(const char *error)	AW_window
highlight()	AW_window
highlight_info	FINAL_TYPE< SEQTYPE >
iBackBone	FINAL_TYPE< SEQTYPE >
iBaseHelix	FINAL_TYPE< SEQTYPE >
iBaseMode	FINAL_TYPE< SEQTYPE >
iBaseNonHelix	FINAL_TYPE< SEQTYPE >
iBaseUnpairHelix	FINAL_TYPE< SEQTYPE >
iColorise	FINAL_TYPE< SEQTYPE >
ED4_terminal::id	ED4_base
ED4_text_terminal::id	ED4_base
ED4_manager::id	ED4_base
ID	FINAL_TYPE< SEQTYPE >
iDispCursorPos	FINAL_TYPE< SEQTYPE >
iDisplayBases	FINAL_TYPE< SEQTYPE >
iDisplayHelix	FINAL_TYPE< SEQTYPE >
iDispPos	FINAL_TYPE< SEQTYPE >
iDispTerInt	FINAL_TYPE< SEQTYPE >
iEndHelix	FINAL_TYPE< SEQTYPE >
iHelixBackBone	FINAL_TYPE< SEQTYPE >
iHelixMidPoint	FINAL_TYPE< SEQTYPE >
iHelixNrs	FINAL_TYPE< SEQTYPE >
iMapSpecies	FINAL_TYPE< SEQTYPE >
iMapSpeciesBase	FINAL_TYPE< SEQTYPE >
iMapSpeciesDels	FINAL_TYPE< SEQTYPE >
iMapSpeciesIns	FINAL_TYPE< SEQTYPE >
iMapSpeciesInsInfo	FINAL_TYPE< SEQTYPE >
iMapSpeciesMiss	FINAL_TYPE< SEQTYPE >
iMapSpeciesPos	FINAL_TYPE< SEQTYPE >
implicit_inc() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode)	ED4_base
ED4_text_terminal::in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode)	ED4_base
ED4_manager::in_border(AW_pos abs_x, AW_pos abs_y, ED4_movemode mode)	ED4_base
TreeNode::in_other_branch_than(const TreeNode *other) const	TreeNode	inline
AP_tree::in_other_branch_than(const TreeNode *other) const	TreeNode	inline
ARB_countedTree::in_other_branch_than(const TreeNode *other) const	TreeNode	inline
TreeNode::in_same_branch_as(const TreeNode *other) const	TreeNode	inline
AP_tree::in_same_branch_as(const TreeNode *other) const	TreeNode	inline
ARB_countedTree::in_same_branch_as(const TreeNode *other) const	TreeNode	inline
inc() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
inc_by(SINT count)	FINAL_TYPE< SEQTYPE >	inline
inc_combine_count()	AP_combinableSeq	inlineprotectedstatic
inc_to(SINT x) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
inc_to_avoid_overflow(SINT x) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
increment_at_commands(int width, int height)	AW_window
indent	XML_Node	protected
Indent() const	XML_Node	inline
indentation_per_level	FINAL_TYPE< SEQTYPE >
index	FINAL_TYPE< SEQTYPE >
index() const	FINAL_TYPE< SEQTYPE >	inline
index_of(const char *search_for) const	CharPtrArray
indexOf(const AP_tree_edge *e) const	FINAL_TYPE< SEQTYPE >	inline
IndexSet typedef	PS_BitSet
indicate_selected(AW_device *d, int gc) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
inform_about_delete(AP_tree *old)	AP_tree_root
init(AliView *aliview)	FINAL_TYPE< SEQTYPE >	inline
init() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
init(AW_root *root, const char *wid, const char *windowname)	FINAL_TYPE< SEQTYPE >
AWT_graphic_parsimony::init(AliView *aliview, AP_sequence *seq_prototype, bool link_to_database_, bool insert_delete_cbs)	AWT_graphic_tree
init_awars(AW_root *awr)	FINAL_TYPE< SEQTYPE >
init_click(const AW::Position &click, int max_distance, AW_bitset filteri)	FINAL_TYPE< SEQTYPE >
init_devices(AW_window *, AW_device *, AWT_canvas *scr) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
init_font(GLuint base, char *f)	FINAL_TYPE< SEQTYPE >
init_tree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
init_tree() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
initial_insert(AP_tree_nlen *new_brother, AP_pars_root *troot)	FINAL_TYPE< SEQTYPE >
initial_insert(AP_tree *new_brother, AP_tree_root *troot) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
initialise(const ArbProbe *pProbe, int nIndex)	FINAL_TYPE< SEQTYPE >
InitMainFont(char *f)	FINAL_TYPE< SEQTYPE >
InputFormat()	InputFormat	inline
insert(AP_tree_nlen *new_brother)	FINAL_TYPE< SEQTYPE >
insert(AP_tree *new_brother) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
insert_default_option(AW_label choice_label, const char *mnemonic, const char *var_value, const char *name_of_color=NULp)	AW_window
insert_default_option(AW_label choice_label, const char *mnemonic, int var_value, const char *name_of_color=NULp)	AW_window
insert_default_option(AW_label choice_label, const char *mnemonic, float var_value, const char *name_of_color=NULp)	AW_window
insert_default_toggle(AW_label toggle_label, const char *mnemonic, const char *var_value)	AW_window
insert_default_toggle(AW_label toggle_label, const char *mnemonic, int var_value)	AW_window
insert_default_toggle(AW_label toggle_label, const char *mnemonic, float var_value)	AW_window
insert_help_topic(const char *labeli, const char *mnemonic, const char *helpText, AW_active mask, const WindowCallback &cb)	AW_window
insert_help_topic(const char *labeli, const char *mnemonic, const char *helpText, AW_active mask, WindowCallbackSimple cb)	AW_window	inline
insert_member(ED4_base *new_member)	ED4_container
insert_menu_topic(const char *id, const char *name, const char *mnemonic, const char *help_text_, AW_active mask, const WindowCallback &wcb)	AW_window
insert_menu_topic(const char *id, const char *name, const char *mnemonic, const char *help_text_, AW_active mask, const CreateWindowCallback &cwcb)	AW_window	inline
insert_menu_topic(const char *id, const char *name, const char *mnemonic, const char *help_text_, AW_active mask, WindowCallbackSimple cb)	AW_window	inline
insert_menu_topic(const char *id, const char *name, const char *mnemonic, const char *help_text_, AW_active mask, CreateWindowCallbackSimple cb)	AW_window	inline
insert_option(AW_label choice_label, const char *mnemonic, const char *var_value, const char *name_of_color=NULp)	AW_window
insert_option(AW_label choice_label, const char *mnemonic, int var_value, const char *name_of_color=NULp)	AW_window
insert_option(AW_label choice_label, const char *mnemonic, float var_value, const char *name_of_color=NULp)	AW_window
insert_sub_menu(const char *name, const char *mnemonic, AW_active mask=AWM_ALL)	AW_window
insert_toggle(AW_label toggle_label, const char *mnemonic, const char *var_value)	AW_window
insert_toggle(AW_label toggle_label, const char *mnemonic, int var_value)	AW_window
insert_toggle(AW_label toggle_label, const char *mnemonic, float var_value)	AW_window
insertMapping(SpeciesID _id, const string &_name)	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::inside_consensus_manager() const	ED4_base	inline
ED4_text_terminal::inside_consensus_manager() const	ED4_base	inline
ED4_manager::inside_consensus_manager() const	ED4_base	inline
ED4_terminal::inside_SAI_manager() const	ED4_base	inline
ED4_text_terminal::inside_SAI_manager() const	ED4_base	inline
ED4_manager::inside_SAI_manager() const	ED4_base	inline
ED4_terminal::inside_species_seq_manager() const	ED4_base	inline
ED4_text_terminal::inside_species_seq_manager() const	ED4_base	inline
ED4_manager::inside_species_seq_manager() const	ED4_base	inline
install_group_changed_callback(const GraphicTreeCallback &gccb)	AWT_graphic_tree	inlinestatic
install_tree_changed_callback(const GraphicTreeCallback &gtcb)	AWT_graphic_tree
TreeNode::intree_distance_to(const TreeNode *other) const	TreeNode	inline
AP_tree::intree_distance_to(const TreeNode *other) const	TreeNode	inline
ARB_countedTree::intree_distance_to(const TreeNode *other) const	TreeNode	inline
invalidate()	SEC_oriented
invalidate_sub_angles() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
invalidate_sub_angles() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
PS_BitSet::invert()	PS_BitSet
PS_BitMap::invert()	PS_BitMap
AW_device::invisible(const AW::Position &pos, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::invisible(const AW::Position &pos, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
is3end() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::is_above_clip(double ypos) const	AW_clipable	inline
AW_simple_device::is_above_clip(double ypos) const	AW_clipable	inline
ED4_terminal::is_abstract_group_manager() const	ED4_base	inline
ED4_text_terminal::is_abstract_group_manager() const	ED4_base	inline
ED4_manager::is_abstract_group_manager() const	ED4_base	inline
is_active_plugin(const ShaderPlugin &plugin) const	ItemShader	inline
TreeNode::is_ancestor_of(const TreeNode *descendant) const	TreeNode	inline
AP_tree::is_ancestor_of(const TreeNode *descendant) const	TreeNode	inline
ARB_countedTree::is_ancestor_of(const TreeNode *descendant) const	TreeNode	inline
ED4_terminal::is_area_manager() const	ED4_base	inline
ED4_text_terminal::is_area_manager() const	ED4_base	inline
ED4_manager::is_area_manager() const	ED4_base	inline
AW_device::is_below_clip(double ypos) const	AW_clipable	inline
AW_simple_device::is_below_clip(double ypos) const	AW_clipable	inline
is_bound_to_species() const	AP_sequence	inline
is_box() const	AW_clicked_element	inline
ED4_terminal::is_bracket_terminal() const	ED4_base	inline
ED4_text_terminal::is_bracket_terminal() const	ED4_base	inline
ED4_manager::is_bracket_terminal() const	ED4_base	inline
ED4_terminal::is_child_of(ED4_manager *Parent)	ED4_base	inline
ED4_text_terminal::is_child_of(ED4_manager *Parent)	ED4_base	inline
ED4_manager::is_child_of(ED4_manager *Parent)	ED4_base	inline
TreeNode::is_clade() const	TreeNode	inline
AP_tree::is_clade() const	TreeNode	inline
ARB_countedTree::is_clade() const	TreeNode	inline
ED4_terminal::is_columnStat_terminal() const	ED4_base	inline
ED4_text_terminal::is_columnStat_terminal() const	ED4_base	inline
ED4_manager::is_columnStat_terminal() const	ED4_base	inline
ED4_terminal::is_consensus_manager() const	ED4_base	inline
ED4_text_terminal::is_consensus_manager() const	ED4_base	inline
ED4_manager::is_consensus_manager() const	ED4_base	inline
ED4_terminal::is_consensus_sequence_terminal() const	ED4_base	inline
ED4_text_terminal::is_consensus_sequence_terminal() const	ED4_base	inline
ED4_manager::is_consensus_sequence_terminal() const	ED4_base	inline
ED4_terminal::is_consensus_terminal() const	ED4_base	inline
ED4_text_terminal::is_consensus_terminal() const	ED4_base	inline
ED4_manager::is_consensus_terminal() const	ED4_base	inline
is_defined() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
is_defined() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
is_defined() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
ED4_terminal::is_device_manager() const	ED4_base	inline
ED4_text_terminal::is_device_manager() const	ED4_base	inline
ED4_manager::is_device_manager() const	ED4_base	inline
