| ancestor_common_with(const TreeNode *other) const | TreeNode | |
| ancestor_common_with(TreeNode *other) | TreeNode | inline |
| announce_tree_constructed() | TreeNode | inline |
| apply_aci_to_remarks(const char *aci, const GBL_call_env &callEnv) | TreeNode | |
| ARB_countedTree(ARB_seqtree_root *tree_root_) | ARB_countedTree | inlineexplicit |
| ARB_seqtree(ARB_seqtree_root *root) | ARB_seqtree | inline |
| at_root() const | TreeNode | inlineprotected |
| bootstrap2branchlen() | TreeNode | |
| branchlen2bootstrap() | TreeNode | |
| calc_clade_level() const | TreeNode | inline |
| calcTreeInfo(ARB_tree_info &info) | ARB_seqtree | |
| compute_tree() OVERRIDE | ARB_countedTree | inlinevirtual |
| contains_marked_species() | ARB_seqtree | |
| count_clades() const | TreeNode | |
| 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(ARB_seqtree_root, ARB_countedTree) | ARB_countedTree | |
| 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_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 =0 | TreeNode | pure virtual |
| 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 |
| has_group_info() const | TreeNode | inline |
| has_no_remark() const | TreeNode | inline |
| has_valid_root_remarks() const | TreeNode | |
| 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 |
| init_tree()=0 | ARB_countedTree | pure 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_inner_node_with_remark() const | TreeNode | inline |
| is_inside(const TreeNode *subtree) const | TreeNode | inline |
| 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 |
| keeledStateInfo() const | TreeNode | inline |
| keelsDownGroup(const TreeNode *toSon) const | TreeNode | inline |
| keelTarget() | TreeNode | inline |
| keelTarget() const | TreeNode | inline |
| leftlen | TreeNode | |
| leftson | TreeNode | |
| mark_subtree() | ARB_seqtree | |
| markAsLeaf() | TreeNode | inline |
| multifurcate() | TreeNode | |
| multifurcate_whole_tree(const multifurc_limits &below) | TreeNode | |
| name | TreeNode | |
| Noncopyable() | Noncopyable | inline |
| parse_bootstrap(double &bootstrap) const | TreeNode | inline |
| relative_position_in(const ARB_countedTree *upgroup) const | ARB_countedTree | |
| remove_bootstrap() | TreeNode | |
| remove_remark() | TreeNode | inline |
| reorder_tree(TreeOrder mode) | TreeNode | |
| replace_seq(AP_sequence *sequence) | ARB_seqtree | protected |
| reset_branchlengths() | TreeNode | |
| reset_length_and_bootstrap() | TreeNode | inline |
| rightlen | TreeNode | |
| rightson | TreeNode | |
| root_distance() const | TreeNode | inline |
| rotate_subtree() | TreeNode | |
| scale_branchlengths(double factor) | TreeNode | |
| self_ref() | TreeNode | inlineprotected |
| 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_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 |
| setKeeledState(int keeledState) | TreeNode | inline |
| sum_child_lengths() const | TreeNode | |
| swap_node_info(TreeNode *other, bool ofKeeledGroups) | TreeNode | inlineprotected |
| swap_sons() | TreeNode | inlinevirtual |
| take_seq() | ARB_seqtree | inlineprotected |
| TreeNode(TreeRoot *root) | TreeNode | inline |
| unkeelGroup() | TreeNode | inline |
| unlink_from_DB() | TreeNode | |
| unlink_from_father() | TreeNode | inlineprotected |
| use_as_remark(const SmartCharPtr &newRemark) | TreeNode | inline |
| ~ARB_countedTree() OVERRIDE | ARB_countedTree | inlineprotected |
| ~ARB_seqtree() OVERRIDE | ARB_seqtree | protected |
| ~TreeNode() | TreeNode | inlineprotectedvirtual |
