Raw content of Bio::Map::MapI # $Id: MapI.pm,v 1.6 2002/10/22 07:45:15 lapp Exp $ # # BioPerl module for Bio::Map::MapI # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::MapI - Interface for describing Map objects in bioperl =head1 SYNOPSIS # get a MapI somehowe my $name = $map->name(); # string my $length = $map->length(); # integer my $species= $map->species; # Bio::Species my $type = $map->type(); # genetic/sts/rh/ =head1 DESCRIPTION This object describes the basic functionality of a Map in bioperl. Maps are anything from Genetic Map to Sequence Map to and Assembly Map to Restriction Enzyme to FPC. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Map::MapI; use vars qw(@ISA); use strict; use Bio::Root::RootI; use Carp; @ISA = qw(Bio::Root::RootI); =head2 species Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : L<Bio::Species> object Args : (optional) Bio::Species =cut sub species{ my ($self) = @_; $self->throw_not_implemented(); } =head2 units Title : units Usage : $map->units('cM'); Function: Get/Set units for a map Returns : units for a map Args : units for a map (string) =cut sub units{ my ($self) = @_; $self->throw_not_implemented(); } =head2 type Title : type Usage : my $type = $map->type Function: Get/Set Map type Returns : String coding map type Args : (optional) string =cut sub type { my ($self) = @_; $self->throw_not_implemented(); } =head2 name Title : name Usage : my $name = $map->name Function: Get/Set Map name Returns : Map name Args : (optional) string =cut sub name { my ($self) = @_; $self->throw_not_implemented(); } =head2 length Title : length Usage : my $length = $map->length(); Function: Retrieves the length of the map, It is possible for the length to be unknown for maps such as Restriction Enzyme, will return undef in that case Returns : integer representing length of map in current units will return undef if length is not calculateable Args : none =cut sub length{ my ($self) = @_; $self->throw_not_implemented(); } =head2 unique_id Title : unique_id Usage : my $id = $map->unique_id; Function: Get/Set the unique ID for this map Returns : a unique identifier Args : [optional] new identifier to set =cut sub unique_id{ my ($self,$id) = @_; $self->throw_not_implemented(); } =head2 add_element Title : add_element Usage : $map->add_element($marker) Function: Add a Bio::Map::MappableI object to the Map Returns : none Args : Bio::Map::MappableI object =cut sub add_element{ my ($self) = @_; $self->throw_not_implemented(); } =head2 each_element Title : each_element Usage : my @elements = $map->each_element; Function: Retrieves all the elements in a map unordered Returns : Array of Map elements (L<Bio::Map::MarkerI>) Args : =cut sub each_element{ my ($self) = @_; $self->throw_not_implemented(); } 1;