/ 
BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Map::Relative

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