Bio::Cluster
UniGeneI
Summary
Bio::Cluster::UniGeneI - abstract interface of UniGene object
Package variables
No package variables defined.
Inherit
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.
Methods
Methods description
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
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Title : species
Usage : $obj->species($newval)
Function: Get the species object for this Unigene cluster.
Example :
Returns : value of species (a Bio::Species object)
Args : |
Methods code
sub unigene_id
{ my ($self) = @_;
$self->throw_not_implemented;} | sub title
{ my ($self) = @_;
$self->throw_not_implemented;} | sub gene
{ my ($self) = @_;
$self->throw_not_implemented;} | sub cytoband
{ my ($self) = @_;
$self->throw_not_implemented;} | sub mgi
{ my ($self) = @_;
$self->throw_not_implemented;} | sub locuslink
{ my ($self) = @_;
$self->throw_not_implemented;} | sub homol
{ my ($self) = @_;
$self->throw_not_implemented;} | sub restr_expr
{ my ($self) = @_;
$self->throw_not_implemented;} | sub gnm_terminus
{ my ($self) = @_;
$self->throw_not_implemented;} | sub scount
{ my ($self) = @_;
$self->throw_not_implemented;} | sub express
{ my ($self) = @_;
$self->throw_not_implemented;} | sub chromosome
{ my ($self) = @_;
$self->throw_not_implemented;} | sub sts
{ my ($self) = @_;
$self->throw_not_implemented;} | sub txmap
{ my ($self) = @_;
$self->throw_not_implemented;} | sub protsim
{ my ($self) = @_;
$self->throw_not_implemented;} | sub sequence
{ my ($self) = @_;
$self->throw_not_implemented;} | sub species
{ shift->throw_not_implemented(); } | General documentation
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
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 | Top |
Email andrew at cbbc.murdoch.edu.au
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
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)
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
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 :
Title : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
Returns : a number
Title : get_members
Usage : Bio::ClusterI->get_members(($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 :