is_endings_segment()	FINAL_TYPE< SEQTYPE >	inline
is_expose_callback(AW_area area, AnyWinCB f)	AW_window
ED4_terminal::is_flag_header_terminal() const	ED4_base	inline
ED4_text_terminal::is_flag_header_terminal() const	ED4_base	inline
ED4_manager::is_flag_header_terminal() const	ED4_base	inline
ED4_terminal::is_flag_terminal() const	ED4_base	inline
ED4_text_terminal::is_flag_terminal() const	ED4_base	inline
ED4_manager::is_flag_terminal() const	ED4_base	inline
is_focus_callback(AnyWinCB f)	AW_window
is_folded_group() const	AP_tree	inline
ED4_terminal::is_group_manager() const	ED4_base	inline
ED4_text_terminal::is_group_manager() const	ED4_base	inline
ED4_manager::is_group_manager() const	ED4_base	inline
is_hidden() const	FINAL_TYPE< SEQTYPE >	inlinevirtual
is_highlighted() const	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::is_in_folded_group() const	ED4_base
ED4_text_terminal::is_in_folded_group() const	ED4_base
ED4_manager::is_in_folded_group() const	ED4_base
TreeNode::is_inner_node_with_remark() const	TreeNode	inline
AP_tree::is_inner_node_with_remark() const	TreeNode	inline
ARB_countedTree::is_inner_node_with_remark() const	TreeNode	inline
TreeNode::is_inside(const TreeNode *subtree) const	TreeNode	inline
AP_tree::is_inside(const TreeNode *subtree) const	TreeNode	inline
ARB_countedTree::is_inside(const TreeNode *subtree) const	TreeNode	inline
is_inside_folded_group() const	AP_tree
is_itemlist_member() const	FINAL_TYPE< SEQTYPE >	inline
TreeNode::is_keeled_group() const	TreeNode	inline
AP_tree::is_keeled_group() const	TreeNode	inline
ARB_countedTree::is_keeled_group() const	TreeNode	inline
TreeNode::is_leaf() const	TreeNode	inline
AP_tree::is_leaf() const	TreeNode	inline
ARB_countedTree::is_leaf() const	TreeNode	inline
AW_device::is_leftof_clip(double xpos) const	AW_clipable	inline
AW_simple_device::is_leftof_clip(double xpos) const	AW_clipable	inline
TreeNode::is_leftson() const	TreeNode	inline
AP_tree::is_leftson() const	TreeNode	inline
ARB_countedTree::is_leftson() const	TreeNode	inline
is_line() const	AW_clicked_element	inline
ED4_terminal::is_line_terminal() const	ED4_base	inline
ED4_text_terminal::is_line_terminal() const	ED4_base	inline
ED4_manager::is_line_terminal() const	ED4_base	inline
awt_viewport::is_linked_item() const	awt_mask_item	inline
awt_mask_item::is_linked_item() const	awt_mask_item	inline
is_local_mask() const	FINAL_TYPE< SEQTYPE >	inline
is_logically_zoomed()	AWT_graphic_tree	inline
AP_tree::is_lower_son() const	ARB_seqtree	inline
ARB_countedTree::is_lower_son() const	ARB_seqtree	inline
ED4_terminal::is_manager() const	ED4_base	inline
ED4_text_terminal::is_manager() const	ED4_base	inline
ED4_manager::is_manager() const	ED4_base	inline
ED4_terminal::is_multi_name_manager() const	ED4_base	inline
ED4_text_terminal::is_multi_name_manager() const	ED4_base	inline
ED4_manager::is_multi_name_manager() const	ED4_base	inline
ED4_terminal::is_multi_sequence_manager() const	ED4_base	inline
ED4_text_terminal::is_multi_sequence_manager() const	ED4_base	inline
ED4_manager::is_multi_sequence_manager() const	ED4_base	inline
ED4_terminal::is_multi_species_manager() const	ED4_base	inline
ED4_text_terminal::is_multi_species_manager() const	ED4_base	inline
ED4_manager::is_multi_species_manager() const	ED4_base	inline
ED4_terminal::is_name_manager() const	ED4_base	inline
ED4_text_terminal::is_name_manager() const	ED4_base	inline
ED4_manager::is_name_manager() const	ED4_base	inline
TreeNode::is_normal_group() const	TreeNode	inline
AP_tree::is_normal_group() const	TreeNode	inline
ARB_countedTree::is_normal_group() const	TreeNode	inline
ED4_terminal::is_orf_terminal() const	ED4_base	inline
ED4_text_terminal::is_orf_terminal() const	ED4_base	inline
ED4_manager::is_orf_terminal() const	ED4_base	inline
AW_device::is_outside_clip(AW::Position pos) const	AW_clipable	inline
AW_device::is_outside_clip(AW::Rectangle rect) const	AW_clipable	inline
AW_simple_device::is_outside_clip(AW::Position pos) const	AW_clipable	inline
AW_simple_device::is_outside_clip(AW::Rectangle rect) const	AW_clipable	inline
is_polygon() const	AW_clicked_element	inline
ED4_terminal::is_pure_text_terminal() const	ED4_base	inline
ED4_text_terminal::is_pure_text_terminal() const	ED4_base	inline
ED4_manager::is_pure_text_terminal() const	ED4_base	inline
is_resize_callback(AW_area area, AnyWinCB f)	AW_window
AW_device::is_rightof_clip(double xpos) const	AW_clipable	inline
AW_simple_device::is_rightof_clip(double xpos) const	AW_clipable	inline
TreeNode::is_rightson() const	TreeNode	inline
AP_tree::is_rightson() const	TreeNode	inline
ARB_countedTree::is_rightson() const	TreeNode	inline
ED4_terminal::is_root_group_manager() const	ED4_base	inline
ED4_text_terminal::is_root_group_manager() const	ED4_base	inline
ED4_manager::is_root_group_manager() const	ED4_base	inline
is_root_loop() const	FINAL_TYPE< SEQTYPE >
TreeNode::is_root_node() const	TreeNode	inline
AP_tree::is_root_node() const	TreeNode	inline
ARB_countedTree::is_root_node() const	TreeNode	inline
ED4_terminal::is_SAI_manager() const	ED4_base	inline
ED4_text_terminal::is_SAI_manager() const	ED4_base	inline
ED4_manager::is_SAI_manager() const	ED4_base	inline
ED4_terminal::is_SAI_terminal() const	ED4_base	inline
ED4_text_terminal::is_SAI_terminal() const	ED4_base	inline
ED4_manager::is_SAI_terminal() const	ED4_base	inline
ED4_terminal::is_sequence_info_terminal() const	ED4_base	inline
ED4_text_terminal::is_sequence_info_terminal() const	ED4_base	inline
ED4_manager::is_sequence_info_terminal() const	ED4_base	inline
ED4_terminal::is_sequence_manager() const	ED4_base	inline
ED4_text_terminal::is_sequence_manager() const	ED4_base	inline
ED4_manager::is_sequence_manager() const	ED4_base	inline
ED4_terminal::is_sequence_terminal() const	ED4_base	inline
ED4_text_terminal::is_sequence_terminal() const	ED4_base	inline
ED4_manager::is_sequence_terminal() const	ED4_base	inline
is_shown() const	AW_window
is_some_brother(const ParagraphTree *other) const	FINAL_TYPE< SEQTYPE >	inline
TreeNode::is_son_of(const TreeNode *Father) const	TreeNode	inline
AP_tree::is_son_of(const TreeNode *Father) const	TreeNode	inline
ARB_countedTree::is_son_of(const TreeNode *Father) const	TreeNode	inline
TreeNode::is_son_of_root() const	TreeNode	inline
AP_tree::is_son_of_root() const	TreeNode	inline
ARB_countedTree::is_son_of_root() const	TreeNode	inline
ED4_terminal::is_spacer_terminal() const	ED4_base	inline
ED4_text_terminal::is_spacer_terminal() const	ED4_base	inline
ED4_manager::is_spacer_terminal() const	ED4_base	inline
ED4_terminal::is_species_manager() const	ED4_base	inline
ED4_text_terminal::is_species_manager() const	ED4_base	inline
ED4_manager::is_species_manager() const	ED4_base	inline
ED4_terminal::is_species_name_terminal() const	ED4_base	inline
ED4_text_terminal::is_species_name_terminal() const	ED4_base	inline
ED4_manager::is_species_name_terminal() const	ED4_base	inline
ED4_terminal::is_species_seq_manager() const	ED4_base	inline
ED4_text_terminal::is_species_seq_manager() const	ED4_base	inline
ED4_manager::is_species_seq_manager() const	ED4_base	inline
ED4_terminal::is_species_seq_terminal() const	ED4_base	inline
ED4_text_terminal::is_species_seq_terminal() const	ED4_base	inline
ED4_manager::is_species_seq_terminal() const	ED4_base	inline
is_species_updated()	AP_tree_root
ED4_terminal::is_terminal() const	ED4_base	inline
ED4_text_terminal::is_terminal() const	ED4_base	inline
ED4_manager::is_terminal() const	ED4_base	inline
is_text() const	AW_clicked_element	inline
ED4_terminal::is_text_terminal() const	ED4_base	inline
ED4_text_terminal::is_text_terminal() const	ED4_base	inline
ED4_manager::is_text_terminal() const	ED4_base	inline
is_tree_updated()	AP_tree_root
AP_tree::is_upper_son() const	ARB_seqtree	inline
ARB_countedTree::is_upper_son() const	ARB_seqtree	inline
is_valid_between(size_t pos) const	AliData	inline
is_valid_part(size_t start, size_t count) const	AliData	inline
is_valid_pos(size_t pos) const	AliData	inline
awt_viewport::is_viewport() const	awt_mask_item	inline
awt_mask_item::is_viewport() const	awt_mask_item	inline
iShapeHelix	FINAL_TYPE< SEQTYPE >
iShapeNonHelix	FINAL_TYPE< SEQTYPE >
iShapeUnpairHelix	FINAL_TYPE< SEQTYPE >
IslandHopping class	FINAL_TYPE< SEQTYPE >	friend
IslandHopping()	FINAL_TYPE< SEQTYPE >	inline
IslandHoppingParameter(bool use_user_freqs_, double fT_, double fC_, double fA_, double fG_, double rTC_, double rTA_, double rTG_, double rCA_, double rCG_, double rAG_, double dist_, double supp_, double gapA_, double gapB_, double gapC_, double thres_)	FINAL_TYPE< SEQTYPE >
isMatched(const ArbStringList &rCladeList, bool &bPartialMatch, double dThreshold, double dCladeMarkedThreshold, double dCladePartiallyMarkedThreshold) const	FINAL_TYPE< SEQTYPE >
isMatched(const std::string &rName, double dThreshold) const	FINAL_TYPE< SEQTYPE >
isReadonly()	FINAL_TYPE< SEQTYPE >	inline
isRootsideFixpoint() const	FINAL_TYPE< SEQTYPE >	inline
iStartHelix	FINAL_TYPE< SEQTYPE >
item()	awt_linked_to_item	inline
ItemQueryKey(GBDATA *gb_main, const char *field_name)	FINAL_TYPE< SEQTYPE >	inline
ItemShader(const std::string &id_, const std::string &description_, ReshadeCallback rcb, int undefined_gc_)	ItemShader	inline
ItemShader_impl(AW_gc_manager *gcman_, const string &id_, const string &description_, const string &help_id_, ReshadeCallback rcb, int undef_gc)	FINAL_TYPE< SEQTYPE >	inline
iterate() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
journal	FINAL_TYPE< SEQTYPE >
justify_branch_lenghs(GBDATA *gb_main)	AP_tree
TreeNode::keeledStateInfo() const	TreeNode	inline
AP_tree::keeledStateInfo() const	TreeNode	inline
ARB_countedTree::keeledStateInfo() const	TreeNode	inline
TreeNode::keelsDownGroup(const TreeNode *toSon) const	TreeNode	inline
AP_tree::keelsDownGroup(const TreeNode *toSon) const	TreeNode	inline
ARB_countedTree::keelsDownGroup(const TreeNode *toSon) const	TreeNode	inline
TreeNode::keelTarget()	TreeNode	inline
TreeNode::keelTarget() const	TreeNode	inline
AP_tree::keelTarget()	TreeNode	inline
AP_tree::keelTarget() const	TreeNode	inline
ARB_countedTree::keelTarget()	TreeNode	inline
ARB_countedTree::keelTarget() const	TreeNode	inline
keywords	FINAL_TYPE< SEQTYPE >
ED4_terminal::kill_object()	ED4_terminal
ED4_text_terminal::kill_object()	ED4_terminal
