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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bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/
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_ $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 : 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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.