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#include <TreeNode.h>

Inheritance diagram for FINAL_TYPE< SEQTYPE >:

Collaboration diagram for FINAL_TYPE< SEQTYPE >:

Public Types
enum	ClickPreference { PREFER_NEARER, PREFER_LINE, PREFER_TEXT }

Public Types inherited from Dragged
enum	DragAction { DRAGGING, DROPPED }

Public Types inherited from ValueTuple
typedef SmartPtr< ValueTuple >	ShadedValue

Public Types inherited from AliData
enum	memop { COPY_TO, COMPARE_WITH, CHECK_DELETE }

Public Types inherited from PS_BitSet
typedef set< long >	IndexSet

Public Member Functions
	SimpleCmmd (const char *cmd, NoArgFun fun_)

int	call (Interpreter &interpret) const OVERRIDE

	ArgCommand (const char *cmd, ArgFun fun_, CallMode emode_=STANDARD_CALL)

int	call (Interpreter &interpret) const OVERRIDE

	CompressionTree (CompressionRoot *croot)

unsigned	get_leaf_count () const OVERRIDE

void	compute_tree () OVERRIDE

	DEFINE_TREE_ACCESSORS (CompressionRoot, CompressionTree)

	SimpleTree (SimpleRoot *sroot)

unsigned	get_leaf_count () const OVERRIDE

void	compute_tree () OVERRIDE

	awt_input_mask_descriptor (const char title_, const char maskname_, const char *itemtypename_, bool local, bool hidden_)

	awt_input_mask_descriptor (const awt_input_mask_descriptor &other)

virtual	~awt_input_mask_descriptor ()

awt_input_mask_descriptor &	operator= (const awt_input_mask_descriptor &other)

const char *	get_title () const

const char *	get_maskname () const

const char *	get_internal_maskname () const

const char *	get_itemtypename () const

bool	is_local_mask () const

bool	is_hidden () const

	awt_marked_checkbox (awt_input_mask_global &global_, const std::string &label_)

	~awt_marked_checkbox () OVERRIDE

GB_ERROR	link_to (GBDATA *gb_new_item) OVERRIDE

GB_ERROR	relink () OVERRIDE

void	awar_changed () OVERRIDE

void	db_changed () OVERRIDE

void	general_item_change () OVERRIDE

void	build_widget (AW_window *aws) OVERRIDE

	awt_script (awt_input_mask_global &global_, const std::string &script_)

	~awt_script () OVERRIDE

std::string	get_value () const OVERRIDE

GB_ERROR	set_value (const std::string &) OVERRIDE

	awt_script_viewport (awt_input_mask_global &global_, const awt_script *script_, const std::string &label_, long field_width_)

	~awt_script_viewport () OVERRIDE

GB_ERROR	link_to (GBDATA *gb_new_item) OVERRIDE

GB_ERROR	relink () OVERRIDE

void	build_widget (AW_window *aws) OVERRIDE

void	awar_changed () OVERRIDE

void	db_changed () OVERRIDE

	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)

virtual	~awt_input_mask ()

void	show ()

void	hide ()

void	set_reload_on_reinit (bool dest)

bool	reload_on_reinit () const

AW_window_simple *&	get_window ()

const awt_input_mask_global &	mask_global () const

awt_input_mask_global &	mask_global ()

void	add_handler (awt_mask_item_ptr handler)

void	relink ()

void	unlink ()

	SizeAwareTree (TreeRoot *root)

	DEFINE_TREE_RELATIVES_ACCESSORS (SizeAwareTree)

unsigned	get_leaf_count () const OVERRIDE

void	compute_tree () OVERRIDE

	Embl ()

	~Embl () OVERRIDE

void	reinit () OVERRIDE

Format	format () const OVERRIDE

	GenBank ()

	~GenBank () OVERRIDE

bool	locus_contains_date () const

char *	get_date () const

void	reinit () OVERRIDE

Format	format () const OVERRIDE

	Macke ()

	~Macke () OVERRIDE

void	add_remark (const char *rem)

void	add_remark (const char key, const char Str)

int	get_rem_count () const

const char *	get_rem (int idx) const

char *	copy_multi_rem (int &idx, int offset) const

void	add_remarks_from (const GenBank &gbk)

void	reinit () OVERRIDE

const char *	get_id () const

Format	format () const OVERRIDE

	concrete_counter (nestable *owner, SINT overall_count)

	~concrete_counter () OVERRIDE

void	auto_subtitles (const char *prefix) OVERRIDE

bool	has_auto_subtitles () OVERRIDE

void	inc () OVERRIDE

void	implicit_inc () OVERRIDE

void	inc_to (SINT x) OVERRIDE

void	inc_to_avoid_overflow (SINT x) OVERRIDE

void	inc_by (SINT count)

void	done () OVERRIDE

counter *	clone (nestable *owner, SINT overall_count) const OVERRIDE

void	child_updates_gauge (double child_gauge) OVERRIDE

	child_progress (nestable parent_, const char title, SINT overall_count, const weightable &speed_)

	~child_progress () OVERRIDE

SmartPtr< nestable >	create_child_progress (const char *title, SINT overall_count, const weightable &speed_) OVERRIDE

void	set_text (int level, const char *text) OVERRIDE

void	update_gauge (double gauge) OVERRIDE

	StrArray ()

	~StrArray () OVERRIDE

void	erase ()

void	put (char *elem)

void	put_before (int insert_before, char *elem)

char *	replace (int i, char *elem)

	MultiFileReader (const CharPtrArray &files_)

	~MultiFileReader ()

GB_ERROR	get_error () const

const string &	getFilename () const OVERRIDE

	GroupTreeRoot (AliView aliView, AP_sequence seqTempl, bool add_delete_callbacks)

	~GroupTreeRoot () OVERRIDE

TreeNode *	makeNode () const OVERRIDE

void	destroyNode (TreeNode *node) const OVERRIDE

	GroupTree (GroupTreeRoot *root)

void	init_tree () OVERRIDE

	DEFINE_TREE_RELATIVES_ACCESSORS (GroupTree)

void	map_species2tip (Species2Tip &mapping)

unsigned	update_leaf_counters ()

void	tag_leaf ()

unsigned	get_tagged_count () const

void	clear_tags ()

float	tagged_rate () const

	ClusterTreeRoot (AliView aliview, AP_sequence seqTemplate_, AP_FLOAT maxDistance_, size_t minClusterSize_)

	~ClusterTreeRoot () OVERRIDE

TreeNode *	makeNode () const OVERRIDE

void	destroyNode (TreeNode *node) const OVERRIDE

	DEFINE_DOWNCAST_ACCESSORS (ClusterTree, get_root_node, ARB_seqtree_root::get_root_node())

GB_ERROR	find_clusters ()

unsigned	get_minClusterSize () const

AP_FLOAT	get_maxDistance () const

	ClusterTree (ClusterTreeRoot *tree_root_)

	DEFINE_TREE_ACCESSORS (ClusterTreeRoot, ClusterTree)

	OVERRIDE_SEQ_ACCESSORS (AP_combinableSeq, ARB_countedTree)

unsigned	get_cluster_count () const

unsigned	get_leaf_count () const OVERRIDE

ClusterState	get_state () const

void	init_tree () OVERRIDE

void	detect_clusters (arb_progress &progress)

const LeafRelations *	get_sequence_dists () const

AP_FLOAT	get_min_bases () const

	ED4_main_manager (const char id, AW_pos width, AW_pos height, ED4_manager parent)

void	set_top_middle_spacer_terminal (ED4_terminal *top_middle_spacer_)

void	set_top_middle_line_terminal (ED4_terminal *top_middle_line_)

ED4_terminal *	get_top_middle_spacer_terminal () const

ED4_terminal *	get_top_middle_line_terminal () const

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_manager)

void	Show (bool refresh_all, bool is_cleared) OVERRIDE

void	resize_requested_children () OVERRIDE

void	clear_whole_background ()

	ED4_species_manager (ED4_species_type type_, const char id, AW_pos width, AW_pos height, ED4_manager parent)

	~ED4_species_manager () OVERRIDE

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_manager)

ED4_species_type	get_type () const

bool	is_highlighted () const

void	set_highlighted (bool highlight)

bool	setCursorTo (ED4_cursor *cursor, int seq_pos, bool unfold_groups, ED4_CursorJumpType jump_type)

void	add_sequence_changed_cb (const ED4_species_managerCallback &cb)

void	remove_sequence_changed_cb (const ED4_species_managerCallback &cb)

void	do_callbacks ()

ED4_species_name_terminal *	get_name_terminal () const

	E4B_AVOID_UNNEEDED_CASTS (tree_terminal)

void	draw () OVERRIDE

	ED4_tree_terminal (const char id, AW_pos width, AW_pos height, ED4_manager parent)

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_terminal)

void	draw () OVERRIDE

int	get_length () const OVERRIDE

ED4_sequence_terminal *	corresponding_sequence_terminal () const

	ED4_columnStat_terminal (GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

	~ED4_columnStat_terminal () OVERRIDE

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_text_terminal)

	ED4_species_name_terminal (GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

	~ED4_species_name_terminal () OVERRIDE

GB_CSTR	get_displayed_text () const

int	get_length () const OVERRIDE

ED4_sequence_terminal *	corresponding_sequence_terminal () const

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_text_terminal)

	ED4_flag_header_terminal (GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

GB_CSTR	get_displayed_text () const

int	get_length () const OVERRIDE

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_text_terminal)

	ED4_sequence_info_terminal (const char id, AW_pos width, AW_pos height, ED4_manager parent)

ED4_species_name_terminal *	corresponding_species_name_terminal () const

void	draw () OVERRIDE

GBDATA *	data ()

const GBDATA *	data () const

int	get_length () const OVERRIDE

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_text_terminal)

	E4B_AVOID_UNNEEDED_CASTS (pure_text_terminal)

	ED4_pure_text_terminal (const char id, AW_pos width, AW_pos height, ED4_manager parent)

int	get_length () const OVERRIDE

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_text_terminal)

void	Show (bool refresh_all, bool is_cleared) OVERRIDE

void	draw () OVERRIDE

	ED4_spacer_terminal (const char id, bool shallDraw_, AW_pos width, AW_pos height, ED4_manager parent)

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_terminal)

void	draw () OVERRIDE

	ED4_flag_terminal (const char id, AW_pos width, AW_pos height, ED4_manager parent)

GBDATA *	get_species () const

void	handle_left_click (const AW::Position &click)

	DECLARE_DUMP_FOR_LEAFCLASS (ED4_terminal)

	Section (string name_, SectionType type_, size_t lineno_)

virtual	~Section ()

const Ostrings &	Content () const

Ostrings &	Content ()

SectionType	get_type () const

size_t	line_number () const OVERRIDE

const string &	getName () const

void	setName (const string &name_)

virtual	~ParagraphTree ()

ParagraphType	get_type () const

bool	is_itemlist_member () const

unsigned	get_enumeration () const

EnumerationType	get_enum_type () const

const char *	readable_type () const

size_t	countTextNodes ()

bool	contains (ParagraphTree *that)

ParagraphTree *	predecessor (ParagraphTree *before_this)

void	append (ParagraphTree *new_brother)

bool	is_some_brother (const ParagraphTree *other) const

ParagraphTree *	takeAllInFrontOf (ParagraphTree *after)

ParagraphTree *	firstListMember ()

ParagraphTree *	nextListMemberAfter (const ParagraphTree &previous)

ParagraphTree *	nextListMember () const

ParagraphTree *	firstWithLessIndentThan (int wanted_indentation)

void	format_indentations ()

void	format_lists ()

void	xml_write ()

	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_)

virtual	~IslandHoppingParameter ()

