Bio::Map
MappableI
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Summary
Bio::Map::MappableI - An object that can be placed in a map
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# do not use this module directly
# See Bio::Map::Mappable for an example of
# implementation.
Description
This object handles the generic notion of an element placed on a
(linear) Map. A Mappable can have multiple positions in multiple maps, such as
is the case of Restriction enzyme cut sites on sequence maps. For exact
information about a mappable's position in a map one must query the associate
PositionI objects which are accessible through the get_positions() method.
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 : add_position
Usage : $mappable->add_position($position);
Function: Add a position to this mappable (defining where on which map it is).
Returns : n/a
Args : Bio::Map::PositionI object |
Title : get_positions
Usage : my @positions = $mappable->get_positions();
Function: Get all the Positions of this Mappable (sorted).
Returns : Array of Bio::Map::PositionI objects
Args : none for all, OR
Bio::Map::MapI object for positions on the given map, AND/OR some
other true value to avoid sorting |
Title : purge_positions
Usage : $mappable->purge_positions();
Function: Remove positions from this mappable.
Returns : n/a
Args : none to remove all positions, OR
Bio::Map::PositionI object to remove just that Position, OR
Bio::Map::MapI object to remove only those positions on the given
map |
Title : known_maps
Usage : my @maps = $marker->known_maps()
Function: Returns the maps that this mappable is found on
Returns : Array of Bio::Map::MapI objects
Args : none |
Title : name
Usage : my $name = $marker->name();
$marker->name($new_name);
Function: Get/Set the name for this Mappable.
Returns : A scalar representing the current name of this Mappable
Args : none to get
string to set |
Title : id
Usage : my $id = $marker->id();
$marker->id($new_id);
Function: Get/Set the id for this Mappable.
Returns : A scalar representing the current id of this Mappable
Args : none to get
string to set |
Title : in_map
Usage : if ($marker->in_map($map)) {...}
Function: Tests if this mappable is found on a specific map
Returns : boolean
Args : Bio::Map::MapI |
Title : equals
Usage : if ($mappable->equals($other_mappable)) {...}
my @equal_positions = $mappable->equals($other_mappable);
Function: Finds the positions in this mappable that are equal to any
comparison positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, the key => value pairs below
-map => Bio::Map::MapI : optionally a Map to only consider
positions on the given map
-relative => Bio::Map::RelativeI : optionally a Relative to ask if
the Positions equal in terms of
their relative position to the
thing described by that Relative |
Title : overlaps
Usage : if ($mappable->overlaps($other_mappable)) {...}
my @overlapping_positions = $mappable->overlaps($other_mappable);
Function: Finds the positions in this mappable that overlap with any
comparison positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, the key => value pairs below
-map => Bio::Map::MapI : optionally a Map to only consider
positions on the given map
-relative => Bio::Map::RelativeI : optionally a Relative to ask if
the Positions overlap in terms of
their relative position to the
thing described by that Relative |
Title : contains
Usage : if ($mappable->contains($other_mappable)) {...}
my @container_positions = $mappable->contains($other_mappable);
Function: Finds the positions in this mappable that contain any comparison
positions.
Returns : array of Bio::Map::PositionI objects
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to (mandatory)
arg #2 = optionally, the key => value pairs below
-map => Bio::Map::MapI : optionally a Map to only consider
positions on the given map
-relative => Bio::Map::RelativeI : optionally a Relative to ask if
the Positions contains in terms of
their relative position to the
thing described by that Relative |
Title : intersection
Usage : my $position = $mappable->intersection($other_mappable);
my $position = Bio::Map::Mappable->intersection(\@mappables);
Function: Make the position that is at the intersection of all positions of all
supplied mappables.
Returns : Bio::Map::PositionI object or undef (if not all positions overlap)
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to, or an array ref of such objects (mandatory)
arg #2 = optionally, the key => value pairs below
-map => Bio::Map::MapI : optionally a Map to only consider
positions on the given map
-relative => Bio::Map::RelativeI : optionally a Relative to to ask
how the Positions intersect in
terms of their relative position
to the thing described by that
Relative |
Title : union
Usage : my $position = $mappable->union($other_mappable);
my $position = Bio::Map::Mappable->union(@mappables);
Function: Make the minimal position that contains all of the positions of all
supplied mappables.
Returns : Bio::Map::PositionI object or undef (if not all positions overlap)
Args : arg #1 = Bio::Map::MappableI OR Bio::Map::PositionI to compare
this one to, or an array ref of such objects (mandatory)
arg #2 = optionally, the key => value pairs below
-map => Bio::Map::MapI : optionally a Map to only consider
positions on the given map
-relative => Bio::Map::RelativeI : optionally a Relative to to ask
if the union of the Positions in
terms of their relative position
to the thing described by that
Relative |
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 add_position
{ my $self = shift;
$self->get_position_handler->add_positions(@_); } | sub get_positions
{ my ($self, $thing, $no_sort) = @_;
my $map;
if (ref($thing) && $thing->isa('Bio::Map::MapI')) {
$map = $thing;
}
else {
$no_sort = $thing;
}
my @positions = $self->get_position_handler->get_positions($map);
return @positions if @positions == 1;
unless ($no_sort) {
@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 known_maps
{ my $self = shift;
return $self->get_position_handler->get_other_entities; } | sub name
{ my $self = shift;
$self->throw_not_implemented();} | sub id
{ my $self = shift;
$self->throw_not_implemented();} | sub in_map
{ my $self = shift;
$self->throw_not_implemented(); } | sub equals
{ my $self = shift;
$self->throw_not_implemented();} | sub overlaps
{ my $self = shift;
$self->throw_not_implemented();} | sub contains
{ my $self = shift;
$self->throw_not_implemented();} | sub intersection
{ my $self = shift;
$self->throw_not_implemented();} | sub union
{ 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
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bioperl-l@bioperl.org - General discussion
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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and
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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 Mappables and other entities, so are
implemented at the interface level
| PositionHandlerI-related methods | Top |
These are fundamental to coordination of Mappables 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
| MappableI-specific methods | Top |
| RangeI-related Methods | Top |
They throw an error if start and end are not defined in the Positions of the
Mappables supplied.