Bio::Map OrderedPosition
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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
Bio::Map::Position
Inherit
Bio::Map::Position
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
equalsDescriptionCode
greater_thanDescriptionCode
less_thanDescriptionCode
newDescriptionCode
orderDescriptionCode
Methods description
equalscode    nextTop
 Title   : equals
 Usage   : if( $mappable->equals($mapable2)) ...
 Function: Test if a position is equal to another position.
 Returns : boolean
 Args    : Bio::Map::PositionI
greater_thancodeprevnextTop
 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
less_thancodeprevnextTop
 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
newcodeprevnextTop
 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
ordercodeprevnextTop
 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 $new_position.
Methods code
equalsdescriptionprevnextTop
sub equals {
   my ($self,$compare) = @_;
   return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
   return ( $compare->order == $self->order);
}

# admittedly these are really the best comparisons in the world
# but it is a first pass we'll need to refine the algorithm or not 
# provide general comparisions and require these to be implemented
# by objects closer to the specific type of data
}
greater_thandescriptionprevnextTop
sub greater_than {
   my ($self,$compare) = @_;
   return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
   return ( $compare->order > $self->order);
}

1;
}
less_thandescriptionprevnextTop
sub less_than {
   my ($self,$compare) = @_;
   return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition'));
   return ( $compare->order < $self->order);
}
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
#    $self->{'_order'} = [];
  
    my ($map, $marker, $value, $order) = 
	$self->_rearrange([qw( MAP 
			       MARKER 
			       VALUE
			       ORDER
			       )], @args);
#    print join ("|-|", ($map, $marker, $value, $order)), "\n";
    $map     && $self->map($map);
    $marker  && $self->marker($marker);
    $value   && $self->value($value);
    $order   && $self->order($order);

    return $self;
}
orderdescriptionprevnextTop
sub order {
    my ($self,$order) = @_;
    if ($order) {
	# no point in keeping the old ones
	$self->{'_order'} = $order;
    }
    return $self->{'_order'};
}
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/MailList.shtml  - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
AUTHOR - Chad MatsallaTop
Email bioinformatics1@dieselwurks.com
CONTRIBUTORSTop
Lincoln Stein, lstein@cshl.org
Heikki Lehvaslaiho, heikki@ebi.ac.uk
Jason Stajich, jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Map::Position functionsTop
known_mapsTop
 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
in_mapTop
 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
each_position_valueTop
 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
add_position_valueTop
 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
purge_position_valuesTop
 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