	IslandHopping ()

void	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)

virtual	~IslandHopping ()

void	set_alignment_length (int len)

void	set_ref_sequence (const char *ref_seq)

void	set_toAlign_sequence (const char *toAlign_seq)

void	set_helix (const char *hel)

void	set_range (ExplicitRange range)

const char *	get_result () const

const char *	get_result_ref () const

int	get_result_length () const

bool	was_aligned () const

GB_ERROR	do_align ()

	ConfigMarkerDisplay (SmartPtr< ConstStrArray > config_, GBDATA *gb_main_)

const char *	get_marker_name (int markerIdx) const OVERRIDE

void	retrieve_marker_state (const char *speciesName, NodeMarkers &node) OVERRIDE

void	handle_click (int markerIdx, AW_MouseButton button, AWT_graphic_exports &exports) OVERRIDE

	nt_item_type_species_selector ()

	~nt_item_type_species_selector () OVERRIDE

const char *	get_self_awar () const OVERRIDE

size_t	get_self_awar_content_length () const OVERRIDE

GBDATA *	current (AW_root root, GBDATA gb_main) const OVERRIDE

const char *	getKeyPath () const OVERRIDE

	AP_pars_root (AliView aliView, AP_sequence seq_proto, bool add_delete_callbacks, const group_scaling *scaling)

TreeNode *	makeNode () const OVERRIDE

void	destroyNode (TreeNode *node) const OVERRIDE

GB_ERROR	saveToDB () OVERRIDE

AP_UPDATE_FLAGS	check_update () OVERRIDE

bool	was_saved () const

	AP_tree_nlen (AP_pars_root *troot)

	DEFINE_TREE_ACCESSORS (AP_pars_root, AP_tree_nlen)

	OVERRIDE_SEQ_ACCESSORS (AP_combinableSeq, AP_tree)

void	unhash_sequence ()

Mutations	costs (char *mutPerSite=NULp)

Mutations	stored_costs () const

bool	rememberState (AP_STACK_MODE, Level frame_level)

void	revertToPreviousState (Level curr_frameLevel, bool &rootPopped)

void	restore (NodeState &state)

void	restore_nondestructive (const NodeState &state)

bool	acceptCurrentState (Level frame_level)

Level	last_remembered_frame () const

bool	may_be_recollected () const

const StateStack &	get_states () const

bool	recalc_marked_from_sons ()

void	recalc_marked_from_sons_and_forward_upwards ()

void	insert (AP_tree_nlen *new_brother)

void	initial_insert (AP_tree_nlen new_brother, AP_pars_root troot)

AP_tree_nlen *	REMOVE () OVERRIDE

void	swap_sons () OVERRIDE

void	swap_assymetric (AP_TREE_SIDE mode)

void	moveNextTo (AP_tree_nlen *new_brother, AP_FLOAT rel_pos)

void	set_root () OVERRIDE

void	moveTo (AP_tree_edge *e)

void	insert (AP_tree *new_brother) OVERRIDE

void	initial_insert (AP_tree new_brother, AP_tree_root troot) OVERRIDE

void	moveNextTo (AP_tree *node, AP_FLOAT rel_pos) OVERRIDE

void	exchange (AP_tree_nlen *other)

void	parsimony_rec (char *mutPerSite=NULp)

Mutations	nn_interchange_rec (EdgeSpec whichEdges, AP_BL_MODE mode)

AP_FLOAT	nn_interchange (AP_FLOAT parsimony, AP_BL_MODE mode)

void	setBranchlen (double leftLen, double rightLen)

const char *	fullname () const

const char *	sortByName ()

int	indexOf (const AP_tree_edge *e) const

AP_tree_edge *	edgeTo (const AP_tree_nlen *brother) const

AP_tree_edge *	nextEdge (const AP_tree_edge *afterThatEdge=NULp) const

int	unusedEdgeIndex () const

void	linkAllEdges (AP_tree_edge edge1, AP_tree_edge edge2, AP_tree_edge *edge3)

void	unlinkAllEdges (AP_tree_edge edgePtr1, AP_tree_edge edgePtr2, AP_tree_edge **edgePtr3)

char *	getSequenceCopy ()

	fake_agt (ArbParsimony &parsimony_)

	~fake_agt () OVERRIDE

void	init (AliView *aliview)

void	read_tree_settings () OVERRIDE

	ArbMatchResultSet ()

	ArbMatchResultSet (const ArbProbe *pProbe)

	ArbMatchResultSet (const ArbMatchResultSet &rCopy)

	DECLARE_ASSIGNMENT_OPERATOR (ArbMatchResultSet)

virtual	~ArbMatchResultSet ()

void	initialise (const ArbProbe *pProbe, int nIndex)

bool	add (const char pName, const char pFullName, const char pMatchPart, const char pResult, const ArbProbeMatchWeighting &rMatchWeighting)

bool	addComment (const char *pComment)

void	findMaximumWeight (double &dMaximumWeight) const

const ArbMatchResultPtrByStringMultiMap &	resultMap () const

bool	isMatched (const ArbStringList &rCladeList, bool &bPartialMatch, double dThreshold, double dCladeMarkedThreshold, double dCladePartiallyMarkedThreshold) const

bool	isMatched (const std::string &rName, double dThreshold) const

const ArbStringList &	commentList () const

bool	hasResults () const

const ArbProbe *	probe () const

void	headline (const char *pHeadline, int nEndFullName)

const std::string &	headline () const

int	endFullName () const

void	enumerateResults (ArbMatchResultPtrByDoubleMultiMap &rMap, int nMaxFullName)

int	index () const

bool	get (const long _row, const long _col) OVERRIDE

bool	set (const long _row, const long _col, const bool _value) OVERRIDE

void	setTrue (const long _row, const long _col) OVERRIDE

void	setFalse (const long _row, const long _col) OVERRIDE

bool	load (PS_FileBuffer *_file) OVERRIDE

bool	copy (const PS_BitMap_Fast *_other_bitmap)

bool	reserve (const long _capacity) OVERRIDE

	PS_BitMap_Fast (const bool _bias, const long _capacity)

void	recalcCounters ()

long	getCountFor (const long _index)

long	getTrueIndicesFor (const long _index, PS_BitSet::IndexSet &_index_set) OVERRIDE

long	getFalseIndicesFor (const long _index, PS_BitSet::IndexSet &_index_set) OVERRIDE

long	getTrueIndicesForRow (const long _row, PS_BitSet::IndexSet &_index_set)

long	getFalseIndicesForRow (const long _row, PS_BitSet::IndexSet &_index_set)

long	getCountOfTrues () OVERRIDE

bool	get (const long _row, const long _col) OVERRIDE

bool	set (const long _row, const long _col, const bool _value) OVERRIDE

void	setTrue (const long _row, const long _col) OVERRIDE

void	setFalse (const long _row, const long _col) OVERRIDE

void	print (FILE *out) OVERRIDE

void	printGNUplot (const char _title, char _buffer, PS_FileBuffer *_file) OVERRIDE

bool	load (PS_FileBuffer *_file) OVERRIDE

bool	copy (const PS_BitMap_Counted *_other_bitmap)

bool	reserve (const long _capacity) OVERRIDE

	PS_BitMap_Counted (PS_FileBuffer *_file)

	PS_BitMap_Counted (const bool _bias, const long _capacity)

	~PS_BitMap_Counted () OVERRIDE

bool	Get (const long _index) OVERRIDE

bool	Set (const long _index, const bool _value) OVERRIDE

void	setTrue (const long _index) OVERRIDE

void	setFalse (const long _index) OVERRIDE

bool	reserve (const long _capacity) OVERRIDE

	PS_BitSet_Fast (PS_FileBuffer *_file, const long _fill_index=-1)

	PS_BitSet_Fast (bool _bias, long _capacity)

bool	load ()

bool	save ()

bool	saveTo (const char *_filename)

bool	merge (const char *_other_db_name)

PS_NodePtr	getRootNode ()

const PS_NodePtr	getConstRootNode ()

bool	getIDForName (SpeciesID &_id, const string &_name)

bool	getNameForID (const SpeciesID _id, string &_name)

bool	insertMapping (SpeciesID _id, const string &_name)

void	setMappings (Name2IDMap &_name2id, ID2NameMap &_id2name)

SpeciesID	getMaxID ()

SpeciesID	getMinID ()

long	getSpeciesCount ()

bool	isReadonly ()

void	reinit (const char *_name, bool _readonly)

	PS_Database (const char *_name, bool _readonly)

	~PS_Database () OVERRIDE

	OpenGLGraphics ()

virtual	~OpenGLGraphics ()

void	WinToScreenCoordinates (int x, int y, GLdouble *screenPos)

void	ScreenToWinCoordinates (int x, int y, GLdouble *winPos)

void	PrintString (float x, float y, float z, char s, void font)

void	init_font (GLuint base, char *f)

void	print_string (GLuint base, char *s)

void	InitMainFont (char *f)

void	SetOpenGLBackGroundColor ()

ColorRGBf	ConvertGCtoRGB (int gc)

void	SetColor (int gc)

ColorRGBf	GetColor (int gc)

void	DrawBox (float x, float y, float width, float height)

	GLRenderer ()

virtual	~GLRenderer ()

void	DisplayMolecule (Structure3D *cStr)

void	DisplayMoleculeName (int w, int h, Structure3D *cStr)

void	DisplayMoleculeMask (int w, int h)

void	DoHelixMapping ()

void	DisplayHelices ()

void	DisplayHelixBackBone ()

void	DisplayHelixNumbers ()

void	DisplayBasePositions ()

void	DisplayMappedSpBasePositions ()

void	DisplayMappedSpInsertions ()

void	DisplayHelixMidPoints (Texture2D *cImages)

void	BeginTexturizer ()

void	EndTexturizer ()

void	TexturizeStructure (Texture2D cImages, Structure3D cStructure)

void	fixInvalidHelixPositions (int maxHelixNumber)

	Texture2D ()

virtual	~Texture2D ()

void	LoadGLTextures ()

size_t	getMsaLen ()

const vector< size_t > &	getPositionMap ()

VecVecType *	getSequences ()

GB_ERROR	get_error () const

bool	has_error () const

	AlignedSequenceLoader (class GBDATA *gb_main)

	~AlignedSequenceLoader ()

Cma *	getCma ()

GB_ERROR	saveSAI (GBDATA *gb_main, vector< size_t > clusters, double threshold)

vector< char >	normalizeClusters (vector< size_t > clusters)

AlignedSequenceLoader *	getLoader ()

GB_ERROR	get_error () const

bool	has_error () const

	Analyser (class GBDATA *gb_main)

virtual	~Analyser ()

MatrixXd	computeMutualInformation (VecVecType &seq)

MatrixXd	computeMutualInformationP (VecVecType &seq)

VectorXi	computeClusters (list< MITuple > mituples, size_t size, double threshold)

list< MITuple >	compute_mituples (MatrixXd mutualInformation)

MatrixXd	getMI ()

MatrixXd	getMIp ()

MatrixXd	getEntropy ()

MatrixXd	getJointEntropy ()

VectorXi	getClusters ()

	Cma (vector< string > &alph, int seq_number)

virtual	~Cma ()

	SEC_graphic (AW_root aw_root, GBDATA gb_main)

	~SEC_graphic () OVERRIDE

AW_gc_manager *	init_devices (AW_window , AW_device , AWT_canvas *scr) OVERRIDE

void	show (AW_device *device) OVERRIDE

void	handle_command (AW_device *device, AWT_graphic_event &event) OVERRIDE

GB_ERROR	load_from_DB (GBDATA gb_main, const char name) OVERRIDE

GB_ERROR	save_to_DB (GBDATA gb_main, const char name) OVERRIDE

void	check_for_DB_update (GBDATA *gb_main) OVERRIDE

void	notify_synchronized (GBDATA *gb_main) OVERRIDE

GB_ERROR	write_data_to_db (const char data, const char x_string) const

GB_ERROR	read_data_from_db (char data, char x_string) const

void	request_update (SEC_update_request req)