AW_window::label(const char *label)	AW_window
label_length(int length)	AW_window
label_widget(void *wgt, AW_label str, char *mnemonic=NULp, int width=0, int alignment=0)	AW_window
last_remembered_frame() const	FINAL_TYPE< SEQTYPE >	inline
last_saved	FINAL_TYPE< SEQTYPE >	mutable
LatestSon()	FINAL_TYPE< SEQTYPE >	inline
lazy_load_sequence() const	AP_sequence	inline
leftAttachAbspos() const	FINAL_TYPE< SEQTYPE >	inline
leftAttachPoint() const	FINAL_TYPE< SEQTYPE >	inline
TreeNode::leftlen	TreeNode
AP_tree::leftlen	TreeNode
ARB_countedTree::leftlen	TreeNode
TreeNode::leftson	TreeNode
AP_tree::leftson	TreeNode
ARB_countedTree::leftson	TreeNode
length() const	NamedCommand	inline
AW_device::line(int gc, const AW::LineVector &Line, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::line(int gc, const AW::Position &pos1, const AW::Position &pos2, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::line(int gc, AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::line(int gc, const AW::LineVector &Line, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::line(int gc, const AW::Position &pos1, const AW::Position &pos2, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::line(int gc, AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
line_number() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
LinearTuple(float val_)	FINAL_TYPE< SEQTYPE >	inline
lineError(const string &msg) const	LineReader
lineError(const char *msg) const	LineReader	inline
LineReader()	LineReader	inline
link_to(GBDATA *gb_new_item) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
link_to(GBDATA *gb_new_item) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
linkAllEdges(AP_tree_edge *edge1, AP_tree_edge *edge2, AP_tree_edge *edge3)	FINAL_TYPE< SEQTYPE >
AP_tree_root::linkToDB(int *zombies, int *duplicates) __ATTR__USERESULT	ARB_seqtree_root
ARB_seqtree_root::linkToDB(int *zombies, int *duplicates) __ATTR__USERESULT	ARB_seqtree_root
load(PS_FileBuffer *_file) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
load(PS_FileBuffer *_file) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
load()	FINAL_TYPE< SEQTYPE >	inline
PS_BitSet::load(PS_FileBuffer *_file, const long _fill_index)	PS_BitSet
load_from_DB(GBDATA *gb_main, const char *name) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
load_or_reset_config_cb(const char *cfgstr)	FINAL_TYPE< SEQTYPE >
load_or_reset_config_cb(const char *cfgstr, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
load_subtree_info()	AP_tree
load_xfig(const char *file, bool resize=true)	AW_window
loadFromDB(const char *name) FINAL_OVERRIDE	AP_tree_root	virtual
LoadGLTextures()	FINAL_TYPE< SEQTYPE >
local_id(const char *id) const	AW_window
locate_selected_group(AP_tree *in_subtree)	AWT_graphic_tree	inline
lock() const	ArbRefCount	inline
locus	FINAL_TYPE< SEQTYPE >
locus_contains_date() const	FINAL_TYPE< SEQTYPE >	inline
Macke()	FINAL_TYPE< SEQTYPE >	inline
make(const char *config)	FINAL_TYPE< SEQTYPE >	static
make(const char *config)	FINAL_TYPE< SEQTYPE >	static
SaiOperator::make(SaiOperatorType type, const char *config)	SaiOperator	static
ValueTuple::make(float f)	ValueTuple	static
ValueTuple::make(float f1, float f2)	ValueTuple	static
ValueTuple::make(float f1, float f2, float f3)	ValueTuple	static
makeNode() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
makeNode() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
makeNode() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
makeNode() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
makeWindowPopper(const CreateWindowCallback &cwcb)	AW_window	inlinestatic
makeWindowReplacer(const CreateWindowCallback &cwcb)	AW_window	inlinestatic
map_species2tip(Species2Tip &mapping)	FINAL_TYPE< SEQTYPE >
mark_angle_absolute()	SEC_oriented	inline
mark_deep_leafs(int min_depth, double min_rootdist, int &found_max_depth, double &found_max_rootdist)	AP_tree
mark_degenerated_branches(double degeneration_factor)	AP_tree
mark_duplicates()	AP_tree
mark_long_branches(double min_rel_diff, double min_abs_diff, double &found_max_abs_diff)	AP_tree
mark_sequence_set(bool is_set)	AP_sequence	inlineprotected
mark_species_in_rest_of_tree(AP_tree *at, int mark)	AWT_graphic_tree
mark_species_in_tree(AP_tree *at, int mark)	AWT_graphic_tree
mark_species_in_tree_that(AP_tree *at, int mark, bool(*condition)(GBDATA *, void *), void *cd)	AWT_graphic_tree
AP_tree::mark_subtree()	ARB_seqtree
ARB_countedTree::mark_subtree()	ARB_seqtree
TreeNode::markAsLeaf()	TreeNode	inline
AP_tree::markAsLeaf()	TreeNode	inline
ARB_countedTree::markAsLeaf()	TreeNode	inline
MarkerDisplay(int numMarkers_)	MarkerDisplay	inline
mask_global() const	FINAL_TYPE< SEQTYPE >	inline
mask_global()	FINAL_TYPE< SEQTYPE >	inline
matches(const char *code) const OVERRIDE	NamedCommand	inlinevirtual
max_columns(GBDATA *gb_main) const	FINAL_TYPE< SEQTYPE >
max_index	PS_BitSet	protected
max_row	PS_BitMap	protected
maxSize() const	SEC_constrainted	inline
may_be_recollected() const	FINAL_TYPE< SEQTYPE >	inline
member(ED4_index i) const	ED4_container	inline
members() const	ED4_container	inline
members_ok() const	ED4_container
memop enum name	AliData
memsize() const	AliData	inline
merge(const char *_other_db_name)	FINAL_TYPE< SEQTYPE >
mergeWith(SEC_segment *other, SEC_loop *target_loop)	FINAL_TYPE< SEQTYPE >
message(char *title, int ms)	AW_window
minSize() const	SEC_constrainted	inline
mix(float my_ratio, const ValueTuple &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
mix(float my_ratio, const ValueTuple &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
mix(float my_ratio, const ValueTuple &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
mouseX	FINAL_TYPE< SEQTYPE >
mouseY	FINAL_TYPE< SEQTYPE >
move(int from, int to)	CharPtrArray
move_group_to(AP_tree *new_group) __ATTR__USERESULT	AP_tree
move_member(ED4_index old_pos, ED4_index new_pos)	ED4_container
move_region(AW_pos src_x, AW_pos src_y, AW_pos width, AW_pos height, AW_pos dest_x, AW_pos dest_y)	FINAL_TYPE< SEQTYPE >	virtual
move_requested_by_child(ED4_move_info *moveinfo)	ED4_manager
move_requested_by_parent(ED4_move_info *mi)	ED4_manager
moveNextTo(AP_tree_nlen *new_brother, AP_FLOAT rel_pos)	FINAL_TYPE< SEQTYPE >
moveNextTo(AP_tree *node, AP_FLOAT rel_pos) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
moveTo(AP_tree_edge *e)	FINAL_TYPE< SEQTYPE >	inline
MultiFileReader(const CharPtrArray &files_)	FINAL_TYPE< SEQTYPE >
TreeNode::multifurcate()	TreeNode
AP_tree::multifurcate()	TreeNode
ARB_countedTree::multifurcate()	TreeNode
TreeNode::multifurcate_whole_tree(const multifurc_limits &below)	TreeNode
AP_tree::multifurcate_whole_tree(const multifurc_limits &below)	TreeNode
ARB_countedTree::multifurcate_whole_tree(const multifurc_limits &below)	TreeNode
mutations_if_combined_with(const AP_combinableSeq *other) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
mutations_if_combined_with(const AP_combinableSeq *other) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
name	FINAL_TYPE< SEQTYPE >
Writer::name() const =0	Writer	pure virtual
NamedCommand(const char *cmd)	NamedCommand	inline
nbk	FINAL_TYPE< SEQTYPE >
NDS_Labeler(NDS_Type type_)	FINAL_TYPE< SEQTYPE >	explicit
negate()	QueryKey	inline
AW_device::new_gc(int gc)	AW_stylable
AW_simple_device::new_gc(int gc)	AW_stylable
QueryKey::next() const	QueryKey	inline
SEC_base_part::next()	SEC_base_part	inline
SEC_base_part::next() const	SEC_base_part	inline
nextEdge(const AP_tree_edge *afterThatEdge=NULp) const	FINAL_TYPE< SEQTYPE >
nextListMember() const	FINAL_TYPE< SEQTYPE >	inline
nextListMemberAfter(const ParagraphTree &previous)	FINAL_TYPE< SEQTYPE >	inline
nn_interchange(AP_FLOAT parsimony, AP_BL_MODE mode)	FINAL_TYPE< SEQTYPE >
nn_interchange_rec(EdgeSpec whichEdges, AP_BL_MODE mode)	FINAL_TYPE< SEQTYPE >
Noncopyable()	Noncopyable	inlineprivate
noncounting_combine_seq(const AP_combinableSeq *lefts, const AP_combinableSeq *rights)	AP_combinableSeq	inline
normalizeClusters(vector< size_t > clusters)	FINAL_TYPE< SEQTYPE >
notify_synchronized(GBDATA *gb_main) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
nt_item_type_species_selector()	FINAL_TYPE< SEQTYPE >	inline
number_of_timed_title_changes	AW_window
ObjectSize	FINAL_TYPE< SEQTYPE >
Writer::ok() const =0	Writer	pure virtual
Writer::ok() const	Writer	inline
CharPtrArray::ok() const	CharPtrArray	inlineprotected
on_hide(const WindowCallback &call_on_hide)	AW_window
on_hide(WindowCallbackSimple call_on_hide)	AW_window	inline
open(const char *path) __ATTR__USERESULT	FINAL_TYPE< SEQTYPE >
open(FILE *out) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
opened	XML_Node	protected
Opened() const	XML_Node	inline
OpenGLGraphics()	FINAL_TYPE< SEQTYPE >
operate_on_mem(void *mem, size_t start, size_t count, memop op) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
operator<<(std::ostream &, const AP_tree_nlen *)	FINAL_TYPE< SEQTYPE >	friend
operator=(const awt_input_mask_descriptor &other)	FINAL_TYPE< SEQTYPE >
operator==(const AW_clicked_element &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
operator[](int i) const	CharPtrArray	inline
optimize_space()	CharPtrArray	inline
organism	FINAL_TYPE< SEQTYPE >
orientationChanged() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
orientationChanged() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
os	FINAL_TYPE< SEQTYPE >
otherLoop(const SEC_loop *loop) const	FINAL_TYPE< SEQTYPE >
Writer::out(char ch)=0	Writer	pure virtual
Writer::out(const char *text)	Writer	inlinevirtual
Out()	FINAL_TYPE< SEQTYPE >	inline
outf(const char *format,...) __ATTR__FORMAT_MEMBER(1)	Writer	virtual
outsideLoop() const	FINAL_TYPE< SEQTYPE >
overlay_color_groups() const	ItemShader	inline
overlay_marked() const	ItemShader	inline
OVERRIDE_SEQ_ACCESSORS(AP_combinableSeq, ARB_countedTree)	FINAL_TYPE< SEQTYPE >
OVERRIDE_SEQ_ACCESSORS(AP_combinableSeq, AP_tree)	FINAL_TYPE< SEQTYPE >
owner()	ED4_container	inline
owner() const	ED4_container	inline
p_w	AW_window
paint(AW_device *device)	FINAL_TYPE< SEQTYPE >
paint(AW_device *device, SEC_helix_strand *previous_strand_pointer)	FINAL_TYPE< SEQTYPE >
paint(AW_device *device)	FINAL_TYPE< SEQTYPE >
paint_constraints(AW_device *device)	FINAL_TYPE< SEQTYPE >
paint_constraints(AW_device *device)	FINAL_TYPE< SEQTYPE >
