# get map objects somehow

  # a marker with complex localisation
  $o_usat = new Bio::Map::Marker (-name=>'Chad Super Marker 2',
				  -positions => [ [$map1, $position1], 
                                                  [$map1, $position2] 
						] );

  # The markers deal with Bio::Map::Position objects which can also
  # be explicitely created and passed on to markers as an array ref:
  $o_usat2 = new Bio::Map::Marker (-name=>'Chad Super Marker 3',
				  -positions => [ $pos1, 
                                                  $pos2 
						] );

  # a marker with unique position in a map
  $marker1 = new Bio::Map::Marker (-name=>'hypervariable1',
				   -map => $map1,
				   -position => 100
				   );

  # an other way of creating a marker with unique position in a map:
  $marker2 = new Bio::Map::Marker (-name=>'hypervariable2');
  $map1->add_element($marker2);
  $marker2->position(100);

  # position method is a short cut for get/setting unique positions
  # which overwrites previous values
  # to place a marker to other maps or to have multiple positions 
  # for a map within the same map use add_position()

  $marker2->add_position(200);	# new position in the same map
  $marker2->add_position($map2,200); # new map

  # setting a map() in a marker or adding a marker into a map are
  # identical mathods. Both set the bidirectional connection which is
  # used by the marker to remember its latest, default map.

  # Regardes of how marker positions are created, they are stored and
  # returned as Bio::Map::PositionI objects:

  # unique position
  print $marker1->position->value, "\n";
  # several positions
  foreach $pos ($marker2->each_position($map1)) {
     print $pos->value, "\n";
  }

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
	bless($self, ref $class || $class);
	
    my ($name, $default_map, $map, $position, $positions) = 
	$self->_rearrange([qw(NAME
				  DEFAULT_MAP
			      MAP
			      POSITION
			      POSITIONS
			      )], @args);
    
    if ($name) { $self->name($name); } 
    else {$self->name('Unnamed marker'); }
    
    $map         && $self->default_map($map);
	$default_map && $self->default_map($default_map);
    $position    && $self->position($position); 
    $positions   && $self->positions($positions);
 
    return $self;

	my ($self, $map) = @_;
	if (defined $map) {
		$self->thow("This is [$map], not Bio::Map::MapI object") unless $map->isa('Bio::Map::MapI');
		$self->{'_default_map'} = $map;
	}
	return $self->{'_default_map'} || return;

	my ($self, $map, $value) = @_;
	$map ||= $self->default_map;
	if ($value) {
		$self->throw("Value better be scalar, not [$value]") unless ref($value) eq '';
	}
	
	my $pos = new Bio::Map::Position();
	$pos->map($map) if $map;
    $pos->value($value) if $value;
    $pos->element($self);
	return $pos;

    my ($self, $pos, $pos_actual) = @_;
    
	if ($pos) {
		$self->purge_positions;
		$self->add_position($pos, $pos_actual);
	}
    
    my @positions = $self->each_position;
    $self->warn('This marker has more than one Position, returning the most recently added') if scalar @positions > 1;
    return pop(@positions);

    my ($self, $pos, $pos_actual) = @_;
    $self->throw("Must give a Position") unless defined $pos;
    
    my $map = $self->default_map;
	my $pos_map;
	if (ref($pos)) {
		if (ref($pos) eq 'ARRAY') {
			($pos, $pos_actual) = @{$pos};
			unless ($pos && $pos_actual && ref($pos)) {
				$self->throw("Supplied an array ref but did not contain two values, the first an object");
			}
		}
		
		if ($pos->isa('Bio::Map::PositionI')) {
			$pos_map = $pos->map;
			$self->default_map($pos_map) unless $map;
			$map = $pos_map if $pos_map;
		}
		elsif ($pos->isa('Bio::Map::MapI')) {
			$self->default_map($pos) unless $map;
			$map = $pos;
			$pos = $pos_actual;
		}
		else {
			$self->throw("This is [$pos], not a Bio::Map::PositionI or Bio::Map::MapI object");
		}
	}
	
	$self->throw("You need to give a marker a default map before you can set positions without explicit map!" ) unless $map;
	
	if (ref($pos) && $pos->isa('Bio::Map::PositionI')) {
		$pos->map($map) unless $pos_map;
		$self->SUPER::add_position($pos);
	}
	else {
		$self->get_position_object($map, $pos); # adds position to us
	}

    my ($self, $args_ref) = @_;
    
    foreach my $arg (@{$args_ref}) {
        if (ref($arg) eq 'ARRAY') {
            $self->add_position(@{$arg});
        }
        else {
            $self->add_position($arg);
        }
    }

	my ($self, $query) = @_;
	$self->throw("Must supply an argument") unless defined($query);
    
	if (ref($query) eq '') {
		foreach my $map ($self->known_maps) {
			my $uid = $map->unique_id;
			if ($uid) {
				($uid eq $query) && return 1;
			}
		}
	}
    else {
		return $self->SUPER::in_map($query);
	}
    
    return 0;

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://bugzilla.open-bio.org/

 Title   : map
 Function: This is a synonym of the default_map() method

		   *** does not actually add this marker to the map! ***

 Status  : deprecated, will be removed in next version