	SEC_helix (SEC_root root, SEC_helix_strand to_root, SEC_helix_strand *from_root)

	~SEC_helix () OVERRIDE

void	calculate_helix_size ()

void	calculate_helix_coordinates ()

void	save (std::ostream &out, int indent, const XString &x_string)

GB_ERROR	read (std::istream &in, int version, double &old_angle_in)

size_t	get_base_length ()

SEC_helix_strand *	strandToRoot () const

SEC_helix_strand *	strandToOutside () const

SEC_helix_strand *	strandAwayFrom (const SEC_loop *loop) const

SEC_helix_strand *	strandTowards (const SEC_loop *loop) const

SEC_loop *	otherLoop (const SEC_loop *loop) const

SEC_loop *	rootsideLoop () const

SEC_loop *	outsideLoop () const

bool	hasLoop (SEC_loop *loop) const

void	setFixpoints (const Position &rootside, const Position &outside)

void	flip ()

void	fixAngleBugs (int version)

void	invalidate_sub_angles () OVERRIDE

SEC_BASE_TYPE	getType () const OVERRIDE

void	reset_angles () OVERRIDE

const Position &	get_fixpoint () const OVERRIDE

void	orientationChanged () OVERRIDE

void	sizeChanged () OVERRIDE

	SEC_helix_strand ()

	~SEC_helix_strand () OVERRIDE

GB_ERROR	read (SEC_loop *loop_, std::istream &in, int version)

void	paint (AW_device *device)

void	unlink (bool fromOtherStrandAsWell)

void	paint_strands (AW_device *device, const Vector &strand_dir, const double &strand_length)

void	paint_constraints (AW_device *device)

const SEC_root *	get_root () const

SEC_root *	get_root ()

const SEC_helix *	get_helix () const

SEC_helix *	get_helix ()

const SEC_helix_strand *	get_other_strand () const

SEC_helix_strand *	get_other_strand ()

const Position &	get_fixpoint () const

bool	isRootsideFixpoint () const

bool	pointsToRoot () const

bool	pointsToOutside () const

bool	is3end () const

const Position &	rightAttachPoint () const

const Position &	leftAttachPoint () const

const Position &	startAttachPoint () const

const Position &	endAttachPoint () const

int	rightAttachAbspos () const

int	leftAttachAbspos () const

int	startAttachAbspos () const

int	endAttachAbspos () const

void	setFixpoint (const Position &p)

void	setAttachPoints (const Position &left, const Position &right)

const SEC_segment *	get_next_segment () const

SEC_segment *	get_next_segment ()

SEC_segment *	get_previous_segment ()

const SEC_loop *	get_origin_loop () const

SEC_loop *	get_origin_loop ()

SEC_loop *	get_destination_loop ()

SEC_loop *	get_rootside_loop ()

void	set_origin_loop (SEC_loop *loop_)

void	set_next_segment (SEC_segment *next_segment_)

	SEC_segment ()

	~SEC_segment () OVERRIDE

void	save (std::ostream &out, int indent, const XString &x_string)

GB_ERROR	read (SEC_loop *loop_, std::istream &in, int version)

void	calculate_segment_size ()

void	calculate_segment_coordinates (const Position &start, const Position &end)

void	paint (AW_device device, SEC_helix_strand previous_strand_pointer)

void	unlink ()

void	prepare_paint (SEC_helix_strand *previous_strand_pointer, double &gamma, double &eta, double &radius, int &base_count, double &angle_step)

void	mergeWith (SEC_segment other, SEC_loop target_loop)

SEC_helix_strand *	split (size_t start, size_t end, SEC_segment **new_segment)

int	is_endings_segment ()

void	delete_pointer_2 (SEC_helix_strand *strand)

SEC_helix_strand *	get_previous_strand ()

const SEC_helix_strand *	get_next_strand () const

SEC_helix_strand *	get_next_strand ()

const SEC_loop *	get_loop () const

SEC_loop *	get_loop ()

double	get_alpha ()

void	set_next_strand (SEC_helix_strand *strand)

void	set_loop (SEC_loop *loop_)

	SEC_loop (SEC_root *root_)

	~SEC_loop () OVERRIDE

void	save (std::ostream &out, int indent, const XString &x_string)

GB_ERROR	read (SEC_helix_strand *rootside_strand, std::istream &in, int version, double loop_angle)

void	calculate_loop_size ()

void	calculate_loop_coordinates ()

void	paint (AW_device *device)

void	paint_constraints (AW_device *device)

const Position &	get_center () const

const double &	get_circumference () const

bool	is_root_loop () const

SEC_helix_strand *	get_rootside_strand () const

SEC_helix *	get_rootside_helix () const

SEC_helix_strand *	get_fixpoint_strand () const

SEC_helix *	get_fixpoint_helix () const

void	set_fixpoint_strand (SEC_helix_strand *strand)

void	toggle_root (SEC_loop *root_loop)

void	set_center (const Position &p)

void	fixAngleBugs (int version)

void	invalidate_sub_angles () OVERRIDE

SEC_BASE_TYPE	getType () const OVERRIDE

void	reset_angles () OVERRIDE

const Position &	get_fixpoint () const OVERRIDE

void	orientationChanged () OVERRIDE

void	sizeChanged () OVERRIDE

	ItemQueryKey (GBDATA gb_main, const char field_name)

	~ItemQueryKey ()

char *	get_target_data (const QueryTarget &target, GB_ERROR &error) const OVERRIDE

const char *	get_name () const OVERRIDE

bool	iterate () const OVERRIDE

void	reset () const OVERRIDE

GBDATA *	get_first_field (GBDATA *gb_item) const

	GroupSearchRoot ()

	~GroupSearchRoot () FINAL_OVERRIDE

	DEFINE_TREE_ROOT_ACCESSORS (GroupSearchRoot, GroupSearchTree)

TreeNode *	makeNode () const OVERRIDE

void	destroyNode (TreeNode *node) const OVERRIDE

	GroupSearchTree (GroupSearchRoot *root)

	DEFINE_TREE_RELATIVES_ACCESSORS (GroupSearchTree)

unsigned	get_leaf_count () const FINAL_OVERRIDE

void	compute_tree () OVERRIDE

unsigned	get_marked_count () const

unsigned	get_zombie_count () const

double	get_average_ingroup_distance () const

size_t	unitsize () const OVERRIDE

bool	has_slice () const OVERRIDE

AliDataPtr	create_gap (size_t gapsize, const UnitPair &gapinfo) const OVERRIDE

AliDataPtr	slice_down (size_t start, size_t count) const OVERRIDE

int	operate_on_mem (void *mem, size_t start, size_t count, memop op) const OVERRIDE

int	cmp_data (size_t start, const AliData &other, size_t ostart, size_t count) const OVERRIDE

UnitPtr	unit_left_of (size_t pos) const OVERRIDE

UnitPtr	unit_right_of (size_t pos) const OVERRIDE

	AliFormatCommand (size_t wanted_len_)

AliDataPtr	apply (AliDataPtr to, GB_ERROR &error) const OVERRIDE

GB_ERROR	check_applicable_to (const Alignment &ali, size_t &resulting_ali_length) const OVERRIDE

	ItemShader_impl (AW_gc_manager *gcman_, const string &id_, const string &description_, const string &help_id_, ReshadeCallback rcb, int undef_gc)

void	register_plugin (ShaderPluginPtr plugin) OVERRIDE

bool	activate_plugin (const string &plugin_id) OVERRIDE

bool	activate_plugin_impl (const string &plugin_id)

std::string	active_plugin_name () const OVERRIDE

const char *	shader_awar (const char *name) const

const char *	tmp_shader_awar (const char *name) const

void	init_awars (AW_root *awr)

void	init () OVERRIDE

void	check_dimension_change () OVERRIDE

void	popup_config_window (AW_root *awr) OVERRIDE

void	configure_active_plugin (AW_root *awr)

void	selected_plugin_changed_cb (AW_root *awr)

void	selected_range_changed_cb (AW_root *awr)

void	configure_colors_cb (AW_window *aww)

void	phase_changed_cb (AW_root *awr)

void	reset_phasing_cb (AW_root *awr) const

char *	store_config_cb () const

void	load_or_reset_config_cb (const char *cfgstr)

	LinearTuple (float val_)

	~LinearTuple () OVERRIDE

bool	is_defined () const OVERRIDE

ShadedValue	clone () const OVERRIDE

int	range_offset (const Phaser &phaser) const OVERRIDE

ShadedValue	reverse_mix (float other_ratio, const LinearTuple &other) const OVERRIDE

ShadedValue	mix (float my_ratio, const ValueTuple &other) const OVERRIDE

	PlanarTuple (float val1_, float val2_)

	~PlanarTuple () OVERRIDE

bool	is_defined () const OVERRIDE

ShadedValue	clone () const OVERRIDE

int	range_offset (const Phaser &phaser) const OVERRIDE

ShadedValue	reverse_mix (float other_ratio, const PlanarTuple &other) const OVERRIDE

ShadedValue	mix (float my_ratio, const ValueTuple &other) const OVERRIDE

	SpatialTuple (float val1_, float val2_, float val3_)

	~SpatialTuple () OVERRIDE

bool	is_defined () const OVERRIDE

ShadedValue	clone () const OVERRIDE

int	range_offset (const Phaser &phaser) const OVERRIDE

ShadedValue	reverse_mix (float other_ratio, const SpatialTuple &other) const OVERRIDE

ShadedValue	mix (float my_ratio, const ValueTuple &other) const OVERRIDE

	NDS_Labeler (NDS_Type type_)

virtual	~NDS_Labeler ()

const char *	speciesLabel (GBDATA gb_main, GBDATA gb_species, TreeNode species, const char tree_name) const OVERRIDE

const char *	groupLabel (GBDATA gb_main, GBDATA gb_group, TreeNode species, const char tree_name) const OVERRIDE

NDS_Type	get_NDS_Type () const

long	max_columns (GBDATA *gb_main) const

	SaiTranslator (char default_translation)

std::string	get_config () const OVERRIDE

ErrorOrString	apply (const SaiCalcEnv &calcEnv) const OVERRIDE

void	addTranslation (const char *from, char to)

void	deduceTranslations (class ConfigMapping &mapping) const

	SaiMatrixTranslator (SaiOperatorPtr Default)

std::string	get_config () const OVERRIDE

ErrorOrString	apply (const SaiCalcEnv &calcEnv) const OVERRIDE

void	addOperator (const char *from, SaiOperatorPtr to)

	AP_sequence_parsimony (const AliView *aliview)

	~AP_sequence_parsimony () OVERRIDE

const char *	get_sequence () const

const unsigned char *	get_usequence () const

AP_combinableSeq *	dup () const OVERRIDE

Mutations	combine_seq (const AP_combinableSeq lefts, const AP_combinableSeq rights, char *mutation_per_site) OVERRIDE

Mutations	mutations_if_combined_with (const AP_combinableSeq *other) OVERRIDE

void	partial_match (const AP_combinableSeq part, long overlap, long *penalty) const OVERRIDE

uint32_t	checksum () const OVERRIDE

int	cmp_combined (const AP_combinableSeq *other) const OVERRIDE

	AP_sequence_protein (const AliView *aliview)

	~AP_sequence_protein () OVERRIDE

const AP_PROTEINS *	get_sequence () const

AP_combinableSeq *	dup () const OVERRIDE

Mutations	combine_seq (const AP_combinableSeq lefts, const AP_combinableSeq rights, char *mutation_per_site=NULp) OVERRIDE

