Bio::Map Marker
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Summary
Bio::Map::Marker - An central map object representing a generic marker
that can have multiple location in several maps.
Package variables
No package variables defined.
Included modules
Bio::Map::Position
Inherit
Bio::Map::Mappable Bio::Map::MarkerI
Synopsis
  # get map objects somehow
# a marker with complex localisation $o_usat = Bio::Map::Marker->new(-name=>'Chad Super Marker 2', -positions => [ [$map1, $position1], [$map1, $position2] ] ); # The markers deal with Bio::Map::Position objects which can also # be explicitly created and passed on to markers as an array ref: $o_usat2 = Bio::Map::Marker->new(-name=>'Chad Super Marker 3', -positions => [ $pos1, $pos2 ] ); # a marker with unique position in a map $marker1 = Bio::Map::Marker->new(-name=>'hypervariable1', -map => $map1, -position => 100 ); # another way of creating a marker with unique position in a map: $marker2 = Bio::Map::Marker->new(-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"; }
See Bio::Map::Position and Bio::Map::PositionI for more information.
Description
A Marker is a Bio::Map::Mappable with some properties particular to markers.
It also offers a number of convienience methods to make dealing with map
elements easier.
Methods
newDescriptionCode
default_mapDescriptionCode
get_position_objectDescriptionCode
positionDescriptionCode
add_positionDescriptionCode
positionsDescriptionCode
in_mapDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $marker = Bio::Map::Marker->new( -name => 'Whizzy marker',
-position => $position);
Function: Builds a new Bio::Map::Marker object
Returns : Bio::Map::Marker
Args :
-name => name of this microsatellite
[optional], string,default 'Unknown'
-default_map => the default map for this marker, a Bio::Map::MapI
-position => map position for this marker, a Bio::Map::PositionI
-positions => array ref of Bio::Map::PositionI objects
position and positions can also take as values anything the corresponding methods can take
default_mapcodeprevnextTop
 Title   : default_map
Usage : my $map = $marker->default_map();
Function: Get/Set the default map for the marker.
Returns : Bio::Map::MapI
Args : [optional] new Bio::Map::MapI
get_position_objectcodeprevnextTop
 Title   : get_position_class
Usage : my $position = $marker->get_position_object();
Function: To get an object of the default Position class
for this Marker. Subclasses should redefine this method.
The Position returned needs to be a Bio::Map::PositionI with
-element set to self.
Returns : Bio::Map::PositionI
Args : none for an 'empty' PositionI object, optionally
Bio::Map::MapI and value string to set the Position's -map and -value
attributes.
positioncodeprevnextTop
 Title   : position
Usage : my $position = $mappable->position();
$mappable->position($position);
Function: Get/Set the Position of this Marker (where it is on which map),
purging all other positions before setting.
Returns : Bio::Map::PositionI
Args : Bio::Map::PositionI
OR
Bio::Map::MapI AND
scalar
OR
scalar, but only if the marker has a default map
add_positioncodeprevnextTop
 Title   : add_position
Usage : $marker->add_position($position);
Function: Add a Position to this marker
Returns : n/a
Args : Bio::Map::PositionI
OR
Bio::Map::MapI AND
scalar
OR
scalar, but only if the marker has a default map
positionscodeprevnextTop
 Title   : positions
Usage : $marker->positions([$pos1, $pos2, $pos3]);
Function: Add multiple Bio::Map::PositionI to this marker
Returns : n/a
Args : array ref of $map/value tuples or array ref of Bio::Map::PositionI
in_mapcodeprevnextTop
 Title   : in_map
Usage : if ( $marker->in_map($map) ) {}
Function: Tests if this marker is found on a specific map
Returns : boolean
Args : a map unique id OR Bio::Map::MapI
Methods code
newdescriptionprevnextTop
sub new {
    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 $self;
}
default_mapdescriptionprevnextTop
sub default_map {
	my ($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 $self->{'_default_map'} || return;
}
get_position_objectdescriptionprevnextTop
sub get_position_object {
	my ($self, $map, $value) = @_;
	$map ||= $self->default_map;
	if ($value) {
		$self->throw("Value better be scalar, not [$value]") unless ref($value) eq '';
	}

	my $pos = Bio::Map::Position->new();
	$pos->map($map) if $map;
    $pos->value($value) if defined($value);
    $pos->element($self);
	return $pos;
}
positiondescriptionprevnextTop
sub position {
    my ($self, $pos, $pos_actual) = @_;

	if ($pos) {
		$self->purge_positions;
		$self->add_position($pos, $pos_actual);
	}

    my @positions = $self->each_position;
    $self->warn('This marker has more than one Position, returning the most recently added') if scalar @positions > 1;
    return pop(@positions);
}
add_positiondescriptionprevnextTop
sub add_position {
    my ($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, $pos); # adds position to us
}
}
positionsdescriptionprevnextTop
sub positions {
    my ($self, $args_ref) = @_;

    foreach my $arg (@{$args_ref}) {
        if (ref($arg) eq 'ARRAY') {
            $self->add_position(@{$arg});
        }
        else {
            $self->add_position($arg);
        }
    }
}
in_mapdescriptionprevnextTop
sub in_map {
	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;
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
SupportTop
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Chad MatsallaTop
Email bioinformatics1@dieselwurks.com
CONTRIBUTORSTop
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Lincoln Stein lstein@cshl.org
Jason Stajich jason@bioperl.org
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
mapTop
 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