Bio::Cluster UniGeneI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::Cluster::UniGeneI - abstract interface of UniGene object
Package variables
No package variables defined.
Inherit
Bio::ClusterI
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
unigene_idDescriptionCode
titleDescriptionCode
geneDescriptionCode
cytobandDescriptionCode
mgiDescriptionCode
locuslinkDescriptionCode
homolDescriptionCode
restr_exprDescriptionCode
gnm_terminusDescriptionCode
scountDescriptionCode
expressDescriptionCode
chromosomeDescriptionCode
stsDescriptionCode
txmapDescriptionCode
protsimDescriptionCode
sequenceDescriptionCode
speciesDescriptionCode
Methods description
unigene_idcode    nextTop
 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
titlecodeprevnextTop
 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
genecodeprevnextTop
 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
cytobandcodeprevnextTop
 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
mgicodeprevnextTop
 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
locuslinkcodeprevnextTop
 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
homolcodeprevnextTop
 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_exprcodeprevnextTop
 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_terminuscodeprevnextTop
 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
scountcodeprevnextTop
 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
expresscodeprevnextTop
 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
chromosomecodeprevnextTop
 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
stscodeprevnextTop
 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
txmapcodeprevnextTop
 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
protsimcodeprevnextTop
 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
sequencecodeprevnextTop
 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
speciescodeprevnextTop
 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
unigene_iddescriptionprevnextTop
sub unigene_id {
    my ($self) = @_;
    $self->throw_not_implemented;
}
titledescriptionprevnextTop
sub title {
    my ($self) = @_;
    $self->throw_not_implemented;
}
genedescriptionprevnextTop
sub gene {
    my ($self) = @_;
    $self->throw_not_implemented;
}
cytobanddescriptionprevnextTop
sub cytoband {
    my ($self) = @_;
    $self->throw_not_implemented;
}
mgidescriptionprevnextTop
sub mgi {
    my ($self) = @_;
    $self->throw_not_implemented;
}
locuslinkdescriptionprevnextTop
sub locuslink {
    my ($self) = @_;
    $self->throw_not_implemented;
}
homoldescriptionprevnextTop
sub homol {
    my ($self) = @_;
    $self->throw_not_implemented;
}
restr_exprdescriptionprevnextTop
sub restr_expr {
    my ($self) = @_;
    $self->throw_not_implemented;
}
gnm_terminusdescriptionprevnextTop
sub gnm_terminus {
    my ($self) = @_;
    $self->throw_not_implemented;
}
scountdescriptionprevnextTop
sub scount {
    my ($self) = @_;
    $self->throw_not_implemented;
}
expressdescriptionprevnextTop
sub express {
    my ($self) = @_;
    $self->throw_not_implemented;
}
chromosomedescriptionprevnextTop
sub chromosome {
    my ($self) = @_;
    $self->throw_not_implemented;
}
stsdescriptionprevnextTop
sub sts {
    my ($self) = @_;
    $self->throw_not_implemented;
}
txmapdescriptionprevnextTop
sub txmap {
    my ($self) = @_;
    $self->throw_not_implemented;
}
protsimdescriptionprevnextTop
sub protsim {
    my ($self) = @_;
    $self->throw_not_implemented;
}
sequencedescriptionprevnextTop
sub sequence {
    my ($self) = @_;
    $self->throw_not_implemented;
}
speciesdescriptionprevnextTop
sub species {
    shift->throw_not_implemented();
}
General documentation
FEEDBACKTop
  #
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Andrew MacgregorTop
Email andrew at cbbc.murdoch.edu.au
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
Methods inherited from Bio::ClusterITop
display_idTop
 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)
descriptionTop
 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
sizeTop
 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_scoreTop
 Title   : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
Returns : a number
get_membersTop
 Title   : get_members
Usage : Bio::ClusterI->get_members(($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 :