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lib/Bio/Variation/VariantI.pm  view on Meta::CPAN

=cut


sub upStreamSeq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'upstreamseq'} = $value;
    }
   return $self->{'upstreamseq'};
}


=head2 dnStreamSeq

 Title   : dnStreamSeq
 Usage   : $obj->dnStreamSeq();
 Function:

            Sets and returns dnstream flanking sequence string.  If
            value is not set, returns false. The sequence should be
            >=25 characters long, if possible.

 Example :
 Returns : string or false
 Args    : string

=cut


sub dnStreamSeq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'dnstreamseq'} = $value;
    }
    return $self->{'dnstreamseq'};

}


=head2 label

 Title   : label
 Usage   : $obj->label();
 Function:

            Sets and returns mutation event label(s).  If value is not
            set, or no argument is given returns false.  Each
            instantiable class needs to implement this method. Valid
            values are listed in 'Mutation event controlled vocabulary' in
            http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.

 Example :
 Returns : string
 Args    : string

=cut


sub label {
    my ($self,$value) = @_;
    $self->throw_not_implemented();
}



=head2 status

 Title   : status
 Usage   : $obj->status()
 Function:

           Returns the status of the sequence change object.
           Valid values are: 'suspected' and 'proven'

 Example : $obj->status('proven');
 Returns : scalar
 Args    : valid string (optional, for setting)


=cut


sub status {
   my ($self,$value) = @_;
   my %status = (suspected => 1,
		 proven => 1
		 );

   if( defined $value) {
       $value = lc $value;
       if ($status{$value}) {
	   $self->{'status'} = $value;
       }
       else {
	   $self->throw("$value is not valid status value!");
       }
    }
   if( ! exists $self->{'status'} ) {
       return "$self";
   }
   return $self->{'status'};
}


=head2 proof

 Title   : proof
 Usage   : $obj->proof()
 Function:

           Returns the proof of the sequence change object.
           Valid values are: 'computed' and 'experimental'.

 Example : $obj->proof('computed');
 Returns : scalar
 Args    : valid string (optional, for setting)


=cut