Christopher Fields > BioPerl > Bio::Cluster::UniGeneI

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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://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    : 
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