| analyse_distances() | AP_tree | |
| ancestor_common_with(const TreeNode *other) const | TreeNode | |
| ancestor_common_with(TreeNode *other) | TreeNode | inline |
| announce_tree_constructed() | TreeNode | inline |
| AP_tree(AP_tree_root *troot) | AP_tree | inlineexplicit |
| AP_tree_root class | AP_tree | friend |
| apply_aci_to_remarks(const char *aci, const GBL_call_env &callEnv) | TreeNode | |
| ARB_seqtree(ARB_seqtree_root *root) | ARB_seqtree | inline |
| at_root() const | TreeNode | inlineprotected |
| bootstrap2branchlen() | TreeNode | |
| branchlen2bootstrap() | TreeNode | |
| buildLeafList(AP_tree **&list, long &num) | AP_tree | |
| calc_clade_level() const | TreeNode | inline |
| calcTreeInfo(ARB_tree_info &info) | ARB_seqtree | |
| cantMoveNextTo(AP_tree *new_brother) | AP_tree | |
| colorize(GB_HASH *hashptr) | AP_tree | |
| compute_tree() FINAL_OVERRIDE | AP_tree | virtual |
| contains_marked_species() | ARB_seqtree | |
| count_clades() const | TreeNode | |
| count_leafs() const | AP_tree | |
| DEFINE_READ_ACCESSORS(TreeNode *, get_father, father) | TreeNode | |
| DEFINE_READ_ACCESSORS(TreeNode *, get_leftson, leftson) | TreeNode | |
| DEFINE_READ_ACCESSORS(TreeNode *, get_rightson, rightson) | TreeNode | |
| DEFINE_TREE_ACCESSORS(AP_tree_root, AP_tree) | AP_tree | |
| ARB_seqtree::DEFINE_TREE_ACCESSORS(ARB_seqtree_root, ARB_seqtree) | ARB_seqtree | |
| destroy() | TreeNode | inlineprotected |
| destroy(TreeRoot *viaRoot) | TreeNode | inlineprotected |
| destroy(TreeNode *that) | TreeNode | inlinestatic |
| destroy(TreeNode *that, TreeRoot *root) | TreeNode | inlinestatic |
| father | TreeNode | |
| find_parent_clade() const | TreeNode | inline |
| find_parent_clade() | TreeNode | inline |
| find_parent_with_groupInfo(bool skipKeeledBrothers=false) const | TreeNode | inline |
| find_parent_with_groupInfo(bool skipKeeledBrothers=false) | TreeNode | inline |
| findLeafNamed(const char *wantedName) | TreeNode | |
| fixDeletedSon() | TreeNode | |
| fixKeeledOrientation() | TreeNode | inlineprotected |
| forget_origin() | TreeNode | inline |
| forget_relatives() | TreeNode | inline |
| gb_node | TreeNode | |
| get_angle() const | AP_tree | inline |
| get_branchlength() const | TreeNode | inline |
| get_branchlength_unrooted() const | TreeNode | inline |
| get_brother() | TreeNode | inline |
| get_brother() const | TreeNode | inline |
| get_group_name() const | TreeNode | inline |
| get_leaf_count() const OVERRIDE | AP_tree | inlinevirtual |
| get_linewidth() const | AP_tree | inline |
| get_remark() const | TreeNode | inline |
| get_remark_ptr() const | TreeNode | inline |
| get_root_node() const | TreeNode | inline |
| get_root_node() | TreeNode | inline |
| get_seq() | ARB_seqtree | inline |
| get_seq() const | ARB_seqtree | inline |
| get_tree_root() const | TreeNode | inline |
| get_tree_shader() | AP_tree | inlinestatic |
| gr | AP_tree | |
| has_correct_mark_flags() const | AP_tree | |
| has_group_info() const | TreeNode | inline |
| has_no_remark() const | TreeNode | inline |
| has_valid_root_remarks() const | TreeNode | |
| hasName(const char *Name) const | AP_tree | inline |
| hasSequence() const | ARB_seqtree | inline |
| in_other_branch_than(const TreeNode *other) const | TreeNode | inline |
| in_same_branch_as(const TreeNode *other) const | TreeNode | inline |
| initial_insert(AP_tree *new_brother, AP_tree_root *troot) | AP_tree | virtual |
| insert(AP_tree *new_brother) | AP_tree | virtual |
| intree_distance_to(const TreeNode *other) const | TreeNode | inline |
| is_ancestor_of(const TreeNode *descendant) const | TreeNode | inline |
| is_clade() const | TreeNode | inline |
| is_folded_group() const | AP_tree | inline |
| is_inner_node_with_remark() const | TreeNode | inline |
| is_inside(const TreeNode *subtree) const | TreeNode | inline |
| is_inside_folded_group() const | AP_tree | |
| is_keeled_group() const | TreeNode | inline |
| is_leaf() const | TreeNode | inline |
| is_leftson() const | TreeNode | inline |
