Provided by: libbio-perl-perl_1.7.2-3_all
Bio::Map::RelativeI - Interface for describing what a Position's coordiantes are relative to.
# do not use this module directly # See Bio::Map::Relative for an example of # implementation.
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.
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AUTHOR - Sendu Bala
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 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 got 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 got 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