Bio::Species(3pm)					User Contributed Perl Documentation					 Bio::Species(3pm)

NAME

       Bio::Species - Generic species object.

SYNOPSIS

	   $species = Bio::Species->new(-classification => [@classification]);
					   # Can also pass classification
					   # array to new as below

	   $species->classification(qw( sapiens Homo Hominidae
					Catarrhini Primates Eutheria
					Mammalia Vertebrata Chordata
					Metazoa Eukaryota ));

	   $genus = $species->genus();

	   $bi = $species->binomial();	   # $bi is now "Homo sapiens"

	   # For storing common name
	   $species->common_name("human");

	   # For storing subspecies
	   $species->sub_species("accountant");

DESCRIPTION

       NOTE: This class is planned for deprecation in favor of the simpler Bio::Taxon.	Please use that class instead.

       Provides a very simple object for storing phylogenetic information. The classification is stored in an array, which is a list of nodes in a
       phylogenetic tree. Access to getting and setting species and genus is provided, but not to any of the other node types (eg: "phylum",
       "class", "order", "family"). There's plenty of scope for making the model more sophisticated, if this is ever needed.

       A methods are also provided for storing common names, and subspecies.

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/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

       James Gilbert email jgrg@sanger.ac.uk

CONTRIBUTORS

       Sendu Bala, bix@sendu.me.uk Chris Fields, cjfields at bioperl dot org

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::Species->new(-classification => @class)
	Function: Build a new Species object
	Returns : Bio::Species object
	Args	: -ncbi_taxid	  => NCBI taxonomic ID (optional)
		  -classification => arrayref of classification

   classification
	Title	: classification
	Usage	: $self->classification(@class_array);
		  @classification = $self->classification();
	Function: Get/set the lineage of this species. The array provided must be in
		  the order ... ---> SPECIES, GENUS ---> KINGDOM ---> etc.
	Example : $obj->classification(qw( 'Homo sapiens' Homo Hominidae
		  Catarrhini Primates Eutheria Mammalia Vertebrata
		  Chordata Metazoa Eukaryota));
	Returns : Classification array
	Args	: Classification array
			OR
		  A reference to the classification array. In the latter case
		  if there is a second argument and it evaluates to true,
		  names will not be validated. NB: in any case, names are never
		  validated anyway.

   ncbi_taxid
	Title	: ncbi_taxid
	Usage	: $obj->ncbi_taxid($newval)
	Function: Get/set the NCBI Taxon ID
	Returns : the NCBI Taxon ID as a string
	Args	: newvalue to set or undef to unset (optional)

   common_name
	Title	: common_name
	Usage	: $self->common_name( $common_name );
		  $common_name = $self->common_name();
	Function: Get or set the common name of the species
	Example : $self->common_name('human')
	Returns : The common name in a string
	Args	: String, which is the common name (optional)

   division
	Title	: division
	Usage	: $obj->division($newval)
	Function: Genbank Division for a species
	Returns : value of division (a scalar)
	Args	: value of division (a scalar)

   species
	Title	: species
	Usage	: $self->species( $species );
		  $species = $self->species();
	Function: Get or set the species name.
		  Note that this is  NOT genus and species
		  -- use $self->binomial() for that.
	Example : $self->species('sapiens');
	Returns : species name as string (NOT genus and species)
	Args	: species name as string (NOT genus and species)

   genus
	Title	: genus
	Usage	: $self->genus( $genus );
		  $genus = $self->genus();
	Function: Get or set the scientific genus name.
	Example : $self->genus('Homo');
	Returns : Scientific genus name as string
	Args	: Scientific genus name as string

   sub_species
	Title	: sub_species
	Usage	: $obj->sub_species($newval)
	Function: Get or set the scientific subspecies name.
	Returns : value of sub_species
	Args	: newvalue (optional)

   variant
	Title	: variant
	Usage	: $obj->variant($newval)
	Function: Get/set variant information for this species object (strain,
		  isolate, etc).
	Example :
	Returns : value of variant (a scalar)
	Args	: new value (a scalar or undef, optional)

   binomial
	Title	: binomial
	Usage	: $binomial = $self->binomial();
		  $binomial = $self->binomial('FULL');
	Function: Returns a string "Genus species", or "Genus species subspecies",
		  if the first argument is 'FULL' (and the species has a subspecies).
	Args	: Optionally the string 'FULL' to get the full name including
		  the subspecies.
	Note	: This is just munged from the taxon() name

   validate_species_name
	Title	: validate_species_name
	Usage	: $result = $self->validate_species_name($string);
	Function: Validate the species portion of the binomial
	Args	: string
	Notes	: The string following the "genus name" in the NCBI binomial is so
		  variable that it's not clear that this is a useful function. Consider
		  the binomials "Simian 11 rotavirus (serotype 3 / strain
		  SA11-Patton)", or "St. Thomas 3 rotavirus", straight from GenBank.
		  This is particularly problematic in microbes and viruses. As such,
		  this isn't actually used automatically by any Bio::Species method.

   organelle
	Title	: organelle
	Usage	: $self->organelle( $organelle );
		  $organelle = $self->organelle();
	Function: Get or set the organelle name
	Example : $self->organelle('Chloroplast')
	Returns : The organelle name in a string
	Args	: String, which is the organelle name
	Note	: TODO: We currently do not know where the organelle definition will
		  eventually go.  This is stored in the source seqfeature, though,
		  so the information isn't lost.

   Delegation
       The following methods delegate to the internal Bio::Taxon instance. This is mainly to allow code continue using older methods, with the
       mind to migrate to using Bio::Taxon and related methods when this class is deprecated.

   taxon
	Title	 : taxon
	Usage	 : $obj->taxon
	Function : retrieve the internal Bio::Taxon instance
	Returns  : A Bio::Taxon. If one is not previously set,
		   an instance is created lazily
	Args	 : Bio::Taxon (optional)

   tree
	Title	 : tree
	Usage	 : $obj->tree
	Function : Returns a Bio::Tree::Tree object
	Returns  : A Bio::Tree::Tree. If one is not previously set,
		   an instance is created lazily
	Args	 : Bio::Tree::Tree (optional)

perl v5.14.2							    2012-03-02							 Bio::Species(3pm)