Raw content of Bio::Cluster::UniGeneI
<![CDATA[# $Id: UniGeneI.pm,v 1.9 2002/10/25 22:49:03 lapp Exp $
#
# BioPerl module for Bio::Cluster::UniGeneI.pm
#
# Cared for by Andrew Macgregor <andrew@anatomy.otago.ac.nz>
#
# Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
# Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
# http://anatomy.otago.ac.nz/meg
#
# You may distribute this module under the same terms as perl itself
#
# _history
# April 31, 2002 - Initial implementation by Andrew Macgregor
# POD documentation - main docs before the code
=head1 NAME
Bio::Cluster::UniGeneI - abstract interface of UniGene object
=head1 SYNOPSIS
#
=head1 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
L<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.
L<Bio::Cluster::UniGeneI> inherits from L<Bio::ClusterI>, so you can
use it wherever a cluster object is expected.
=head1 FEEDBACK
#
=head2 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://bio.perl.org/MailList.html - About the mailing lists
=head2 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 email
or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Andrew Macgregor
Email andrew@anatomy.otago.ac.nz
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
# Let the code begin...
package Bio::Cluster::UniGeneI;
use vars qw(@ISA $VERSION);
use strict;
use Bio::ClusterI;
$VERSION = '1.0';
@ISA = qw(Bio::ClusterI);
=head2 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
=cut
sub unigene_id {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub title {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub gene {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub cytoband {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub mgi {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 locuslink
Title : locuslink
Usage : locuslink();
Function: Returns or stores a reference to an array containing locuslink data.
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
=cut
sub locuslink {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub gnm_terminus {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub scount {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 express
Title : express
Usage : express();
Function: Returns or stores a reference to an array containing tissue expression data.
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
=cut
sub express {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 chromosome
Title : chromosome
Usage : chromosome();
Function: Returns or stores a reference to an array containing chromosome lines
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
=cut
sub chromosome {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 sts
Title : sts
Usage : sts();
Function: Returns or stores a reference to an array containing sts lines
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
=cut
sub sts {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 txmap
Title : txmap
Usage : txmap();
Function: Returns or stores a reference to an array containing txmap lines
Returns : An array reference
Args : None or an array reference
=cut
sub txmap {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 protsim
Title : protsim
Usage : protsim();
Function: Returns or stores a reference to an array containing protsim lines
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
=cut
sub protsim {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 sequence
Title : sequence
Usage : sequence();
Function: Returns or stores a reference to an array containing sequence data
This should really only be used by ClusterIO, not directly
Returns : An array reference
Args : None or an array reference
=cut
sub sequence {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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 :
=cut
sub species{
shift->throw_not_implemented();
}
=head1 Methods inherited from L<Bio::ClusterI>
=cut
=head2 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)
=cut
=head2 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
=cut
=head2 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 :
=cut
=head2 cluster_score
Title : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
Returns : a number
=cut
=head2 get_members
Title : get_members
Usage : Bio::ClusterI->get_members(($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 :
=cut
1;
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