--- name: "Bio::Taxonomy::Taxon" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.2-3" release: "Debian 10 (Buster)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Taxonomy::Taxon" --- # Bio::Taxonomy::Taxon(3pm) Generic Taxonomic Entity object ## NAME Bio::Taxonomy::Taxon - Generic Taxonomic Entity object ## SYNOPSIS ``` # NB: This module is deprecated. Use Bio::Taxon instead. use Bio::Taxonomy::Taxon; my $taxonA = Bio::Taxonomy::Taxon->new(); my $taxonL = Bio::Taxonomy::Taxon->new(); my $taxonR = Bio::Taxonomy::Taxon->new(); my $taxon = Bio::Taxonomy::Taxon->new(); $taxon->add_Descendents($taxonL); $taxon->add_Descendents($taxonR); my $species = $taxon->species; ``` ## DESCRIPTION Makes a taxonomic unit suitable for use in a taxonomic tree ## AUTHOR Dan Kortschak email **kortschak@rsbs.anu.edu.au** ## CONTRIBUTORS Sendu Bala: bix@sendu.me.uk ## 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 = Bio::Taxonomy::Taxon->new(); Function: Builds a new Bio::Taxonomy::Taxon object Returns : Bio::Taxonomy::Taxon Args : -descendents => array pointer to descendents (optional) -branch_length => branch length [integer] (optional) -taxon => taxon -id => unique taxon id for node (from NCBI's list preferably) -rank => the taxonomic level of the node (also from NCBI) ``` ### add\_Descendent ``` Title : add_Descendent Usage : $taxon->add_Descendent($taxon); Function: Adds a descendent to a taxon Returns : number of current descendents for this taxon Args : Bio::Taxonomy::Taxon boolean flag, true if you want to ignore the fact that you are adding a second node with the same unique id (typically memory location reference in this implementation). default is false and will throw an error if you try and overwrite an existing node. ``` ### each\_Descendent ``` Title : each_Descendent($sortby) Usage : my @taxa = $taxon->each_Descendent; Function: all the descendents for this taxon (but not their descendents i.e. not a recursive fetchall) Returns : Array of Bio::Taxonomy::Taxon objects Args : $sortby [optional] "height", "creation" or coderef to be used to sort the order of children taxa. ``` ### remove\_Descendent ``` Title : remove_Descendent Usage : $taxon->remove_Descedent($taxon_foo); Function: Removes a specific taxon from being a Descendent of this taxon Returns : nothing Args : An array of Bio::taxonomy::Taxon objects which have be previously passed to the add_Descendent call of this object. ``` ### remove\_all\_Descendents ``` Title : remove_all_Descendents Usage : $taxon->remove_All_Descendents() Function: Cleanup the taxon's reference to descendents and reset their ancestor pointers to undef, if you don't have a reference to these objects after this call they will be cleanedup - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none ``` ### get\_Descendents ``` Title : get_Descendents Usage : my @taxa = $taxon->get_Descendents; Function: Recursively fetch all the taxa and their descendents *NOTE* This is different from each_Descendent Returns : Array or Bio::Taxonomy::Taxon objects Args : none ``` ### ancestor ``` Title : ancestor Usage : $taxon->ancestor($newval) Function: Set the Ancestor Returns : value of ancestor Args : newvalue (optional) ``` ### branch\_length ``` Title : branch_length Usage : $obj->branch_length($newval) Function: Example : Returns : value of branch_length Args : newvalue (optional) ``` ### description ``` Title : description Usage : $obj->description($newval) Function: Returns : value of description Args : newvalue (optional) ``` ### rank ``` Title : rank Usage : $obj->rank($newval) Function: Set the taxonomic rank Returns : taxonomic rank of taxon Args : newvalue (optional) ``` ### taxon ``` Title : taxon Usage : $obj->taxon($newtaxon) Function: Set the name of the taxon Example : Returns : name of taxon Args : newtaxon (optional) ``` ### id ``` Title : id Usage : $obj->id($newval) Function: Example : Returns : value of id Args : newvalue (optional) ``` ### internal\_id ``` Title : internal_id Usage : my $internalid = $taxon->internal_id Function: Returns the internal unique id for this taxon (a monotonically increasing number for this in-memory implementation but could be a database determined unique id in other implementations) Returns : unique id Args : none ``` ### \_creation\_id ``` Title : _creation_id Usage : $obj->_creation_id($newval) Function: a private method signifying the internal creation order Returns : value of _creation_id Args : newvalue (optional) ``` ### is\_Leaf ``` Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean Args : none ``` ### to\_string ``` Title : to_string Usage : my $str = $taxon->to_string() Function: For debugging, provide a taxon as a string Returns : string Args : none ``` ### height ``` Title : height Usage : my $len = $taxon->height Function: Returns the height of the tree starting at this taxon. Height is the maximum branchlength. Returns : The longest length (weighting branches with branch_length) to a leaf Args : none ``` ### invalidate\_height ``` Title : invalidate_height Usage : private helper method Function: Invalidate our cached value of the taxon's height in the tree Returns : nothing Args : none ``` ### classify ``` Title : classify Usage : @obj->classify() Function: a method to return the classification of a species Returns : name of taxon and ancestor's taxon recursively Args : boolean to specify whether we want all taxa not just ranked levels ``` ### has\_rank ``` Title : has_rank Usage : $obj->has_rank($rank) Function: a method to query ancestors' rank Returns : boolean Args : $rank ``` ### has\_taxon ``` Title : has_taxon Usage : $obj->has_taxon($taxon) Function: a method to query ancestors' taxa Returns : boolean Args : Bio::Taxonomy::Taxon object ``` ### distance\_to\_root ``` Title : distance_to_root Usage : $obj->distance_to_root Function: a method to query ancestors' taxa Returns : number of links to root Args : ``` ### recent\_common\_ancestor ``` Title : recent_common_ancestor Usage : $obj->recent_common_ancestor($taxon) Function: a method to query find common ancestors Returns : Bio::Taxonomy::Taxon of query or undef if no ancestor of rank Args : Bio::Taxonomy::Taxon ``` ### species ``` Title : species Usage : $obj=$taxon->species; Function: Returns a Bio::Species object reflecting the taxon's tree position Returns : a Bio::Species object Args : none ```