Bio::EnsEMBL::Compara::GeneTreeNode Class Reference

Inheritance diagram for Bio::EnsEMBL::Compara::GeneTreeNode:

List of all members.

---

Class Summary

Description

Specific subclass of NestedSet to add functionality when the nodes of this tree
are GeneTreeMember objects and the tree is a representation of a gene derived
Phylogenetic tree

Definition at line 17 of file GeneTreeNode.pm.

Available Methods
protected	_add_neighbor_link_to_hash ()
protected	_add_nodeI_to_node ()
protected	_distance ()
protected	_internal_newick_format ()
protected	_internal_newick_format_ryo ()
protected	_internal_nhx_format ()
protected	_internal_print_tree ()
protected	_internal_string_tree ()
protected	_invert_tree_above ()
protected void	_load_tags ()
protected	_parent_id ()
protected	_recursive_get_all_leaves ()
protected Listref	_recursive_get_all_sorted_leaves ()
protected	_root_id ()
protected	_set_parent_link ()
protected	_unlink_node_in_hash ()
protected	_walk_graph_until ()
public Subclass	adaptor ()
public Undef	add_child ()
public Boolean	add_tag ()
public	all_links_in_graph ()
public	all_nodes_in_graph ()
public	alloc ()
public void	AUTOLOAD ()
public	build_leftright_indexing ()
public	cascade_unlink ()
public Array	children ()
public	consensus_cigar_line ()
public Bio::EnsEMBL::Compara::NestedSet	copy ()
public	copy_graph ()
public	copy_shallow_links ()
public	create_directed_link_to_node ()
public Compara::Graph::Link	create_link_to_node ()
public	dealloc ()
public	delete_lineage ()
public	delete_tag ()
public	DESTROY ()
public Undef	disavow_parent ()
public Float	distance_to_ancestor ()
public Float	distance_to_node ()
public Int	distance_to_parent ()
public	distance_to_root ()
public	each_child ()
public	equals ()
public	extract_subtree_from_leaves ()
public Bio::EnsEMBL::Compara::NestedSet	find_first_shared_ancestor ()
public	find_first_shared_ancestor_from_leaves ()
public	find_leaf_by_name ()
public	find_leaf_by_node_id ()
public	find_node_by_name ()
public	find_node_by_node_id ()
public Undef	flatten_tree ()
public Listref	get_all_adjacent_subtrees ()
public Listref	get_all_ancestors ()
public Reference	get_all_leaves ()
public	get_all_leaves_indexed ()
public Listref	get_all_nodes ()
public Listref	get_all_nodes_by_tag_value ()
public Listref	get_all_sorted_leaves ()
public Listref	get_all_subnodes ()
public Array	get_all_tags ()
public ArrayRef	get_all_values_for_tag ()
public	get_child_count ()
public	get_leaf_by_Member ()
public	get_SimpleAlign ()
public Scalar	get_tagvalue ()
public Hashref	get_tagvalue_hash ()
public	get_TreeI ()
public Scalar	get_value_for_tag ()
public	has_ancestor ()
public	has_child ()
public	has_neighbor ()
public	has_parent ()
public Boolean	has_tag ()
public	init ()
public	is_leaf ()
public	is_member_of ()
public	is_subset_of ()
public Bio::EnsEMBL::Compara::GeneTreeNode	keep_nodes_by_taxon_ids ()
public	left_index ()
public	like ()
public	link_count ()
public	link_for_neighbor ()
public Array	links ()
public	load_children_if_needed ()
public Int	max_depth ()
public Int	max_distance ()
public	merge_children ()
public	merge_node_via_shared_ancestor ()
public	minimize_node ()
public Bio::EnsEMBL::Compara::NestedSet	minimize_tree ()
public	name ()
public	neighbors ()
public	new ()
public	new_from_newick ()
public	new_from_TreeI ()
public String	newick_format ()
public Undef	newick_simple_format ()
public	nhx_format ()
public	no_autoload_children ()
public Int	node_id ()
public Int	num_leaves ()
public	obj_id ()
public Undef	parent ()
public	parent_link ()
public	print_links ()
public	print_node ()
public Undef	print_tree ()
public Undef	re_root ()
public	refcount ()
public	release ()
public	release_children ()
public Undef	release_tree ()
public Bio::EnsEMBL::Compara::NestedSet	remove_nodes ()
public Bio::EnsEMBL::Compara::GeneTreeNode	remove_nodes_by_taxon_ids ()
public	retain ()
public	right_index ()
public	root ()
public	scale ()
public	scale_max_to ()
public Array	sorted_children ()
public	store ()
public	store_tag ()
public	string_node ()
public	string_tree ()
public	subroot ()
public	tree ()
public	unlink_all ()
public Undef	unlink_neighbor ()

