GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::CLUSTER::UNIGENEI (3)

.ds Aq ’

NAME

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

CONTENTS

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    :



Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::CLUSTER::UNIGENEI (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.