paint_strands(AW_device *device, const Vector &strand_dir, const double &strand_length)	FINAL_TYPE< SEQTYPE >
SEC_base::parent()	SEC_oriented	inline
SEC_base::parent() const	SEC_oriented	inline
SEC_base_part::parent()	SEC_base_part	inline
SEC_base_part::parent() const	SEC_base_part	inline
TreeNode::parse_bootstrap(double &bootstrap) const	TreeNode	inline
AP_tree::parse_bootstrap(double &bootstrap) const	TreeNode	inline
ARB_countedTree::parse_bootstrap(double &bootstrap) const	TreeNode	inline
parsimony_rec(char *mutPerSite=NULp)	FINAL_TYPE< SEQTYPE >
partial_match(const AP_combinableSeq *part, long *overlap, long *penalty) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
partial_match(const AP_combinableSeq *part, long *overlap, long *penalty) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
partiallyMarked	AWT_graphic_tree
pc() const	Command	inline
permit_flag_updates	FINAL_TYPE< SEQTYPE >
phase_changed_cb(AW_root *awr)	FINAL_TYPE< SEQTYPE >	inline
phase_changed_cb(AW_root *awr, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
phaser	ItemShader	protected
picture	AW_window
PlanarTuple(float val1_, float val2_)	FINAL_TYPE< SEQTYPE >	inline
pointsToOutside() const	FINAL_TYPE< SEQTYPE >	inline
pointsToRoot() const	FINAL_TYPE< SEQTYPE >	inline
AW_device::polygon(int gc, AW::FillStyle filled, int npoints, const AW_pos *points, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::polygon(int gc, AW::FillStyle filled, int npos, const AW::Position *pos, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::polygon(int gc, AW::FillStyle filled, int npoints, const AW_pos *points, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_simple_device::polygon(int gc, AW::FillStyle filled, int npos, const AW::Position *pos, AW_bitset filteri=AW_ALL_DEVICES_SCALED)	AW_device	inline
AW_device::pop_clip_scale()	AW_device
AW_simple_device::pop_clip_scale()	AW_device
popup_config_window(AW_root *awr) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
predecessor(ParagraphTree *before_this)	FINAL_TYPE< SEQTYPE >	inline
TreeRoot::predelete()	TreeRoot	inlineprotected
AP_tree_root::predelete()	TreeRoot	inlineprotected
ARB_seqtree_root::predelete()	TreeRoot	inlineprotected
PREFER_LINE enum value	FINAL_TYPE< SEQTYPE >
PREFER_NEARER enum value	FINAL_TYPE< SEQTYPE >
PREFER_TEXT enum value	FINAL_TYPE< SEQTYPE >
AWT_graphic_parsimony::PREPARE_MARK_NONFINAL_CLASS(AWT_graphic_tree)	AWT_graphic_tree
AP_tree::PREPARE_MARK_NONFINAL_CLASS(AP_tree)	AP_tree
AP_tree_root::PREPARE_MARK_NONFINAL_CLASS(AP_tree_root)	AP_tree_root
AP_tree_root::ARB_seqtree_root::PREPARE_MARK_NONFINAL_CLASS(ARB_seqtree_root)	ARB_seqtree_root
ARB_seqtree_root::PREPARE_MARK_NONFINAL_CLASS(ARB_seqtree_root)	ARB_seqtree_root
prepare_paint(SEC_helix_strand *previous_strand_pointer, double &gamma, double &eta, double &radius, int &base_count, double &angle_step)	FINAL_TYPE< SEQTYPE >
print(FILE *out) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
print(FILE *out) const	FINAL_TYPE< SEQTYPE >
PS_BitSet::print(FILE *out, const bool _header, const long _fill_index)	PS_BitSet
print_string(GLuint base, char *s)	FINAL_TYPE< SEQTYPE >
printGNUplot(const char *_title, char *_buffer, PS_FileBuffer *_file) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
PrintString(float x, float y, float z, char *s, void *font)	FINAL_TYPE< SEQTYPE >
probe() const	FINAL_TYPE< SEQTYPE >	inline
PS_BitMap(const bool _bias, const long _max_row, const long _capacity)	PS_BitMap	inlineprotected
PS_BitMap(const bool _bias, const long _capacity)	PS_BitMap	inlineexplicit
PS_BitMap(PS_FileBuffer *_file)	PS_BitMap	inlineexplicit
PS_BitMap_Counted(PS_FileBuffer *_file)	FINAL_TYPE< SEQTYPE >	inlineexplicit
PS_BitMap_Counted(const bool _bias, const long _capacity)	FINAL_TYPE< SEQTYPE >	inlineexplicit
PS_BitMap_Fast(const bool _bias, const long _capacity)	FINAL_TYPE< SEQTYPE >	inlineexplicit
PS_BitSet(const bool _bias, const long _max_index, const long _capacity)	PS_BitSet	inlineprotected
PS_BitSet(const bool _bias, const long _capacity)	PS_BitSet	inlineexplicit
PS_BitSet(PS_FileBuffer *_file, const long _fill_index=-1)	PS_BitSet	inlineexplicit
PS_BitSet_Fast(PS_FileBuffer *_file, const long _fill_index=-1)	FINAL_TYPE< SEQTYPE >	inlineexplicit
PS_BitSet_Fast(bool _bias, long _capacity)	FINAL_TYPE< SEQTYPE >	inlineexplicit
PS_Database(const char *_name, bool _readonly)	FINAL_TYPE< SEQTYPE >	inline
AW_device::push_clip_scale()	AW_device
AW_simple_device::push_clip_scale()	AW_device
put(char *elem)	FINAL_TYPE< SEQTYPE >	inline
put_before(int insert_before, char *elem)	FINAL_TYPE< SEQTYPE >	inline
QueryKey(query_key_type type_)	QueryKey	inline
range_offset(const Phaser &phaser) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
range_offset(const Phaser &phaser) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
range_offset(const Phaser &phaser) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
rates	AP_tree_root
read(std::istream &in, int version, double &old_angle_in)	FINAL_TYPE< SEQTYPE >
read(SEC_loop *loop_, std::istream &in, int version)	FINAL_TYPE< SEQTYPE >
read(SEC_loop *loop_, std::istream &in, int version)	FINAL_TYPE< SEQTYPE >
read(SEC_helix_strand *rootside_strand, std::istream &in, int version, double loop_angle)	FINAL_TYPE< SEQTYPE >
read_cache(const AP_tree *at) const	MarkerDisplay	inline
read_data_from_db(char **data, char **x_string) const	FINAL_TYPE< SEQTYPE >
read_tree_settings() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
readable_type() const	FINAL_TYPE< SEQTYPE >	inline
READONLY	FINAL_TYPE< SEQTYPE >	static
AW_device::ready_to_draw(int gc)	AW_device
AW_simple_device::ready_to_draw(int gc)	AW_device
rebuild_consensi(ED4_base *start_species, ED4_update_flag update_flag)	ED4_manager
recalc_marked_from_sons()	FINAL_TYPE< SEQTYPE >	inline
recalc_marked_from_sons_and_forward_upwards()	FINAL_TYPE< SEQTYPE >	inline
recalc_pos_atShow(AW_PosRecalc pr)	AW_window
recalc_size_atShow(enum AW_SizeRecalc sr)	AW_window
recalcCounters()	FINAL_TYPE< SEQTYPE >
recompute_and_write_folding()	AP_tree
AW_device::reduce_bottom_clip_border(int bottom)	AW_clipable
AW_simple_device::reduce_bottom_clip_border(int bottom)	AW_clipable
AW_device::reduce_left_clip_border(int left)	AW_clipable
AW_simple_device::reduce_left_clip_border(int left)	AW_clipable
AW_device::reduce_right_clip_border(int right)	AW_clipable
AW_simple_device::reduce_right_clip_border(int right)	AW_clipable
AW_device::reduce_top_clip_border(int top)	AW_clipable
AW_simple_device::reduce_top_clip_border(int top)	AW_clipable
AW_device::reduceClipBorders(int top, int bottom, int left, int right)	AW_clipable
AW_simple_device::reduceClipBorders(int top, int bottom, int left, int right)	AW_clipable
refresh_flag_ok()	ED4_manager
refresh_option_menu(AW_option_menu_struct *)	AW_window
refresh_requested_by_child()	ED4_manager
refresh_toggle_field(int toggle_field_number)	AW_window
register_plugin(ShaderPluginPtr plugin) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
reinit() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
reinit() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
reinit() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
reinit(const char *_name, bool _readonly)	FINAL_TYPE< SEQTYPE >
RefContainer< GenbankRef >::reinit_refs()	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::reinit_refs()	RefContainer< Emblref >	inline
relative_position_in(const ARB_countedTree *upgroup) const	ARB_countedTree
relink() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
relink() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
relink()	FINAL_TYPE< SEQTYPE >	inlinevirtual
relink_tree(GBDATA *gb_main, void(*relinker)(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash), GB_HASH *organism_hash)	AP_tree
reload_on_reinit() const	FINAL_TYPE< SEQTYPE >	inline
rememberState(AP_STACK_MODE, Level frame_level)	FINAL_TYPE< SEQTYPE >
remove(int i)	CharPtrArray
REMOVE() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
remove_awar_callbacks(AW_root *root, const RootCallback &cb) const	awt_item_type_selector
remove_awarItem_callbacks()	awt_mask_awar_item	protected
TreeNode::remove_bootstrap()	TreeNode
AP_tree::remove_bootstrap()	TreeNode
ARB_countedTree::remove_bootstrap()	TreeNode
ED4_terminal::remove_callbacks() FINAL_OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::remove_callbacks() FINAL_OVERRIDE	ED4_terminal	virtual
ED4_manager::remove_callbacks() OVERRIDE	ED4_manager	virtual
remove_db_callbacks()	awt_linked_to_item	protectedvirtual
remove_delete_callback(const ED4_managerCallback &cb)	ED4_manager	inline
remove_leafs(AWT_RemoveType awt_remove_type)	AP_tree_root
remove_member(ED4_base *member)	ED4_container
awt_viewport::remove_name()	awt_mask_item
awt_mask_item::remove_name()	awt_mask_item
TreeNode::remove_remark()	TreeNode	inline
AP_tree::remove_remark()	TreeNode	inline
ARB_countedTree::remove_remark()	TreeNode	inline
remove_sequence_changed_cb(const ED4_species_managerCallback &cb)	FINAL_TYPE< SEQTYPE >	inline
remove_son(XML_Node *son_) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
TreeNode::reorder_tree(TreeOrder mode)	TreeNode
AP_tree::reorder_tree(TreeOrder mode)	TreeNode
ARB_countedTree::reorder_tree(TreeOrder mode)	TreeNode
reorderTree(TreeOrder mode)	AWT_graphic_tree
repeated(char ch, int repeat)	Writer	inline
replace(int i, char *elem)	FINAL_TYPE< SEQTYPE >	inline
AP_tree::replace_seq(AP_sequence *sequence)	ARB_seqtree	protected
ARB_countedTree::replace_seq(AP_sequence *sequence)	ARB_seqtree	protected
ED4_terminal::request_refresh(int clear=1) FINAL_OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::request_refresh(int clear=1) FINAL_OVERRIDE	ED4_terminal	virtual
ED4_manager::request_refresh(int clear=1) FINAL_OVERRIDE	ED4_manager	virtual
ED4_terminal::request_resize()	ED4_base	inline
ED4_text_terminal::request_resize()	ED4_base	inline
ED4_manager::request_resize()	ED4_base	inline
ED4_terminal::request_resize_of_linked()	ED4_base
ED4_text_terminal::request_resize_of_linked()	ED4_base
ED4_manager::request_resize_of_linked()	ED4_base
request_update(SEC_update_request req)	FINAL_TYPE< SEQTYPE >	inline
reserve(const long _capacity) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
reserve(const long _capacity) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
