ARB
Public Member Functions | Protected Member Functions | Friends | List of all members
ARB_seqtree Class Reference

#include <ARB_Tree.hxx>

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Collaboration diagram for ARB_seqtree:
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Public Member Functions

 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 ()
 
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
 
virtual void compute_tree ()=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

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)
 

Friends

GB_ERROR ARB_seqtree_root::loadFromDB (const char *name)
 
GB_ERROR ARB_seqtree_root::linkToDB (int *zombies, int *duplicates)
 
void ARB_seqtree_root::unlinkFromDB ()
 

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
TreeNodefather
 
TreeNodeleftson
 
TreeNoderightson
 
GBT_LEN leftlen
 
GBT_LEN rightlen
 
GBDATAgb_node
 
charname
 

Detailed Description

Definition at line 119 of file ARB_Tree.hxx.

Constructor & Destructor Documentation

ARB_seqtree::~ARB_seqtree ( )
protected

Definition at line 184 of file ARB_Tree.cxx.

ARB_seqtree::ARB_seqtree ( ARB_seqtree_root root)
inline

Definition at line 149 of file ARB_Tree.hxx.

Member Function Documentation

AP_sequence* ARB_seqtree::take_seq ( )
inlineprotected

Definition at line 139 of file ARB_Tree.hxx.

References NULp, and result.

void ARB_seqtree::replace_seq ( AP_sequence sequence)
protected

Definition at line 256 of file ARB_Tree.cxx.

References NULp, and set_seq().

ARB_seqtree::DEFINE_TREE_ACCESSORS ( ARB_seqtree_root  ,
ARB_seqtree   
)
void ARB_seqtree::calcTreeInfo ( ARB_tree_info info)
bool ARB_seqtree::is_upper_son ( ) const
inline

Definition at line 159 of file ARB_Tree.hxx.

References TreeNode::is_leftson().

Referenced by ARB_countedTree::relative_position_in().

bool ARB_seqtree::is_lower_son ( ) const
inline

Definition at line 160 of file ARB_Tree.hxx.

References TreeNode::is_rightson().

AP_sequence* ARB_seqtree::get_seq ( )
inline

Definition at line 162 of file ARB_Tree.hxx.

Referenced by AP_tree_root::remove_leafs().

const AP_sequence* ARB_seqtree::get_seq ( ) const
inline

Definition at line 163 of file ARB_Tree.hxx.

AP_sequence* ARB_seqtree::set_seq ( AP_sequence sequence)
inline

Definition at line 164 of file ARB_Tree.hxx.

References at_assert.

Referenced by replace_seq().

bool ARB_seqtree::hasSequence ( ) const
inline

Definition at line 174 of file ARB_Tree.hxx.

References AP_sequence::hasSequence().

void ARB_seqtree::mark_subtree ( )

Definition at line 188 of file ARB_Tree.cxx.

References TreeNode::gb_node, GB_write_flag(), and TreeNode::is_leaf().

Referenced by ap_mark_degenerated().

bool ARB_seqtree::contains_marked_species ( )

Friends And Related Function Documentation

GB_ERROR ARB_seqtree_root::loadFromDB ( const char name)
friend
GB_ERROR ARB_seqtree_root::linkToDB ( int zombies,
int duplicates 
)
friend

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