Bio::Taxonomy::Node - A node in a represented taxonomy use Bio::Taxonomy::Node; # typically you will get a Node from a Bio::DB::Taxonomy object # but here is how you initialize one my $node = new Bio::Taxonomy::Node(-name => $name, -object_id => $oid, -parent_id => $pid, -rank => $rank, -division => $div, -dbh => $dbh); my $dbh = new Bio::DB::Taxonomy(-source => 'flatfile', -directory=> '/tmp', -nodesfile=> '/path/to/nodes.dmp', -namesfile=> '/path/to/names.dmp'); my $hum_node = $dbh->get_Taxonomy_Node(-name => 'Homo sapiens'); my $hum_node2= $dbh->get_Taxonomy_Node(-taxonid => '9606'); print "rank is ", $hum_node->rank, "\n"; print "classification is ", join(" ", $hum_node->classification),"\n"; print "division is ", $node->division, "\n"; This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediete nodes not just the species nodes and can relate their connections.

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email jason-at-bioperl-dot-org Describe contact details here Juguang Xiao, juguang@tll.org.sg Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Taxonomy::Node(); Function: Builds a new Bio::Taxonomy::Node object Returns : an instance of Bio::Taxonomy::Node Args : -dbh => a reference to a Bio::DB::Taxonomy object -name => a string representing the node name -object_id => unique identifier - typically NCBI Taxid

db_handle
Title : db_handle Usage : $obj->db_handle($newval) Function: Get/Set Bio::DB::Taxonomy Handle Returns : value of db_handle (a scalar) (Bio::DB::Taxonomy object) Args : on set, new value (a scalar or undef, optional) Bio::DB::Taxonomy object

factory
Title: factory Usage: $factory->factory($newval); Function: Get/Set Bio::Taxonomy::FactoryI implementation Returns: Bio:;Taxonomy::FactoryI Args: Bio::Taxonomy::FactoryI

rank
Title : rank Usage : $obj->rank($newval) Function: Example : Returns : value of rank (a scalar) Args : on set, new value (a scalar or undef, optional)

object_id
Title : object_id Usage : $obj->object_id($newval) Function: Example : Returns : value of object_id (a scalar) Args : on set, new value (a scalar or undef, optional)

version
Title : version Usage : $obj->version($newval) Function: Example : Returns : value of version (a scalar) Args : on set, new value (a scalar or undef, optional)

authority
Title : authority Usage : $obj->authority($newval) Function: Example : Returns : value of authority (a scalar) Args : on set, new value (a scalar or undef, optional)

namespace
Title : namespace Usage : $obj->namespace($newval) Function: Example : Returns : value of namespace (a scalar) Args : on set, new value (a scalar or undef, optional)

parent_id
Title : parent_id Usage : $obj->parent_id($newval) Function: Example : Returns : value of parent_id (a scalar) Args : on set, new value (a scalar or undef, optional)

get_Parent_Node
Title : get_Parent_Node Usage : my $parentnode = $node->get_Parent_Node() Function: Retrieve the full Parent node from the database Returns : Bio::Taxonomy::Node Args : none

node_name
Title : node_name Usage : $obj->node_name($newval) Function: Example : Returns : value of node_name (a scalar) Args : on set, new value (a scalar or undef, optional)

classification
Title : classification Usage : $self->classification(@class_array); @classification = $self->classification(); Function: Fills Returns the classification list in the object. The array provided must be in the order SPECIES, GENUS ---> KINGDOM. Checks are made that species is in lower case, and all other elements are in title case. Returns : Classification array Args : none - this can be set directly

division
Title : division Usage : $obj->division($newval) Function: Example : Returns : value of division (a scalar) Args : on set, new value (a scalar or undef, optional)

show_all
Title : show_all Usage : $obj->show_all($newval) Function: Boolean flag whether or not we should show all intermediete nodes that do not have actual ranks. Returns : value of show_all (a scalar) Args : on set, new value (a scalar or undef, optional)

name
Title: name Usage: $obj->name('scientific', 'sapiens'); $obj->name('common', 'human', 'man'); my @names = @{$obj->name('common')}; Function: Get and set the names Returns: names (a array reference) Args: Arg1 => the name_class. You can assign any text, but the words 'scientific' and 'common' have the special meaning, as scientific name and common name, respectively. Arg2 .. => the names

scientific_name
Title: scientific_name Usage: my $new_val = $obj->scientific_name($newval); Function: Get/Set the scientific name Returns: a scalar text value Args: a scalar text value

parent_taxon_id
Title : parent_taxon_id Usage : $self->parent_taxon_id($newval); $val = $self->parent_taxon_id; Function: Get/Set for parent_taxon_id Return : Args :