---

Method Documentation

protected Bio::EnsEMBL::Compara::Graph::Node::_add_neighbor_link_to_hash

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_add_nodeI_to_node

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_distance

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_internal_newick_format

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_internal_newick_format_ryo

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_internal_nhx_format

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_internal_print_tree

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_internal_string_tree

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_invert_tree_above

(

)

[inherited]

Undocumented method

Code:

protected void Bio::EnsEMBL::Compara::Taggable::_load_tags

(

)

[inherited]

  Description: loads all the tags (from the database) if possible.
               Otherwise, an empty hash is created
  Example    : $ns_node->_load_tags();
  Returntype : none
  Exceptions : none
  Caller     : internal

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_parent_id

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_recursive_get_all_leaves

(

)

[inherited]

Undocumented method

Code:

protected Listref Bio::EnsEMBL::Compara::NestedSet::_recursive_get_all_sorted_leaves

(

)

[inherited]

  Arg [1]     : hashref $score_by_node
  Example     : my $sorted_leaves = $object->_recursive_get_all_sorted_leaves($score_by_node);
  Description : Recursive code for the get_all_sorted_leaves() method
  Returntype  : listref of Bio::EnsEMBL::Compara::NestedSet (sorted leaves)
  Exceptions  : none
  Caller      : private
  Status      : Stable

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_root_id

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::NestedSet::_set_parent_link

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::Graph::Node::_unlink_node_in_hash

(

)

[inherited]

Undocumented method

Code:

protected Bio::EnsEMBL::Compara::Graph::Node::_walk_graph_until

(

)

[inherited]

Undocumented method

Code:

public Subclass Bio::EnsEMBL::Compara::Graph::CGObject::adaptor

(

)

[inherited]

  Arg [1]    : (opt.) subcalss of Bio::EnsEMBL::DBSQL::BaseAdaptor
  Example    : my $object_adaptor = $object->adaptor();
  Example    : $object->adaptor($object_adaptor);
  Description: Getter/Setter for the adaptor this object uses for database
               interaction.
  Returntype : subclass of Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general

Code:

Reimplemented in Bio::EnsEMBL::Compara::SpeciesSet.

public Undef Bio::EnsEMBL::Compara::NestedSet::add_child

(

)

[inherited]

  Overview   : attaches child nestedset node to this nested set
  Arg [1]    : Bio::EnsEMBL::Compara::NestedSet $child
  Arg [2]    : (opt.) distance between this node and child
  Example    : $self->add_child($child);
  Returntype : undef
  Exceptions : if child is undef or not a NestedSet subclass
  Caller     : general

Code:

public Boolean Bio::EnsEMBL::Compara::Taggable::add_tag

(

)

[inherited]

  Description: adds metadata tags to a node.  Both tag and value are added
               as metdata with the added ability to retreive the value given
               the tag (like a perl hash). In case of one to many relation i.e.
               one tag and different values associated with it, the values are
               returned in a array reference.
  Arg [1]    : <string> tag
  Arg [2]    : <string> value
  Arg [3]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $ns_node->add_tag('scientific name', 'Mammalia');
               $ns_node->add_tag('lost_taxon_id', 9593, 1);
  Returntype : Boolean indicating if the tag could be added
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::Graph::Node::all_links_in_graph

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::all_nodes_in_graph

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::alloc

(

)

[inherited]

Undocumented method

Code:

public void Bio::EnsEMBL::Compara::Taggable::AUTOLOAD

(

)

[inherited]

  Description: matches the get_value_for_XXX calls to get_value_for_tag('XXX') and other calls
  Returntype : none
  Exceptions : none
  Caller     : system