Mutations	mutations_if_combined_with (const AP_combinableSeq *other) OVERRIDE

void	partial_match (const AP_combinableSeq part, long overlap, long *penalty) const OVERRIDE

uint32_t	checksum () const OVERRIDE

int	cmp_combined (const AP_combinableSeq *other) const OVERRIDE

	BranchRotator (AW_device device_, AP_tree node_, const LineVector &clicked_branch_, const Position &mousepos, AWT_graphic_exports &exports_)

void	draw_drag_indicator (AW_device *IF_DEBUG(same_device), int drag_gc) const OVERRIDE

	ArbWriter (string ta, string f, int c)

	~ArbWriter ()

void	addSequence (GBDATA *gbspec) OVERRIDE

void	finish () OVERRIDE

	AwtiExportWriter (GBDATA _gbmain, const char _dbname, const char eft, const char out, int c)

void	addSequence (GBDATA *gbspec) OVERRIDE

void	finish () OVERRIDE

	AW_device_print (AW_common *common_)

GB_ERROR	open (const char *path) __ATTR__USERESULT

void	close ()

void	set_color_mode (bool mode)

AW_DEVICE_TYPE	type ()

void	draw_text (int gc, const char *textBuffer, size_t textStart, size_t textLen, const AW::Position &pos)

	AW_clicked_polygon ()

	AW_clicked_polygon (const AW_clicked_polygon &other)

	DECLARE_ASSIGNMENT_OPERATOR (AW_clicked_polygon)

	~AW_clicked_polygon ()

void	assign (int npos_, const AW::Position pos_, int distance_, const AW_pos &nearest_rel_pos_, const AW_click_cd click_cd_)

bool	operator== (const AW_clicked_element &other) const OVERRIDE

AW::Position	get_attach_point () const OVERRIDE

AW::Rectangle	get_bounding_box () const OVERRIDE

int	indicate_selected (AW_device *d, int gc) const OVERRIDE

AW_clicked_element *	clone () const OVERRIDE

const AW::Position *	get_polygon (int &posCount) const

	AW_device_click (AW_common *common_)

AW_DEVICE_TYPE	type () OVERRIDE

void	init_click (const AW::Position &click, int max_distance, AW_bitset filteri)

const AW_clicked_element *	best_click (ClickPreference prefer=PREFER_NEARER)

	AW_repeated_question ()

virtual	~AW_repeated_question ()

void	add_help (const char *help_file)

int	get_answer (const char unique_id, const char question, const char buttons, const char to_all, bool add_abort)

	AW_window_simple ()

	~AW_window_simple ()

void	init (AW_root root, const char wid, const char *windowname)

	AW_device_Xm (AW_common *commoni)

AW_common_Xm *	get_common () const

AW_DEVICE_TYPE	type ()

void	clear (AW_bitset filteri)

void	clear_part (const AW::Rectangle &rect, AW_bitset filteri)

void	flush ()

void	move_region (AW_pos src_x, AW_pos src_y, AW_pos width, AW_pos height, AW_pos dest_x, AW_pos dest_y)

	XML_Attribute (const std::string &name_, const std::string &content_)

virtual	~XML_Attribute ()

XML_Attribute *	append_to (XML_Attribute *queue)

void	print (FILE *out) const

	XML_Tag (const std::string &name_)

	~XML_Tag () OVERRIDE

void	add_attribute (const std::string &name_, const std::string &content_)

void	add_attribute (const std::string &name_, int value)

void	add_son (XML_Node *son_, bool son_is_tag) OVERRIDE

void	remove_son (XML_Node *son_) OVERRIDE

void	open (FILE *out) OVERRIDE

void	close (FILE *out) OVERRIDE

void	set_on_extra_line (bool oel)

	XML_Document (const std::string &name_, const std::string &dtd_, FILE *out_)

virtual	~XML_Document ()

XML_Node *	LatestSon ()

void	set_LatestSon (XML_Node *latest_son_)

XML_Tag &	getRoot ()

void	add_attribute (const std::string &name_, const std::string &content_)

FILE *	Out ()

Public Member Functions inherited from XML_Node
	XML_Node (bool is_tag)

virtual	~XML_Node ()

int	Indent () const

bool	Opened () const

Public Member Functions inherited from AW_device
	AW_device (class AW_common *common_)

virtual	~AW_device ()

const AW_click_cd *	get_click_cd () const

AW_bitset	get_filter () const

void	reset ()

const AW_screen_area &	get_area_size () const

AW::Rectangle	get_rtransformed_cliprect () const

void	set_filter (AW_bitset filteri)

void	push_clip_scale ()

void	pop_clip_scale ()

bool	ready_to_draw (int gc)

bool	line (int gc, const AW::LineVector &Line, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	line (int gc, const AW::Position &pos1, const AW::Position &pos2, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	line (int gc, AW_pos x0, AW_pos y0, AW_pos x1, AW_pos y1, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	text (int gc, const SizedCstr &cstr, const AW::Position &pos, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)

bool	text (int gc, const char *str, const AW::Position &pos, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)

bool	text (int gc, const char *str, AW_pos x, AW_pos y, AW_pos alignment=0.0, AW_bitset filteri=AW_ALL_DEVICES_UNSCALED)

bool	invisible (const AW::Position &pos, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	box (int gc, AW::FillStyle filled, const AW::Rectangle &rect, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	box (int gc, AW::FillStyle filled, const AW::Position &pos, const AW::Vector &size, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	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)

bool	circle (int gc, AW::FillStyle filled, const AW::Position &center, const AW::Vector &radius, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	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)

bool	circle (int gc, AW::FillStyle filled, const AW::Rectangle &rect, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	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)

bool	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)

bool	polygon (int gc, AW::FillStyle filled, int npoints, const AW_pos *points, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	polygon (int gc, AW::FillStyle filled, int npos, const AW::Position *pos, AW_bitset filteri=AW_ALL_DEVICES_SCALED)

bool	text_overlay (int gc, const SizedCstr &cstr, const AW::Position &pos, AW_pos alignment, AW_bitset filteri, TextOverlayCallback toc, AW_CL cduser=0)

void	clear_part (AW_pos x, AW_pos y, AW_pos width, AW_pos height, AW_bitset filteri)

virtual void	fast ()

virtual void	slow ()

Public Member Functions inherited from AW_zoomable
	AW_zoomable ()

virtual	~AW_zoomable ()

void	zoom (AW_pos scale)

AW_pos	get_scale () const

AW_pos	get_unscale () const

AW::Vector	get_offset () const

void	rotate (AW_pos angle)

void	set_offset (const AW::Vector &off)

void	shift (const AW::Vector &doff)

void	reset ()

double	transform_size (const double &size) const

double	rtransform_size (const double &size) const

double	rtransform_pixelsize (int pixelsize) const

AW::Vector	transform (const AW::Vector &vec) const

AW::Vector	rtransform (const AW::Vector &vec) const

AW::Position	transform (const AW::Position &pos) const

AW::Position	rtransform (const AW::Position &pos) const

AW::LineVector	transform (const AW::LineVector &lvec) const

AW::LineVector	rtransform (const AW::LineVector &lvec) const

AW::Rectangle	transform (const AW::Rectangle &rect) const

AW::Rectangle	rtransform (const AW::Rectangle &rect) const

void	transform (AW_pos x, AW_pos y, AW_pos &xout, AW_pos &yout) const

void	rtransform (AW_pos x, AW_pos y, AW_pos &xout, AW_pos &yout) const

Public Member Functions inherited from AW_stylable
	AW_stylable (AW_common *common_)

virtual	~AW_stylable ()

AW_common *	get_common () const

void	new_gc (int gc)

void	set_grey_level (int gc, AW_grey_level grey_level)

AW_grey_level	get_grey_level (int gc)

void	set_font (int gc, AW_font fontnr, int size, int *found_size)

void	set_line_attributes (int gc, short width, AW_linestyle style)

void	set_function (int gc, AW_function function)

void	establish_default (int gc)

void	set_foreground_color (int gc, AW_color_idx color)

int	get_string_size (int gc, long textlen) const

int	get_string_size (int gc, const SizedCstr &cstr) const

const AW_font_limits &	get_font_limits (int gc, char c) const

int	get_available_fontsizes (int gc, AW_font font_nr, int *available_sizes)

void	reset_style ()

Public Member Functions inherited from AW_clipable
	AW_clipable (const AW_screen_area &screen)

virtual	~AW_clipable ()

bool	is_below_clip (double ypos) const

bool	is_above_clip (double ypos) const

bool	is_leftof_clip (double xpos) const

bool	is_rightof_clip (double xpos) const

bool	is_outside_clip (AW::Position pos) const

bool	is_outside_clip (AW::Rectangle rect) const

bool	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)

bool	clip (const AW::LineVector &line, AW::LineVector &clippedLine)

bool	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)

bool	box_clip (const AW::Rectangle &rect, AW::Rectangle &clippedRect)

bool	box_clip (int npos, const AW::Position pos, int &nclippedPos, AW::Position &clippedPos)

bool	force_into_clipbox (const AW::Position &pos, AW::Position &forcedPos)

void	set_top_clip_border (int top, bool allow_oversize=false)

void	set_bottom_clip_border (int bottom, bool allow_oversize=false)

void	set_bottom_clip_margin (int bottom, bool allow_oversize=false)

void	set_left_clip_border (int left, bool allow_oversize=false)

void	set_right_clip_border (int right, bool allow_oversize=false)

const AW_screen_area &	get_cliprect () const

void	set_clipall ()

bool	completely_clipped () const

bool	allow_top_font_overlap () const

bool	allow_bottom_font_overlap () const

bool	allow_left_font_overlap () const

bool	allow_right_font_overlap () const

const AW_font_overlap &	get_font_overlap () const

void	set_top_font_overlap (bool allow)

void	set_bottom_font_overlap (bool allow)

void	set_left_font_overlap (bool allow)

void	set_right_font_overlap (bool allow)

void	set_vertical_font_overlap (bool allow)

void	set_horizontal_font_overlap (bool allow)

void	set_font_overlap (bool allow)

void	set_font_overlap (const AW_font_overlap &fo)

void	reduce_top_clip_border (int top)

void	reduce_bottom_clip_border (int bottom)

void	reduce_left_clip_border (int left)

void	reduce_right_clip_border (int right)

int	reduceClipBorders (int top, int bottom, int left, int right)

Public Member Functions inherited from AW_window
	AW_window ()

virtual	~AW_window ()

const char *	window_local_awarname (const char *localname, bool tmp=true)

class AW_awar *	window_local_awar (const char *localname, bool tmp=true)

void	create_window_variables ()

void	recalc_pos_atShow (AW_PosRecalc pr)

void	recalc_size_atShow (enum AW_SizeRecalc sr)

AW_PosRecalc	get_recalc_pos_atShow () const

void	reset_layout (const char *YYYYMMDD)

void	allow_delete_window (bool allow_close)

void	on_hide (const WindowCallback &call_on_hide)

void	on_hide (WindowCallbackSimple call_on_hide)

void	run_focus_callback ()

void	run_popup_callbacks ()

void	show_modal ()

void	set_window_title_intern (char *title)

void	update_label (Widget widget, const char *var_value)

void	update_toggle (Widget widget, const char *var_value, AW_CL cd)

void	update_input_field (Widget widget, const char *var_value)

void	update_text_field (Widget widget, const char *var_value)

void	update_scaler (Widget widget, AW_awar *awar, AW_ScalerType scalerType)

void	create_invisible (int columns)

void *	_create_option_entry (AW_VARIABLE_TYPE type, const char name, const char mnemonic, const char *name_of_color)

void	refresh_toggle_field (int toggle_field_number)

void	_set_activate_callback (void *widget)

void	increment_at_commands (int width, int height)

AW_color_idx	alloc_named_data_color (int colnum, const char *colorname)

void	_get_area_size (AW_area area, AW_screen_area *square)

int	label_widget (void wgt, AW_label str, char mnemonic=NULp, int width=0, int alignment=0)

