Provided by: libbio-perl-perl_1.6.901-2_all bug

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