- AUTHOR - Sendu Bala
Bio::Map::Relative - Represents what a Position's coordiantes are relative to.
# 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
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.
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.
firstname.lastname@example.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
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.
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:
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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)
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
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
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.
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
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
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