reserve(const long _capacity) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
CharPtrArray::reserve(size_t forElems)	CharPtrArray	inline
reserve_space(size_t forElems, bool alloc_ahead)	CharPtrArray	inlineprotected
reset() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
AW_device::reset()	AW_device
AW_simple_device::reset()	AW_device
LineReader::reset()	LineReader	inlineprotected
reset_angle()	AP_tree	inline
reset_angles() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
reset_angles() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
TreeNode::reset_branchlengths()	TreeNode
AP_tree::reset_branchlengths()	TreeNode
ARB_countedTree::reset_branchlengths()	TreeNode
reset_layout(const char *YYYYMMDD)	AW_window
TreeNode::reset_length_and_bootstrap()	TreeNode	inline
AP_tree::reset_length_and_bootstrap()	TreeNode	inline
ARB_countedTree::reset_length_and_bootstrap()	TreeNode	inline
reset_linewidth()	AP_tree	inline
reset_phasing_cb(AW_root *awr) const	FINAL_TYPE< SEQTYPE >	inline
reset_phasing_cb(AW_window *aww, const ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
reset_scrolled_picture_size()	AW_window
AW_device::reset_style()	AW_stylable
AW_simple_device::reset_style()	AW_stylable
reset_subtree_angles()	AP_tree
reset_subtree_layout()	AP_tree
reset_subtree_linewidths()	AP_tree
reset_subtree_spreads()	AP_tree
resize(int newsize)	CharPtrArray	inline
ED4_terminal::resize_dynamic()	ED4_base	inline
ED4_text_terminal::resize_dynamic()	ED4_base	inline
ED4_manager::resize_dynamic()	ED4_base	inline
RefContainer< GenbankRef >::resize_refs(int new_size)	RefContainer< GenbankRef >	inline
RefContainer< Emblref >::resize_refs(int new_size)	RefContainer< Emblref >	inline
resize_requested_by_child()	ED4_manager	inline
ED4_terminal::resize_requested_by_link(ED4_base *link)	ED4_base	inline
ED4_text_terminal::resize_requested_by_link(ED4_base *link)	ED4_base	inline
ED4_manager::resize_requested_by_link(ED4_base *link)	ED4_base	inline
resize_requested_children() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
ED4_terminal::resolve_pointer_to_char_pntr(int *str_len=NULp) const FINAL_OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::resolve_pointer_to_char_pntr(int *str_len=NULp) const FINAL_OVERRIDE	ED4_terminal	virtual
ED4_terminal::resolve_pointer_to_string_copy(int *str_len=NULp) const FINAL_OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::resolve_pointer_to_string_copy(int *str_len=NULp) const FINAL_OVERRIDE	ED4_terminal	virtual
ResourceStack::destroy_edges()	FINAL_TYPE< SEQTYPE >	friend
ResourceStack::destroy_nodes()	FINAL_TYPE< SEQTYPE >	friend
rest_tree_has_marks(AP_tree *at)	AWT_graphic_tree
restore(NodeState &state)	FINAL_TYPE< SEQTYPE >
restore_at_from(const AW_at_storage &stored)	AW_window	inline
restore_nondestructive(const NodeState &state)	FINAL_TYPE< SEQTYPE >
resultMap() const	FINAL_TYPE< SEQTYPE >	inline
retrieve_marker_state(const char *speciesName, NodeMarkers &node) OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
reverse_mix(float other_ratio, const LinearTuple &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
reverse_mix(float other_ratio, const PlanarTuple &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
reverse_mix(float other_ratio, const SpatialTuple &other) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
ValueTuple::reverse_mix(float, const class NoTuple &) const	ValueTuple	inlinevirtual
ValueTuple::reverse_mix(float, const class LinearTuple &) const	ValueTuple	inlinevirtual
ValueTuple::reverse_mix(float, const class PlanarTuple &) const	ValueTuple	inlinevirtual
ValueTuple::reverse_mix(float, const class SpatialTuple &) const	ValueTuple	inlinevirtual
revertToPreviousState(Level curr_frameLevel, bool &rootPopped)	FINAL_TYPE< SEQTYPE >
rightAttachAbspos() const	FINAL_TYPE< SEQTYPE >	inline
rightAttachPoint() const	FINAL_TYPE< SEQTYPE >	inline
TreeNode::rightlen	TreeNode
AP_tree::rightlen	TreeNode
ARB_countedTree::rightlen	TreeNode
TreeNode::rightson	TreeNode
AP_tree::rightson	TreeNode
ARB_countedTree::rightson	TreeNode
rna	FINAL_TYPE< SEQTYPE >
rna_or_dna	FINAL_TYPE< SEQTYPE >
TreeNode::root_distance() const	TreeNode	inline
AP_tree::root_distance() const	TreeNode	inline
ARB_countedTree::root_distance() const	TreeNode	inline
rootsideLoop() const	FINAL_TYPE< SEQTYPE >
AW_device::rotate(AW_pos angle)	AW_zoomable
AW_simple_device::rotate(AW_pos angle)	AW_zoomable
TreeNode::rotate_subtree()	TreeNode
AP_tree::rotate_subtree()	TreeNode
ARB_countedTree::rotate_subtree()	TreeNode
ED4_terminal::route_down_hierarchy(const ED4_route_cb &cb)	ED4_base	virtual
ED4_manager::route_down_hierarchy(const ED4_route_cb &cb) FINAL_OVERRIDE	ED4_manager	virtual
AW_device::rtransform(const AW::Vector &vec) const	AW_zoomable	inline
AW_device::rtransform(const AW::Position &pos) const	AW_zoomable	inline
AW_device::rtransform(const AW::LineVector &lvec) const	AW_zoomable	inline
AW_device::rtransform(const AW::Rectangle &rect) const	AW_zoomable	inline
AW_device::rtransform(AW_pos x, AW_pos y, AW_pos &xout, AW_pos &yout) const	AW_zoomable	inline
AW_simple_device::rtransform(const AW::Vector &vec) const	AW_zoomable	inline
AW_simple_device::rtransform(const AW::Position &pos) const	AW_zoomable	inline
AW_simple_device::rtransform(const AW::LineVector &lvec) const	AW_zoomable	inline
AW_simple_device::rtransform(const AW::Rectangle &rect) const	AW_zoomable	inline
AW_simple_device::rtransform(AW_pos x, AW_pos y, AW_pos &xout, AW_pos &yout) const	AW_zoomable	inline
AW_device::rtransform_pixelsize(int pixelsize) const	AW_zoomable	inline
AW_simple_device::rtransform_pixelsize(int pixelsize) const	AW_zoomable	inline
AW_device::rtransform_size(const double &size) const	AW_zoomable	inline
AW_simple_device::rtransform_size(const double &size) const	AW_zoomable	inline
ruler_awar(const char *name)	AWT_graphic_tree
run_focus_callback()	AW_window
run_popup_callbacks()	AW_window
safe_remove(int i)	CharPtrArray	inline
SaiMatrixTranslator(SaiOperatorPtr Default)	FINAL_TYPE< SEQTYPE >	inline
SaiOperator(SaiOperatorType type_)	SaiOperator	inline
SaiTranslator(char default_translation)	FINAL_TYPE< SEQTYPE >	inline
save()	FINAL_TYPE< SEQTYPE >	inline
save(std::ostream &out, int indent, const XString &x_string)	FINAL_TYPE< SEQTYPE >
save(std::ostream &out, int indent, const XString &x_string)	FINAL_TYPE< SEQTYPE >
save(std::ostream &out, int indent, const XString &x_string)	FINAL_TYPE< SEQTYPE >
PS_BitSet::save(PS_FileBuffer *_file)	PS_BitSet
PS_BitMap::save(PS_FileBuffer *_file)	PS_BitMap
save_to_DB(GBDATA *gb_main, const char *name) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
saveSAI(GBDATA *gb_main, vector< size_t > clusters, double threshold)	FINAL_TYPE< SEQTYPE >
saveTo(const char *_filename)	FINAL_TYPE< SEQTYPE >	inline
saveToDB() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
TreeNode::scale_branchlengths(double factor)	TreeNode
AP_tree::scale_branchlengths(double factor)	TreeNode
ARB_countedTree::scale_branchlengths(double factor)	TreeNode
ScreenToWinCoordinates(int x, int y, GLdouble *winPos)	FINAL_TYPE< SEQTYPE >
screenXmax	FINAL_TYPE< SEQTYPE >
screenYmax	FINAL_TYPE< SEQTYPE >
ED4_terminal::scroll_into_view(ED4_window *ed4w)	ED4_terminal
ED4_text_terminal::scroll_into_view(ED4_window *ed4w)	ED4_terminal
ED4_terminal::search_ID(const char *id) OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::search_ID(const char *id) OVERRIDE	ED4_terminal	virtual
ED4_manager::search_ID(const char *id) FINAL_OVERRIDE	ED4_manager	virtual
search_member(ED4_extension *location, ED4_properties prop)	ED4_container
search_spec_child_rek(ED4_level level)	ED4_manager
search_target_species(ED4_extension *location, ED4_properties prop, ED4_base **found_member, ED4_level return_level)	ED4_container
SEC_base(SEC_root *Root)	SEC_base	inline
SEC_base_part()	SEC_base_part	inline
SEC_constrainted()	SEC_constrainted	inline
SEC_graphic(AW_root *aw_root, GBDATA *gb_main)	FINAL_TYPE< SEQTYPE >
SEC_helix class	FINAL_TYPE< SEQTYPE >	friend
SEC_helix(SEC_root *root, SEC_helix_strand *to_root, SEC_helix_strand *from_root)	FINAL_TYPE< SEQTYPE >
SEC_helix_strand()	FINAL_TYPE< SEQTYPE >
SEC_loop(SEC_root *root_)	FINAL_TYPE< SEQTYPE >
SEC_oriented()	SEC_oriented	inline
sec_root	FINAL_TYPE< SEQTYPE >
SEC_segment()	FINAL_TYPE< SEQTYPE >
Section(string name_, SectionType type_, size_t lineno_)	FINAL_TYPE< SEQTYPE >	inline
select_group(AP_tree *node)	AWT_graphic_tree	inline
select_group(GBDATA *gb_group)	AWT_graphic_tree	inline
select_mode(int mode)	AW_window
selected_plugin_changed_cb(AW_root *awr)	FINAL_TYPE< SEQTYPE >	inline
selected_plugin_changed_cb(AW_root *awr, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
selected_range_changed_cb(AW_root *awr)	FINAL_TYPE< SEQTYPE >	inline
selected_range_changed_cb(AW_root *awr, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
SEC_base::self() const	SEC_base	inline
SEC_base_part::self() const	SEC_base_part	inline
TreeNode::self_ref()	TreeNode	inlineprotected
AP_tree::self_ref()	TreeNode	inlineprotected
ARB_countedTree::self_ref()	TreeNode	inlineprotected
sens_mask(AW_active mask)	AW_window
sep______________()	AW_window
seqabbr	FINAL_TYPE< SEQTYPE >
set(const long _row, const long _col, const bool _value) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
set(const long _row, const long _col, const bool _value) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
Set(const long _index, const bool _value) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
set_abs_angle(const Angle &abs)	SEC_oriented	inline
set_abs_angle(const double &abs)	SEC_oriented	inline
set_alignment_length(int len)	FINAL_TYPE< SEQTYPE >	inline
set_angle(float angle)	AP_tree	inline
set_background(const char *colorname, Widget w)	AW_window	protected
TreeNode::set_bootstrap(double bootstrap)	TreeNode	inline
AP_tree::set_bootstrap(double bootstrap)	TreeNode	inline
ARB_countedTree::set_bootstrap(double bootstrap)	TreeNode	inline
TreeRoot::set_bootstrap_seen(bool seen)	TreeRoot	inline
AP_tree_root::set_bootstrap_seen(bool seen)	TreeRoot	inline
ARB_seqtree_root::set_bootstrap_seen(bool seen)	TreeRoot	inline
ED4_terminal::set_both_links(ED4_base *ref)	ED4_base	inline
ED4_text_terminal::set_both_links(ED4_base *ref)	ED4_base	inline
ED4_manager::set_both_links(ED4_base *ref)	ED4_base	inline
set_bottom_area_height(int height)	AW_window