AW_root *	get_root ()

void	show ()

void	hide ()

void	activate ()

bool	is_shown () const

void	hide_or_notify (const char *error)

void	message (char *title, int ms)

void	set_window_title (const char *title)

const char *	get_window_title () const

const char *	get_window_id () const

const char *	local_id (const char *id) const

void	set_info_area_height (int height)

void	set_bottom_area_height (int height)

void	set_popup_callback (const WindowCallback &wcb)

void	set_focus_callback (const WindowCallback &wcb)

bool	is_focus_callback (AnyWinCB f)

void	set_expose_callback (AW_area area, const WindowCallback &wcb)

void	set_resize_callback (AW_area area, const WindowCallback &wcb)

void	set_input_callback (AW_area area, const WindowCallback &wcb)

void	set_motion_callback (AW_area area, const WindowCallback &wcb)

void	set_double_click_callback (AW_area area, const WindowCallback &wcb)

bool	is_expose_callback (AW_area area, AnyWinCB f)

bool	is_resize_callback (AW_area area, AnyWinCB f)

void	get_event (AW_event *eventi) const

void	force_expose ()

AW_device *	get_device (AW_area area)

AW_device_click *	get_click_device (AW_area area, int mousex, int mousey, int max_distance)

AW_device_size *	get_size_device (AW_area area)

AW_device_print *	get_print_device (AW_area area)

AW_common *	get_common (AW_area area)

void	create_menu (const char name, const char mnemonic, AW_active mask=AWM_ALL)

void	insert_sub_menu (const char name, const char mnemonic, AW_active mask=AWM_ALL)

void	insert_menu_topic (const char id, const char name, const char mnemonic, const char help_text_, AW_active mask, const WindowCallback &wcb)

void	insert_menu_topic (const char id, const char name, const char mnemonic, const char help_text_, AW_active mask, const CreateWindowCallback &cwcb)

void	insert_menu_topic (const char id, const char name, const char mnemonic, const char help_text_, AW_active mask, WindowCallbackSimple cb)

void	insert_menu_topic (const char id, const char name, const char mnemonic, const char help_text_, AW_active mask, CreateWindowCallbackSimple cb)

void	sep______________ ()

void	close_sub_menu ()

void	insert_help_topic (const char labeli, const char mnemonic, const char *helpText, AW_active mask, const WindowCallback &cb)

void	insert_help_topic (const char labeli, const char mnemonic, const char *helpText, AW_active mask, WindowCallbackSimple cb)

int	create_mode (const char pixmap, const char help_text_, AW_active mask, const WindowCallback &cb)

void	select_mode (int mode)

void	tell_scrolled_picture_size (AW_screen_area rectangle)

void	tell_scrolled_picture_size (AW_world rectangle)

AW_pos	get_scrolled_picture_width () const

AW_pos	get_scrolled_picture_height () const

void	reset_scrolled_picture_size ()

void	get_scrollarea_size (AW_screen_area *square)

void	calculate_scrollbars ()

void	set_vertical_scrollbar_position (int position)

void	set_horizontal_scrollbar_position (int position)

void	set_vertical_change_callback (const WindowCallback &wcb)

void	set_horizontal_change_callback (const WindowCallback &wcb)

void	set_vertical_scrollbar_top_indent (int indent)

void	set_horizontal_scrollbar_left_indent (int indent)

void	update_scrollbar_settings_from_awars (AW_orientation orientation)

void	create_user_geometry_awars (int posx, int posy, int width, int height)

void	get_window_size (int &width, int &height)

void	window_fit ()

void	load_xfig (const char *file, bool resize=true)

void	draw_line (int x1, int y1, int x2, int y2, int width, bool resize)

void	label_length (int length)

void	button_length (int length)

void	button_height (int height)

int	get_button_length () const

void	highlight ()

void	auto_increment (int dx, int dy)

void	auto_space (int xspace, int yspace)

void	shadow_width (int shadow_thickness)

void	TuneBackground (Widget w, int modStrength)

void	TuneOrSetBackground (Widget w, const char *color, int modStrength)

void	at (int x, int y)

void	at_x (int x)

void	at_y (int y)

void	at_shift (int x, int y)

void	at_newline ()

void	at (const char *id)

bool	at_ifdef (const char *id)

void	label (const char *label)

void	get_at_position (int x, int y) const

int	get_at_xposition () const

int	get_at_yposition () const

void	dump_at_position (const char *debug_label) const

void	at_attach (int x, int y)

void	at_attach_to (bool attach_x, bool attach_y, int xoff, int yoff)

void	at_unattach ()

void	unset_at_commands ()

void	store_at_to (AW_at_storage &storage)

void	restore_at_from (const AW_at_storage &stored)

void	sens_mask (AW_active mask)

void	help_text (const char *id)

void	callback (const WindowCallback &cb)

void	callback (const CreateWindowCallback &cwcb)

void	callback (CreateWindowCallbackSimple cb)

void	callback (WindowCallbackSimple cb)

void	d_callback (const WindowCallback &cb)

void	create_button (const char macro_name, AW_label label, const char mnemonic=NULp, const char *color=NULp)

void	create_autosize_button (const char macro_name, AW_label label, const char mnemonic=NULp, unsigned xtraSpace=1)

Widget	get_last_widget () const

void	create_toggle (const char *awar_name)

void	create_inverse_toggle (const char *awar_name)

void	create_toggle (const char awar_name, const char nobitmap, const char *yesbitmap, int buttonWidth=0)

void	create_text_toggle (const char var_name, const char noText, const char *yesText, int buttonWidth=0)

void	create_input_field (const char *awar_name, int columns=0)

void	create_text_field (const char *awar_name, int columns=20, int rows=4)

void	create_input_field_with_scaler (const char *awar_name, int textcolumns=4, int scaler_length=250, AW_ScalerType scalerType=AW_SCALER_LINEAR)

AW_option_menu_struct *	create_option_menu (const char *awar_name)

void	clear_option_menu (AW_option_menu_struct *oms)

void	insert_option (AW_label choice_label, const char mnemonic, const char var_value, const char *name_of_color=NULp)

void	insert_default_option (AW_label choice_label, const char mnemonic, const char var_value, const char *name_of_color=NULp)

void	insert_option (AW_label choice_label, const char mnemonic, int var_value, const char name_of_color=NULp)

void	insert_default_option (AW_label choice_label, const char mnemonic, int var_value, const char name_of_color=NULp)

void	insert_option (AW_label choice_label, const char mnemonic, float var_value, const char name_of_color=NULp)

void	insert_default_option (AW_label choice_label, const char mnemonic, float var_value, const char name_of_color=NULp)

void	update_option_menu ()

void	refresh_option_menu (AW_option_menu_struct *)

void	create_toggle_field (const char *awar_name, AW_label label, AW_orientation orientation=AW_VERTICAL)

void	create_toggle_field (const char *awar_name, AW_orientation orientation=AW_VERTICAL)

void	insert_toggle (AW_label toggle_label, const char mnemonic, const char var_value)

void	insert_default_toggle (AW_label toggle_label, const char mnemonic, const char var_value)

void	insert_toggle (AW_label toggle_label, const char *mnemonic, int var_value)

void	insert_default_toggle (AW_label toggle_label, const char *mnemonic, int var_value)

void	insert_toggle (AW_label toggle_label, const char *mnemonic, float var_value)

void	insert_default_toggle (AW_label toggle_label, const char *mnemonic, float var_value)

void	update_toggle_field ()

AW_selection_list *	create_selection_list (const char *awar_name, int columns, int rows)

AW_selection_list *	create_selection_list (const char *awar_name)

Public Member Functions inherited from AW_simple_device
	AW_simple_device (AW_common *common_)

Public Member Functions inherited from AW_clicked_element
virtual	~AW_clicked_element ()

AW_CL	cd1 () const

AW_CL	cd2 () const

bool	does_exist () const

bool	is_text () const

bool	is_line () const

bool	is_box () const

bool	is_polygon () const

double	get_rel_pos () const

int	get_distance () const

AW::LineVector	get_connecting_line (const AW_clicked_element &other) const

Public Member Functions inherited from Writer
	Writer ()

virtual	~Writer ()

virtual bool	ok () const =0

virtual void	out (char ch)=0

virtual const char *	name () const =0

virtual void	throw_write_error () const __ATTR__NORETURN

virtual int	out (const char *text)

virtual int	outf (const char *format,...) __ATTR__FORMAT_MEMBER(1)

void	repeated (char ch, int repeat)

virtual	~Writer ()

const char *	get_error () const

bool	ok () const

Public Member Functions inherited from Dragged
	Dragged (AWT_graphic_exports &exports_)

virtual void	draw_drag_indicator (AW_device *device, int drag_gc) const =0

void	do_drag (const AW_clicked_element *drag_target, const Position &mousepos)

void	do_drop (const AW_clicked_element *drop_target, const Position &mousepos)

void	hide_drag_indicator (AW_device *device, int drag_gc) const

Public Member Functions inherited from AWT_command_data
virtual	~AWT_command_data ()

Public Member Functions inherited from AP_combinableSeq
	AP_combinableSeq (const AliView *aliview)

virtual	~AP_combinableSeq ()

AP_FLOAT	weighted_base_count () const

Mutations	noncounting_combine_seq (const AP_combinableSeq lefts, const AP_combinableSeq rights)

bool	combinedEquals (const AP_combinableSeq *other) const

Public Member Functions inherited from AP_sequence
	AP_sequence (const AliView *aliview)

virtual	~AP_sequence ()

GB_ERROR	bind_to_species (GBDATA *gb_species)

void	unbind_from_species ()

bool	is_bound_to_species () const

GBDATA *	get_bound_species_data () const

void	lazy_load_sequence () const

void	ensure_sequence_loaded () const

bool	hasSequence () const

void	forget_sequence ()

size_t	get_sequence_length () const

const AP_filter *	get_filter () const

const AP_weights *	get_weights () const

const AliView *	get_aliview () const

Public Member Functions inherited from SaiOperator
	SaiOperator (SaiOperatorType type_)

virtual	~SaiOperator ()

SaiOperatorType	get_type () const

std::string	get_description () const

Public Member Functions inherited from TreeLabeler
virtual	~TreeLabeler ()

Public Member Functions inherited from ValueTuple
virtual	~ValueTuple ()

virtual ShadedValue	reverse_mix (float, const class NoTuple &) const

virtual ShadedValue	reverse_mix (float, const class LinearTuple &) const

virtual ShadedValue	reverse_mix (float, const class PlanarTuple &) const

virtual ShadedValue	reverse_mix (float, const class SpatialTuple &) const

Public Member Functions inherited from ItemShader
	ItemShader (const std::string &id_, const std::string &description_, ReshadeCallback rcb, int undefined_gc_)

virtual	~ItemShader ()

bool	deactivate_plugin ()

bool	is_active_plugin (const ShaderPlugin &plugin) const

const std::string &	get_id () const

const std::string &	get_description () const

bool	active () const

bool	overlay_marked () const

bool	overlay_color_groups () const

ShadedValue	shade (GBDATA *gb_item) const

int	to_GC (const ShadedValue &val) const

void	trigger_reshade_callback (ReshadeMode mode)

Public Member Functions inherited from AliEditCommand
virtual	~AliEditCommand ()

Public Member Functions inherited from AliData
	AliData (size_t size_)

virtual	~AliData ()

void	clear_error () const

void	set_error (GB_ERROR error) const

void	copyPartTo (void *mem, size_t start, size_t count) const

int	cmpPartWith (const void *mem, size_t start, size_t count) const

GB_ERROR	check_delete_allowed (size_t start, size_t count) const

size_t	elems () const

size_t	memsize () const

void	copyTo (void *mem) const

bool	empty () const

int	cmp_whole_data (const AliData &other) const

bool	equals (const AliData &other) const

bool	differs_from (const AliData &other) const

bool	is_valid_pos (size_t pos) const

bool	is_valid_between (size_t pos) const

bool	is_valid_part (size_t start, size_t count) const

Public Member Functions inherited from TreeNode
bool	is_leaf () const

void	markAsLeaf ()

