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)