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FINAL_TYPE< SEQTYPE > Class Template Reference

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#include <TreeNode.h>

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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< ValueTupleShadedValue
 
- Public Types inherited from AliData
enum  memop { COPY_TO, COMPARE_WITH, CHECK_DELETE }
 
- Public Types inherited from PS_BitSet
typedef set< longIndexSet
 

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_descriptoroperator= (const awt_input_mask_descriptor &other)
 
const charget_title () const
 
const charget_maskname () const
 
const charget_internal_maskname () const
 
const charget_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_globalmask_global () const
 
awt_input_mask_globalmask_global ()
 
void add_handler (awt_mask_item_ptr handler)
 
void relink ()
 
void unlink ()
 
 SizeAwareTree (TreeRoot *root)
 
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
 
charget_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 charget_rem (int idx) const
 
charcopy_multi_rem (int &idx, int offset) const
 
void add_remarks_from (const GenBank &gbk)
 
void reinit () OVERRIDE
 
const charget_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
 
counterclone (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)
 
 ~child_progress () OVERRIDE
 
SmartPtr< nestablecreate_child_progress (const char *title, SINT overall_count) 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)
 
charreplace (int i, char *elem)
 
 MultiFileReader (const CharPtrArray &files_)
 
 ~MultiFileReader ()
 
GB_ERROR get_error () const
 
const stringgetFilename () const OVERRIDE
 
 GroupTreeRoot (AliView *aliView, AP_sequence *seqTempl, bool add_delete_callbacks)
 
 ~GroupTreeRoot () OVERRIDE
 
TreeNodemakeNode () 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
 
TreeNodemakeNode () 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 LeafRelationsget_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_terminalget_top_middle_spacer_terminal () const
 
ED4_terminalget_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_selected () const
 
void set_selected (bool select)
 
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_terminalget_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_terminalcorresponding_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_terminalcorresponding_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_terminalcorresponding_species_name_terminal () const
 
void draw () OVERRIDE
 
GBDATAdata ()
 
const GBDATAdata () 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)
 
GBDATAget_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 OstringsContent () const
 
OstringsContent ()
 
SectionType get_type () const
 
size_t line_number () const OVERRIDE
 
const stringgetName () 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 charreadable_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 charget_result () const
 
const charget_result_ref () const
 
int get_result_length () const
 
bool was_aligned () const
 
GB_ERROR do_align ()
 
 ConfigMarkerDisplay (SmartPtr< ConstStrArray > config_, GBDATA *gb_main_)
 
const charget_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 charget_self_awar () const OVERRIDE
 
size_t get_self_awar_content_length () const OVERRIDE
 
GBDATAcurrent (AW_root *root, GBDATA *gb_main) const OVERRIDE
 
const chargetKeyPath () const OVERRIDE
 
 AP_pars_root (AliView *aliView, AP_sequence *seq_proto, bool add_delete_callbacks, const group_scaling *scaling)
 
TreeNodemakeNode () 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 StateStackget_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_nlenREMOVE () 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 charfullname () const
 
const charsortByName ()
 
int indexOf (const AP_tree_edge *e) const
 
AP_tree_edgeedgeTo (const AP_tree_nlen *brother) const
 
AP_tree_edgenextEdge (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)
 
chargetSequenceCopy ()
 
 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 ArbStringListcommentList () const
 
bool hasResults () const
 
const ArbProbeprobe () const
 
void headline (const char *pHeadline, int nEndFullName)
 
const std::stringheadline () 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
 
size_t getMsaLen ()
 
vector< size_t > * getPositionMap ()
 
VecVecTypegetSequences ()
 
 AlignedSequenceLoader ()
 
virtual ~AlignedSequenceLoader ()
 
CmagetCma ()
 
GB_ERROR saveSAI (vector< size_t > clusters, double threshold)
 
vector< charnormalizeClusters (vector< size_t > clusters)
 
AlignedSequenceLoadergetLoader ()
 
 Analyser ()
 
virtual ~Analyser ()
 
MatrixXd computeMutualInformation (VecVecType &seq)
 
MatrixXd computeMutualInformationP (VecVecType &seq)
 
VectorXi computeClusters (list< MITuple > mituples, size_t size, double threshold)
 
list< MITuplecompute_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_managerinit_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_strandstrandToRoot () const
 
