Raw content of Bio::Map::Marker
<![CDATA[# BioPerl module for Bio::Map::Marker
#
# 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::Marker - An central map object representing a generic marker
that can have multiple location in several maps.
=head1 SYNOPSIS
# get map objects somehow
# a marker with complex localisation
$o_usat = new Bio::Map::Marker (-name=>'Chad Super Marker 2',
-positions => [ [$map1, $position1],
[$map1, $position2]
] );
# The markers deal with Bio::Map::Position objects which can also
# be explicitely created and passed on to markers as an array ref:
$o_usat2 = new Bio::Map::Marker (-name=>'Chad Super Marker 3',
-positions => [ $pos1,
$pos2
] );
# a marker with unique position in a map
$marker1 = new Bio::Map::Marker (-name=>'hypervariable1',
-map => $map1,
-position => 100
)
# an other way of creating a marker with unique position in a map:
$marker2 = new Bio::Map::Marker (-name=>'hypervariable2');
$map1->add_marker($marker2);
$marker2->position(100);
# position method is a short cut for get/set'ing unigue positions
# which overwrites previous values
# to place a marker to other maps or to have multiple positions
# for a map within the same map use add_position()
$marker2->add_position(200); # new position in the same map
$marker2->add_position($map2,200); # new map
# setting a map() in a marker or adding a marker into a map are
# identical mathods. Both set the bidirectional connection which is
# used by the marker to remember its latest, default map.
# Regardes of how marker positions are created, they are stored and
# returned as Bio::Map::PositionI objects:
# unique position
print $marker1->position->value, "\n";
# several positions
foreach $pos ($marker2->each_position($map1)) {
print $pos->value, "\n";
}
See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
=head1 DESCRIPTION
This object handles the notion of a generic marker. This marker will
have a name and a position in a map.
This object is intended to be used by a marker parser like Mapmaker.pm
and then blessed into the proper type of marker (ie Microsatellite) by
the calling script.
=head2 Design principles
A Marker is a central object in Bio::Map name space. A Map is a holder
class for objects. A Marker has a Position in a Map. A Marker can be
compared to an other Markers using boolean methods. Positions can have
non-numeric values or other methods to store the locations, so they
have a method numeric() which does the conversion.
A Marker has a convinience method position() which is able to create
Positions of required class from scalars by calling method
get_position_object().
For more complex situations, a Marker can have multiple positions in
multiple Maps. It is therefore possible to extract Positions (all or
belonging to certain Map) and compare Markers to them. It is up to the
programmer to make sure position values and Maps they belong to can be
sensibly compared.
=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
Heikki Lehvaslaiho heikki@ebi.ac.uk
Lincoln Stein lstein@cshl.org
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::Marker;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Map::MarkerI;
use Bio::Map::Position;
@ISA = qw(Bio::Root::Root Bio::Map::MarkerI);
=head2 new
Title : new
Usage : $o_marker = new Bio::Map::Marker( -name => 'Whizzy marker',
-position => $position);
Function: Builds a new Bio::Map::Marker object
Returns : Bio::Map::Marker
Args :
-name => name of this microsatellite
[optional], string,default 'Unknown'
-positions => map position for this marker, [optional]
Bio::Map::PositionI-inherited obj, no default)
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_positions'} = [];
my ($name, $map, $position, $positions) =
$self->_rearrange([qw(NAME
MAP
POSITION
POSITIONS
)], @args);
if ($name) { $self->name($name); }
else {$self->name('Unnamed marker'); }
$position && $self->position($position);
$positions && $self->positions($positions);
$map && $self->map($map);
return $self;
}
=head2 name
Title : name
Usage : $o_usat->name($new_name) _or_
my $name = $o_usat->name()
Function: Get/Set the name for this Microsatellite
Returns : A scalar representing the current name of this marker
Args : If provided, the current name of this marker
will be set to $new_name.
