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.
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_order);
my $order = $o_position->order();
Function: Get/set the order position of this position in a map.
Returns : int, the order of this position
Args : none to get, OR int to set |
Title : sortable
Usage : my $num = $position->sortable();
Function: Read-only method that is guaranteed to return a value suitable
for correctly sorting this kind of position amongst other positions
of the same kind on the same map. Note that sorting different kinds
of position together is unlikely to give sane results.
Returns : numeric
Args : none |
Title : equals
Usage : if ($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 = $class->SUPER::new(@args);
my ($order) = $self->_rearrange([qw(ORDER)], @args);
$order && $self->order($order);
return $self;} | sub order
{ my ($self, $order) = @_;
if ($order) {
$self->{'_order'} = $order;
}
return $self->{'_order'} || return;} | sub sortable
{ my $self = shift;
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/wiki/Mailing_lists - 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 the
web:
http://bugzilla.open-bio.org/
| AUTHOR - Chad Matsalla | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _