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


       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);

           # 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 -
           my $abs_start = $pos->start; # $abs_start == 300

           # 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.


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AUTHOR - Sendu Bala



       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

                  (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

        Returns : the string 'map', 'element' or 'position', or undef
        Args    : none

        Title   : map
        Usage   : my $int = $relative->map();
        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();
        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();
        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();
        Function: Get/set a textual description of what this relative describes.
        Returns : string
        Args    : none to get, OR
                  string to set