SEC_helix_strandstrandToOutside () const
 
SEC_helix_strandstrandAwayFrom (const SEC_loop *loop) const
 
SEC_helix_strandstrandTowards (const SEC_loop *loop) const
 
SEC_loopotherLoop (const SEC_loop *loop) const
 
SEC_looprootsideLoop () const
 
SEC_loopoutsideLoop () 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 Positionget_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_rootget_root () const
 
SEC_rootget_root ()
 
const SEC_helixget_helix () const
 
SEC_helixget_helix ()
 
const SEC_helix_strandget_other_strand () const
 
SEC_helix_strandget_other_strand ()
 
const Positionget_fixpoint () const
 
bool isRootsideFixpoint () const
 
bool pointsToRoot () const
 
bool pointsToOutside () const
 
bool is3end () const
 
const PositionrightAttachPoint () const
 
const PositionleftAttachPoint () const
 
const PositionstartAttachPoint () const
 
const PositionendAttachPoint () 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_segmentget_next_segment () const
 
SEC_segmentget_next_segment ()
 
SEC_segmentget_previous_segment ()
 
const SEC_loopget_origin_loop () const
 
SEC_loopget_origin_loop ()
 
SEC_loopget_destination_loop ()
 
SEC_loopget_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_strandsplit (size_t start, size_t end, SEC_segment **new_segment)
 
int is_endings_segment ()
 
void delete_pointer_2 (SEC_helix_strand *strand)
 
SEC_helix_strandget_previous_strand ()
 
const SEC_helix_strandget_next_strand () const
 
SEC_helix_strandget_next_strand ()
 
const SEC_loopget_loop () const
 
SEC_loopget_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 Positionget_center () const
 
const double & get_circumference () const
 
bool is_root_loop () const
 
SEC_helix_strandget_rootside_strand () const
 
SEC_helixget_rootside_helix () const
 
SEC_helix_strandget_fixpoint_strand () const
 
SEC_helixget_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 Positionget_fixpoint () const OVERRIDE
 
void orientationChanged () OVERRIDE
 
void sizeChanged () OVERRIDE
 
 ItemQueryKey (GBDATA *gb_main, const char *field_name)
 
 ~ItemQueryKey ()
 
charget_target_data (const QueryTarget &target, GB_ERROR &error) const OVERRIDE
 
const charget_name () const OVERRIDE
 
bool iterate () const OVERRIDE
 
void reset () const OVERRIDE
 
GBDATAget_first_field (GBDATA *gb_item) const
 
 GroupSearchRoot ()
 
 ~GroupSearchRoot () FINAL_OVERRIDE
 
 DEFINE_TREE_ROOT_ACCESSORS (GroupSearchRoot, GroupSearchTree)
 
TreeNodemakeNode () 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 charshader_awar (const char *name) const
 
const chartmp_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
 
charstore_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
 
 AP_sequence_parsimony (const AliView *aliview)
 
 ~AP_sequence_parsimony () OVERRIDE
 
const charget_sequence () const
 
const unsigned charget_usequence () const
 
AP_combinableSeqdup () 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_PROTEINSget_sequence () const
 
AP_combinableSeqdup () 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_elementclone () const OVERRIDE
 
const AW::Positionget_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_elementbest_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_Xmget_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_Attributeappend_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_NodeLatestSon ()
 
void set_LatestSon (XML_Node *latest_son_)
 
XML_TaggetRoot ()
 
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_cdget_click_cd () const
 
AW_bitset get_filter () const
 
void reset ()
 
const AW_screen_areaget_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_commonget_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_limitsget_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_areaget_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_overlapget_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 charwindow_local_awarname (const char *localname, bool tmp=true)
 
class AW_awarwindow_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 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 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_rootget_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 charget_window_title () const
 
const charget_window_id () const
 
const charlocal_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_deviceget_device (AW_area area)
 
AW_device_click * get_click_device (AW_area area, int mousex, int mousey, int max_distance)
 
AW_device_sizeget_size_device (AW_area area)
 
AW_device_print * get_print_device (AW_area area)
 
AW_commonget_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_structcreate_option_menu (const char *awar_name, bool fallback2default)
 
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, const char *mnemonic)
 
void create_toggle_field (const char *awar_name, int orientation=0)
 
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_listcreate_selection_list (const char *awar_name, int columns, int rows, bool fallback2default)
 