=cut
sub name {
my ($self,$name) = @_;
my $last = $self->{'_name'};
if ($name) {
$self->{'_name'} = $name;
}
return $last;
}
=head2 map
Title : map
Usage : my $mymap = $marker->map();
Function: Get/Set the default map for the marker.
This is set by L<Bio::Map::CytoMap::add_element> method
Returns : L<Bio::Map::MapI>
Args : [optional] new L<Bio::Map::MapI>
=cut
sub map {
my ($self,$map) = @_;
if( defined $map ) {
$self->thow('This is [$map], not Bio::Map::MapI object')
unless $map->isa('Bio::Map::MapI');
$self->{'_default_map'} = $map;
}
return $self->{'_default_map'};
}
=head2 get_position_object
Title : get_position_class
Usage : my $pos = $marker->get_position_object();
Function: To get an object of the default Position class
for this Marker. Subclasses should redefine this method.
The Position needs to be Bio::Map::PositionI.
Returns : Bio::Map::Position
Args : none
See L<Bio::Map::Position> and L<Bio::Map::PositionI> for more information.
=cut
sub get_position_object {
my ($self) = @_;
return new Bio::Map::Position();
}
=head2 position
Title : position
Usage : $position = $mappable->position($map); OR
$mappable->position($position); # $position can be Bio::Map::PositionI
$mappable->position(100); # or scalar if the marker has a default map
$mappable->position($map, 100); # if not give explicit $map
Function: Get/Set the Bio::Map::PositionI for a mappable element
in a specific Map
Adds the marker to a map automatically if Map is given.
Altenaitvely, you can add the merker to the map first
(L<Bio::Map::Map::add_element>) to set the default map
Returns : Bio::Map::PositionI
Args : $position - Bio::Map::PositionI # Position we want to set
OR
$map - Bio::Map::MapI AND
scalar
OR
scalar, but only if the marker has been added to a map
=cut
sub position {
my ($self, $pos, $secondary_pos) = @_;
my ($map);
POS: {
if ($pos) {
if (ref($pos) eq 'SCALAR' || ref($pos) eq '') {
$map = $self->map;
}
elsif (ref($pos) eq 'ARRAY') {
$map = $pos->[0];
$pos = $pos->[1];
}
elsif ($pos->isa('Bio::Map::PositionI')) {
$pos->marker($self);
$self->purge_positions;
$self->add_position($pos);
$map = $pos->map;
$map->add_element($self) unless defined($self->map) && $self->map eq $map;
last POS;
}
elsif ($pos->isa('Bio::Map::MapI')) {
$map = $pos;
$pos = $secondary_pos;
} else {
$map = $self->map;
}
$self->throw("You need to add a marker to a map before ".
"you can set positions without explicit map!" )
unless $map;
$self->throw("Position better be scalar, not [$pos=". ref($pos) ."]")
unless ref($pos) eq 'SCALAR' || ref($pos) eq '';
my $newpos = $self->get_position_object;
$newpos->map($map);
$newpos->value($pos);
$newpos->marker($self);
$map->add_element($self) unless defined($self->map) && $self->map eq $map;
$self->purge_positions;
$self->add_position($newpos)
}
}
my @array = $self->each_position();
$self->warn('More than one value is associated with this position')
if scalar @array > 1;
return $array[0];
}
=head2 add_position
Title : add_position
Usage : $position->add_position($position)
Function: Add the Position to the Marker container.
If you are using this method, you need to
add the Marker to the Map yourself
Returns : none
Args : Position - Reference to Bio::Map::PositionI
=cut
sub add_position{
my ($self, $pos) = @_;
$self->throw("Must give a Position") unless defined $pos;
$self->throw("Must give a Bio::Map::PositionI, not [". ref($pos) ."]")
unless $pos->isa('Bio::Map::PositionI');
my $map = $pos->map;
$map->add_element($self) unless defined($self->map) && $self->map eq $map;
push @{$self->{'_positions'}}, $pos;
}
=head2 positions
Title : positions
Usage : $mappable->positions([$pos1, $pos2, $pos3]);
Function: Add multiple Bio::Map::PositionI for a mappable element
in a Map.
Returns : boolean
Args : array ref of $map/value tuples or array ref of Positions
=cut
sub positions {
my ($self, $arrayref) = @_;
my ($map);
$self->throw_not_implemented();
}
=head2 each_position
Title : each_position
Usage : my @positions = $position->each_position('mapname');
Function: Retrieve a list of Positions
Returns : Array of L<Bio::Map::PositionI>
Args : none
=cut
sub each_position {
my ($self,$mapname) = @_;
$self->warn("Retrieving positions in a named map only is ".
"not implemented. Getting all.") if $mapname;
return @{$self->{'_positions'}};
}
=head2 purge_positions
Title : purge_positions
Usage : $marker->purge_positions
Function: Remove all the position values stored for a Marker
Returns : none
Args : [optional] only purge values for a given map
=cut
sub purge_positions{
my ($self, $map) = @_;
$self->warn("Retrieving positions in a named map only, not implemented ") if $map;
$self->{'_positions'} = [];
}
=head2 known_maps
Title : known_maps
Usage : my @maps = $marker->known_maps
Function: Returns the list of maps that this position has values for
Returns : list of Bio::Map::MapI unique ids
Args : none
=cut
sub known_maps{
my ($self) = @_;
my %hash;
foreach my $pos ($self->each_position) {
$hash{$pos->map->unique_id} = 1;
}
return keys %hash;
}
=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
=cut
sub in_map{
my ($self,$map) = @_;
$self->throw("Need an argument") unless $map;
if (ref($map) && $map->isa('Bio::Map::MapI')) {
foreach my $pos ($self->each_position) {
return 1 if $pos->map eq $map;
}
} else { # assuming a scalar
foreach my $pos ($self->each_position) {
return 1 if $pos->map->unique_id eq $map;
}
}
return 0;
}
=head2 Comparison methods
=cut
=head2 tuple
Title : tuple
Usage : ($me, $you) = $self->_tuple($compare)
Function: Utility ethod to extract numbers and test for missing values.
Returns : tuple values
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub tuple {
my ($self,$compare) = @_;
my ($me, $you) = (-1, -1);
$self->warn("Trying to compare [". $self->name. "] to nothing.") &&
return ($me, $you) unless defined $compare;
$self->warn("[". $self->name. "] has no position.") &&
return ($me, $you) unless $self->position;
$me = $self->position->numeric;
if( $compare->isa('Bio::Map::MappableI') ){
$self->warn("[". $compare->name. "] has no position.") &&
return ($me, $you) unless $compare->position;
$you = $compare->position->numeric;
return ($me, $you);
} elsif( $compare->isa('Bio::Map::PositionI') ) {
$you = $compare->numeric;
return ($me, $you);
} else {
$self->warn("Can only run equals with Bio::Map::MappableI or ".
"Bio::Map::PositionI not [$compare]");
}
return ($me, $you);
}
=head2 equals
Title : equals
Usage : if( $mappable->equals($mapable2)) ...
Function: Test if a position is equal to another position
Returns : boolean
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub equals {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 if $me == -1 or $you == -1 ;
return $me == $you;
}
=head2 less_than
Title : less_than
Usage : if( $mappable->less_than($m2) ) ...
Function: Tests if a position is less than another position
Returns : boolean
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub less_than {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 if $me == -1 or $you == -1 ;
return $me < $you;
}
=head2 greater_than
Title : greater_than
Usage : if( $mappable->greater_than($m2) ) ...
Function: Tests if position is greater than another position
Returns : boolean
Args : Bio::Map::MappableI or Bio::Map::PositionI
=cut
sub greater_than {
my ($self,$compare) = @_;
my ($me, $you) = $self->tuple($compare);
return 0 if $me == -1 or $you == -1 ;
return $me > $you;
}
1;
]]>