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Bio::Map::Marker.3pm

NAME

Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps.

SYNOPSIS

   # get map objects somehow
 
   # a marker with complex localisation
   $o_usat = Bio::Map::Marker->new(-name=>'Chad Super Marker 2',
                                   -positions => [ [$map1, $position1], 
                                                   [$map1, $position2] 
                                                 ] );
 
   # The markers deal with Bio::Map::Position objects which can also
   # be explicitely created and passed on to markers as an array ref:
   $o_usat2 = Bio::Map::Marker->new(-name=>'Chad Super Marker 3',
                                   -positions => [ $pos1, 
                                                   $pos2 
                                                 ] );
 
   # a marker with unique position in a map
   $marker1 = Bio::Map::Marker->new(-name=>'hypervariable1',
                                    -map => $map1,
                                    -position => 100
                                    );
 
   # an other way of creating a marker with unique position in a map:
   $marker2 = Bio::Map::Marker->new(-name=>'hypervariable2');
   $map1->add_element($marker2);
   $marker2->position(100);
 
   # position method is a short cut for get/setting unique positions
   # which overwrites previous values
   # to place a marker to other maps or to have multiple positions 
   # for a map within the same map use add_position()
 
   $marker2->add_position(200);  # new position in the same map
   $marker2->add_position($map2,200); # new map
 
   # setting a map() in a marker or adding a marker into a map are
   # identical mathods. Both set the bidirectional connection which is
   # used by the marker to remember its latest, default map.
 
   # Regardes of how marker positions are created, they are stored and
   # returned as Bio::Map::PositionI objects:
 
   # unique position
   print $marker1->position->value, "\n";
   # several positions
   foreach $pos ($marker2->each_position($map1)) {
      print $pos->value, "\n";
   }
 
 

See Bio::Map::Position and Bio::Map::PositionI for more information.

DESCRIPTION

A Marker is a Bio::Map::Mappable with some properties particular to markers. It also offers a number of convienience methods to make dealing with map elements easier.

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 - Chad Matsalla

Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org 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 $marker = Bio::Map::Marker->new( -name => 'Whizzy marker',
                                                   -position => $position);
  Function: Builds a new Bio::Map::Marker object
  Returns : Bio::Map::Marker
  Args    :
            -name    => name of this microsatellite 
                        [optional], string,default 'Unknown'
            -default_map => the default map for this marker, a Bio::Map::MapI
            -position => map position for this marker, a Bio::Map::PositionI
            -positions => array ref of Bio::Map::PositionI objects
 
            position and positions can also take as values anything the
            corresponding methods can take
 
 

default_map

  Title   : default_map
  Usage   : my $map = $marker->default_map();
  Function: Get/Set the default map for the marker.
  Returns : L<Bio::Map::MapI>
  Args    : [optional] new L<Bio::Map::MapI>
 
 

map

  Title   : map
  Function: This is a synonym of the default_map() method
 
                    *** does not actually add this marker to the map! ***
 
  Status  : deprecated, will be removed in next version
 
 

get_position_object

  Title   : get_position_class
  Usage   : my $position = $marker->get_position_object();
  Function: To get an object of the default Position class
            for this Marker. Subclasses should redefine this method.
            The Position returned needs to be a L<Bio::Map::PositionI> with
                    -element set to self.
  Returns : L<Bio::Map::PositionI>
  Args    : none for an 'empty' PositionI object, optionally
            Bio::Map::MapI and value string to set the Position's -map and -value
            attributes.
 
 

position

  Title   : position
  Usage   : my $position = $mappable->position();
                    $mappable->position($position);
  Function: Get/Set the Position of this Marker (where it is on which map),
            purging all other positions before setting.
  Returns : L<Bio::Map::PositionI>
  Args    : Bio::Map::PositionI
             OR
            Bio::Map::MapI AND
            scalar
             OR
            scalar, but only if the marker has a default map
 
 

add_position

  Title   : add_position
  Usage   : $marker->add_position($position);
  Function: Add a Position to this marker
  Returns : n/a
  Args    : Bio::Map::PositionI
             OR
            Bio::Map::MapI AND
            scalar
             OR
            scalar, but only if the marker has a default map
 
 

positions

  Title   : positions
  Usage   : $marker->positions([$pos1, $pos2, $pos3]);
  Function: Add multiple Bio::Map::PositionI to this marker
  Returns : n/a
  Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI
 
 

in_map

  Title   : in_map
  Usage   : if ( $marker->in_map($map) ) {}
  Function: Tests if this marker is found on a specific map
  Returns : boolean
  Args    : a map unique id OR Bio::Map::MapI