table of contents
| Bio::Map::Marker(3pm) | User Contributed Perl Documentation | 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 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¶
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://github.com/bioperl/bioperl-live/issues
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
| 2018-10-27 | perl v5.26.2 |