# $Id: MapI.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Map::MapI # # Please direct questions and support issues to # # Cared for by Sendu Bala # # 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 somehow 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 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/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =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 the web: http://bugzilla.open-bio.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.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 strict; use Bio::Map::PositionHandler; use base qw(Bio::Map::EntityI Bio::AnnotatableI); =head2 EntityI methods These are fundamental to coordination of Maps and other entities, so are implemented at the interface level =cut =head2 get_position_handler Title : get_position_handler Usage : my $position_handler = $entity->get_position_handler(); Function: Gets a PositionHandlerI that $entity is registered with. Returns : Bio::Map::PositionHandlerI object Args : none =cut sub get_position_handler { my $self = shift; unless (defined $self->{_eh}) { my $ph = Bio::Map::PositionHandler->new(-self => $self); $self->{_eh} = $ph; $ph->register; } return $self->{_eh}; } =head2 PositionHandlerI-related methods These are fundamental to coordination of Maps and other entities, so are implemented at the interface level =cut =head2 get_positions Title : get_positions Usage : my @positions = $mappable->get_positions(); Function: Get all the Positions on this Map (sorted). Returns : Array of L objects Args : none for all, OR L object for positions of the given Mappable =cut sub get_positions { my ($self, $mappable) = @_; my @positions = $self->get_position_handler->get_positions($mappable); # precompute sortable for effieciency and to avoid bugs @positions = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [$_->sortable, $_] } @positions; return @positions; } =head2 each_position Title : each_position Function: Synonym of the get_positions() method. Status : deprecated, will be removed in next version =cut *each_position = \&get_positions; =head2 purge_positions Title : purge_positions Usage : $map->purge_position(); Function: Remove all positions from this map. Notifies the positions they are no longer on this map. Returns : n/a Args : none to remove all positions, OR L object to remove just that Position, OR L object to remove only those positions of the given mappable =cut sub purge_positions { my ($self, $thing) = @_; $self->get_position_handler->purge_positions($thing); } =head2 get_elements Title : get_elements Usage : my @elements = $map->get_elements; Function: Retrieves all the elements on a map (unordered) Returns : Array of Map elements (L) Args : none =cut sub get_elements { my $self = shift; return $self->get_position_handler->get_other_entities; } =head2 each_element Title : each_element Function: Synonym of the get_elements() method. Status : deprecated, will be removed in the next version =cut =head2 common_elements Title : common_elements Usage : my @common_elements = $map->common_elements(\@other_maps); my @common_elements = Bio::Map::SimpleMap->common_elements(\@maps); Function: Find the elements that are common to multiple maps. Returns : array of Bio::Map::MappableI Args : arg #1 = L to compare this one to, or an array ref of such objects (mandatory) arg #2 = optionally, one or more of the key => value pairs below -min_num => int : the minimum number of input maps an element must be found on before before returned [default is 1] -min_percent => number : as above, but the minimum percentage of input maps [default is 100 - note that this will effectively override all other options] -require_self => 1|0 : require that all output elements at least be on the calling map [default is 1, has no effect when the second usage form is used] -required => \@maps : require that all output elements be on at least all the maps supplied here =cut sub common_elements { my ($self, $maps_ref, @extra_args) = @_; $self->throw("Must supply a reference first argument") unless ref($maps_ref); my @maps; if (ref($maps_ref) eq 'ARRAY') { @maps = @{$maps_ref}; } elsif ($maps_ref->isa('Bio::Map::MapI')) { @maps = ($maps_ref); } if (ref($self)) { unshift(@maps, $self); } $self->throw("Need at least 2 maps") unless @maps >= 2; my %args = (-min_num => 1, -min_percent => 100, -require_self => 1, -required => undef, @extra_args); my $min_num = $args{-min_num}; if ($args{-min_percent}) { my $mn = @maps / 100 * $args{-min_percent}; if ($mn > $min_num) { $min_num = $mn; } } my %required = map { $_ => 1 } $args{-required} ? @{$args{-required}} : (); $required{$self} = 1 if ref($self) && $args{-require_self}; my @required = keys %required; my %map_elements; my %elements; my %count; foreach my $map (@maps) { $map_elements{$map} = {}; foreach my $element ($map->get_elements) { $map_elements{$map}->{$element} = 1; $elements{$element} = $element; $count{$element}++; } } my @elements; ELEMENT: while (my ($key, $value) = each %elements) { $count{$key} >= $min_num or next; foreach my $required (@required) { exists $map_elements{$required}->{$key} or next ELEMENT; } push(@elements, $value); } return @elements; } =head2 MapI-specific methods =cut =head2 species Title : species Usage : my $species = $map->species; Function: Get/Set Species for a map Returns : L object Args : (optional) Bio::Species =cut sub species{ my $self = shift; $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 = shift; $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 = shift; $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 = shift; $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 0 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 = shift; $self->throw_not_implemented(); } 1;