/ 
BioPerl-1.007000_004
River stage two • 60 direct dependents • 65 total dependents
/ 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 = Bio::Map::OrderedPosition->new(-order => 1,
			-positions => [ [ $map, 22.3] ] );
	# the second marker in the sequence, 15.6 units from the fist one
    my $position2 = Bio::Map::OrderedPosition->new(-order => 2,
			-positions => [ [ $map, 37.9] ] );
	# the third marker in the sequence, coincidental with the second
	# marker
    my $position3 = Bio::Map::OrderedPosition->new(-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/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chad Matsalla

Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Jason Stajich, jason@bioperl.org Sendu Bala, bix@sendu.me.uk

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 = Bio::Map::OrderedPosition->new();
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_order);
          my $order = $o_position->order();
Function: Get/set the order position of this position in a map.
Returns : int, the order of this position
Args    : none to get, OR int to set

sortable

Title   : sortable
Usage   : my $num = $position->sortable();
Function: Read-only method that is guaranteed to return a value suitable
          for correctly sorting this kind of position amongst other positions
          of the same kind on the same map. Note that sorting different kinds
          of position together is unlikely to give sane results.
Returns : numeric
Args    : none

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