/ 
bioperl-1.0.2
/ Bio::Map::OrderedPosition

NAME

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.

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.

FEEDBACK

Mailing Lists

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 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://bioperl.org/bioperl-bugs/

AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

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

APPENDIX

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