	DEFINE_READ_ACCESSORS (TreeNode *, get_father, father)

	DEFINE_READ_ACCESSORS (TreeNode *, get_leftson, leftson)

	DEFINE_READ_ACCESSORS (TreeNode *, get_rightson, rightson)

bool	is_son_of (const TreeNode *Father) const

bool	is_leftson () const

bool	is_rightson () const

bool	is_inside (const TreeNode *subtree) const

bool	is_ancestor_of (const TreeNode *descendant) const

bool	in_same_branch_as (const TreeNode *other) const

bool	in_other_branch_than (const TreeNode *other) const

const TreeNode *	ancestor_common_with (const TreeNode *other) const

TreeNode *	ancestor_common_with (TreeNode *other)

bool	is_son_of_root () const

GBT_LEN	get_branchlength () const

void	set_branchlength (GBT_LEN newlen)

GBT_LEN	get_branchlength_unrooted () const

void	set_branchlength_unrooted (GBT_LEN newlen)

GBT_LEN	sum_child_lengths () const

GBT_LEN	root_distance () const

GBT_LEN	intree_distance_to (const TreeNode *other) const

void	remove_bootstrap ()

GB_ERROR	apply_aci_to_remarks (const char *aci, const GBL_call_env &callEnv)

void	reset_branchlengths ()

void	scale_branchlengths (double factor)

void	bootstrap2branchlen ()

void	branchlen2bootstrap ()

GBT_RemarkType	parse_bootstrap (double &bootstrap) const

const char *	get_remark () const

const SmartCharPtr &	get_remark_ptr () const

bool	is_inner_node_with_remark () const

void	use_as_remark (const SmartCharPtr &newRemark)

void	set_remark (const char *newRemark)

void	set_bootstrap (double bootstrap)

void	remove_remark ()

bool	has_no_remark () const

bool	has_valid_root_remarks () const

	TreeNode (TreeRoot *root)

TreeNode *	fixDeletedSon ()

void	unlink_from_DB ()

void	announce_tree_constructed ()

void	forget_origin ()

void	forget_relatives ()

TreeRoot *	get_tree_root () const

const TreeNode *	get_root_node () const

TreeNode *	get_root_node ()

bool	is_root_node () const

TreeNode *	get_brother ()

const TreeNode *	get_brother () const

bool	has_group_info () const

TreeNode *	keelTarget ()

const TreeNode *	keelTarget () const

bool	keelsDownGroup (const TreeNode *toSon) const

void	unkeelGroup ()

int	keeledStateInfo () const

void	setKeeledState (int keeledState)

bool	is_normal_group () const

bool	is_keeled_group () const

bool	is_clade () const

const char *	get_group_name () const

const TreeNode *	find_parent_with_groupInfo (bool skipKeeledBrothers=false) const

TreeNode *	find_parent_with_groupInfo (bool skipKeeledBrothers=false)

const TreeNode *	find_parent_clade () const

TreeNode *	find_parent_clade ()

int	calc_clade_level () const

int	count_clades () const

void	rotate_subtree ()

void	reorder_tree (TreeOrder mode)

TreeNode *	findLeafNamed (const char *wantedName)

GBT_LEN	reset_length_and_bootstrap ()

void	multifurcate ()

void	set_branchlength_preserving (GBT_LEN new_len)

void	multifurcate_whole_tree (const multifurc_limits &below)

Public Member Functions inherited from TreeRoot
	TreeRoot (bool deleteWithNodes_)

virtual	~TreeRoot ()

void	delete_by_node ()

bool	has_bootstrap () const

void	set_bootstrap_seen (bool seen)

	DEFINE_READ_ACCESSORS (TreeNode *, get_root_node, rootNode)

ARB_edge	find_innermost_edge ()

Public Member Functions inherited from QueryKey
	QueryKey (query_key_type type_)

virtual	~QueryKey ()

bool	next () const

query_key_type	get_type () const

void	negate ()

Public Member Functions inherited from SEC_base
	SEC_base (SEC_root *Root)

	~SEC_base () OVERRIDE

AW_CL	self () const

SEC_root *	get_root () const

Public Member Functions inherited from SEC_constrainted
	SEC_constrainted ()

double	drawnSize () const

double	standardSize () const

double	minSize () const

double	maxSize () const

void	setDrawnSize (double size)

void	setStandardSize (double size)

void	setConstraints (double low, double high)

Public Member Functions inherited from SEC_oriented
	SEC_oriented ()

virtual	~SEC_oriented ()

void	invalidate ()

const Angle &	get_abs_angle () const

const Angle &	get_rel_angle () const

void	set_rel_angle (const Angle &rel)

void	set_abs_angle (const Angle &abs)

void	set_rel_angle (const double &rel)

void	set_abs_angle (const double &abs)

void	mark_angle_absolute ()

SEC_base *	parent ()

const SEC_base *	parent () const

Public Member Functions inherited from SEC_base_part
	SEC_base_part ()

virtual	~SEC_base_part ()

SEC_base *	parent ()

const SEC_base *	parent () const

AW_CL	self () const

SEC_root *	get_root () const

SEC_base_part *	next ()

const SEC_base_part *	next () const

const SEC_region *	get_region () const

SEC_region *	get_region ()

void	set_sequence_portion (int start, int end)

size_t	getNextAbspos () const

Public Member Functions inherited from AWT_graphic
	AWT_graphic ()

virtual	~AWT_graphic ()

bool	wants_drag_target () const

void	drag_target_detection (bool detect)

int	get_drag_gc () const

Public Member Functions inherited from PS_BitSet
long	getTrueIndices (IndexSet &_index_set, const long _fill_index)

long	getFalseIndices (IndexSet &_index_set, const long _fill_index)

long	getCountOfTrues (const long _fill_index=-1)

long	getMaxUsedIndex () const

long	getCapacity () const

void	invert ()

void	x_or (const PS_BitSet *_other_set)

void	print (FILE *out, const bool _header, const long _fill_index)

bool	save (PS_FileBuffer *_file)

bool	load (PS_FileBuffer *_file, const long _fill_index)

bool	copy (const PS_BitSet *_other_bitset)

	PS_BitSet (const bool _bias, const long _capacity)

	PS_BitSet (PS_FileBuffer *_file, const long _fill_index=-1)

virtual	~PS_BitSet ()

Public Member Functions inherited from PS_BitMap
bool	triangle_get (const long _row, const long _col)

bool	triangle_set (const long _row, const long _col, const bool _value)

void	invert ()

void	x_or (const PS_BitMap *_other_map)

bool	save (PS_FileBuffer *_file)

bool	copy (const PS_BitMap *_other_bitmap)

	PS_BitMap (const bool _bias, const long _capacity)

	PS_BitMap (PS_FileBuffer *_file)

virtual	~PS_BitMap ()

Public Member Functions inherited from ArbRefCount
	ArbRefCount ()

	ArbRefCount (const ArbRefCount &)

virtual	~ArbRefCount ()

void	lock () const

bool	unlock () const

void	free () const

Public Member Functions inherited from AWT_graphic_parsimony
	AWT_graphic_parsimony (ArbParsimony &parsimony_, GBDATA *gb_main_, AD_map_viewer_cb map_viewer_cb_)

AP_tree_nlen *	get_root_node ()

AP_pars_root *	get_tree_root ()

ArbParsimony &	get_parsimony ()

Public Member Functions inherited from AWT_graphic_tree
	AWT_graphic_tree (AW_root aw_root, GBDATA gb_main, AD_map_viewer_cb map_viewer_cb)

	~AWT_graphic_tree () OVERRIDE

void	filled_box (int gc, const AW::Position &pos, int pixel_width)

void	empty_box (int gc, const AW::Position &pos, int pixel_width)

void	diamond (int gc, const AW::Position &pos, int pixel_radius)

const char *	ruler_awar (const char *name)

void	set_line_attributes_for (AP_tree *at) const

void	update_structure () FINAL_OVERRIDE

void	apply_zoom_settings_for_treetype (AWT_canvas *ntw)

int	draw_branch_line (int gc, const AW::Position &root, const AW::Position &leaf, AW_bitset filter)

bool	warn_inappropriate_mode (AWT_COMMAND_MODE mode)

AW_root *	get_root () const

GBDATA *	get_gbmain () const

AP_tree_root *	get_tree_root ()

AP_tree *	get_root_node ()

const AP_tree *	get_root_node () const

AP_tree *	get_logical_root ()

const AP_tree *	get_logical_root () const

bool	is_logically_zoomed ()

void	set_logical_root_to (AP_tree *node)

void	init (AliView aliview, AP_sequence seq_prototype, bool link_to_database_, bool insert_delete_cbs)

AW_gc_manager *	init_devices (AW_window , AW_device , AWT_canvas *ntw) OVERRIDE

void	show (AW_device *device) OVERRIDE

const AW::Position &	get_cursor () const

const AW::Position &	get_group_cursor () const

void	handle_command (AW_device *device, AWT_graphic_event &event) OVERRIDE

long	mark_species_in_tree (AP_tree *at, int mark)

long	mark_species_in_tree_that (AP_tree at, int mark, bool(condition)(GBDATA , void ), void *cd)

void	mark_species_in_rest_of_tree (AP_tree *at, int mark)

bool	tree_has_marks (AP_tree *at)

bool	rest_tree_has_marks (AP_tree *at)

void	detect_group_state (AP_tree at, AWT_graphic_tree_group_state state, AP_tree *skip_this_son)

bool	group_tree (AP_tree *at, CollapseMode mode, int color_group)

void	group_rest_tree (AP_tree *at, CollapseMode mode, int color_group)

void	reorderTree (TreeOrder mode)

void	toggle_group (AP_tree *at)

GB_ERROR	load_from_DB (GBDATA gb_main, const char name) FINAL_OVERRIDE __ATTR__USERESULT

GB_ERROR	save_to_DB (GBDATA gb_main, const char name) FINAL_OVERRIDE __ATTR__USERESULT

void	check_for_DB_update (GBDATA *gb_main) FINAL_OVERRIDE

void	notify_synchronized (GBDATA *gb_main) FINAL_OVERRIDE

void	fast_sync_changed_folding (AP_tree *parent_of_all_changes)

void	set_tree_style (AP_tree_display_style style, AWT_canvas *ntw)

AP_tree_display_style	get_tree_style () const

double	get_irs_tree_ruler_scale_factor () const

void	show_ruler (AW_device *device, int gc)

void	get_zombies_and_duplicates (int &zomb, int &dups) const

void	hide_marker_display ()

void	set_marker_display (MarkerDisplay *display)

MarkerDisplay *	get_marker_display ()

void	install_tree_changed_callback (const GraphicTreeCallback &gtcb)

void	uninstall_tree_changed_callback ()

void	auto_unfold (AP_tree *want_visible)

void	forget_auto_unfolded ()

void	select_group (AP_tree *node)

void	select_group (GBDATA *gb_group)

void	deselect_group ()

const Group &	get_selected_group () const

AP_tree *	locate_selected_group (AP_tree *in_subtree)

void	dislocate_selected_group ()

	PREPARE_MARK_NONFINAL_CLASS (AWT_graphic_tree)

Public Member Functions inherited from AP_tree
	AP_tree (AP_tree_root *troot)

	DEFINE_TREE_ACCESSORS (AP_tree_root, AP_tree)

void	recompute_and_write_folding ()

unsigned	count_leafs () const

void	load_subtree_info ()

int	colorize (GB_HASH *hashptr)

void	uncolorize ()

void	swap_sons () OVERRIDE

GB_ERROR	cantMoveNextTo (AP_tree *new_brother)

