Ewan Birney


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.


    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]] );


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.


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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:


AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com


Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk Jason Stajich, jason@bioperl.org


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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_
 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.

Bio::Map::Position functions


 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


 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