Bio::Map::Mappable - An object representing a generic map element that can have multiple locations in several maps.
# 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"; }
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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>
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
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
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
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
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
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
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
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
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
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
To install BioPerl, copy and paste the appropriate command in to your terminal.
cpanm
cpanm BioPerl
CPAN shell
perl -MCPAN -e shell install BioPerl
For more information on module installation, please visit the detailed CPAN module installation guide.