view release on metacpan or  search on metacpan

Bio/Map/FPCMarker.pm  view on Meta::CPAN

    return $self->{'_subgroup'} || 0;
}

=head2 position

 Title   : position
 Usage   : $markerpos = $markerobj->position($ctg);
 Function: get the position of the marker in the contig
 Returns : scalar representing the position of the markernumber of
           the contig
 Args    : $ctg is necessary to look for the position of the marker
           in that contig.

 *** This has nothing to do with an actual Bio::Map::PositionI object ***

=cut

sub position {
    my ($self,$ctg) = @_;
    return 0 unless defined $ctg;

    return 0 unless( defined $self->{'_position'} &&
		     defined $self->{'_position'}{$ctg});
    return $self->{'_position'}{$ctg};
}

=head2 remark

 Title   : remark
 Usage   : $markerremark = $markerobj->remark();
 Function: get the remarks for this marker
 Returns : scalar of newline-separated markers
 Args    : none

=cut

sub remark {
    my ($self) = shift;
    return $self->{'_remark'} = shift if @_;
    return $self->{'_remark'};
}

=head2 each_cloneid

 Title   : each_cloneid
 Usage   : my @clones  = $map->each_cloneid();
 Function: retrieves all the clone ids in a map unordered
 Returns : list of strings (ids)
 Args    : none

 *** This only supplies the ids set with the set_clones method ***
 *** It has nothing to do with actual Bio::Map::MappableI objects ***

=cut

sub each_cloneid {
    my ($self) = @_;
    return $self->_each_element('clones');
}

=head2 each_contigid

 Title   : each_contigid
 Usage   : my @contigs = $map->each_contigid();
 Function: retrieves all the contig ids in a map unordered
 Returns : list of strings (ids)
 Args    : none

 *** This only supplies the ids set with the set_contigs method ***
 *** It has nothing to do with actual Bio::Map::MapI objects ***

=cut

sub each_contigid {
    my ($self) = @_;
    return $self->_each_element('contigs');
}

sub _each_element{
    my ($self, $type) = @_;

    $type = 'clones' unless defined $type;
    $type = lc("_$type");

    return keys %{$self->{$type} || {}};
}

=head2 set_clones

 Title   : set_clones
 Usage   : $marker->set_clones(\%clones)
 Function: Set the clone ids hashref
 Returns : None
 Args    : Hashref of clone ids

 *** This only sets a hash of ids ***
 *** It has nothing to do with actual Bio::Map::MappableI objects ***

=cut

sub set_clones{
   my ($self,$clones) = @_;
   if( defined $clones && ref($clones) =~ /HASH/ ) {
       $self->{'_clones'} = $clones;
   }
}

=head2 set_contigs

 Title   : set_contigs
 Usage   : $marker->set_contigs(\%contigs)
 Function: Set the contig ids hashref
 Returns : None
 Args    : Hashref of contig ids

 *** This only sets a hash of ids ***
 *** It has nothing to do with actual Bio::Map::MapI objects ***

=cut

sub set_contigs{
   my ($self,$contigs) = @_;
   if( defined $contigs && ref($contigs) =~ /HASH/ ) {
       $self->{'_contigs'} = $contigs;
   }
}

=head2 set_positions

 Title   : set_positions
 Usage   : $marker->set_positions(\%markerpos)
 Function: Set the positions hashref
 Returns : None
 Args    : Hashref of marker positions