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Bio::Cluster::UniGeneI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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    :