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Summary

Bio::EnsEMBL::ExternalData::Expression::SeqTag

Package variables

Included modules

Inherit

Bio::DBLinkContainerI

Synopsis

    @contig = $db->get_Contigs();

    $clone = $db->get_Clone();

    @genes    = $clone->get_all_Genes();

Description

Represents information on one Clone

Methods

Methods description

 Title   : adaptor
 Usage   : $obj->adaptor($newval)
 Function: 
 Example : 
 Returns : value of adaptor
 Args    : newvalue (optional)

 Title   : add_DBLink
 Usage   : $self->add_DBLink($ref)
 Function: adds a link object
 Example :
 Returns :
 Args    :

 Title   : each_DBLink
 Usage   : foreach $ref ( $self->each_DBlink() )
 Function: gets an array of DBlink of objects
 Example :
 Returns :
 Args    :

 Title   : frequency
 Usage   : $obj->frequency($newval)
 Function: 
 Example : 
 Returns : value  of frequency
 Args    : newvalue (optional)

 Title   : id
 Usage   : $obj->id($newval)
 Function: 
 Example : 
 Returns : value of tag id
 Args    : newvalue (optional)

 Title   : name
 Usage   : $obj->name($newval)
 Function: 
 Example : 
 Returns : value  of name
 Args    : newvalue (optional)

 Title   : new
 Usage   : 
 Function: 
 Example : 
 Returns : SeqTag object
 Args    :

 Title   : relative_frequency
 Usage   : $obj->realtive_frequency($newval)
 Function: 
 Example : 
 Returns : value  of realtive_frequency
 Args    : newvalue (optional)

 Title   : source
 Usage   : $obj->source($newval)
 Function: 
 Example : 
 Returns : value of source
 Args    : newvalue (optional)

Methods code

sub _set_from_args {

    my ($self,@args)=@_;

    my ($id,$source,$name,$frequency,$relative_frequency)=@args;

    $self->id($id);
    $self->source($source);
    $self->name($name);
    $self->frequency($frequency);
    $self->relative_frequency($relative_frequency);

}

sub adaptor {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'adaptor'} = $value;
    }
    return $obj->{'adaptor'};

}

sub add_DBLink {

   my ($self,$com) = @_;
   if( ! $com->isa('Bio::Annotation::DBLink') ) {
       $self->throw("Is not a link object but a  [$com]");
   }
   push(@{$self->{'link'}},$com);

}

sub each_DBLink {

   my ($self) = @_;

   return @{$self->{'link'}} if defined $self->{'link'};

}

sub frequency {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_frequency'} = $value;
    }
    return $obj->{'_frequency'};

}

sub id {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_id'} = $value;
    }
    return $obj->{'_id'};

}

sub name {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_name'} = $value;
    }
    return $obj->{'_name'};

}

sub new {

    my ($class,$adaptor,@args) = @_;

    my $self = {};
    bless $self,$class;

    $self->adaptor($adaptor);
    $self->_set_from_args(@args);

    return $self;

}

sub relative_frequency {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_relative_frequency'} = $value;
    }
    return $obj->{'_relative_frequency'};

}

sub source {

   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_source'} = $value;
    }
    return $obj->{'_source'};

}

General documentation

Describe contact details here

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _