Bio::Map::Marker(3pm) | User Contributed Perl Documentation | Bio::Map::Marker(3pm) |
Bio::Map::Marker - An central map object representing a generic marker that can have multiple location in several maps.
# 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 explicitly 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 ); # another 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.
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.
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Email bioinformatics1@dieselwurks.com
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein lstein@cshl.org Jason Stajich jason@bioperl.org Sendu Bala bix@sendu.me.uk
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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>
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
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.
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
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
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
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
2018-10-27 | perl v5.26.2 |