GB_ERROR	tree_write_tree_rek (GBDATA *gb_tree)

GB_ERROR	relink () __ATTR__USERESULT

int	get_linewidth () const

void	set_linewidth (int width)

void	reset_linewidth ()

void	set_linewidth_recursive (int width)

float	get_angle () const

void	set_angle (float angle)

void	reset_angle ()

void	buildLeafList (AP_tree **&list, long &num)

GB_ERROR	move_group_to (AP_tree *new_group) __ATTR__USERESULT

bool	is_folded_group () const

bool	is_inside_folded_group () const

void	mark_duplicates ()

const char *	mark_long_branches (double min_rel_diff, double min_abs_diff, double &found_max_abs_diff)

const char *	mark_deep_leafs (int min_depth, double min_rootdist, int &found_max_depth, double &found_max_rootdist)

double	mark_degenerated_branches (double degeneration_factor)

const char *	analyse_distances ()

void	justify_branch_lenghs (GBDATA *gb_main)

void	relink_tree (GBDATA gb_main, void(relinker)(GBDATA &ref_gb_node, char &ref_name, GB_HASH organism_hash), GB_HASH organism_hash)

void	reset_subtree_spreads ()

void	reset_subtree_angles ()

void	reset_subtree_linewidths ()

void	reset_subtree_layout ()

bool	hasName (const char *Name) const

bool	has_correct_mark_flags () const

	PREPARE_MARK_NONFINAL_CLASS (AP_tree)

template<>
ShadedValue	update_subtree_information (const group_scaling &gscaling)

Public Member Functions inherited from ARB_seqtree
	ARB_seqtree (ARB_seqtree_root *root)

	DEFINE_TREE_ACCESSORS (ARB_seqtree_root, ARB_seqtree)

void	calcTreeInfo (ARB_tree_info &info)

bool	is_upper_son () const

bool	is_lower_son () const

AP_sequence *	get_seq ()

const AP_sequence *	get_seq () const

AP_sequence *	set_seq (AP_sequence *sequence)

bool	hasSequence () const

void	mark_subtree ()

bool	contains_marked_species ()

Public Member Functions inherited from AP_tree_root
	AP_tree_root (AliView aliView, AP_sequence seq_proto, bool add_delete_callbacks, const group_scaling *scaling)

	~AP_tree_root () OVERRIDE

	DEFINE_TREE_ROOT_ACCESSORS (AP_tree_root, AP_tree)

void	change_root (TreeNode old, TreeNode newroot) FINAL_OVERRIDE

GB_ERROR	loadFromDB (const char *name) FINAL_OVERRIDE

GB_ERROR	saveToDB () OVERRIDE

void	update_timers ()

bool	is_tree_updated ()

bool	is_species_updated ()

const group_scaling *	get_group_scaling () const

void	inform_about_delete (AP_tree *old)

void	set_root_changed_callback (AP_rootChangedCb cb, void *cd)

void	set_node_deleted_callback (AP_nodeDelCb cb, void *cd)

long	remove_leafs (AWT_RemoveType awt_remove_type)

	PREPARE_MARK_NONFINAL_CLASS (AP_tree_root)

Public Member Functions inherited from ARB_seqtree_root
	ARB_seqtree_root (AliView aliView, AP_sequence seqTempl, bool add_delete_callbacks)

	~ARB_seqtree_root () OVERRIDE

	DEFINE_TREE_ROOT_ACCESSORS (ARB_seqtree_root, ARB_seqtree)

const AliView *	get_aliview () const

const AP_filter *	get_filter () const

const AP_weights *	get_weights () const

GBDATA *	get_gb_main () const

GBDATA *	get_gb_tree () const

void	tree_deleted_cb (GBDATA *gb_tree_del)

const char *	get_tree_name () const

const AP_sequence *	get_seqTemplate () const

GB_ERROR	linkToDB (int zombies, int duplicates) __ATTR__USERESULT

void	unlinkFromDB ()

	PREPARE_MARK_NONFINAL_CLASS (ARB_seqtree_root)

Public Member Functions inherited from awt_item_type_selector
	awt_item_type_selector (awt_item_type for_type)

virtual	~awt_item_type_selector ()

awt_item_type	get_item_type () const

void	add_awar_callbacks (AW_root *root, const RootCallback &cb) const

void	remove_awar_callbacks (AW_root *root, const RootCallback &cb) const

Public Member Functions inherited from MarkerDisplay
	MarkerDisplay (int numMarkers_)

virtual	~MarkerDisplay ()

const NodeMarkers *	read_cache (const AP_tree *at) const

void	write_cache (const AP_tree *at, const NodeMarkers &markers)

void	flush_cache ()

bool	cache_is_flushed () const

int	size () const

Public Member Functions inherited from MessageAttachable
virtual	~MessageAttachable ()

LineAttachedMessage	attached_message (const string &message) const

void	attach_warning (const string &message) const

Public Member Functions inherited from ED4_terminal
	DECLARE_DUMP_FOR_BASECLASS (ED4_terminal, ED4_base)

void	changed_by_database () OVERRIDE

bool	calc_bounding_box () FINAL_OVERRIDE

ED4_returncode	draw_drag_box (AW_pos x, AW_pos y, GB_CSTR text=NULp, int cursor_y=-1)

void	request_refresh (int clear=1) FINAL_OVERRIDE

void	update_requested_children () OVERRIDE

void	delete_requested_children () OVERRIDE

void	Delete () OVERRIDE

ED4_returncode	event_sent_by_parent (AW_event event, AW_window aww) OVERRIDE

ED4_returncode	kill_object ()

ED4_base *	search_ID (const char *id) OVERRIDE

char *	resolve_pointer_to_string_copy (int *str_len=NULp) const FINAL_OVERRIDE

const char *	resolve_pointer_to_char_pntr (int *str_len=NULp) const FINAL_OVERRIDE

void	remove_callbacks () FINAL_OVERRIDE

GB_ERROR	write_sequence (const char *seq, int seq_len)

void	scroll_into_view (ED4_window *ed4w)

bool	setCursorTo (ED4_cursor *cursor, int seq_pos, bool unfoldGroups, ED4_CursorJumpType jump_type)

bool	is_hidden () const FINAL_OVERRIDE

	ED4_terminal (const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

	~ED4_terminal () OVERRIDE

Public Member Functions inherited from ED4_base
void	draw_bb (int color)

	DECLARE_DUMP_FOR_ROOTCLASS (ED4_base)

GBDATA *	get_species_pointer () const

void	set_species_pointer (GBDATA *gbd)

bool	has_callback () const

int	adjust_clipping_rectangle ()

void	resize_dynamic ()

ED4_returncode	clear_background (int color=0)

void	set_links (ED4_base width_ref, ED4_base height_ref)

void	set_both_links (ED4_base *ref)

void	set_property (ED4_properties prop)

void	clr_property (ED4_properties prop)

bool	has_property (ED4_properties prop) const

void	calc_rel_coords (AW_pos x, AW_pos y)

void	calc_world_coords (AW_pos x, AW_pos y) const

const AW::Position &	calc_world_coords () const

void	update_world_coords_cache () const

AW::Rectangle	get_win_area (ED4_window *ed4w) const

void	request_resize ()

void	request_resize_of_linked ()

void	resize_requested_by_link (ED4_base *link)

void	set_update ()

int	calc_group_depth ()

void	check_all ()

short	in_border (AW_pos abs_x, AW_pos abs_y, ED4_movemode mode)

ED4_returncode	set_width ()

ED4_AREA_LEVEL	get_area_level (ED4_multi_species_manager **multi_species_manager=NULp) const

ED4_manager *	get_parent (ED4_level lev) const

void	unlink_from_parent ()

bool	has_parent (ED4_manager *Parent)

bool	is_child_of (ED4_manager *Parent)

ED4_group_manager *	is_in_folded_group () const

char *	get_name_of_species ()

ED4_terminal *	get_next_terminal ()

ED4_terminal *	get_prev_terminal ()

void	generate_configuration_string (GBS_strstruct &buffer)

const ED4_terminal *	get_consensus_relevant_terminal () const

	ED4_base (const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

virtual	~ED4_base ()

int	is_terminal () const

int	is_text_terminal () const

int	is_species_name_terminal () const

int	is_sequence_info_terminal () const

int	is_sequence_terminal () const

int	is_orf_terminal () const

int	is_pure_text_terminal () const

int	is_columnStat_terminal () const

int	is_bracket_terminal () const

int	is_spacer_terminal () const

int	is_line_terminal () const

int	is_flag_header_terminal () const

int	is_flag_terminal () const

int	is_manager () const

int	is_sequence_manager () const

int	is_multi_name_manager () const

int	is_name_manager () const

int	is_multi_species_manager () const

int	is_multi_sequence_manager () const

int	is_device_manager () const

int	is_group_manager () const

int	is_root_group_manager () const

int	is_abstract_group_manager () const

int	is_species_manager () const

int	is_area_manager () const

	E4B_DECL_CASTOP (area_manager)

	E4B_DECL_CASTOP (abstract_group_manager)

	E4B_DECL_CASTOP (bracket_terminal)

	E4B_DECL_CASTOP (columnStat_terminal)

	E4B_DECL_CASTOP (consensus_sequence_terminal)

	E4B_DECL_CASTOP (device_manager)

	E4B_DECL_CASTOP (group_manager)

	E4B_DECL_CASTOP (line_terminal)

	E4B_DECL_CASTOP (manager)

	E4B_DECL_CASTOP (multi_name_manager)

	E4B_DECL_CASTOP (multi_sequence_manager)

	E4B_DECL_CASTOP (multi_species_manager)

	E4B_DECL_CASTOP (name_manager)

	E4B_DECL_CASTOP (orf_terminal)

	E4B_DECL_CASTOP (pure_text_terminal)

	E4B_DECL_CASTOP (root_group_manager)

	E4B_DECL_CASTOP (sequence_info_terminal)

	E4B_DECL_CASTOP (sequence_manager)

	E4B_DECL_CASTOP (sequence_terminal)

	E4B_DECL_CASTOP (spacer_terminal)

	E4B_DECL_CASTOP (species_manager)

	E4B_DECL_CASTOP (species_name_terminal)

	E4B_DECL_CASTOP (terminal)

	E4B_DECL_CASTOP (text_terminal)

	E4B_DECL_CASTOP (flag_header_terminal)

	E4B_DECL_CASTOP (flag_terminal)

ED4_species_manager *	containing_species_manager () const

bool	is_consensus_manager () const

bool	is_SAI_manager () const

bool	is_species_seq_manager () const

ED4_species_type	get_species_type () const

bool	inside_consensus_manager () const

bool	inside_SAI_manager () const

bool	inside_species_seq_manager () const

bool	is_consensus_terminal () const

bool	is_SAI_terminal () const

bool	is_species_seq_terminal () const

bool	is_consensus_sequence_terminal () const

Public Member Functions inherited from ED4_text_terminal
	E4B_AVOID_UNNEEDED_CASTS (text_terminal)

void	deleted_from_database () OVERRIDE

	ED4_text_terminal (const ED4_objspec &spec_, GB_CSTR id, AW_pos width, AW_pos height, ED4_manager *parent)

	~ED4_text_terminal () OVERRIDE

	DECLARE_DUMP_FOR_BASECLASS (ED4_text_terminal, ED4_terminal)

Public Member Functions inherited from ED4_manager
	E4B_AVOID_UNNEEDED_CASTS (manager)

	DECLARE_DUMP_FOR_BASECLASS (ED4_manager, ED4_base)

void	add_delete_callback (const ED4_managerCallback &cb)

void	remove_delete_callback (const ED4_managerCallback &cb)

int	refresh_flag_ok ()

void	changed_by_database () OVERRIDE

void	deleted_from_database () OVERRIDE

bool	calc_bounding_box () FINAL_OVERRIDE

ED4_returncode	distribute_children ()

