Public Member Functions | Protected Member Functions | List of all members
ARB_countedTree Class Referenceabstract

#include <ARB_Tree.hxx>

Inheritance diagram for ARB_countedTree:
Inheritance graph
Collaboration diagram for ARB_countedTree:
Collaboration graph

Public Member Functions

 ARB_countedTree (ARB_seqtree_root *tree_root_)
 DEFINE_TREE_ACCESSORS (ARB_seqtree_root, ARB_countedTree)
virtual void init_tree ()=0
void compute_tree () OVERRIDE
size_t relative_position_in (const ARB_countedTree *upgroup) const
- 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 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 ()
GB_ERROR apply_aci_to_remarks (const char *aci, const GBL_call_env &callEnv)
void reset_branchlengths ()
void scale_branchlengths (double factor)
void bootstrap2branchlen ()
void branchlen2bootstrap ()
GBT_RemarkType parse_bootstrap (double &bootstrap) const
const 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 ()
virtual unsigned get_leaf_count () const =0
void forget_origin ()
void forget_relatives ()
TreeRootget_tree_root () const
const TreeNodeget_root_node () const
TreeNodeget_root_node ()
bool is_root_node () const
virtual void set_root ()
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
virtual void swap_sons ()
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 Noncopyable
 Noncopyable ()

Protected Member Functions

 ~ARB_countedTree () 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 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)

Additional Inherited Members

- Static Public Member Functions inherited from TreeNode
static void destroy (TreeNode *that)
static void destroy (TreeNode *that, TreeRoot *root)
- Public Attributes inherited from TreeNode
GBT_LEN leftlen
GBT_LEN rightlen

Detailed Description

Definition at line 195 of file ARB_Tree.hxx.

Constructor & Destructor Documentation

ARB_countedTree::~ARB_countedTree ( )

Definition at line 197 of file ARB_Tree.hxx.

ARB_countedTree::ARB_countedTree ( ARB_seqtree_root tree_root_)

Definition at line 199 of file ARB_Tree.hxx.

Member Function Documentation

ARB_countedTree::DEFINE_TREE_ACCESSORS ( ARB_seqtree_root  ,
virtual void ARB_countedTree::init_tree ( )
pure virtual
void ARB_countedTree::compute_tree ( )

Implements TreeNode.

Reimplemented in FINAL_TYPE< SEQTYPE >.

Definition at line 212 of file ARB_Tree.hxx.

size_t ARB_countedTree::relative_position_in ( const ARB_countedTree upgroup) const

The documentation for this class was generated from the following files: