Bio::Map::Relative(3pm) 				User Contributed Perl Documentation				   Bio::Map::Relative(3pm)

NAME

       Bio::Map::Relative - Represents what a Position's coordiantes are relative to.

SYNOPSIS

	   # Get a Bio::Map::PositionI somehow
	   my $pos = Bio::Map::Position->new(-value => 100);

	   # its co-ordinates are implicitly relative to the start of its map
	   my $implicit_relative = $pos->relative;
	   my $type = $implicit_relative->type; # $type eq 'map'
	   my $value = $implicit_relative->$type(); # $value == 0

	   # make its co-ordinates relative to another Position
	   my $pos_we_are_relative_to = Bio::Map::Position->new(-value => 200);
	   my $relative = Bio::Map::Relative->new(-position => $pos_we_are_relative_to);
	   $pos->relative($relative);

	   # Get the start co-ordinate of $pos relative to $pos_we_are_relative_to
	   my $start = $pos->start; # $start == 100

	   # Get the start co-ordinate of $pos relative to the start of the map
	   my $abs_start = $relative->absolute_conversion($pos); # $abs_start == 300
	   # - or -
	   $pos->absolute(1);
	   my $abs_start = $pos->start; # $abs_start == 300
	   $pos->absolute(0);

	   # Get the start co-ordinate of $pos relative to a third Position
	   my $pos_frame_of_reference = Bio::Map::Position->new(-value => 10);
	   my $relative2 = Bio::Map::Relative->new(-position => $pos_frame_of_reference);
	   my $start = $pos->start($relative2); # $start == 290

DESCRIPTION

       A Relative object is used to describe what the co-ordinates (numerical(), start(), end()) of a Position are relative to. By default they
       are implicitly assumed to be relative to the start of the map the Position is on.  But setting the relative() of a Position to one of these
       objects lets us define otherwise.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala
       Email 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 $relative = Bio::Map::Relative->new();
	Function: Build a new Bio::Map::Relative object.
	Returns : Bio::Map::Relative object
	Args	: -map => int		: coordinates are relative to this point on the
					  Position's map [default is map => 0, ie.
					  relative to the start of the map],
		  -element => Mappable	: or relative to this element's (a
					  Bio::Map::MappableI) position in the map
					  (only works if the given element has only one
					  position in the map the Position belongs to),
		  -position => Position : or relative to this other Position (a
					  Bio::Map::PositionI, fails if the other
					  Position is on a different map to this map)

		  -description => string: Free text description of what this relative
					  describes

		  (To say a Position is relative to something and upstream of it,
		   the Position's start() co-ordinate should be set negative)

   absolute_conversion
	Title	: absolute_conversion
	Usage	: my $absolute_coord = $relative->absolute_conversion($pos);
	Function: Convert the start co-ordinate of the supplied position into a number
		  relative to the start of its map.
	Returns : scalar number
	Args	: Bio::Map::PositionI object

   type
	Title	: type
	Usage	: my $type = $relative->type();
	Function: Get the type of thing we are relative to. The types correspond
		  to a method name, so the value of what we are relative to can
		  subsequently be found by $value = $relative->$type;

		  Note that type is set by the last method that was set, or during
		  new().

	Returns : the string 'map', 'element' or 'position', or undef
	Args	: none

   map
	Title	: map
	Usage	: my $int = $relative->map();
		  $relative->map($int);
	Function: Get/set the distance from the start of the map that the Position's
		  co-ordiantes are relative to.
	Returns : int
	Args	: none to get, OR
		  int to set; a value of 0 means relative to the start of the map.

   element
	Title	: element
	Usage	: my $element = $relative->element();
		  $relative->element($element);
	Function: Get/set the map element (Mappable) the Position is relative to. If
		  the Mappable has more than one Position on the Position's map, we
		  will be relative to the Mappable's first Position on the map.
	Returns : Bio::Map::MappableI
	Args	: none to get, OR
		  Bio::Map::MappableI to set

   position
	Title	: position
	Usage	: my $position = $relative->position();
		  $relative->position($position);
	Function: Get/set the Position your Position is relative to. Your Position
		  will be made relative to the start of this supplied Position. It
		  makes no difference what maps the Positions are on.
	Returns : Bio::Map::PositionI
	Args	: none to get, OR
		  Bio::Map::PositionI to set

   description
	Title	: description
	Usage	: my $description = $relative->description();
		  $relative->description($description);
	Function: Get/set a textual description of what this relative describes.
	Returns : string
	Args	: none to get, OR
		  string to set

perl v5.14.2							    2012-03-02						   Bio::Map::Relative(3pm)