
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.
Method Documentation
protected Bio::EnsEMBL::Compara::Graph::Node::_add_neighbor_link_to_hash | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_add_nodeI_to_node | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_distance | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_internal_newick_format | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_internal_newick_format_ryo | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_internal_nhx_format | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_internal_print_tree | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_internal_string_tree | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_invert_tree_above | ( | ) | [inherited] |
Undocumented method

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
protected Bio::EnsEMBL::Compara::NestedSet::_parent_id | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_recursive_get_all_leaves | ( | ) | [inherited] |
Undocumented method

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

protected Bio::EnsEMBL::Compara::NestedSet::_root_id | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::NestedSet::_set_parent_link | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::Graph::Node::_unlink_node_in_hash | ( | ) | [inherited] |
Undocumented method

protected Bio::EnsEMBL::Compara::Graph::Node::_walk_graph_until | ( | ) | [inherited] |
Undocumented method

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

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

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

public Bio::EnsEMBL::Compara::Graph::Node::all_links_in_graph | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::all_nodes_in_graph | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::CGObject::alloc | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::NestedSet::build_leftright_indexing | ( | ) | [inherited] |
Undocumented method

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

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.

public Bio::EnsEMBL::Compara::GeneTreeNode::consensus_cigar_line | ( | ) |
Undocumented method

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

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

public Bio::EnsEMBL::Compara::Graph::Node::copy_shallow_links | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::create_directed_link_to_node | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::NestedSet::dealloc | ( | ) | [inherited] |
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)

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

public Bio::EnsEMBL::Compara::Graph::CGObject::DESTROY | ( | ) | [inherited] |
Undocumented method

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

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

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

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

public Bio::EnsEMBL::Compara::NestedSet::distance_to_root | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::each_child | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::equals | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::extract_subtree_from_leaves | ( | ) | [inherited] |
Undocumented method

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
public Bio::EnsEMBL::Compara::NestedSet::find_first_shared_ancestor_from_leaves | ( | ) | [inherited] |
Undocumented method
public Bio::EnsEMBL::Compara::NestedSet::find_leaf_by_name | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::find_leaf_by_node_id | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::find_node_by_name | ( | ) | [inherited] |
public Bio::EnsEMBL::Compara::NestedSet::find_node_by_node_id | ( | ) | [inherited] |
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

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 :

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 :

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

Reimplemented in Bio::EnsEMBL::Compara::GenomicAlignTree.
public Bio::EnsEMBL::Compara::NestedSet::get_all_leaves_indexed | ( | ) | [inherited] |
Undocumented method

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

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 :

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

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

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
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

public Bio::EnsEMBL::Compara::NestedSet::get_child_count | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::GeneTreeNode::get_leaf_by_Member | ( | ) |
Undocumented method

public Bio::EnsEMBL::Compara::GeneTreeNode::get_SimpleAlign | ( | ) |
Undocumented method

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

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

public Bio::EnsEMBL::Compara::NestedSet::get_TreeI | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::NestedSet::has_ancestor | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::has_child | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::has_neighbor | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::has_parent | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::NestedSet::init | ( | ) | [inherited] |
public Bio::EnsEMBL::Compara::NestedSet::is_leaf | ( | ) | [inherited] |
public Bio::EnsEMBL::Compara::NestedSet::is_member_of | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::is_subset_of | ( | ) | [inherited] |
Undocumented method

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)

public Bio::EnsEMBL::Compara::NestedSet::left_index | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::like | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::link_count | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::link_for_neighbor | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::NestedSet::load_children_if_needed | ( | ) | [inherited] |
Undocumented method

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

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

public Bio::EnsEMBL::Compara::NestedSet::merge_children | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::merge_node_via_shared_ancestor | ( | ) | [inherited] |
Undocumented method
public Bio::EnsEMBL::Compara::NestedSet::minimize_node | ( | ) | [inherited] |
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

public Bio::EnsEMBL::Compara::Graph::CGObject::name | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::Compara::GeneTreeMember, and Bio::EnsEMBL::Compara::GenomicAlignTree.
public Bio::EnsEMBL::Compara::Graph::Node::neighbors | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::CGObject::new | ( | ) | [inherited] |
Undocumented method

Reimplemented in Bio::EnsEMBL::Compara::Graph::Link, and Bio::EnsEMBL::Compara::SpeciesSet.
public Bio::EnsEMBL::Compara::NestedSet::new_from_newick | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::new_from_TreeI | ( | ) | [inherited] |
Undocumented method

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

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

public Bio::EnsEMBL::Compara::NestedSet::nhx_format | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::no_autoload_children | ( | ) | [inherited] |
Undocumented method

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

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)

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

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

public Bio::EnsEMBL::Compara::NestedSet::parent_link | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::print_links | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::print_node | ( | ) | [inherited] |
Undocumented method

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)

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

public Bio::EnsEMBL::Compara::Graph::CGObject::refcount | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::CGObject::release | ( | ) | [inherited] |
Undocumented method

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

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

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)

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)

public Bio::EnsEMBL::Compara::Graph::CGObject::retain | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::right_index | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::GeneTreeNode::root | ( | ) |
public Bio::EnsEMBL::Compara::NestedSet::scale | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::scale_max_to | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::Graph::CGObject::store | ( | ) | [inherited] |
Undocumented method

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

public Bio::EnsEMBL::Compara::NestedSet::string_node | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::string_tree | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::NestedSet::subroot | ( | ) | [inherited] |
Undocumented method

public Bio::EnsEMBL::Compara::GeneTreeNode::tree | ( | ) |
Undocumented method

public Bio::EnsEMBL::Compara::Graph::Node::unlink_all | ( | ) | [inherited] |
Undocumented method

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

The documentation for this class was generated from the following file:
- Bio/EnsEMBL/Compara/GeneTreeNode.pm