Bio::Map MarkerI
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Summary
Bio::Map::MarkerI - Interface for basic marker functionality
Package variables
No package variables defined.
Inherit
Bio::Map::MappableI
Synopsis
    # do not use this module directly
# See Bio::Map::Marker for an example of
# implementation.
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.
Methods
get_position_objectDescriptionCode
positionDescriptionCode
positionsDescriptionCode
default_mapDescriptionCode
Methods description
get_position_objectcode    nextTop
 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 Bio::Map::PositionI with
-element set to self.
Returns : 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.
positioncodeprevnextTop
 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 : Bio::Map::PositionI
Args : Bio::Map::PositionI
OR
Bio::Map::MapI AND
scalar
OR
scalar, but only if the marker has a default map
positionscodeprevnextTop
 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
default_mapcodeprevnextTop
 Title   : default_map
Usage : my $map = $marker->default_map();
Function: Get/Set the default map for the marker.
Returns : Bio::Map::MapI
Args : [optional] new Bio::Map::MapI
Methods code
get_position_objectdescriptionprevnextTop
sub get_position_object {
    my $self = shift;
    $self->throw_not_implemented();
}
positiondescriptionprevnextTop
sub position {
    my $self = shift;
    $self->throw_not_implemented();
}
positionsdescriptionprevnextTop
sub positions {
    my $self = shift;
    $self->throw_not_implemented();
}
default_mapdescriptionprevnextTop
sub default_map {
    my $self = shift;
    $self->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
CONTRIBUTORSTop
Heikki Lehvaslaiho heikki-at-bioperl-dot-org
Lincoln Stein lstein@cshl.org
Jason Stajich jason@bioperl.org
Chad Matsalla bioinformatics1@dieselwurks.com
Sendu Bala bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
in_mapTop
 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