AW_device::set_bottom_clip_border(int bottom, bool allow_oversize=false)	AW_clipable
AW_simple_device::set_bottom_clip_border(int bottom, bool allow_oversize=false)	AW_clipable
AW_device::set_bottom_clip_margin(int bottom, bool allow_oversize=false)	AW_clipable
AW_simple_device::set_bottom_clip_margin(int bottom, bool allow_oversize=false)	AW_clipable
AW_device::set_bottom_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_bottom_font_overlap(bool allow)	AW_clipable	inline
TreeNode::set_branchlength(GBT_LEN newlen)	TreeNode	inline
AP_tree::set_branchlength(GBT_LEN newlen)	TreeNode	inline
ARB_countedTree::set_branchlength(GBT_LEN newlen)	TreeNode	inline
TreeNode::set_branchlength_preserving(GBT_LEN new_len)	TreeNode
AP_tree::set_branchlength_preserving(GBT_LEN new_len)	TreeNode
ARB_countedTree::set_branchlength_preserving(GBT_LEN new_len)	TreeNode
TreeNode::set_branchlength_unrooted(GBT_LEN newlen)	TreeNode	inline
AP_tree::set_branchlength_unrooted(GBT_LEN newlen)	TreeNode	inline
ARB_countedTree::set_branchlength_unrooted(GBT_LEN newlen)	TreeNode	inline
set_center(const Position &p)	FINAL_TYPE< SEQTYPE >	inline
AW_device::set_clipall()	AW_clipable	inline
AW_simple_device::set_clipall()	AW_clipable	inline
AW_device::set_cliprect(const AW_screen_area &rect)	AW_clipable	inlineprotected
AW_simple_device::set_cliprect(const AW_screen_area &rect)	AW_clipable	inlineprotected
set_color_mode(bool mode)	FINAL_TYPE< SEQTYPE >	inline
set_double_click_callback(AW_area area, const WindowCallback &wcb)	AW_window
AliData::set_error(GB_ERROR error) const	AliData	inline
set_expose_callback(AW_area area, const WindowCallback &wcb)	AW_window
AW_device::set_filter(AW_bitset filteri)	AW_device
AW_simple_device::set_filter(AW_bitset filteri)	AW_device
set_fixpoint_strand(SEC_helix_strand *strand)	FINAL_TYPE< SEQTYPE >	inline
set_focus_callback(const WindowCallback &wcb)	AW_window
AW_device::set_font(int gc, AW_font fontnr, int size, int *found_size)	AW_stylable
AW_simple_device::set_font(int gc, AW_font fontnr, int size, int *found_size)	AW_stylable
AW_device::set_font_overlap(bool allow)	AW_clipable	inline
AW_device::set_font_overlap(const AW_font_overlap &fo)	AW_clipable	inline
AW_simple_device::set_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_font_overlap(const AW_font_overlap &fo)	AW_clipable	inline
AW_device::set_foreground_color(int gc, AW_color_idx color)	AW_stylable
AW_simple_device::set_foreground_color(int gc, AW_color_idx color)	AW_stylable
AW_device::set_function(int gc, AW_function function)	AW_stylable
AW_simple_device::set_function(int gc, AW_function function)	AW_stylable
AP_tree_root::set_gb_tree(GBDATA *gbTree)	ARB_seqtree_root	inlineprotected
ARB_seqtree_root::set_gb_tree(GBDATA *gbTree)	ARB_seqtree_root	inlineprotected
AP_tree_root::set_gb_tree_and_name(GBDATA *gbTree, const char *name)	ARB_seqtree_root	inlineprotected
ARB_seqtree_root::set_gb_tree_and_name(GBDATA *gbTree, const char *name)	ARB_seqtree_root	inlineprotected
AW_device::set_grey_level(int gc, AW_grey_level grey_level)	AW_stylable
AW_simple_device::set_grey_level(int gc, AW_grey_level grey_level)	AW_stylable
set_helix(const char *hel)	FINAL_TYPE< SEQTYPE >	inline
set_highlighted(bool highlight)	FINAL_TYPE< SEQTYPE >	inline
set_horizontal_change_callback(const WindowCallback &wcb)	AW_window
AW_device::set_horizontal_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_horizontal_font_overlap(bool allow)	AW_clipable	inline
set_horizontal_scrollbar_left_indent(int indent)	AW_window
set_horizontal_scrollbar_position(int position)	AW_window
set_info_area_height(int height)	AW_window
set_input_callback(AW_area area, const WindowCallback &wcb)	AW_window
set_item(GBDATA *new_item)	awt_linked_to_item	inlineprotected
set_LatestSon(XML_Node *latest_son_)	FINAL_TYPE< SEQTYPE >	inline
AW_device::set_left_clip_border(int left, bool allow_oversize=false)	AW_clipable
AW_simple_device::set_left_clip_border(int left, bool allow_oversize=false)	AW_clipable
AW_device::set_left_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_left_font_overlap(bool allow)	AW_clipable	inline
AW_device::set_line_attributes(int gc, short width, AW_linestyle style)	AW_stylable
AW_simple_device::set_line_attributes(int gc, short width, AW_linestyle style)	AW_stylable
set_line_attributes_for(AP_tree *at) const	AWT_graphic_tree	inline
set_linewidth(int width)	AP_tree	inline
set_linewidth_recursive(int width)	AP_tree
ED4_terminal::set_links(ED4_base *width_ref, ED4_base *height_ref)	ED4_base
ED4_text_terminal::set_links(ED4_base *width_ref, ED4_base *height_ref)	ED4_base
ED4_manager::set_links(ED4_base *width_ref, ED4_base *height_ref)	ED4_base
set_logical_root_to(AP_tree *node)	AWT_graphic_tree	inline
set_loop(SEC_loop *loop_)	FINAL_TYPE< SEQTYPE >	inline
set_marker_display(MarkerDisplay *display)	AWT_graphic_tree	inline
set_motion_callback(AW_area area, const WindowCallback &wcb)	AW_window
awt_viewport::set_name(const std::string &name_, bool is_global)	awt_mask_item
awt_mask_item::set_name(const std::string &name_, bool is_global)	awt_mask_item
set_next_segment(SEC_segment *next_segment_)	FINAL_TYPE< SEQTYPE >	inline
set_next_strand(SEC_helix_strand *strand)	FINAL_TYPE< SEQTYPE >	inline
set_node_deleted_callback(AP_nodeDelCb cb, void *cd)	AP_tree_root
AW_device::set_offset(const AW::Vector &off)	AW_zoomable	inline
AW_simple_device::set_offset(const AW::Vector &off)	AW_zoomable	inline
set_on_extra_line(bool oel)	FINAL_TYPE< SEQTYPE >	inline
set_origin_loop(SEC_loop *loop_)	FINAL_TYPE< SEQTYPE >	inline
set_parameters(bool use_user_freqs, double fT, double fC, double fA, double fG, double rTC, double rTA, double rTG, double rCA, double rCG, double rAG, double dist, double supp, double gapA, double gapB, double gapC, double thres)	FINAL_TYPE< SEQTYPE >	inline
set_popup_callback(const WindowCallback &wcb)	AW_window
ED4_terminal::set_property(ED4_properties prop)	ED4_base	inline
ED4_text_terminal::set_property(ED4_properties prop)	ED4_base	inline
ED4_manager::set_property(ED4_properties prop)	ED4_base	inline
set_range(ExplicitRange range)	FINAL_TYPE< SEQTYPE >	inline
set_ref_sequence(const char *ref_seq)	FINAL_TYPE< SEQTYPE >	inline
set_rel_angle(const Angle &rel)	SEC_oriented	inline
set_rel_angle(const double &rel)	SEC_oriented	inline
set_reload_on_reinit(bool dest)	FINAL_TYPE< SEQTYPE >	inline
TreeNode::set_remark(const char *newRemark)	TreeNode	inline
AP_tree::set_remark(const char *newRemark)	TreeNode	inline
ARB_countedTree::set_remark(const char *newRemark)	TreeNode	inline
set_resize_callback(AW_area area, const WindowCallback &wcb)	AW_window
AW_device::set_right_clip_border(int right, bool allow_oversize=false)	AW_clipable
AW_simple_device::set_right_clip_border(int right, bool allow_oversize=false)	AW_clipable
AW_device::set_right_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_right_font_overlap(bool allow)	AW_clipable	inline
set_root() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
set_root_changed_callback(AP_rootChangedCb cb, void *cd)	AP_tree_root
AP_tree::set_seq(AP_sequence *sequence)	ARB_seqtree	inline
ARB_countedTree::set_seq(AP_sequence *sequence)	ARB_seqtree	inline
set_sequence_portion(int start, int end)	SEC_base_part	inline
set_space(size_t new_allocated)	CharPtrArray	inlineprotected
set_species_data(GBDATA *gb_species_data_)	FINAL_TYPE< SEQTYPE >	inlinestatic
ED4_terminal::set_species_pointer(GBDATA *gbd)	ED4_base	inline
ED4_text_terminal::set_species_pointer(GBDATA *gbd)	ED4_base	inline
ED4_manager::set_species_pointer(GBDATA *gbd)	ED4_base	inline
set_text(int level, const char *text) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
set_threshold(double aThreshold)	FINAL_TYPE< SEQTYPE >	static
set_toAlign_sequence(const char *toAlign_seq)	FINAL_TYPE< SEQTYPE >	inline
AW_device::set_top_clip_border(int top, bool allow_oversize=false)	AW_clipable
AW_simple_device::set_top_clip_border(int top, bool allow_oversize=false)	AW_clipable
AW_device::set_top_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_top_font_overlap(bool allow)	AW_clipable	inline
set_top_middle_line_terminal(ED4_terminal *top_middle_line_)	FINAL_TYPE< SEQTYPE >	inline
set_top_middle_spacer_terminal(ED4_terminal *top_middle_spacer_)	FINAL_TYPE< SEQTYPE >	inline
TreeNode::set_tree_root(TreeRoot *new_root)	TreeNode	protected
AP_tree::set_tree_root(TreeRoot *new_root)	TreeNode	protected
ARB_countedTree::set_tree_root(TreeRoot *new_root)	TreeNode	protected
set_tree_shader(AP_TreeShader *new_shader)	AP_tree	static
set_tree_style(AP_tree_display_style style, AWT_canvas *ntw)	AWT_graphic_tree
ED4_terminal::set_update()	ED4_base	inline
ED4_text_terminal::set_update()	ED4_base	inline
ED4_manager::set_update()	ED4_base	inline
set_value(const std::string &) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
set_vertical_change_callback(const WindowCallback &wcb)	AW_window
AW_device::set_vertical_font_overlap(bool allow)	AW_clipable	inline
AW_simple_device::set_vertical_font_overlap(bool allow)	AW_clipable	inline
set_vertical_scrollbar_position(int position)	AW_window
set_vertical_scrollbar_top_indent(int indent)	AW_window
ED4_terminal::set_width()	ED4_base
ED4_text_terminal::set_width()	ED4_base
ED4_manager::set_width()	ED4_base
set_window_title(const char *title)	AW_window
set_window_title_intern(char *title)	AW_window
setAttachPoints(const Position &left, const Position &right)	FINAL_TYPE< SEQTYPE >	inline
setBranchlen(double leftLen, double rightLen)	FINAL_TYPE< SEQTYPE >	inline
SetColor(int gc)	FINAL_TYPE< SEQTYPE >
setConstraints(double low, double high)	SEC_constrainted	inline
setCursorTo(ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type)	FINAL_TYPE< SEQTYPE >
setDrawnSize(double size)	SEC_constrainted	inline
setFalse(const long _row, const long _col) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
setFalse(const long _row, const long _col) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
setFalse(const long _index) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
setFixpoint(const Position &p)	FINAL_TYPE< SEQTYPE >	inline
setFixpoints(const Position &rootside, const Position &outside)	FINAL_TYPE< SEQTYPE >
TreeNode::setKeeledState(int keeledState)	TreeNode	inline
AP_tree::setKeeledState(int keeledState)	TreeNode	inline
