Bio-Cluster
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lib/Bio/Cluster/FamilyI.pm view on Meta::CPAN
Title : family_id
Usage : Bio::Cluster::FamilyI->family_id("znfp");
Function: get/set for the family id
Returns : the family id
Args : the family id
=cut
sub family_id{
shift->throw_not_implemented();
}
=head2 family_score
Title : family_score
Usage : Bio::Cluster::FamilyI->family_score(95);
Function: get/set for the score of algorithm used to generate
the family if present
Returns : the score
Args : the score
=cut
sub family_score {
shift->throw_not_implemented();
}
=head1 Methods inherited from L<Bio::ClusterI>
=cut
=head2 display_id
Title : display_id
lib/Bio/Cluster/SequenceFamily.pm view on Meta::CPAN
Function: Constructor for SequenceFamily object
Returns : Bio::Cluster::SequenceFamily object
See L<Bio::Cluster::SequenceFamily>.
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($id,$description,$version,$annot_score,
$family_score,$members) = $self->_rearrange([qw(FAMILY_ID DESCRIPTION VERSION
ANNOTATION_SCORE
FAMILY_SCORE MEMBERS)],@args);
$self->{'_members'} = [];
$id && $self->family_id($id);
$description && $self->description($description);
$version && $self->version($version);
$annot_score && $self->annotation_score($annot_score);
$family_score && $self->family_score($family_score);
$members && $self->add_members($members);
return $self;
}
=head2 version
Title : version
Usage : $family->version("1.0");
lib/Bio/Cluster/UniGeneI.pm view on Meta::CPAN
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 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
=cut
sub homol {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 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
=cut
sub restr_expr {
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 :
lib/Bio/ClusterI.pm view on Meta::CPAN
Title : display_id
Usage :
Function: Get the display name or identifier for the cluster
Returns : a string
Args :
=cut
sub display_id{
shift->throw_not_implemented();
}
=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
sub description{
shift->throw_not_implemented();
}
=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
sub size {
shift->throw_not_implemented();
}
=head2 cluster_score
Title : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
Returns : a number
=cut
sub cluster_score{
shift->throw_not_implemented();
}
=head2 get_members
Title : get_members
Usage : Bio::ClusterI->get_members(($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
sub get_members {
shift->throw_not_implemented();
}
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