AW_selection_listcreate_selection_list (const char *awar_name, bool fallback2default)
 
- 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 charname () 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 charget_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
 
GBDATAget_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_filterget_filter () const
 
const AP_weightsget_weights () const
 
const AliViewget_aliview () const
 
- 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::stringget_id () const
 
const std::stringget_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 TreeNodeancestor_common_with (const TreeNode *other) const
 
TreeNodeancestor_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 ()
 
void reset_branchlengths ()
 
void scale_branchlengths (double factor)
 
void bootstrap2branchlen ()
 
void branchlen2bootstrap ()
 
GBT_RemarkType parse_bootstrap (double &bootstrap) const
 
const charget_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)
 
TreeNodefixDeletedSon ()
 
void unlink_from_DB ()
 
void announce_tree_constructed ()
 
void forget_origin ()
 
void forget_relatives ()
 
TreeRootget_tree_root () const
 
const TreeNodeget_root_node () const
 
TreeNodeget_root_node ()
 
bool is_root_node () const
 
TreeNodeget_brother ()
 
const TreeNodeget_brother () const
 
bool has_group_info () const
 
TreeNodekeelTarget ()
 
const TreeNodekeelTarget () 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 charget_group_name () const
 
const TreeNodefind_parent_with_groupInfo (bool skipKeeledBrothers=false) const
 
TreeNodefind_parent_with_groupInfo (bool skipKeeledBrothers=false)
 
const TreeNodefind_parent_clade () const
 
TreeNodefind_parent_clade ()
 
int calc_clade_level () const
 
int count_clades () const
 
void rotate_subtree ()
 
void reorder_tree (TreeOrder mode)
 
TreeNodefindLeafNamed (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_rootget_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 Angleget_abs_angle () const
 
const Angleget_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_baseparent ()
 
const SEC_baseparent () const
 
- Public Member Functions inherited from SEC_base_part
 SEC_base_part ()
 
virtual ~SEC_base_part ()
 
SEC_baseparent ()
 
const SEC_baseparent () const
 
AW_CL self () const
 
SEC_rootget_root () const
 
SEC_base_partnext ()
 
const SEC_base_partnext () const
 
const SEC_regionget_region () const
 
SEC_regionget_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 ()
 
ArbParsimonyget_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 charruler_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_rootget_root () const
 
GBDATAget_gbmain () const
 
AP_tree_rootget_tree_root ()
 
AP_treeget_root_node ()
 
const AP_treeget_root_node () const
 
AP_treeget_logical_root ()
 
const AP_treeget_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_managerinit_devices (AW_window *, AW_device *, AWT_canvas *ntw) OVERRIDE
 
void show (AW_device *device) OVERRIDE
 
const AW::Positionget_cursor () const
 
const AW::Positionget_group_cursor () const
 
void handle_command (AW_device *device, AWT_graphic_event &event) OVERRIDE
 
void mark_species_in_tree (AP_tree *at, int mark)
 
void 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)
 
void mark_species_in_rest_of_tree_that (AP_tree *at, int mark, bool(*condition)(GBDATA *, void *), void *cd)
 
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)
 
MarkerDisplayget_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 Groupget_selected_group () const
 
AP_treelocate_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 charmark_long_branches (double min_rel_diff, double min_abs_diff, double &found_max_abs_diff)
 
const charmark_deep_leafs (int min_depth, double min_rootdist, int &found_max_depth, double &found_max_rootdist)
 
double mark_degenerated_branches (double degeneration_factor)
 
const charanalyse_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_sequenceget_seq ()
 
const AP_sequenceget_seq () const
 
AP_sequenceset_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_scalingget_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 AliViewget_aliview () const
 
const AP_filterget_filter () const
 
const AP_weightsget_weights () const
 
GBDATAget_gb_main () const
 
GBDATAget_gb_tree () const
 
void tree_deleted_cb (GBDATA *gb_tree_del)
 
const charget_tree_name () const
 
const AP_sequenceget_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 NodeMarkersread_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_basesearch_ID (const char *id) OVERRIDE
 
charresolve_pointer_to_string_copy (int *str_len=NULp) const FINAL_OVERRIDE
 
const charresolve_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)
 
GBDATAget_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::Positioncalc_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_managerget_parent (ED4_level lev) const
 
void unlink_from_parent ()
 
bool has_parent (ED4_manager *Parent)
 
bool is_child_of (ED4_manager *Parent)
 
