- AUTHOR - Jason Stajich
Bio::Map::Position - A single position of a Marker, or the range over which that marker lies, in a Map
use Bio::Map::Position; my $position = Bio::Map::Position->new(-map => $map, -element => $marker, -value => 100 ); my $position_with_range = Bio::Map::Position->new(-map => $map, -element => $marker, -start => 100, -length => 10 );
This object is an implementation of the PositionI interface that handles the specific values of a position. This allows a map element (e.g. Marker) to have multiple positions within a map and still be treated as a single entity.
This handles the concept of a relative map in which the order of elements and the distance between them is known, but does not directly handle the case when distances are unknown - in that case arbitrary values must be assigned for position values.
No units are assumed here - units are handled by context of which Map a position is placed in or the subclass of this Position.
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.
email@example.com - 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:
Lincoln Stein, firstname.lastname@example.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Chad Matsalla, email@example.com Sendu Bala, firstname.lastname@example.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::Map::Position->new(); Function: Builds a new Bio::Map::Position object Returns : Bio::Map::Position Args : -map => Bio::Map::MapI object -element => Bio::Map::MappableI object -relative => Bio::Map::RelativeI object * If this position has no range, or if a single value can describe the range * -value => scalar : something that describes the single point position or range of this Position, most likely an int * Or if this position has a range, at least two of * -start => int : value of the start co-ordinate -end => int : value of the end co-ordinate -length => int : length of the range
Title : relative Usage : my $relative = $position->relative(); $position->relative($relative); Function: Get/set the thing this Position's coordinates (numerical(), start(), end()) are relative to, as described by a Relative object. Returns : Bio::Map::RelativeI (default is one describing "relative to the start of the Position's map") Args : none to get, OR Bio::Map::RelativeI to set
Title : absolute Usage : my $absolute = $position->absolute(); $position->absolute($absolute); Function: Get/set how this Position's co-ordinates (numerical(), start(), end()) are reported. When absolute is off, co-ordinates are relative to the thing described by relative(). Ie. the value returned by start() will be the same as the value you set start() to. When absolute is on, co-ordinates are converted to be relative to the start of the map. So if relative() currently points to a Relative object describing "relative to another position which is 100 bp from the start of the map", this Position's start() had been set to 50 and absolute() returns 1, $position->start() will return 150. If absolute() returns 0 in the same situation, $position->start() would return 50. Returns : boolean (default 0) Args : none to get, OR boolean to set
Title : value Usage : my $pos = $position->value; Function: Get/Set the value for this postion Returns : scalar, value Args : [optional] new value to set
Title : numeric Usage : my $num = $position->numeric; Function: Read-only method that is guaranteed to return a numeric representation of the start of this position. Returns : scalar numeric Args : none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes.
Title : start Usage : my $start = $position->start(); $position->start($start); Function: Get/set the start co-ordinate of this position. Returns : the start of this position Args : scalar numeric to set, OR none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes.
Title : end Usage : my $end = $position->end(); $position->end($end); Function: Get/set the end co-ordinate of this position. Returns : the end of this position Args : scalar numeric to set, OR none to get the co-ordinate normally (see absolute() method), OR Bio::Map::RelativeI to get the co-ordinate converted to be relative to what this Relative describes.
Title : length Usage : $length = $position->length(); Function: Get/set the length of this position's range, changing the end() if necessary. Getting and even setting the length will fail if both start() and end() are not already defined. Returns : the length of this range Args : none to get, OR scalar numeric (>0) to set.
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
Title : toString Usage : print $position->toString(), "\n"; Function: stringifies this range Returns : a string representation of the range of this Position Args : optional Bio::Map::RelativeI to have the co-ordinates reported relative to the thing described by that Relative
Title : absolute_relative Usage : my $rel = $position->absolute_relative(); Function: Get a relative describing the start of the map. This is useful for supplying to the coordinate methods (start(), end() etc.) to get the temporary effect of having set absolute(1). Returns : Bio::Map::Relative Args : none