Provided by: libbio-perl-perl_1.6.923-1_all bug

NAME

       Bio::Map::Position - A single position of a Marker, or the range over which
                            that marker lies, in a Map

SYNOPSIS

           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
                                                 );

DESCRIPTION

       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.

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 - Jason Stajich

       Email jason@bioperl.org

CONTRIBUTORS

       Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Chad
       Matsalla, bioinformatics1@dieselwurks.com Sendu Bala, 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 $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

   relative
         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

   absolute
         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

   value
        Title   : value
        Usage   : my $pos = $position->value;
        Function: Get/Set the value for this postion
        Returns : scalar, value
        Args    : [optional] new value to set

   numeric
        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.

   start
         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.

   end
         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.

   length
         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.

   sortable
        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

   toString
         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

   absolute_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