ED4_group_manageris_in_folded_group () const
 
charget_name_of_species ()
 
ED4_terminalget_next_terminal ()
 
ED4_terminalget_prev_terminal ()
 
void generate_configuration_string (GBS_strstruct &buffer)
 
const ED4_terminalget_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_basefind_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_baseget_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_baseget_competent_child (AW_pos x, AW_pos y, ED4_properties relevant_prop)
 
ED4_baseget_competent_clicked_child (AW_pos x, AW_pos y, ED4_properties relevant_prop)
 
ED4_basesearch_spec_child_rek (ED4_level level)
 
ED4_basesearch_ID (const char *id) FINAL_OVERRIDE
 
void remove_callbacks () OVERRIDE
 
ED4_terminalget_first_terminal (int start_index=0) const
 
ED4_terminalget_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_managerowner ()
 
const ED4_managerowner () const
 
ED4_basemember (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)
 
virtual 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 charoperator[] (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 charget_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 GenbankRefget_ref (int num) const
 
GenbankRefget_ref (int num)
 
const GenbankRefget_latest_ref () const
 
GenbankRefget_latest_ref ()
 
GenbankRefget_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 Emblrefget_ref (int num) const
 
Emblrefget_ref (int num)
 
const Emblrefget_latest_ref () const
 
Emblrefget_latest_ref ()
 
Emblrefget_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::stringget_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_awarawar () const
 
AW_awarawar ()
 
- Public Member Functions inherited from awt_mask_item
 awt_mask_item (awt_input_mask_global &global_)
 
virtual ~awt_mask_item ()
 
const awt_input_mask_globalmask_global () const
 
awt_input_mask_globalmask_global ()
 
bool has_name () const
 
const std::stringget_name () const
 
GB_ERROR set_name (const std::string &name_, bool is_global)
 
GB_ERROR remove_name ()
 
const awt_viewportto_viewport () const
 
awt_viewportto_viewport ()
 
const awt_linked_to_itemto_linked_item () const
 
awt_linked_to_itemto_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 ()
 
GBDATAitem ()
 
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 Locationpc () const
 

Static Public Member Functions

static const child_progresscalling_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 chargetSAIname ()
 
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 charstore_config_cb (ItemShader_impl *shader)
 
static void load_or_reset_config_cb (const char *cfgstr, ItemShader_impl *shader)
 
- 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 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_TreeShaderget_tree_shader ()
 
- Static Public Member Functions inherited from ED4_base
static void touch_world_cache ()
 

Public Attributes

int index
 
int sons
 
charID
 
chardateu
 
chardatec
 
chardescription
 
charos
 
characcession
 
charkeywords
 
chardr
 
RDP_comments comments
 
charlocus
 
chardefinition
 
charsource
 
charorganism
 
charseqabbr
 
charname
 
int rna_or_dna
 
charatcc
 
charrna
 
chardate
 
charnbk
 
characs
 
charauthor
 
charjournal
 
charwho
 
charstrain
 
charsubspecies
 
ED4_selection_entryselection_info
 
bool dragged
 
SEQTYPE * templ
 
LocallyModify< intpermit_flag_updates
 
AW_rootaw_root
 
SEC_rootsec_root
 
GBDATAgb_struct
 
GBDATAgb_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_rgbcolor_table
 
int number_of_timed_title_changes
 
AW_window_Motifp_w
 
AW_cb_callback
 
AW_cb_d_callback
 
charwindow_name
 
charwindow_defaults_name
 window title More...
 
int slider_pos_vertical
 window id More...
 
int slider_pos_horizontal
 current position of the vertical slider More...
 
bool window_is_shown
 current position of the horizontal slider More...
 
