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Bio::Map::Position.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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