Code:

public Bio::EnsEMBL::Compara::NestedSet::build_leftright_indexing

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::cascade_unlink

(

)

[inherited]

  Overview   : release all neighbors and clear arrays and hashes
               will cause potential deletion of neighbors if refcount reaches Zero.
  Example    : $self->cascade_unlink
  Returntype : $self
  Exceptions : none
  Caller     : general

Code:

public Array Bio::EnsEMBL::Compara::NestedSet::children

(

)

[inherited]

  Overview   : returns a list of NestedSet nodes directly under this parent node
  Example    : my @children = @{$object->children()};
  Returntype : array reference of Bio::EnsEMBL::Compara::NestedSet objects (could be empty)
  Exceptions : none
  Caller     : general
  Algorithm  : new algorithm for fetching children:
                for each link connected to this NestedsSet node, a child is defined if
                  old: the link is not my parent_link
                  new: the link's neighbors' parent_link is the link
               This allows one (with a carefully coded algorithm) to overlay a tree on top
               of a fully connected graph and use the parent/children methods of NestedSet
               to walk the 'tree' substructure of the graph.  
               Trees that are really just trees are still trees.

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode::consensus_cigar_line

(

)

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::copy

(

)

[inherited]

  Overview   : creates copy of tree starting at this node going down
  Example    : my $clone = $self->copy;
  Returntype : Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

Reimplemented in Bio::EnsEMBL::Compara::GeneTreeMember, Bio::EnsEMBL::Compara::GenomicAlignTree, and Bio::EnsEMBL::Compara::NCBITaxon.

public Bio::EnsEMBL::Compara::Graph::Node::copy_graph

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::copy_shallow_links

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::create_directed_link_to_node

(

)

[inherited]

Undocumented method

Code:

public Compara::Graph::Link Bio::EnsEMBL::Compara::Graph::Node::create_link_to_node

(

)

[inherited]

  Overview   : attaches neighbor Graph::Node to this nested set
  Arg [1]    : Bio::EnsEMBL::Compara::Graph::Node $node
  Arg [2]    : (opt.) <float> distance to node
  Example    : $self->add_child($node);
  Returntype : Compara::Graph::Link object
  Exceptions : if neighbor is undef or not a NestedSet subclass
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::dealloc

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::delete_lineage

(

)

[inherited]

  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $node
  Example     : $tree->delete_lineage($node);
  Description : Removes $node from tree. Nodes should be in the tree.
  Returntype  : 
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)

Code:

public Bio::EnsEMBL::Compara::Taggable::delete_tag

(

)

[inherited]

  Description: removes a tag from the metadata. If the value is provided, it tries
               to delete only it (if present). Otherwise, it just clears the tag,
               whatever value it was containing
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <string> value
  Example    : $ns_node->remove_tag('scientific name', 'Mammalia');
               $ns_node->remove_tag('lost_taxon_id', 9593);
  Returntype : 0 if the tag couldn't be removed,
               1 if it is only in the PERL object,
               2 if it is also stored in the database
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::DESTROY

(

)

[inherited]

Undocumented method

Code:

public Undef Bio::EnsEMBL::Compara::NestedSet::disavow_parent

(

)

[inherited]

  Overview   : unlink and release self from its parent
               might cause self to delete if refcount reaches Zero.
  Example    : $self->disavow_parent
  Returntype : undef
  Caller     : general

Code:

public Float Bio::EnsEMBL::Compara::NestedSet::distance_to_ancestor

(

)

[inherited]

  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $ancestor
  Example     : my $distance = $this_node->distance_to_ancestor($ancestor);
  Description : Calculates the distance in the tree between this node and
                its ancestor $ancestor
  Returntype  : float
  Exceptions  : throws if $ancestor is not an ancestor of this node.
  Caller      : general
  Status      : Stable

Code:

public Float Bio::EnsEMBL::Compara::NestedSet::distance_to_node

(

)

[inherited]

  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $node
  Example     : my $distance = $this_node->distance_to_node($other_node);
  Description : Calculates the distance in the tree between these
                two nodes.
  Returntype  : float
  Exceptions  : returns undef if no ancestor can be found, no distances are
                defined in the tree, etc.
  Caller      : general
  Status      : Stable

