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Bio-Cluster-1.7.3
River stage two • 1 direct dependent • 12 total dependents
/ Bio::Cluster::UniGeneI

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
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    :