Raw content of Bio::EnsEMBL::Analysis::Tools::Pmatch::ProteinHit
<![CDATA[# holds a pmatch protein hit - simply the name(idenitifier) of the protein
# and a list of ContigHit objects
package Bio::EnsEMBL::Analysis::Tools::Pmatch::ProteinHit;
use Bio::Root::Object;
@ISA = qw(Bio::Root::Object);
=head2 new
Title : new
Usage :
Function:
Example :
Returns :
Args : constructor
=cut
sub new {
my ($class, @args) = @_;
my $self = bless {}, $class;
my ($id) = $self->_rearrange(['ID'], @args);
$self->throw("No id") unless defined $id;
$self->id($id);
return $self;
}
=head2 id
Title : id
Usage :
Function: get/set for contig id
Example :
Returns :
Args :
=cut
sub id {
my ($self,$id) = @_;
if ($id) {
$self->{'id'} = $id;
}
return $self->{'id'};
}
=head2 add_ContigHit
Title : add_ContigHit
Usage :
Function: adds a ContigHit into $self->{_contig_hits}
Example :
Returns :
Args :
=cut
sub add_ContigHit {
my ($self,$hit) = @_;
$self->throw('No contig hit') unless defined $hit;
$self->throw('$contig is not a Bio::EnsEMBL::Analysis::Tools::Pmatch::ContigHit') unless $hit->isa("Bio::EnsEMBL::Analysis::Tools::Pmatch::ContigHit");
$self->{_contig_hits}{$hit->id()} = $hit;
}
=head2 each_ContigHit
Title : each_ContigHit
Usage :
Function: returns all entries in $self->{_contig_hits}
Example :
Returns :
Args :
=cut
sub each_ContigHit {
my ($self) = @_;
return values %{$self->{_contig_hits}};
}
=head2 get_ContigHit
Title : get_ContigHit
Usage :
Function: returns entries for a particular contig in $self->{_contig_hits}
Example :
Returns :
Args :
=cut
sub get_ContigHit {
my ($self,$contig) = @_;
return ($self->{_contig_hits}{$contig}) if defined $contig;
return undef;
}
1;
]]>