Code:

public Int Bio::EnsEMBL::Compara::NestedSet::distance_to_parent

(

)

[inherited]

  Arg [1]    : (opt.) <int or double> distance
  Example    : my $dist = $object->distance_to_parent();
  Example    : $object->distance_to_parent(1.618);
  Description: Getter/Setter for the distance between this child and its parent
  Returntype : integer node_id
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::distance_to_root

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::each_child

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::equals

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::extract_subtree_from_leaves

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::find_first_shared_ancestor

(

)

[inherited]

  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $node
  Example     : my $ancestor = $this_node->find_first_shared_ancestor($other_node);
  Description : Gets the first common ancestor between this node and the other one.
  Returntype  : Bio::EnsEMBL::Compara::NestedSet object
  Exceptions  :
  Caller      : general
  Status      : Stable

Code:

public Bio::EnsEMBL::Compara::NestedSet::find_first_shared_ancestor_from_leaves

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::find_leaf_by_name

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::find_leaf_by_node_id

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::find_node_by_name

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::find_node_by_node_id

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Undef Bio::EnsEMBL::Compara::NestedSet::flatten_tree

(

)

[inherited]

  Overview   : Removes all internal nodes and attaches leaves to the tree root, creating
               a "flattened" star tree structure.
  Example    : $node->flatten_tree();
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general

Code:

public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_adjacent_subtrees

(

)

[inherited]

  Arg 1       : 
  Example     : my @subtrees = @{$node->get_all_adjacent_subtrees};
  Description : Returns subtree 'root' nodes where the subtree is adjacent
                to this node. Used e.g. by the web code for the 'collapse 
                other nodes' action 
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : EnsEMBL::Web::Component::Gene::ComparaTree
  Status      :

Code:

public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_ancestors

(

)

[inherited]

  Arg 1       : 
  Example     : my @ancestors = @{$node->get_all_ancestors};
  Description : Returns all ancestor nodes for a given node
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      :

Code:

public Reference Bio::EnsEMBL::Compara::NestedSet::get_all_leaves

(

)

[inherited]

 Title   : get_all_leaves
 Usage   : my @leaves = @{$tree->get_all_leaves};
 Function: searching from the given starting node, searches and creates list
           of all leaves in this subtree and returns by reference
 Example :
 Returns : reference to list of NestedSet objects (all leaves)
 Args    : none

Code:

Reimplemented in Bio::EnsEMBL::Compara::GenomicAlignTree.

public Bio::EnsEMBL::Compara::NestedSet::get_all_leaves_indexed

(

)

[inherited]

Undocumented method

Code:

public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_nodes

(

)

[inherited]

  Arg 1       : hashref $node_hash [used for recursivity, do not use it!]
  Example     : my $all_nodes = $root->get_all_nodes();
  Description : Returns this and all underlying sub nodes
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      : Stable

Code:

public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_nodes_by_tag_value

(

)

[inherited]

  Arg 1       : tag_name
  Arg 2       : tag_value (optional)
  Example     : my $all_nodes = $root->get_all_nodes_by_tagvalue('taxon_name'=>'Mamalia');
  Description : Returns all underlying nodes that have a tag of the given name, and optionally a value of the given value.
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      :

Code:

public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_sorted_leaves

(

)

[inherited]

  Arg [1]     : Bio::EnsEMBL::Compara::NestedSet $top_leaf
  Arg [...]   : (optional) Bio::EnsEMBL::Compara::NestedSet $secondary_priority_leaf
  Example     : my $sorted_leaves = $object->get_all_sorted_leaves($human_leaf);
  Example     : my $sorted_leaves = $object->get_all_sorted_leaves($human_leaf, $mouse_leaf);
  Description : Sorts the tree such as $top_leaf is the first leave and returns
                all the other leaves in the order defined by the tree.
                It is possible to define as many secondary top leaves as you require
                to sort other branches of the tree. The priority to sort the trees
                is defined by the order in which you specify the leaves.
  Returntype  : listref of Bio::EnsEMBL::Compara::NestedSet (all sorted leaves)
  Exceptions  : none
  Caller      : general
  Status      : Stable

Code:

public Listref Bio::EnsEMBL::Compara::NestedSet::get_all_subnodes

(

)

[inherited]

  Arg 1       : hashref $node_hash [used for recursivity, do not use it!]
  Example     : my $all_nodes = $root->get_all_nodes();
  Description : Returns all underlying sub nodes
  ReturnType  : listref of Bio::EnsEMBL::Compara::NestedSet objects
  Exceptions  : none
  Caller      : general
  Status      : Stable

Code:

public Array Bio::EnsEMBL::Compara::Taggable::get_all_tags

(

)

[inherited]

  Description: returns an array of all the available tags
  Example    : $ns_node->get_all_tags();
  Returntype : Array
  Exceptions : none
  Caller     : general

Code:

public ArrayRef Bio::EnsEMBL::Compara::Taggable::get_all_values_for_tag

(

)

[inherited]

  Description: returns all the values of the tag, or $default (undef
               if not provided) if the tag doesn't exist. In case of
               a single value, it is wrapped with an array
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : ArrayRef
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::get_child_count

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode::get_leaf_by_Member

(

)

Undocumented method

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode::get_SimpleAlign

(

)

Undocumented method

Code:

public Scalar Bio::EnsEMBL::Compara::Taggable::get_tagvalue

(

)

[inherited]

  Description: returns the value(s) of the tag, or $default (undef
               if not provided) if the tag doesn't exist.
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : Scalar or ArrayRef
  Exceptions : none
  Caller     : general

Code:

public Hashref Bio::EnsEMBL::Compara::Taggable::get_tagvalue_hash

(

)

[inherited]

  Description: returns the underlying hash that contains all
               the tags
  Example    : $ns_node->get_tagvalue_hash();
  Returntype : Hashref
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::get_TreeI

(

)

[inherited]

Undocumented method

Code:

public Scalar Bio::EnsEMBL::Compara::Taggable::get_value_for_tag

(

)

[inherited]

  Description: returns the value of the tag, or $default (undef
               if not provided) if the tag doesn't exist. In case
               of multiple values, the first one is returned.
  Arg [1]    : <string> tag
  Arg [2]    : (optional) <scalar> default
  Example    : $ns_node->get_tagvalue('scientific name');
  Returntype : Scalar
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::has_ancestor

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::has_child

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::has_neighbor

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::has_parent

(

)

[inherited]

Undocumented method

Code:

public Boolean Bio::EnsEMBL::Compara::Taggable::has_tag

(

)

[inherited]

  Description: indicates whether the tag exists in the metadata
  Arg [1]    : <string> tag
  Example    : $ns_node->has_tag('scientific name');
  Returntype : Boolean
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::init

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::is_leaf

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet::is_member_of

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::is_subset_of

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode Bio::EnsEMBL::Compara::GeneTreeNode::keep_nodes_by_taxon_ids

(

)

  Arg [1]     : arrayref of taxon_ids
  Example     : my $ret_tree = $tree->keep_nodes_by_taxon_ids($taxon_ids);
  Description : Returns the tree with kept nodes in taxon_id list.
  Returntype  : Bio::EnsEMBL::Compara::GeneTreeNode object
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)

Code:

public Bio::EnsEMBL::Compara::NestedSet::left_index

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::like

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::link_count

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::link_for_neighbor

(

)

[inherited]

Undocumented method

Code:

public Array Bio::EnsEMBL::Compara::Graph::Node::links

(

)

[inherited]

  Overview   : returns a list of Compara::Graph::Link connected to this node
  Example    : my @links = @{self->links()};
  Returntype : array reference of Bio::EnsEMBL::Compara::Graph::Link objects (could be empty)
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::load_children_if_needed

(

)

[inherited]

Undocumented method

Code:

public Int Bio::EnsEMBL::Compara::NestedSet::max_depth

(

)

[inherited]

 Title   : max_depth
 Args    : none
 Usage   : $tree_node->max_depth;
 Function: searching from the given starting node, calculates the maximum depth to a leaf
 Returns : int

Code:

public Int Bio::EnsEMBL::Compara::NestedSet::max_distance

(

)

[inherited]

 Title   : max_distance
 Args    : none
 Usage   : $tree_node->max_distance;
 Function: searching from the given starting node, calculates the maximum distance to a leaf
 Returns : int

Code:

public Bio::EnsEMBL::Compara::NestedSet::merge_children

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::merge_node_via_shared_ancestor

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::minimize_node

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::minimize_tree

(

)

[inherited]

  Arg [1]     : -none-
  Example     : $leaf->disavow_parent();
                $tree = $tree->minimize_tree();
  Description : Returns the tree after removing internal nodes that do not
                represent an multi- or bi-furcation anymore. This is typically
                required after disavowing a node. Please ensure you use the
                object returned by the method and not the original object
                anymore!
  Returntype  : Bio::EnsEMBL::Compara::NestedSet object
  Exceptions  :
  Caller      : general
  Status      : Stable

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::name

(

)

[inherited]

Undocumented method

Code:

Reimplemented in Bio::EnsEMBL::Compara::GeneTreeMember, and Bio::EnsEMBL::Compara::GenomicAlignTree.

public Bio::EnsEMBL::Compara::Graph::Node::neighbors

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::new

(

)

[inherited]

Undocumented method

Code:

Reimplemented in Bio::EnsEMBL::Compara::Graph::Link, and Bio::EnsEMBL::Compara::SpeciesSet.

public Bio::EnsEMBL::Compara::NestedSet::new_from_newick

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::new_from_TreeI

(

)

[inherited]

Undocumented method

Code:

public String Bio::EnsEMBL::Compara::NestedSet::newick_format

(

)

[inherited]

  Arg [1]     : string $format_mode
  Example     : $this_node->newick_format("full");
  Description : Prints this tree in Newick format. Several modes are
                available: full, display_label_composite, simple, species,
                species_short_name, ncbi_taxon, ncbi_name, njtree and phylip
  Returntype  : string
  Exceptions  :
  Caller      : general
  Status      : Stable

Code:

public Undef Bio::EnsEMBL::Compara::NestedSet::newick_simple_format

(

)

[inherited]

  Arg [1]     : -none-
  Example     : $this_node->newick_simple_format();
  Description : Prints this tree in simple Newick format. This is an
                alias for $this_node->newick_format("simple");
  Returntype  : undef
  Exceptions  :
  Caller      : general
  Status      : Stable

Code:

public Bio::EnsEMBL::Compara::NestedSet::nhx_format

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::no_autoload_children

(

)

[inherited]

Undocumented method

Code:

public Int Bio::EnsEMBL::Compara::Graph::Node::node_id

(

)

[inherited]

  Arg [1]    : (opt.) integer node_id
  Example    : my $nsetID = $object->node_id();
  Example    : $object->node_id(12);
  Description: Getter/Setter for the node_id of this object in the database
  Returntype : integer node_id
  Exceptions : none
  Caller     : general

Code:

public Int Bio::EnsEMBL::Compara::NestedSet::num_leaves

(

)

[inherited]

  Example     : my $num_leaves = $node->num_leaves
  Description : Returns the number of leaves underlying the node
  ReturnType  : integer
  Exceptions  : none
  Caller      : general
  Status      : At risk (relies on left and right indexes)

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::obj_id

(

)

[inherited]

  Example    : my $nsetID = $object->obj_id();
  Description: returns the unique identifier of this object.  
  Returntype : <string> uuid
  Exceptions : none
  Caller     : general

Code:

public Undef Bio::EnsEMBL::Compara::NestedSet::parent

(

)

[inherited]

  Overview   : returns the parent NestedSet object for this node
  Example    : my $my_parent = $object->parent();
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::parent_link

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::print_links

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::print_node

(

)

[inherited]

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::Graph::Node.

Reimplemented in Bio::EnsEMBL::Compara::GeneTreeMember, and Bio::EnsEMBL::Compara::NCBITaxon.

public Undef Bio::EnsEMBL::Compara::NestedSet::print_tree

(

)

[inherited]

  Arg [1]     : int $scale
  Example     : $this_node->print_tree(100);
  Description : Prints this tree in ASCII format. The scale is used to define
                the width of the tree in the output
  Returntype  : undef
  Exceptions  :
  Caller      : general
  Status      : At risk (as the output might change)

Code:

public Undef Bio::EnsEMBL::Compara::NestedSet::re_root

(

)

[inherited]

  Overview   : rearranges the tree structure so that the root is moved to 
               beetween this node and its parent.  If the old root was more than
	       bifurcated (2 children) a new node is created where it was to hold
	       the multiple children that arises from the re-rooting.  
	       The old root is returned.
  Example    : $node->re_root();
  Returntype : undef or Bio::EnsEMBL::Compara::NestedSet
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::refcount

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::release

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::release_children

(

)

[inherited]

  Overview   : recursive releases all children
               will cause potential deletion of children if refcount reaches Zero.
  Example    : $self->release_children
  Returntype : $self
  Exceptions : none
  Caller     : general

Code:

public Undef Bio::EnsEMBL::Compara::GeneTreeNode::release_tree

(

)

  Overview   : Removes the to/from GeneTree reference to
               allow freeing memory 
  Example    : $self->release_tree;
  Returntype : undef
  Exceptions : none
  Caller     : general

Code:

Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

public Bio::EnsEMBL::Compara::NestedSet Bio::EnsEMBL::Compara::NestedSet::remove_nodes

(

)

[inherited]

  Arg [1]     : arrayref Bio::EnsEMBL::Compara::NestedSet $nodes
  Example     : my $ret_tree = $tree->remove_nodes($nodes);
  Description : Returns the tree with removed nodes in list. Nodes should be in the tree.
  Returntype  : Bio::EnsEMBL::Compara::NestedSet object
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode Bio::EnsEMBL::Compara::GeneTreeNode::remove_nodes_by_taxon_ids

(

)

  Arg [1]     : arrayref of taxon_ids
  Example     : my $ret_tree = $tree->remove_nodes_by_taxon_ids($taxon_ids);
  Description : Returns the tree with removed nodes in taxon_id list.
  Returntype  : Bio::EnsEMBL::Compara::GeneTreeNode object
  Exceptions  :
  Caller      : general
  Status      : At risk (behaviour on exceptions could change)

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::retain

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::right_index

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode::root

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::Compara::NestedSet.

public Bio::EnsEMBL::Compara::NestedSet::scale

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::scale_max_to

(

)

[inherited]

Undocumented method

Code:

public Array Bio::EnsEMBL::Compara::NestedSet::sorted_children

(

)

[inherited]

  Overview   : returns a sorted list of NestedSet nodes directly under this parent node
               sort so that internal nodes<leaves and then on distance
  Example    : my @kids = @{$object->ordered_children()};
  Returntype : array reference of Bio::EnsEMBL::Compara::NestedSet objects (could be empty)
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::Graph::CGObject::store

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Taggable::store_tag

(

)

[inherited]

  Description: calls add_tag and then stores the tag in the database. Has the
               exact same arguments as add_tag
  Arg [1]    : <string> tag
  Arg [2]    : <string> value
  Arg [3]    : (optional) <int> allows overloading the tag with different values
               default is 0 (no overloading allowed, one tag points to one value)
  Example    : $ns_node->store_tag('scientific name', 'Mammalia');
               $ns_node->store_tag('lost_taxon_id', 9593, 1);
  Returntype : 0 if the tag couldn't be stored,
               1 if it is only in the PERL object,
               2 if it is also stored in the database
  Exceptions : none
  Caller     : general

Code:

public Bio::EnsEMBL::Compara::NestedSet::string_node

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::string_tree

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::NestedSet::subroot

(

)

[inherited]

Undocumented method

Code:

public Bio::EnsEMBL::Compara::GeneTreeNode::tree

(

)

Undocumented method

Code:

public Bio::EnsEMBL::Compara::Graph::Node::unlink_all

(

)

[inherited]

Undocumented method

Code:

public Undef Bio::EnsEMBL::Compara::Graph::Node::unlink_neighbor

(

)

[inherited]

  Overview   : unlink and release neighbor from self if its mine
               might cause neighbor to delete if refcount reaches Zero.
  Arg [1]    : $node Bio::EnsEMBL::Compara::Graph::Node instance
  Example    : $self->unlink_neighbor($node);
  Returntype : undef
  Caller     : general

Code:

---

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

• Bio/EnsEMBL/Compara/GeneTreeNode.pm