Public Member Functions | |
public | new () |
public Int | taxon_id () |
public Int | parent_id () |
public Int | root_id () |
public Hashref | names () |
public | name () |
public String | rank () |
public Int | num_descendants () |
public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor | dba () |
public Bio::EnsEMBL::TaxonomyNode | root () |
public Bio::EnsEMBL::TaxonomyNode | parent () |
public Arrayref | children () |
public Int | is_root () |
public Int | is_leaf () |
public Int | is_branch () |
public void | add_all_descendants () |
public void | add_child () |
public | traverse_tree () |
public Int | count_leaves () |
public Int | distance_to_node () |
public Boolean | has_ancestor () |
public | to_string () |
public | to_tree_string () |
An object representing a node of the NCBI taxonomy, (most often) created by Bio::EnsEMBL::DBSQL::TaxonomyAdaptor.
public void Bio::EnsEMBL::TaxonomyNode::add_all_descendants | ( | ) |
Description : Uses database to fetch all descendants for this node from database and assemble them into a tree Return type : None
public void Bio::EnsEMBL::TaxonomyNode::add_child | ( | ) |
Description : Add child node (if not already present) Argument : Arrayref of Bio::EnsEMBL::TaxonomyNode Return type : None
public Arrayref Bio::EnsEMBL::TaxonomyNode::children | ( | ) |
Description : Getter/setter for arrayref of child nodes for this node (fetched lazily using adaptor) Argument : (optional) Arrayref of Bio::EnsEMBL::TaxonomyNode Return type : Arrayref of Bio::EnsEMBL::TaxonomyNode
public Int Bio::EnsEMBL::TaxonomyNode::count_leaves | ( | ) |
Description : Counts all leaf or DBA nodes below this node Argument : (Optional) closure checking whether to count a node or not Return type : Int
public Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor Bio::EnsEMBL::TaxonomyNode::dba | ( | ) |
Description : Getter/setter for core database adaptor for this node Argument : (optional) Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor Return type : Bio::EnsEMBL::DBSQL::TaxonomyNodeAdaptor
public Int Bio::EnsEMBL::TaxonomyNode::distance_to_node | ( | ) |
Description : Calculate the distance between this and the supplied node in steps via the closest common ancestor Argument : Bio::EnsEMBL::TaxonomyNode Return type : Int
public Boolean Bio::EnsEMBL::TaxonomyNode::has_ancestor | ( | ) |
Description : Test if the ancestors of this node include the supplied node Argument : Putative ancestor Return: 1 if the supplied node is an ancestor of this node
public Int Bio::EnsEMBL::TaxonomyNode::is_branch | ( | ) |
Description : Returns 1 if this is a branch node with more than one direct child Return type : Int
public Int Bio::EnsEMBL::TaxonomyNode::is_leaf | ( | ) |
Description : Returns 1 if this is a leaf node with no children Return type : Int
public Int Bio::EnsEMBL::TaxonomyNode::is_root | ( | ) |
Description : Returns 1 if this is a root node with no parents Return type : Int
public Bio::EnsEMBL::TaxonomyNode::name | ( | ) |
Undocumented method
public Hashref Bio::EnsEMBL::TaxonomyNode::names | ( | ) |
Description : Hashref of names for this node. Hash keys are the class of name, and values are arrays of names (as you can have more than one name for each class) Return type : hashref
public Bio::EnsEMBL::TaxonomyNode::new | ( | ) |
Undocumented method
public Int Bio::EnsEMBL::TaxonomyNode::num_descendants | ( | ) |
Description : Total number of descendants in the tree Return type : Int
public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::TaxonomyNode::parent | ( | ) |
Description : Getter/setter for parent node for this node (fetched lazily using adaptor) Argument : (optional) Bio::EnsEMBL::TaxonomyNode Return type : Bio::EnsEMBL::TaxonomyNode
public Int Bio::EnsEMBL::TaxonomyNode::parent_id | ( | ) |
Taxon ID of the parent of this node Return type : Int
public String Bio::EnsEMBL::TaxonomyNode::rank | ( | ) |
Description : Taxonomic rank Return type : String
public Bio::EnsEMBL::TaxonomyNode Bio::EnsEMBL::TaxonomyNode::root | ( | ) |
Description : Getter/setter for root node for this node (fetched lazily using adaptor) Argument : (optional) Bio::EnsEMBL::TaxonomyNode Return type : Bio::EnsEMBL::TaxonomyNode
public Int Bio::EnsEMBL::TaxonomyNode::root_id | ( | ) |
Description : Taxon ID of the root node for the taxonomy. Return type : Int
public Int Bio::EnsEMBL::TaxonomyNode::taxon_id | ( | ) |
Description : Taxon ID of this node Return type : Int
public Bio::EnsEMBL::TaxonomyNode::to_string | ( | ) |
Description : Return simple string representation of node Argument : (Optional) name_class to display (default is 'scientific name')
public Bio::EnsEMBL::TaxonomyNode::to_tree_string | ( | ) |
Description: Render tree as a string
public Bio::EnsEMBL::TaxonomyNode::traverse_tree | ( | ) |
Description : Walk the tree recursively, invoking the supplied subroutine on each node Argument : Subroutine reference, accepting current node and depth