Bio::Map
OrderedPosition
Summary
Bio::Map::OrderedPosition - Abstracts the notion of a member
of an ordered list of markers. Each marker is a certain distance
from the one in the ordered list before it.
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Map::OrderedPosition;
# the first marker in the sequence
my $position = new Bio::Map::OrderedPosition(-order => 1,
-positions => [ [ $map, 22.3] ] );
# the second marker in the sequence, 15.6 units from the fist one
my $position2 = new Bio::Map::OrderedPosition(-order => 2,
-positions => [ [ $map, 37.9] ] );
# the third marker in the sequence, coincidental with the second
# marker
my $position3 = new Bio::Map::OrderedPosition(-order => 3,
-posititions => [ [ $map, 37.9]] );
Description
This object is an implementation of the PositionI interface and the
Position object handles the specific values of a position.
OrderedPosition is intended to be slightly more specific then Position
but only specific enough for a parser from the MarkerIO subsystem to
create and then pass to a client application to bless into the proper
type. For an example of how this is intended to work, see the
Mapmaker.pm.
No units are assumed here - units are handled by context of which Map
a position is placed in.
Se Bio::Map::Position for additional information.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Map::OrderedPosition();
Function: Builds a new Bio::Map::OrderedPosition object
Returns : Bio::Map::OrderedPosition
Args : -order - The order of this position |
Title : order
Usage : $o_position->order($new_position) _or_
$o_position->order()
Function: get/set the order position of this position in a map
Returns :
Args : If $new_position is provided, the current position of this Position
will be set to $new_position. |
Title : equals
Usage : if( $mappable->equals($mapable2)) ...
Function: Test if a position is equal to another position.
Returns : boolean
Args : Bio::Map::PositionI |
Title : less_than
Usage : if( $mappable->less_than($m2) ) ...
Function: Tests if a position is less than another position
It is assumed that 2 positions are in the same map.
Returns : boolean
Args : Bio::Map::PositionI |
Title : greater_than
Usage : if( $mappable->greater_than($m2) ) ...
Function: Tests if position is greater than another position.
It is assumed that 2 positions are in the same map.
Returns : boolean
Args : Bio::Map::PositionI |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($map, $marker, $value, $order) =
$self->_rearrange([qw( MAP
MARKER
VALUE
ORDER
)], @args);
$map && $self->map($map);
$marker && $self->marker($marker);
$value && $self->value($value);
$order && $self->order($order);
return $self;} | sub order
{ my ($self,$order) = @_;
if ($order) {
$self->{'_order'} = $order;
}
return $self->{'_order'};} | sub equals
{ my ($self,$compare) = @_;
return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
return ( $compare->order == $self->order);} | sub less_than
{ my ($self,$compare) = @_;
return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
return ( $compare->order < $self->order);} | sub greater_than
{ my ($self,$compare) = @_;
return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
return ( $compare->order > $self->order);} | General documentation
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/MailList.shtml - About the mailing lists
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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
| AUTHOR - Chad Matsalla | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Bio::Map::Position functions | Top |
Title : known_maps
Usage : my @maps = $position->known_maps
Function: Returns the list of maps that this position has values for
Returns : list of Bio::Map::MapI unique ids
Args : none
Title : in_map
Usage : if ( $position->in_map($map) ) {}
Function: Tests if a position has values in a specific map
Returns : boolean
Args : a map unique id OR Bio::Map::MapI Title : positions
Usage : my @positions = $position->each_position_value($map);
Function: Retrieve a list of positions coded as strings or ints
Returns : Array of position values for a Map
Args : Bio::Map::MapI object to get positions for
Title : add_position_value
Usage : $position->add_position_value($map,'100');
Function: Add a numeric or string position to the PositionI container
and assoiciate it with a Bio::Map::MapI
Returns : none
Args : $map - Bio::Map::MapI
String or Numeric coding for a position on a map Title : purge_position_values
Usage : $position->purge_position_values
Function: Remove all the position values stored for a position
Returns : none
Args : [optional] only purge values for a given map