ED4_returncode	event_sent_by_parent (AW_event event, AW_window aww) FINAL_OVERRIDE

void	request_refresh (int clear=1) FINAL_OVERRIDE

ED4_returncode	clear_refresh ()

void	update_requested_children () OVERRIDE

void	delete_requested_children () OVERRIDE

void	Delete () FINAL_OVERRIDE

ED4_returncode	move_requested_by_parent (ED4_move_info *mi)

void	create_consensus (ED4_abstract_group_manager upper_group_manager, arb_progress progress)

ARB_ERROR	route_down_hierarchy (const ED4_route_cb &cb) FINAL_OVERRIDE

ED4_base *	find_first_that (ED4_level level, const ED4_basePredicate &fulfills_predicate)

ED4_returncode	move_requested_by_child (ED4_move_info *moveinfo)

void	resize_requested_by_child ()

ED4_returncode	refresh_requested_by_child ()

void	delete_requested_by_child ()

void	update_requested_by_child ()

ED4_base *	get_defined_level (ED4_level lev) const

void	update_consensus (ED4_manager old_parent, ED4_manager new_parent, ED4_base *sequence)

ED4_returncode	rebuild_consensi (ED4_base *start_species, ED4_update_flag update_flag)

ED4_returncode	check_in_bases (ED4_base *added_base)

ED4_returncode	check_out_bases (ED4_base *subbed_base)

ED4_returncode	update_bases (const ED4_base old_base, const ED4_base new_base, PosRange range=PosRange::whole())

ED4_returncode	update_bases (const char old_seq, int old_len, const char new_seq, int new_len, PosRange range=PosRange::whole())

ED4_returncode	update_bases (const char old_seq, int old_len, const ED4_base new_base, PosRange range=PosRange::whole())

ED4_returncode	update_bases (const BaseFrequencies old_table, const BaseFrequencies new_table, PosRange range=PosRange::whole())

ED4_returncode	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_returncode	handle_move (ED4_move_info *moveinfo)

ED4_base *	get_competent_child (AW_pos x, AW_pos y, ED4_properties relevant_prop)

ED4_base *	get_competent_clicked_child (AW_pos x, AW_pos y, ED4_properties relevant_prop)

ED4_base *	search_spec_child_rek (ED4_level level)

ED4_base *	search_ID (const char *id) FINAL_OVERRIDE

void	remove_callbacks () OVERRIDE

ED4_terminal *	get_first_terminal (int start_index=0) const

ED4_terminal *	get_last_terminal (int start_index=-1) const

void	hide_children ()

void	unhide_children ()

bool	is_hidden () const FINAL_OVERRIDE

	ED4_manager (const ED4_objspec &spec_, const char id, AW_pos width, AW_pos height, ED4_manager parent)

	~ED4_manager () OVERRIDE

Public Member Functions inherited from ED4_container
ED4_manager *	owner ()

const ED4_manager *	owner () const

ED4_base *	member (ED4_index i) const

ED4_index	members () const

bool	empty () const

void	clear ()

void	insert_member (ED4_base *new_member)

void	append_member (ED4_base *new_member)

ED4_returncode	remove_member (ED4_base *member)

ED4_index	search_member (ED4_extension *location, ED4_properties prop)

ED4_returncode	search_target_species (ED4_extension location, ED4_properties prop, ED4_base *found_member, ED4_level return_level)

ED4_returncode	move_member (ED4_index old_pos, ED4_index new_pos)

bool	members_ok () const

	ED4_container ()

virtual	~ED4_container ()

Public Member Functions inherited from ARB_countedTree
	ARB_countedTree (ARB_seqtree_root *tree_root_)

	DEFINE_TREE_ACCESSORS (ARB_seqtree_root, ARB_countedTree)

size_t	relative_position_in (const ARB_countedTree *upgroup) const

Public Member Functions inherited from LineReader
	LineReader ()

virtual	~LineReader ()

string	lineError (const string &msg) const

string	lineError (const char *msg) const

void	showFilenameInLineError (bool show)

bool	getLine (string &line)

void	backLine (const string &line)

size_t	getLineNumber () const

void	setLineNumber (size_t line)

void	copyTo (FILE *out)

Public Member Functions inherited from CharPtrArray
void	reserve (size_t forElems)

void	optimize_space ()

size_t	size () const

bool	empty () const

const char *	operator[] (int i) const

void	swap (int i1, int i2)

void	move (int from, int to)

void	remove (int i)

void	safe_remove (int i)

void	resize (int newsize)

void	clear ()

void	sort (CharPtrArray_compare_fun compare, void *client_data)

void	uniq (CharPtrArray_compare_fun compare, void *client_data)

void	sort_and_uniq (CharPtrArray_compare_fun compare, void *client_data)

int	index_of (const char *search_for) const

Public Member Functions inherited from InputFormat
	InputFormat ()

	~InputFormat () OVERRIDE

const char *	get_id () const

Public Member Functions inherited from OutputFormat
virtual	~OutputFormat ()

Public Member Functions inherited from RefContainer< GenbankRef >
void	reinit_refs ()

void	resize_refs (int new_size)

int	get_refcount () const

bool	has_refs () const

const GenbankRef &	get_ref (int num) const

GenbankRef &	get_ref (int num)

const GenbankRef &	get_latest_ref () const

GenbankRef &	get_latest_ref ()

GenbankRef &	get_new_ref ()

Public Member Functions inherited from RefContainer< Emblref >
void	reinit_refs ()

void	resize_refs (int new_size)

int	get_refcount () const

bool	has_refs () const

const Emblref &	get_ref (int num) const

Emblref &	get_ref (int num)

const Emblref &	get_latest_ref () const

Emblref &	get_latest_ref ()

Emblref &	get_new_ref ()

Public Member Functions inherited from awt_viewport
	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 (const awt_mask_awar_item &ref_item, const std::string &label_)

	~awt_viewport () OVERRIDE

const std::string &	get_label () const

Public Member Functions inherited from awt_mask_awar_item
	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 () OVERRIDE

std::string	awar_name () const

const AW_awar *	awar () const

AW_awar *	awar ()

Public Member Functions inherited from awt_mask_item
	awt_mask_item (awt_input_mask_global &global_)

virtual	~awt_mask_item ()

const awt_input_mask_global &	mask_global () const

awt_input_mask_global &	mask_global ()

bool	has_name () const

const std::string &	get_name () const

GB_ERROR	set_name (const std::string &name_, bool is_global)

GB_ERROR	remove_name ()

const awt_viewport *	to_viewport () const

awt_viewport *	to_viewport ()

const awt_linked_to_item *	to_linked_item () const

awt_linked_to_item *	to_linked_item ()

bool	is_viewport () const

bool	is_linked_item () const

Public Member Functions inherited from awt_linked_to_item
	awt_linked_to_item ()

virtual	~awt_linked_to_item ()

GBDATA *	item ()

GB_ERROR	unlink ()

Public Member Functions inherited from NamedCommand
	NamedCommand (const char *cmd)

bool	matches (const char *code) const OVERRIDE

int	length () const

Public Member Functions inherited from Command
virtual	~Command ()

const Location &	pc () const

Static Public Member Functions
static const child_progress *	calling_child_progress ()

static int	threshold_is_set ()

static void	set_threshold (double aThreshold)

static double	get_threshold ()

static ParagraphTree *	buildParagraphTree (const Section &sec)

static const char *	getSAIname ()

static void	set_species_data (GBDATA *gb_species_data_)

static void	trigger_reshade_cb (AW_root , ItemShader_impl shader)

static void	configure_active_plugin_cb (AW_window aww, ItemShader_impl shader)

static void	selected_plugin_changed_cb (AW_root awr, ItemShader_impl shader)

static void	selected_range_changed_cb (AW_root awr, ItemShader_impl shader)

static void	configure_colors_cb (AW_window aww, ItemShader_impl shader)

static void	phase_changed_cb (AW_root awr, ItemShader_impl shader)

static void	reset_phasing_cb (AW_window aww, const ItemShader_impl shader)

static char *	store_config_cb (ItemShader_impl *shader)

static void	load_or_reset_config_cb (const char cfgstr, ItemShader_impl shader)

static ErrorOrSaiOperatorPtr	make (const char *config)

static ErrorOrSaiOperatorPtr	make (const char *config)

Static Public Member Functions inherited from AW_window
static WindowCallback	makeWindowPopper (const CreateWindowCallback &cwcb)

static WindowCallback	makeWindowReplacer (const CreateWindowCallback &cwcb)

Static Public Member Functions inherited from Dragged
static bool	valid_drag_device (AW_device *device)

Static Public Member Functions inherited from AP_combinableSeq
static long	combine_count ()

Static Public Member Functions inherited from SaiOperator
static ErrorOrSaiOperatorPtr	make (SaiOperatorType type, const char *config)

static const char *	type_name (SaiOperatorType type)

Static Public Member Functions inherited from ValueTuple
static ShadedValue	undefined ()

static ShadedValue	make (float f)

static ShadedValue	make (float f1, float f2)

static ShadedValue	make (float f1, float f2, float f3)

Static Public Member Functions inherited from TreeNode
static void	destroy (TreeNode *that)

static void	destroy (TreeNode that, TreeRoot root)

Static Public Member Functions inherited from AWT_graphic_tree
static void	install_group_changed_callback (const GraphicTreeCallback &gccb)

Static Public Member Functions inherited from AP_tree
static void	set_tree_shader (AP_TreeShader *new_shader)

static const AP_TreeShader *	get_tree_shader ()

Static Public Member Functions inherited from ED4_base
static void	touch_world_cache ()

Public Attributes
int	index

int	sons

char *	ID

char *	dateu

char *	datec

char *	description

char *	os

char *	accession

char *	keywords

char *	dr

RDP_comments	comments

char *	locus

char *	definition

char *	source

char *	organism

char *	seqabbr

char *	name

int	rna_or_dna

char *	atcc

char *	rna

char *	date

char *	nbk

char *	acs

char *	author

char *	journal

char *	who

char *	strain

char *	subspecies

ED4_highlighted_entry *	highlight_info

bool	dragged

SEQTYPE *	templ

LocallyModify< int >	permit_flag_updates

int	screenXmax

int	screenYmax

int	mouseX

int	mouseY

bool	displayGrid

ColorRGBf	ApplicationBGColor

float	ObjectSize

int	iDisplayBases

int	iBaseMode

int	iBaseHelix

int	iBaseUnpairHelix

int	iBaseNonHelix

int	iShapeHelix

int	iShapeUnpairHelix

int	iShapeNonHelix

int	iDisplayHelix

int	iHelixMidPoint

int	iHelixBackBone

int	iHelixNrs

int	iDispTerInt

int	iStartHelix

int	iEndHelix

float	fHelixSize

float	fSkeletonSize

int	iColorise

int	iBackBone

int	iDispPos

int	iMapSpecies

int	iMapSpeciesBase

int	iMapSpeciesPos

int	iMapSpeciesDels

int	iMapSpeciesMiss

int	iMapSpeciesIns

int	iMapSpeciesInsInfo

int	iDispCursorPos

OpenGLGraphics *	G

GLuint	texture [SHAPE_MAX]

AW_root *	aw_root

SEC_root *	sec_root

GBDATA *	gb_struct

GBDATA *	gb_struct_ref

long	last_saved

bool	skip_empty_tags
	true -> tags w/o content or attributes are skipped (default = false) More...

size_t	indentation_per_level
	how many columns are used per indentation level (defaults to 1) More...

Public Attributes inherited from AW_window
AW_event	event

unsigned long	click_time

long	color_table_size

AW_rgb *	color_table

int	number_of_timed_title_changes

AW_window_Motif *	p_w

AW_cb *	_callback

AW_cb *	_d_callback

char *	window_name

char *	window_defaults_name
	window title More...

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes