/ 
bioperl-1.4
/ Bio::Taxonomy::Node

NAME

Bio::Taxonomy::Node - A node in a represented taxonomy

SYNOPSIS

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";

DESCRIPTION

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.

FEEDBACK

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/

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

Describe contact details here

CONTRIBUTORS

Juguang Xiao, juguang@tll.org.sg

Additional contributors names and emails here

APPENDIX

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    :