Bio::Map PositionHandlerI
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Map::PositionHandlerI - A Position Handler Interface
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
Synopsis
    # do not use this module directly
    # See Bio::Map::PositionHandler for an example of
    # implementation.
Description
This interface describes the basic methods required for Position Handlers. A
Position Handler copes with the coordination of different Bio::Map::EntityI
objects, adding and removing them from each other and knowning who belongs to
who. These relationships between objects are based around shared Positions,
hence PositionHandler.
Methods
registerDescriptionCode
indexDescriptionCode
get_entityDescriptionCode
mapDescriptionCode
elementDescriptionCode
add_positionsDescriptionCode
get_positionsDescriptionCode
purge_positionsDescriptionCode
get_other_entitiesDescriptionCode
Methods description
registercode    nextTop
 Title   : register
 Usage   : $position_handler->register();
 Function: Ask this Position Handler to look after your entity relationships.
 Returns : n/a
 Args    : none
indexcodeprevnextTop
 Title   : index
 Usage   : my $index = $position_handler->index();
 Function: Get the unique registry index for yourself, generated during the
           resistration process.
 Returns : int
 Args    : none
get_entitycodeprevnextTop
 Title   : get_entity
 Usage   : my $entity = $position_handler->get_entity($index);
 Function: Get the entity that corresponds to the supplied registry index.
 Returns : Bio::Map::EntityI object
 Args    : int
mapcodeprevnextTop
 Title   : map
 Usage   : my $map = $position_handler->map();
           $position_handler->map($map);
 Function: Get/Set the map you are on. You must be a Position.
 Returns : Bio::Map::MapI
 Args    : none to get, OR
           new Bio::Map::MapI to set
elementcodeprevnextTop
 Title   : element
 Usage   : my $element = $position_handler->element();
           $position_handler->element($element);
 Function: Get/Set the map element you are for. You must be a Position.
 Returns : Bio::Map::MappableI
 Args    : none to get, OR
           new Bio::Map::MappableI to set
add_positionscodeprevnextTop
 Title   : add_positions
 Usage   : $position_handler->add_positions($pos1, $pos2, ...);
 Function: Add some positions to yourself. You can't be a position.
 Returns : n/a
 Args    : Array of Bio::Map::PositionI objects
get_positionscodeprevnextTop
 Title   : get_positions
 Usage   : my @positions = $position_handler->get_positions();
 Function: Get all your positions. You can't be a Position.
 Returns : Array of Bio::Map::PositionI objects
 Args    : none for all, OR
           Bio::Map::EntityI object to limit the Positions to those that
           are shared by you and this other entity.
purge_positionscodeprevnextTop
 Title   : purge_positions
 Usage   : $position_handler->purge_positions();
 Function: Remove all positions from yourself. You can't be a Position.
 Returns : n/a
 Args    : none to remove all, OR
           Bio::Map::PositionI object to remove only that entity, OR
           Bio::Map::EntityI object to limit the removal to those Positions that
           are shared by you and this other entity.
get_other_entitiescodeprevnextTop
 Title   : get_other_entities
 Usage   : my @entities = $position_handler->get_other_entities();
 Function: Get all the entities that share your Positions. You can't be a
           Position.
 Returns : Array of Bio::Map::EntityI objects
 Args    : none
Methods code
registerdescriptionprevnextTop
sub register {
    my $self = shift;
    $self->throw_not_implemented();
}
indexdescriptionprevnextTop
sub index {
    my $self = shift;
    $self->throw_not_implemented();
}
get_entitydescriptionprevnextTop
sub get_entity {
        my $self = shift;
    $self->throw_not_implemented();
}
mapdescriptionprevnextTop
sub map {
    my $self = shift;
    $self->throw_not_implemented();
}
elementdescriptionprevnextTop
sub element {
    my $self = shift;
    $self->throw_not_implemented();
}
add_positionsdescriptionprevnextTop
sub add_positions {
    my $self = shift;
    $self->throw_not_implemented();
}
get_positionsdescriptionprevnextTop
sub get_positions {
    my $self = shift;
    $self->throw_not_implemented();
}
purge_positionsdescriptionprevnextTop
sub purge_positions {
    my $self = shift;
    $self->throw_not_implemented();
}
get_other_entitiesdescriptionprevnextTop
sub get_other_entities {
    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 - Sendu BalaTop
Email bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
General methodsTop
Methods for Bio::Map::PositionI objectsTop
Methods for all other Bio::Map::EntityI objectsTop