ARB_countedTree::setKeeledState(int keeledState)	TreeNode	inline
setLineNumber(size_t line)	LineReader	inline
setMappings(Name2IDMap &_name2id, ID2NameMap &_id2name)	FINAL_TYPE< SEQTYPE >	inline
setName(const string &name_)	FINAL_TYPE< SEQTYPE >	inline
SetOpenGLBackGroundColor()	FINAL_TYPE< SEQTYPE >
setStandardSize(double size)	SEC_constrainted	inline
setTrue(const long _row, const long _col) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
setTrue(const long _row, const long _col) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
setTrue(const long _index) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
shade(GBDATA *gb_item) const	ItemShader	inline
ShadedValue typedef	ValueTuple
shader_awar(const char *name) const	FINAL_TYPE< SEQTYPE >	inline
shadow_width(int shadow_thickness)	AW_window
AW_device::shift(const AW::Vector &doff)	AW_zoomable	inline
AW_simple_device::shift(const AW::Vector &doff)	AW_zoomable	inline
Show(bool refresh_all, bool is_cleared) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
Show(bool refresh_all, bool is_cleared) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
show()	FINAL_TYPE< SEQTYPE >	inline
show(AW_device *device) OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
show_modal()	AW_window
show_ruler(AW_device *device, int gc)	AWT_graphic_tree
showFilenameInLineError(bool show)	LineReader	inline
SimpleCmmd(const char *cmd, NoArgFun fun_)	FINAL_TYPE< SEQTYPE >	inline
SimpleRoot class	FINAL_TYPE< SEQTYPE >	friend
SimpleTree(SimpleRoot *sroot)	FINAL_TYPE< SEQTYPE >	inline
MarkerDisplay::size() const	MarkerDisplay	inline
CharPtrArray::size() const	CharPtrArray	inline
SizeAwareRoot class	FINAL_TYPE< SEQTYPE >	friend
SizeAwareTree(TreeRoot *root)	FINAL_TYPE< SEQTYPE >	inline
sizeChanged() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
sizeChanged() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
skip_empty_tags	FINAL_TYPE< SEQTYPE >
slice_down(size_t start, size_t count) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
slider_pos_horizontal	AW_window
slider_pos_vertical	AW_window
slow()	AW_device	virtual
sons	FINAL_TYPE< SEQTYPE >
sort(CharPtrArray_compare_fun compare, void *client_data)	CharPtrArray
sort_and_uniq(CharPtrArray_compare_fun compare, void *client_data)	CharPtrArray	inline
sortByName()	FINAL_TYPE< SEQTYPE >
source	FINAL_TYPE< SEQTYPE >
SpatialTuple(float val1_, float val2_, float val3_)	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::spec	ED4_base
ED4_text_terminal::spec	ED4_base
ED4_manager::spec	ED4_base
species_timer	AP_tree_root
speciesLabel(GBDATA *gb_main, GBDATA *gb_species, TreeNode *species, const char *tree_name) const OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
split(size_t start, size_t end, SEC_segment **new_segment)	FINAL_TYPE< SEQTYPE >
SPOOLER class	FINAL_TYPE< SEQTYPE >	friend
StackFrameData::destroyNode(AP_tree_nlen *node)	FINAL_TYPE< SEQTYPE >	friend
standardSize() const	SEC_constrainted	inline
startAttachAbspos() const	FINAL_TYPE< SEQTYPE >	inline
startAttachPoint() const	FINAL_TYPE< SEQTYPE >	inline
store_at_to(AW_at_storage &storage)	AW_window	inline
store_command_data(AWT_command_data *new_cmd_data)	AWT_graphic_tree	inlineprotected
store_config_cb() const	FINAL_TYPE< SEQTYPE >
store_config_cb(ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
stored_costs() const	FINAL_TYPE< SEQTYPE >	inline
str	CharPtrArray	protected
strain	FINAL_TYPE< SEQTYPE >
strandAwayFrom(const SEC_loop *loop) const	FINAL_TYPE< SEQTYPE >
strandToOutside() const	FINAL_TYPE< SEQTYPE >
strandToRoot() const	FINAL_TYPE< SEQTYPE >	inline
strandTowards(const SEC_loop *loop) const	FINAL_TYPE< SEQTYPE >
StrArray()	FINAL_TYPE< SEQTYPE >	inline
subspecies	FINAL_TYPE< SEQTYPE >
TreeNode::sum_child_lengths() const	TreeNode
AP_tree::sum_child_lengths() const	TreeNode
ARB_countedTree::sum_child_lengths() const	TreeNode
swap(int i1, int i2)	CharPtrArray	inline
swap_assymetric(AP_TREE_SIDE mode)	FINAL_TYPE< SEQTYPE >
TreeNode::swap_node_info(TreeNode *other, bool ofKeeledGroups)	TreeNode	inlineprotected
AP_tree::swap_node_info(TreeNode *other, bool ofKeeledGroups)	TreeNode	inlineprotected
ARB_countedTree::swap_node_info(TreeNode *other, bool ofKeeledGroups)	TreeNode	inlineprotected
swap_sons() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
table	FINAL_TYPE< SEQTYPE >	static
tag_leaf()	FINAL_TYPE< SEQTYPE >	inline
tagged_rate() const	FINAL_TYPE< SEQTYPE >	inline
AP_tree::take_seq()	ARB_seqtree	inlineprotected
ARB_countedTree::take_seq()	ARB_seqtree	inlineprotected
takeAllInFrontOf(ParagraphTree *after)	FINAL_TYPE< SEQTYPE >	inline
tell_scrolled_picture_size(AW_screen_area rectangle)	AW_window
tell_scrolled_picture_size(AW_world rectangle)	AW_window
templ	FINAL_TYPE< SEQTYPE >
AW_device::text(int gc, const SizedCstr &cstr, const AW::Position &pos, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)	AW_device	inline
AW_device::text(int gc, const char *str, const AW::Position &pos, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)	AW_device	inline
AW_device::text(int gc, const char *str, AW_pos x, AW_pos y, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)	AW_device	inline
AW_simple_device::text(int gc, const SizedCstr &cstr, const AW::Position &pos, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)	AW_device	inline
AW_simple_device::text(int gc, const char *str, const AW::Position &pos, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)	AW_device	inline
AW_simple_device::text(int gc, const char *str, AW_pos x, AW_pos y, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)	AW_device	inline
AW_device::text_overlay(int gc, const SizedCstr &cstr, const AW::Position &pos, AW_pos alignment, AW_bitset filteri, TextOverlayCallback toc, AW_CL cduser=0)	AW_device
AW_simple_device::text_overlay(int gc, const SizedCstr &cstr, const AW::Position &pos, AW_pos alignment, AW_bitset filteri, TextOverlayCallback toc, AW_CL cduser=0)	AW_device
texture	FINAL_TYPE< SEQTYPE >
Texture2D()	FINAL_TYPE< SEQTYPE >
TexturizeStructure(Texture2D *cImages, Structure3D *cStructure)	FINAL_TYPE< SEQTYPE >
ED4_terminal::tflag	ED4_terminal
ED4_text_terminal::tflag	ED4_terminal
threshold_is_set()	FINAL_TYPE< SEQTYPE >	static
throw_write_error() const __ATTR__NORETURN	Writer	virtual
tmp_shader_awar(const char *name) const	FINAL_TYPE< SEQTYPE >	inline
to_GC(const ShadedValue &val) const	ItemShader	inline
awt_viewport::to_linked_item() const	awt_mask_item	inline
awt_viewport::to_linked_item()	awt_mask_item	inline
awt_mask_item::to_linked_item() const	awt_mask_item	inline
awt_mask_item::to_linked_item()	awt_mask_item	inline
awt_viewport::to_viewport() const	awt_mask_item	inline
awt_viewport::to_viewport()	awt_mask_item	inline
awt_mask_item::to_viewport() const	awt_mask_item	inline
awt_mask_item::to_viewport()	awt_mask_item	inline
toggle_group(AP_tree *at)	AWT_graphic_tree
toggle_root(SEC_loop *root_loop)	FINAL_TYPE< SEQTYPE >
ED4_terminal::touch_world_cache()	ED4_base	inlinestatic
ED4_text_terminal::touch_world_cache()	ED4_base	inlinestatic
ED4_manager::touch_world_cache()	ED4_base	inlinestatic
AW_device::transform(const AW::Vector &vec) const	AW_zoomable	inline
AW_device::transform(const AW::Position &pos) const	AW_zoomable	inline
AW_device::transform(const AW::LineVector &lvec) const	AW_zoomable	inline
AW_device::transform(const AW::Rectangle &rect) const	AW_zoomable	inline
AW_device::transform(AW_pos x, AW_pos y, AW_pos &xout, AW_pos &yout) const	AW_zoomable	inline
AW_simple_device::transform(const AW::Vector &vec) const	AW_zoomable	inline
AW_simple_device::transform(const AW::Position &pos) const	AW_zoomable	inline
AW_simple_device::transform(const AW::LineVector &lvec) const	AW_zoomable	inline
AW_simple_device::transform(const AW::Rectangle &rect) const	AW_zoomable	inline
AW_simple_device::transform(AW_pos x, AW_pos y, AW_pos &xout, AW_pos &yout) const	AW_zoomable	inline
AW_device::transform_size(const double &size) const	AW_zoomable	inline
AW_simple_device::transform_size(const double &size) const	AW_zoomable	inline
AP_tree_root::tree_deleted_cb(GBDATA *gb_tree_del)	ARB_seqtree_root
ARB_seqtree_root::tree_deleted_cb(GBDATA *gb_tree_del)	ARB_seqtree_root
tree_has_marks(AP_tree *at)	AWT_graphic_tree
tree_timer	AP_tree_root
tree_write_tree_rek(GBDATA *gb_tree)	AP_tree
TreeNode::TreeNode(TreeRoot *root)	TreeNode	inline
AP_tree::TreeNode(TreeRoot *root)	TreeNode	inline
ARB_countedTree::TreeNode(TreeRoot *root)	TreeNode	inline
TreeRoot::TreeRoot(bool deleteWithNodes_)	TreeRoot	inlineexplicit
AP_tree_root::TreeRoot(bool deleteWithNodes_)	TreeRoot	inlineexplicit
ARB_seqtree_root::TreeRoot(bool deleteWithNodes_)	TreeRoot	inlineexplicit
triangle_get(const long _row, const long _col)	PS_BitMap
triangle_set(const long _row, const long _col, const bool _value)	PS_BitMap
trigger_reshade_callback(ReshadeMode mode)	ItemShader	inline
trigger_reshade_cb(AW_root *, ItemShader_impl *shader)	FINAL_TYPE< SEQTYPE >	inlinestatic
TuneBackground(Widget w, int modStrength)	AW_window
TuneOrSetBackground(Widget w, const char *color, int modStrength)	AW_window
type()	FINAL_TYPE< SEQTYPE >	virtual
type() OVERRIDE	FINAL_TYPE< SEQTYPE >	virtual
type()	FINAL_TYPE< SEQTYPE >	virtual
type_name(SaiOperatorType type)	SaiOperator	inlinestatic
unbind_from_species()	AP_sequence
uncolorize()	AP_tree	inline
undefined()	ValueTuple	static
unhash_sequence()	FINAL_TYPE< SEQTYPE >
unhide_children()	ED4_manager
uninstall_tree_changed_callback()	AWT_graphic_tree
uniq(CharPtrArray_compare_fun compare, void *client_data)	CharPtrArray
unit_left_of(size_t pos) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
unit_right_of(size_t pos) const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
unitsize() const OVERRIDE	FINAL_TYPE< SEQTYPE >	inlinevirtual
TreeNode::unkeelGroup()	TreeNode	inline
AP_tree::unkeelGroup()	TreeNode	inline
ARB_countedTree::unkeelGroup()	TreeNode	inline
unlink()	FINAL_TYPE< SEQTYPE >	inline
unlink(bool fromOtherStrandAsWell)	FINAL_TYPE< SEQTYPE >
unlink()	FINAL_TYPE< SEQTYPE >
TreeNode::unlink_from_DB()	TreeNode
AP_tree::unlink_from_DB()	TreeNode
ARB_countedTree::unlink_from_DB()	TreeNode
TreeNode::unlink_from_father()	TreeNode	inlineprotected
AP_tree::unlink_from_father()	TreeNode	inlineprotected
ARB_countedTree::unlink_from_father()	TreeNode	inlineprotected
