Bio::Map MarkerI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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
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:
  http://bugzilla.open-bio.org/
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