SYNOPSIS
# a map element in two different positions on the same map
$map1 = Bio::Map::SimpleMap->new();
$position1 = Bio::Map::Position->new(-map => $map1, -value => 100);
$position2 = Bio::Map::Position->new(-map => $map1, -value => 200);
$mappable = Bio::Map::Mappable->new(-positions => [$position1, $position2] );
# add another position on a different map
$map2 = Bio::Map::SimpleMap->new();
$position3 = Bio::Map::Position->new(-map => $map2, $value => 50);
$mappable->add_position($position3);
# get all the places our map element is found, on a particular map of interest
foreach $pos ($mappable->get_positions($map1)) {
print $pos->value, "\n";
}
DESCRIPTION
This object handles the notion of a generic map element. Mappables are entities with one or more positions on one or more maps.This object is a pure perl implementation of Bio::Map::MappableI. That interface implements some of its own methods so check the docs there for those.
FEEDBACK
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AUTHOR - Sendu Bala
Email [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new
Usage : my $mappable = Bio::Map::Mappable->new();
Function: Builds a new Bio::Map::Mappable object
Returns : Bio::Map::Mappable
Args : -name => string : name of the mappable element
-id => string : id of the mappable element
name
Title : name
Usage : $mappable->name($new_name);
my $name = $mappable->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
id
Title : id
Usage : my $id = $mappable->id();
$mappable->id($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
in_map
Title : in_map
Usage : if ($mappable->in_map($map)) {...}
Function: Tests if this mappable is found on a specific map
Returns : boolean
Args : L<Bio::Map::MapI>
Comparison methods
equals
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 L<Bio::Map::PositionI> objects
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
less_than
Title : less_than
Usage : if ($mappable->less_than($other_mappable)) {...}
my @lesser_positions = $mappable->less_than($other_mappable);
Function: Finds the positions in this mappable that are less than all
comparison positions.
Returns : array of L<Bio::Map::PositionI> objects
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
greater_than
Title : greater_than
Usage : if ($mappable->greater_than($other_mappable)) {...}
my @greater_positions = $mappable->greater_than($other_mappable);
Function: Finds the positions in this mappable that are greater than all
comparison positions.
Returns : array of L<Bio::Map::PositionI> objects
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
overlaps
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 L<Bio::Map::PositionI> objects
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
contains
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 L<Bio::Map::PositionI> objects
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> to compare
this one to (mandatory)
arg #2 = optionally, one or more of the key => value pairs below
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
overlapping_groups
Title : overlapping_groups
Usage : my @groups = $mappable->overlapping_groups($other_mappable);
my @groups = Bio::Map::Mappable->overlapping_groups(\@mappables);
Function: Look at all the positions of all the supplied mappables and group
them according to overlap.
Returns : array of array refs, each ref containing the Bio::Map::PositionI
objects that overlap with each other
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> 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
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
-min_pos_num => int : the minimum number of positions that must
be in a group before it will be returned
[default is 1]
-min_mappables_num => int : the minimum number of different
mappables represented by the
positions in a group before it
will be returned [default is 1]
-min_mappables_percent => number : as above, but the minimum
percentage of input mappables
[default is 0]
-min_map_num => int : the minimum number of different
maps represented by the positions
in a group before it will be
returned [default is 1]
-min_map_percent => number : as above, but the minimum
percentage of maps known by the
input mappables [default is 0]
-require_self => 1|0 : require that at least one of the
calling object's positions be in
each group [default is 1, has no
effect when the second usage form
is used]
-required => \@mappables : require that at least one position
for each mappable supplied in this
array ref be in each group
disconnected_intersections
Title : disconnected_intersections
Usage : @positions = $mappable->disconnected_intersections($other_mappable);
@positions = Bio::Map::Mappable->disconnected_intersections(\@mappables);
Function: Make the positions that are at the intersection of each group of
overlapping positions, considering all the positions of the supplied
mappables.
Returns : new Bio::Map::Mappable who's positions on maps are the calculated
disconnected unions
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> 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
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
-min_pos_num => int : the minimum number of positions that must
be in a group before the intersection will
be calculated and returned [default is 1]
-min_mappables_num => int : the minimum number of different
mappables represented by the
positions in a group before the
intersection will be calculated
and returned [default is 1]
-min_mappables_percent => number : as above, but the minimum
percentage of input mappables
[default is 0]
-min_map_num => int : the minimum number of different
maps represented by the positions
in a group before the intersection
will be calculated and returned
[default is 1]
-min_map_percent => number : as above, but the minimum
percentage of maps known by the
input mappables [default is 0]
-require_self => 1|0 : require that at least one of the
calling object's positions be in
each group [default is 1, has no
effect when the second usage form
is used]
-required => \@mappables : require that at least one position
for each mappable supplied in this
array ref be in each group
disconnected_unions
Title : disconnected_unions
Usage : my @positions = $mappable->disconnected_unions($other_mappable);
my @positions = Bio::Map::Mappable->disconnected_unions(\@mappables);
Function: Make the positions that are the union of each group of overlapping
positions, considering all the positions of the supplied mappables.
Returns : new Bio::Map::Mappable who's positions on maps are the calculated
disconnected unions
Args : arg #1 = L<Bio::Map::MappableI> OR L<Bio::Map::PositionI> 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
-map => MapI : a Bio::Map::MapI to only consider positions
on the given map
-relative => RelativeI : a Bio::Map::RelativeI to calculate in terms
of each Position's relative position to the
thing described by that Relative
-min_pos_num => int : the minimum number of positions that must
be in a group before the union will be
calculated and returned [default is 1]
-min_mappables_num => int : the minimum number of different
mappables represented by the
positions in a group before the
union will be calculated and
returned [default is 1]
-min_mappables_percent => number : as above, but the minimum
percentage of input mappables
[default is 0]
-min_map_num => int : the minimum number of different
maps represented by the positions
in a group before the union will
be calculated and returned
[default is 1]
-min_map_percent => number : as above, but the minimum
percentage of maps known by the
input mappables [default is 0]
-require_self => 1|0 : require that at least one of the
calling object's positions be in
each group [default is 1, has no
effect when the second usage form
is used]
-required => \@mappables : require that at least one position
for each mappable supplied in this
array ref be in each group
tuple
Title : tuple
Usage : Do Not Use!
Function: tuple was supposed to be a private method; this method no longer
does anything
Returns : warning
Args : none
Status : deprecated, will be removed in next version
annotation
Title : annotation
Usage : $mappable->annotation($an_col);
my $an_col = $mappable->annotation();
Function: Get the annotation collection (see Bio::AnnotationCollectionI)
for this annotatable object.
Returns : a Bio::AnnotationCollectionI implementing object, or undef
Args : none to get, OR
a Bio::AnnotationCollectionI implementing object to set