ED4_terminal::unlink_from_parent()	ED4_base
ED4_text_terminal::unlink_from_parent()	ED4_base
ED4_manager::unlink_from_parent()	ED4_base
unlinkAllEdges(AP_tree_edge **edgePtr1, AP_tree_edge **edgePtr2, AP_tree_edge **edgePtr3)	FINAL_TYPE< SEQTYPE >
AP_tree_root::unlinkFromDB()	ARB_seqtree_root
ARB_seqtree_root::unlinkFromDB()	ARB_seqtree_root
unlock() const	ArbRefCount	inline
unset_at_commands()	AW_window
unusedEdgeIndex() const	FINAL_TYPE< SEQTYPE >
update_bases(const ED4_base *old_base, const ED4_base *new_base, PosRange range=PosRange::whole())	ED4_manager
update_bases(const char *old_seq, int old_len, const char *new_seq, int new_len, PosRange range=PosRange::whole())	ED4_manager
update_bases(const char *old_seq, int old_len, const ED4_base *new_base, PosRange range=PosRange::whole())	ED4_manager
update_bases(const BaseFrequencies *old_table, const BaseFrequencies *new_table, PosRange range=PosRange::whole())	ED4_manager
update_bases_and_rebuild_consensi(const char *old_seq, int old_len, ED4_base *species, ED4_update_flag update_flag, PosRange range=PosRange::whole())	ED4_manager
update_consensus(ED4_manager *old_parent, ED4_manager *new_parent, ED4_base *sequence)	ED4_manager
update_gauge(double gauge) OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::update_info	ED4_base
ED4_text_terminal::update_info	ED4_base
ED4_manager::update_info	ED4_base
update_input_field(Widget widget, const char *var_value)	AW_window
update_label(Widget widget, const char *var_value)	AW_window
update_leaf_counters()	FINAL_TYPE< SEQTYPE >
update_option_menu()	AW_window
update_requested_by_child()	ED4_manager
ED4_terminal::update_requested_children() OVERRIDE	ED4_terminal	virtual
ED4_text_terminal::update_requested_children() OVERRIDE	ED4_terminal	virtual
ED4_manager::update_requested_children() OVERRIDE	ED4_manager	virtual
update_scaler(Widget widget, AW_awar *awar, AW_ScalerType scalerType)	AW_window
update_scrollbar_settings_from_awars(AW_orientation orientation)	AW_window
update_subtree_information(const group_scaling &gscaling)	AP_tree
update_text_field(Widget widget, const char *var_value)	AW_window
update_timers()	AP_tree_root
update_toggle(Widget widget, const char *var_value, AW_CL cd)	AW_window
update_toggle_field()	AW_window
ED4_terminal::update_world_coords_cache() const	ED4_base	inline
ED4_text_terminal::update_world_coords_cache() const	ED4_base	inline
ED4_manager::update_world_coords_cache() const	ED4_base	inline
TreeNode::use_as_remark(const SmartCharPtr &newRemark)	TreeNode	inline
AP_tree::use_as_remark(const SmartCharPtr &newRemark)	TreeNode	inline
ARB_countedTree::use_as_remark(const SmartCharPtr &newRemark)	TreeNode	inline
valid_drag_device(AW_device *device)	Dragged	inlinestatic
valid_index(ED4_index idx) const	ED4_container	inlineprotected
AWT_graphic::wants_drag_target() const	AWT_graphic	inline
AWT_graphic_parsimony::wants_drag_target() const	AWT_graphic	inline
warn_inappropriate_mode(AWT_COMMAND_MODE mode)	AWT_graphic_tree
was_aligned() const	FINAL_TYPE< SEQTYPE >	inline
was_saved() const	FINAL_TYPE< SEQTYPE >	inline
weighted_base_count() const	AP_combinableSeq	inline
who	FINAL_TYPE< SEQTYPE >
ED4_terminal::width_link	ED4_base
ED4_text_terminal::width_link	ED4_base
ED4_manager::width_link	ED4_base
window_defaults_name	AW_window
window_fit()	AW_window
window_is_shown	AW_window
window_local_awar(const char *localname, bool tmp=true)	AW_window
window_local_awarname(const char *localname, bool tmp=true)	AW_window
window_name	AW_window
WinToScreenCoordinates(int x, int y, GLdouble *screenPos)	FINAL_TYPE< SEQTYPE >
wm_activate()	AW_window	protected
write_cache(const AP_tree *at, const NodeMarkers &markers)	MarkerDisplay	inline
write_data_to_db(const char *data, const char *x_string) const	FINAL_TYPE< SEQTYPE >
ED4_terminal::write_sequence(const char *seq, int seq_len)	ED4_terminal
ED4_text_terminal::write_sequence(const char *seq, int seq_len)	ED4_terminal
WRITEONLY	FINAL_TYPE< SEQTYPE >	static
Writer()	Writer	inline
PS_BitSet::x_or(const PS_BitSet *_other_set)	PS_BitSet
PS_BitMap::x_or(const PS_BitMap *_other_map)	PS_BitMap
XML_Attribute(const std::string &name_, const std::string &content_)	FINAL_TYPE< SEQTYPE >
XML_Document(const std::string &name_, const std::string &dtd_, FILE *out_)	FINAL_TYPE< SEQTYPE >
XML_Node(bool is_tag)	XML_Node
XML_Tag(const std::string &name_)	FINAL_TYPE< SEQTYPE >
xml_write()	FINAL_TYPE< SEQTYPE >
AW_device::zoom(AW_pos scale)	AW_zoomable
AW_simple_device::zoom(AW_pos scale)	AW_zoomable
~AliData()	AliData	inlinevirtual
~AliEditCommand()	AliEditCommand	inlinevirtual
~AlignedSequenceLoader()	FINAL_TYPE< SEQTYPE >
~Analyser()	FINAL_TYPE< SEQTYPE >	virtual
~AP_combinableSeq()	AP_combinableSeq	inlinevirtual
~AP_sequence()	AP_sequence	inlinevirtual
~AP_sequence_parsimony() OVERRIDE	FINAL_TYPE< SEQTYPE >
~AP_sequence_protein() OVERRIDE	FINAL_TYPE< SEQTYPE >
~AP_tree() OVERRIDE	AP_tree	protected
~AP_tree_nlen() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlineprotected
~AP_tree_root() OVERRIDE	AP_tree_root
~ARB_countedTree() OVERRIDE	ARB_countedTree	inlineprotected
AP_tree::~ARB_seqtree() OVERRIDE	ARB_seqtree	protected
ARB_countedTree::~ARB_seqtree() OVERRIDE	ARB_seqtree	protected
AP_tree_root::~ARB_seqtree_root() OVERRIDE	ARB_seqtree_root
ARB_seqtree_root::~ARB_seqtree_root() OVERRIDE	ARB_seqtree_root
~ArbMatchResultSet()	FINAL_TYPE< SEQTYPE >	virtual
~ArbRefCount()	ArbRefCount	inlinevirtual
~ArbWriter()	FINAL_TYPE< SEQTYPE >	inline
~AW_clicked_element()	AW_clicked_element	inlinevirtual
~AW_clicked_polygon()	FINAL_TYPE< SEQTYPE >	inline
~AW_clipable()	AW_clipable	inlinevirtual
~AW_device()	AW_device	inlinevirtual
~AW_repeated_question()	FINAL_TYPE< SEQTYPE >	inlinevirtual
~AW_stylable()	AW_stylable	inlinevirtual
~AW_window()	AW_window	virtual
~AW_window_simple()	FINAL_TYPE< SEQTYPE >
~AW_zoomable()	AW_zoomable	inlinevirtual
~AWT_command_data()	AWT_command_data	inlinevirtual
~AWT_graphic()	AWT_graphic	inlinevirtual
~AWT_graphic_tree() OVERRIDE	AWT_graphic_tree
~awt_input_mask()	FINAL_TYPE< SEQTYPE >	virtual
~awt_input_mask_descriptor()	FINAL_TYPE< SEQTYPE >	virtual
~awt_item_type_selector()	awt_item_type_selector	inlinevirtual
~awt_linked_to_item()	awt_linked_to_item	inlinevirtual
~awt_marked_checkbox() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~awt_mask_awar_item() OVERRIDE	awt_mask_awar_item	inline
~awt_mask_item()	awt_mask_item	virtual
~awt_script() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~awt_script_viewport() OVERRIDE	FINAL_TYPE< SEQTYPE >
~awt_viewport() OVERRIDE	awt_viewport	inline
~CharPtrArray()	CharPtrArray	inlineprotectedvirtual
~child_progress() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~ClusterTree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlineprotected
~ClusterTreeRoot() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~Cma()	FINAL_TYPE< SEQTYPE >	virtual
~Command()	Command	inlinevirtual
~CompressionTree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlineprotected
~concrete_counter() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~ED4_base()	ED4_base	virtual
~ED4_columnStat_terminal() OVERRIDE	FINAL_TYPE< SEQTYPE >
~ED4_container()	ED4_container	virtual
~ED4_manager() OVERRIDE	ED4_manager
~ED4_species_manager() OVERRIDE	FINAL_TYPE< SEQTYPE >
~ED4_species_name_terminal() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
ED4_terminal::~ED4_terminal() OVERRIDE	ED4_terminal
ED4_text_terminal::~ED4_terminal() OVERRIDE	ED4_terminal
~ED4_text_terminal() OVERRIDE	ED4_text_terminal	inline
~Embl() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~fake_agt() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~GenBank() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~GLRenderer()	FINAL_TYPE< SEQTYPE >	virtual
~GroupSearchRoot() FINAL_OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~GroupTree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlineprotected
~GroupTreeRoot() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~InputFormat() OVERRIDE	InputFormat	inline
~IslandHopping()	FINAL_TYPE< SEQTYPE >	inlinevirtual
~IslandHoppingParameter()	FINAL_TYPE< SEQTYPE >	virtual
~ItemQueryKey()	FINAL_TYPE< SEQTYPE >	inline
~ItemShader()	ItemShader	inlinevirtual
~LinearTuple() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~LineReader()	LineReader	inlinevirtual
~Macke() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~MarkerDisplay()	MarkerDisplay	inlinevirtual
~MessageAttachable()	MessageAttachable	inlinevirtual
~MultiFileReader()	FINAL_TYPE< SEQTYPE >
~NDS_Labeler()	FINAL_TYPE< SEQTYPE >	virtual
~nt_item_type_species_selector() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~OpenGLGraphics()	FINAL_TYPE< SEQTYPE >	virtual
~OutputFormat()	OutputFormat	inlinevirtual
~ParagraphTree()	FINAL_TYPE< SEQTYPE >	inlinevirtual
~PlanarTuple() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~PS_BitMap()	PS_BitMap	inlinevirtual
~PS_BitMap_Counted() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~PS_BitSet()	PS_BitSet	inlinevirtual
~PS_Callback()	PS_Callback	inlineprivatevirtual
~PS_Database() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~QueryKey()	QueryKey	inlinevirtual
~SaiOperator()	SaiOperator	inlinevirtual
~SEC_base() OVERRIDE	SEC_base	inline
~SEC_base_part()	SEC_base_part	inlinevirtual
~SEC_graphic() OVERRIDE	FINAL_TYPE< SEQTYPE >
~SEC_helix() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~SEC_helix_strand() OVERRIDE	FINAL_TYPE< SEQTYPE >
~SEC_loop() OVERRIDE	FINAL_TYPE< SEQTYPE >
~SEC_oriented()	SEC_oriented	inlinevirtual
~SEC_segment() OVERRIDE	FINAL_TYPE< SEQTYPE >
~Section()	FINAL_TYPE< SEQTYPE >	inlinevirtual
~SimpleTree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlineprotected
~SizeAwareTree() OVERRIDE	FINAL_TYPE< SEQTYPE >	inlineprotected
~SpatialTuple() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~StrArray() OVERRIDE	FINAL_TYPE< SEQTYPE >	inline
~Texture2D()	FINAL_TYPE< SEQTYPE >	virtual
~TreeLabeler()	TreeLabeler	inlinevirtual
~TreeNode()	TreeNode	inlineprotectedvirtual
~TreeRoot()	TreeRoot	virtual
~ValueTuple()	ValueTuple	inlinevirtual
~Writer()	Writer	inlinevirtual
~Writer()	Writer	inlinevirtual
~XML_Attribute()	FINAL_TYPE< SEQTYPE >	virtual
~XML_Document()	FINAL_TYPE< SEQTYPE >	virtual
~XML_Node()	XML_Node	virtual
~XML_Tag() OVERRIDE	FINAL_TYPE< SEQTYPE >