AW_screen_areapicture
 
- Public Attributes inherited from TreeNode
TreeNodefather
 
TreeNodeleftson
 
TreeNoderightson
 
GBT_LEN leftlen
 
GBT_LEN rightlen
 
GBDATAgb_node
 
charname
 
- Public Attributes inherited from AWT_graphic
AWT_graphic_exports exports
 
- Public Attributes inherited from AP_tree
AP_tree_members gr
 
- Public Attributes inherited from AP_tree_root
GBDATAgb_tree_gone
 
chargone_tree_name
 
long tree_timer
 
long species_timer
 
AP_ratesrates
 
- Public Attributes inherited from ED4_terminal
struct {
   unsigned int   deleted: 1
 
tflag
 
long curr_timestamp
 
- Public Attributes inherited from ED4_base
const ED4_objspecspec
 
ED4_managerparent
 
ED4_properties dynamic_prop
 
charid
 
ED4_index index
 
ED4_basewidth_link
 
ED4_baseheight_link
 
ED4_extension extension
 
ED4_update_info update_info
 
struct {
   unsigned int   hidden: 1
 
flag
 

Static Public Attributes

static const bool READONLY = true
 
static const bool WRITEONLY = false
 
static chartable
 

Protected Member Functions

 ~CompressionTree () OVERRIDE
 
 ~SimpleTree () OVERRIDE
 
 ~SizeAwareTree () OVERRIDE
 
 ~GroupTree () OVERRIDE
 
 ~ClusterTree () OVERRIDE
 
 ~AP_tree_nlen () OVERRIDE
 
GB_ERROR handleKey (AW_event_type event, AW_key_mod key_modifier, AW_key_code key_code, char key_char)
 
GB_ERROR handleMouse (AW_device *device, AW_event_type event, int button, AWT_COMMAND_MODE cmd, const Position &world, SEC_base *elem, int abspos)
 
- Protected Member Functions inherited from AW_device
bool generic_box (int gc, const AW::Rectangle &rect, AW_bitset filteri)
 
bool generic_circle (int gc, const AW::Position &center, const AW::Vector &radius, AW_bitset filteri)
 
bool generic_polygon (int gc, int npos, const AW::Position *pos, AW_bitset filteri)
 
bool generic_invisible (const AW::Position &pos, AW_bitset filteri)
 
- Protected Member Functions inherited from AW_clipable
int compoutcode (AW_pos xx, AW_pos yy) const
 
void set_cliprect (const AW_screen_area &rect)
 
- Protected Member Functions inherited from AW_window
void create_devices ()
 
void set_background (const char *colorname, Widget w)
 
void wm_activate ()
 
- Protected Member Functions inherited from AW_clicked_element
 AW_clicked_element ()
 
void assign (int distance_, const AW_pos &nearest_rel_pos_, const AW_click_cd *click_cd_)
 
- Protected Member Functions inherited from Dragged
AWT_graphic_exportsget_exports ()
 
- Protected Member Functions inherited from AP_sequence
void mark_sequence_set (bool is_set)
 
void do_lazy_load () const
 
- Protected Member Functions inherited from TreeNode
TreeNode *& self_ref ()
 
void unlink_from_father ()
 
void swap_node_info (TreeNode *other, bool ofKeeledGroups)
 
void fixKeeledOrientation ()
 
void set_tree_root (TreeRoot *new_root)
 
bool at_root () const
 
virtual ~TreeNode ()
 
void destroy ()
 
void destroy (TreeRoot *viaRoot)
 
- Protected Member Functions inherited from TreeRoot
void predelete ()
 
- Protected Member Functions inherited from PS_BitSet
 PS_BitSet (const bool _bias, const long _max_index, const long _capacity)
 
- Protected Member Functions inherited from PS_BitMap
 PS_BitMap (const bool _bias, const long _max_row, const long _capacity)
 
- Protected Member Functions inherited from AWT_graphic_tree
void store_command_data (AWT_command_data *new_cmd_data)
 
AWT_command_dataget_command_data ()
 
- Protected Member Functions inherited from AP_tree
 ~AP_tree () OVERRIDE
 
- Protected Member Functions inherited from ARB_seqtree
AP_sequencetake_seq ()
 
void replace_seq (AP_sequence *sequence)
 
 ~ARB_seqtree () OVERRIDE
 
- Protected Member Functions inherited from ARB_seqtree_root
void set_gb_tree (GBDATA *gbTree)
 
void set_gb_tree_and_name (GBDATA *gbTree, const char *name)
 
- Protected Member Functions inherited from ED4_container
bool valid_index (ED4_index idx) const
 
bool existing_index (ED4_index idx) const
 
- Protected Member Functions inherited from ARB_countedTree
 ~ARB_countedTree () OVERRIDE
 
- Protected Member Functions inherited from LineReader
void reset ()
 
- Protected Member Functions inherited from CharPtrArray
bool ok () const