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Bio::Map::Mappable(3) User Contributed Perl DocumentationBio::Map::Mappable(3)

NAME
       Bio::Map::Mappable - An object representing a generic map element that
       can have	multiple locations in several maps.

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
   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/wiki/Mailing_lists	- About	the mailing lists

   Support
       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.

   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 the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Sendu Bala
       Email bix@sendu.me.uk

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

perl v5.24.1			  2017-07-08		 Bio::Map::Mappable(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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