Christopher Fields > BioPerl-1.6.923 > Bio::Map::Position

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Source   Latest Release: BioPerl-1.6.924

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
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