Bio::Cluster::UniGeneI(3pm)				User Contributed Perl Documentation			       Bio::Cluster::UniGeneI(3pm)

NAME

       Bio::Cluster::UniGeneI - abstract interface of UniGene object

SYNOPSIS

	 #

DESCRIPTION

       This is the general interface for a UniGene cluster representation in Bioperl. You cannot use this module directly, use an implementation
       instead.

       You can create UniGene cluster objects yourself by instantiating Bio::Cluster::UniGene. If you read UniGene clusters from a ClusterIO
       parser, you will get objects implementing this interface, most likely instances of said UniGene class.

       Bio::Cluster::UniGeneI inherits from Bio::ClusterI, so you can use it wherever a cluster object is expected.

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 one
       of the Bioperl mailing lists. 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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

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

AUTHOR - Andrew Macgregor
       Email andrew at cbbc.murdoch.edu.au

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a "_".

   unigene_id
	Title	: unigene_id
	Usage	: unigene_id();
	Function: Returns the unigene_id associated with the object.
	Example : $id = $unigene->unigene_id or $unigene->unigene_id($id)
	Returns : A string
	Args	: None or an id

   title
	Title	: title
	Usage	: title();
	Function: Returns the title associated with the object.
	Example : $title = $unigene->title or $unigene->title($title)
	Returns : A string
	Args	: None or a title

   gene
	Title	: gene
	Usage	: gene();
	Function: Returns the gene associated with the object.
	Example : $gene = $unigene->gene or $unigene->gene($gene)
	Returns : A string
	Args	: None or a gene

   cytoband
	Title	: cytoband
	Usage	: cytoband();
	Function: Returns the cytoband associated with the object.
	Example : $cytoband = $unigene->cytoband or $unigene->cytoband($cytoband)
	Returns : A string
	Args	: None or a cytoband

   mgi
	Title	: mgi
	Usage	: mgi();
	Function: Returns the mgi associated with the object.
	Example : $mgi = $unigene->mgi or $unigene->mgi($mgi)
	Returns : A string
	Args	: None or a mgi

   locuslink
	Title	: locuslink
	Usage	: locuslink();
	Function: Returns or stores a reference to an array containing locuslink data.
		  This should really only be used by ClusterIO, not directly
	Returns : An array reference
	Args	: None or an array reference

   homol
	Title	: homol
	Usage	: homol();
	Function: Returns the homol entry associated with the object.
	Example : $homol = $unigene->homol or $unigene->homol($homol)
	Returns : A string
	Args	: None or a homol entry

   restr_expr
	Title	: restr_expr
	Usage	: restr_expr();
	Function: Returns the restr_expr entry associated with the object.
	Example : $restr_expr = $unigene->restr_expr or $unigene->restr_expr($restr_expr)
	Returns : A string
	Args	: None or a restr_expr entry

   gnm_terminus
	Title	: gnm_terminus
	Usage	: gnm_terminus();
	Function: Returns the gnm_terminus associated with the object.
	Example : $gnm_terminus = $unigene->gnm_terminus or $unigene->gnm_terminus($gnm_terminus)
	Returns : A string
	Args	: None or a gnm_terminus

   scount
	Title	: scount
	Usage	: scount();
	Function: Returns the scount associated with the object.
	Example : $scount = $unigene->scount or $unigene->scount($scount)
	Returns : A string
	Args	: None or a scount

   express
	Title	: express
	Usage	: express();
	Function: Returns or stores a reference to an array containing tissue expression data.
		  This should really only be used by ClusterIO, not directly
	Returns : An array reference
	Args	: None or an array reference

   chromosome
	Title	: chromosome
	Usage	: chromosome();
	Function: Returns or stores a reference to an array containing chromosome lines
		  This should really only be used by ClusterIO, not directly
	Returns : An array reference
	Args	: None or an array reference

   sts
	Title	: sts
	Usage	: sts();
	Function: Returns or stores a reference to an array containing sts lines
		  This should really only be used by ClusterIO, not directly
	Returns : An array reference
	Args	: None or an array reference

   txmap
	Title	: txmap
	Usage	: txmap();
	Function: Returns or stores a reference to an array containing txmap lines
	Returns : An array reference
	Args	: None or an array reference

   protsim
	Title	: protsim
	Usage	: protsim();
	Function: Returns or stores a reference to an array containing protsim lines
		  This should really only be used by ClusterIO, not directly
	Returns : An array reference
	Args	: None or an array reference

   sequence
	Title	: sequence
	Usage	: sequence();
	Function: Returns or stores a reference to an array containing sequence data
		  This should really only be used by ClusterIO, not directly
	Returns : An array reference
	Args	: None or an array reference

   species
	Title	: species
	Usage	: $obj->species($newval)
	Function: Get the species object for this Unigene cluster.
	Example :
	Returns : value of species (a L<Bio::Species> object)
	Args	:

Methods inherited from Bio::ClusterI
   display_id
	Title	: display_id
	Usage	:
	Function: Get/set the display name or identifier for the cluster
	Returns : a string
	Args	: optional, on set the display ID ( a string)

   description
	Title	: description
	Usage	: Bio::ClusterI->description("POLYUBIQUITIN")
	Function: get/set for the consensus description of the cluster
	Returns : the description string
	Args	: Optional the description string

   size
	Title	: size
	Usage	: Bio::ClusterI->size();
	Function: get/set for the size of the family,
		  calculated from the number of members
	Returns : the size of the family
	Args	:

   cluster_score
	Title	: cluster_score
	Usage	: $cluster ->cluster_score(100);
	Function: get/set for cluster_score which
		  represent the score in which the clustering
		  algorithm assigns to this cluster.
	Returns : a number

   get_members
	Title	: get_members
	Usage	: Bio::ClusterI->get_members(($seq1, $seq2));
	Function: retrieve the members of the family by some criteria, for
		  example :
		  $cluster->get_members(-species => 'homo sapiens');

		  Will return all members if no criteria are provided.

	Returns : the array of members
	Args	:

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