Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

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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

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   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://github.com/bioperl/bioperl-live/issues

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    :