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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Reporting Bugs
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/ 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 _

new
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

order
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.

Bio::Map::Position functions

known_maps
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_map
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_value
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_value
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_values
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

equals
Title : equals Usage : if( $mappable->equals($mapable2)) ... Function: Test if a position is equal to another position. Returns : boolean Args : Bio::Map::PositionI

less_than
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

greater_than
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