Raw content of Bio::Map::OrderedPosition # BioPerl module for Bio::Map::OrderedPosition # # Cared for by Chad Matsalla <bioinformatics1@dieselwurks.com> # # Copyright Chad Matsalla # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Map::OrderedPosition - Abstracts the notion of a member of an ordered list of markers. Each marker is a certain distance from the one in the ordered list before it. =head1 SYNOPSIS use Bio::Map::OrderedPosition; # the first marker in the sequence my $position = new Bio::Map::OrderedPosition(-order => 1, -positions => [ [ $map, 22.3] ] ); # the second marker in the sequence, 15.6 units from the fist one my $position2 = new Bio::Map::OrderedPosition(-order => 2, -positions => [ [ $map, 37.9] ] ); # the third marker in the sequence, coincidental with the second # marker my $position3 = new Bio::Map::OrderedPosition(-order => 3, -posititions => [ [ $map, 37.9]] ); =head1 DESCRIPTION This object is an implementation of the PositionI interface and the Position object handles the specific values of a position. OrderedPosition is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO subsystem to create and then pass to a client application to bless into the proper type. For an example of how this is intended to work, see the Mapmaker.pm. No units are assumed here - units are handled by context of which Map a position is placed in. Se Bio::Map::Position for additional information. =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 - Chad Matsalla Email bioinformatics1@dieselwurks.com =head1 CONTRIBUTORS Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki@ebi.ac.uk Jason Stajich, jason@bioperl.org =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::OrderedPosition; use vars qw(@ISA); use strict; use Bio::Map::Position; @ISA = qw(Bio::Map::Position); =head2 new Title : new Usage : my $obj = new Bio::Map::OrderedPosition(); Function: Builds a new Bio::Map::OrderedPosition object Returns : Bio::Map::OrderedPosition Args : -order - The order of this position =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); # $self->{'_order'} = []; my ($map, $marker, $value, $order) = $self->_rearrange([qw( MAP MARKER VALUE ORDER )], @args); # print join ("|-|", ($map, $marker, $value, $order)), "\n"; $map && $self->map($map); $marker && $self->marker($marker); $value && $self->value($value); $order && $self->order($order); return $self; } =head2 order Title : order Usage : $o_position->order($new_position) _or_ $o_position->order() Function: get/set the order position of this position in a map Returns : Args : If $new_position is provided, the current position of this Position will be set to $new_position. =cut sub order { my ($self,$order) = @_; if ($order) { # no point in keeping the old ones $self->{'_order'} = $order; } return $self->{'_order'}; } =head2 Bio::Map::Position functions =cut =head2 known_maps Title : known_maps Usage : my @maps = $position->known_maps Function: Returns the list of maps that this position has values for Returns : list of Bio::Map::MapI unique ids Args : none =head2 in_map Title : in_map Usage : if ( $position->in_map($map) ) {} Function: Tests if a position has values in a specific map Returns : boolean Args : a map unique id OR Bio::Map::MapI =head2 each_position_value Title : positions Usage : my @positions = $position->each_position_value($map); Function: Retrieve a list of positions coded as strings or ints Returns : Array of position values for a Map Args : Bio::Map::MapI object to get positions for =head2 add_position_value Title : add_position_value Usage : $position->add_position_value($map,'100'); Function: Add a numeric or string position to the PositionI container and assoiciate it with a Bio::Map::MapI Returns : none Args : $map - Bio::Map::MapI String or Numeric coding for a position on a map =head2 purge_position_values Title : purge_position_values Usage : $position->purge_position_values Function: Remove all the position values stored for a position Returns : none Args : [optional] only purge values for a given map =head2 equals Title : equals Usage : if( $mappable->equals($mapable2)) ... Function: Test if a position is equal to another position. Returns : boolean Args : Bio::Map::PositionI =cut sub equals{ my ($self,$compare) = @_; return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition')); return ( $compare->order == $self->order); } # admittedly these are really the best comparisons in the world # but it is a first pass we'll need to refine the algorithm or not # provide general comparisions and require these to be implemented # by objects closer to the specific type of data =head2 less_than Title : less_than Usage : if( $mappable->less_than($m2) ) ... Function: Tests if a position is less than another position It is assumed that 2 positions are in the same map. Returns : boolean Args : Bio::Map::PositionI =cut sub less_than{ my ($self,$compare) = @_; return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition')); return ( $compare->order < $self->order); } =head2 greater_than Title : greater_than Usage : if( $mappable->greater_than($m2) ) ... Function: Tests if position is greater than another position. It is assumed that 2 positions are in the same map. Returns : boolean Args : Bio::Map::PositionI =cut sub greater_than{ my ($self,$compare) = @_; return 0 if ( ! defined $compare || ! $compare->isa('Bio::Map::OrderedPosition')); return ( $compare->order > $self->order); } 1;