Bio::Map
MapI
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Summary
Bio::Map::MapI - Interface for describing Map objects in bioperl
Package variables
No package variables defined.
Included modules
Inherit
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/
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.
Methods
Methods description
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 |
Title : get_positions
Usage : my @positions = $mappable->get_positions();
Function: Get all the Positions on this Map (sorted).
Returns : Array of Bio::Map::PositionI objects
Args : none for all, OR
Bio::Map::MappableI object for positions of the given Mappable |
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
Bio::Map::PositionI object to remove just that Position, OR
Bio::Map::MappableI object to remove only those positions of the
given mappable |
Title : get_elements
Usage : my @elements = $map->get_elements;
Function: Retrieves all the elements on a map (unordered)
Returns : Array of Map elements (Bio::Map::MappableI)
Args : none |
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 = Bio::Map::MapI 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 |
Title : species
Usage : my $species = $map->species;
Function: Get/Set Species for a map
Returns : Bio::Species object
Args : (optional) Bio::Species |
Title : units
Usage : $map->units('cM');
Function: Get/Set units for a map
Returns : units for a map
Args : units for a map (string) |
Title : type
Usage : my $type = $map->type
Function: Get/Set Map type
Returns : String coding map type
Args : (optional) string |
Title : name
Usage : my $name = $map->name
Function: Get/Set Map name
Returns : Map name
Args : (optional) string |
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 |
Methods code
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 $self->{_eh};} | sub get_positions
{ my ($self, $mappable) = @_;
my @positions = $self->get_position_handler->get_positions($mappable);
@positions = map { $_->[1] }
sort { $a->[0] <=> $b->[0] }
map { [$_->sortable, $_] }
@positions;
return @positions;} | sub purge_positions
{ my ($self, $thing) = @_;
$self->get_position_handler->purge_positions($thing);} | sub get_elements
{ my $self = shift;
return $self->get_position_handler->get_other_entities;} | sub common_elements
{ my ($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;} | sub species
{ my $self = shift;
$self->throw_not_implemented();} | sub units
{ my $self = shift;
$self->throw_not_implemented();} | sub type
{ my $self = shift;
$self->throw_not_implemented();} | sub name
{ my $self = shift;
$self->throw_not_implemented();} | sub length
{ my $self = shift;
$self->throw_not_implemented();
}
1;} | General documentation
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
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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.
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:
https://redmine.open-bio.org/projects/bioperl/
| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
These are fundamental to coordination of Maps and other entities, so are
implemented at the interface level
| PositionHandlerI-related methods | Top |
These are fundamental to coordination of Maps and other entities, so are
implemented at the interface level
Title : each_position
Function: Synonym of the get_positions() method.
Status : deprecated, will be removed in next version
Title : each_element
Function: Synonym of the get_elements() method.
Status : deprecated, will be removed in the next version