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 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.
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
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Support
Please direct usage questions or support issues to the mailing list: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://github.com/bioperl/bioperl-live/issues
AUTHOR - Chad Matsalla
Email [email protected]CONTRIBUTORS
Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein [email protected] Jason Stajich [email protected] Sendu Bala [email protected]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