| is_lower_son() const | ARB_seqtree | inline |
| is_normal_group() const | TreeNode | inline |
| is_rightson() const | TreeNode | inline |
| is_root_node() const | TreeNode | inline |
| is_son_of(const TreeNode *Father) const | TreeNode | inline |
| is_son_of_root() const | TreeNode | inline |
| is_upper_son() const | ARB_seqtree | inline |
| justify_branch_lenghs(GBDATA *gb_main) | AP_tree | |
| keeledStateInfo() const | TreeNode | inline |
| keelsDownGroup(const TreeNode *toSon) const | TreeNode | inline |
| keelTarget() | TreeNode | inline |
| keelTarget() const | TreeNode | inline |
| leftlen | TreeNode | |
| leftson | TreeNode | |
| load_subtree_info() | AP_tree | |
| mark_deep_leafs(int min_depth, double min_rootdist, int &found_max_depth, double &found_max_rootdist) | AP_tree | |
| mark_degenerated_branches(double degeneration_factor) | AP_tree | |
| mark_duplicates() | AP_tree | |
| mark_long_branches(double min_rel_diff, double min_abs_diff, double &found_max_abs_diff) | AP_tree | |
| mark_subtree() | ARB_seqtree | |
| markAsLeaf() | TreeNode | inline |
| move_group_to(AP_tree *new_group) __ATTR__USERESULT | AP_tree | |
| moveNextTo(AP_tree *new_brother, AP_FLOAT rel_pos) | AP_tree | virtual |
| multifurcate() | TreeNode | |
| multifurcate_whole_tree(const multifurc_limits &below) | TreeNode | |
| name | TreeNode | |
| Noncopyable() | Noncopyable | inline |
| parse_bootstrap(double &bootstrap) const | TreeNode | inline |
| PREPARE_MARK_NONFINAL_CLASS(AP_tree) | AP_tree | |
| recompute_and_write_folding() | AP_tree | |
| relink() __ATTR__USERESULT | AP_tree | |
| relink_tree(GBDATA *gb_main, void(*relinker)(GBDATA *&ref_gb_node, char *&ref_name, GB_HASH *organism_hash), GB_HASH *organism_hash) | AP_tree | |
| REMOVE() | AP_tree | virtual |
| remove_bootstrap() | TreeNode | |
| remove_remark() | TreeNode | inline |
| reorder_tree(TreeOrder mode) | TreeNode | |
| replace_seq(AP_sequence *sequence) | ARB_seqtree | protected |
| reset_angle() | AP_tree | inline |
| reset_branchlengths() | TreeNode | |
| reset_length_and_bootstrap() | TreeNode | inline |
| reset_linewidth() | AP_tree | inline |
| reset_subtree_angles() | AP_tree | |
| reset_subtree_layout() | AP_tree | |
| reset_subtree_linewidths() | AP_tree | |
| reset_subtree_spreads() | AP_tree | |
| rightlen | TreeNode | |
| rightson | TreeNode | |
| root_distance() const | TreeNode | inline |
| rotate_subtree() | TreeNode | |
| scale_branchlengths(double factor) | TreeNode | |
| self_ref() | TreeNode | inlineprotected |
| set_angle(float angle) | AP_tree | inline |
| set_bootstrap(double bootstrap) | TreeNode | inline |
| set_branchlength(GBT_LEN newlen) | TreeNode | inline |
| set_branchlength_preserving(GBT_LEN new_len) | TreeNode | |
| set_branchlength_unrooted(GBT_LEN newlen) | TreeNode | inline |
| set_linewidth(int width) | AP_tree | inline |
| set_linewidth_recursive(int width) | AP_tree | |
| set_remark(const char *newRemark) | TreeNode | inline |
| set_root() | TreeNode | virtual |
| set_seq(AP_sequence *sequence) | ARB_seqtree | inline |
| set_tree_root(TreeRoot *new_root) | TreeNode | protected |
| set_tree_shader(AP_TreeShader *new_shader) | AP_tree | static |
| setKeeledState(int keeledState) | TreeNode | inline |
| sum_child_lengths() const | TreeNode | |
| swap_node_info(TreeNode *other, bool ofKeeledGroups) | TreeNode | inlineprotected |
| swap_sons() OVERRIDE | AP_tree | inlinevirtual |
| take_seq() | ARB_seqtree | inlineprotected |
| tree_write_tree_rek(GBDATA *gb_tree) | AP_tree | |
| TreeNode(TreeRoot *root) | TreeNode | inline |
| uncolorize() | AP_tree | inline |
| unkeelGroup() | TreeNode | inline |
| unlink_from_DB() | TreeNode | |
| unlink_from_father() | TreeNode | inlineprotected |
| update_subtree_information(const group_scaling &gscaling) | AP_tree | |
| use_as_remark(const SmartCharPtr &newRemark) | TreeNode | inline |
| ~AP_tree() OVERRIDE | AP_tree | protected |
| ~ARB_seqtree() OVERRIDE | ARB_seqtree | protected |
| ~TreeNode() | TreeNode | inlineprotectedvirtual |
