Bio::Map::PositionI(3pm)				User Contributed Perl Documentation				  Bio::Map::PositionI(3pm)

NAME

       Bio::Map::PositionI - Abstracts the notion of a position having a value in the context of a marker and a Map

SYNOPSIS

	   # do not use this module directly
	   # See Bio::Map::Position for an example of
	   # implementation.

DESCRIPTION

       This object stores one of the postions that a mappable object (e.g. Marker) may have in a map.

       Positions can have non-numeric values or other methods to store the locations, so they have a method numeric() which does the conversion.
       numeric() returns the position in a form that can be compared between other positions of the same type. It is not necessarily a value
       suitable for sorting positions (it may be the distance from the previous position); for that purpose the result of sortable() should be
       used.

       A 'position', in addition to being a single point, can also be an area and so can be imagined as a range and compared with other positions
       on the basis of overlap, intersection etc.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason-at-bioperl.org

CONTRIBUTORS

       Lincoln Stein, lstein-at-cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Sendu Bala, bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   EntityI methods
	These are fundamental to coordination of Positions and other entities, so are
	implemented at the interface level

   get_position_handler
	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

   PositionHandlerI-related methods
	These are fundamental to coordination of Positions and other entities, so are
	implemented at the interface level

   map
	Title	: map
	Usage	: my $map = $position->map();
		  $position->map($map);
	Function: Get/Set the map the position is in.
	Returns : L<Bio::Map::MapI>
	Args	: none to get
		  new L<Bio::Map::MapI> to set

   element
	Title	: element
	Usage	: my $element = $position->element();
		  $position->element($element);
	Function: Get/Set the element the position is for.
	Returns : L<Bio::Map::MappableI>
	Args	: none to get
		  new L<Bio::Map::MappableI> to set

   marker
	Title	: marker
	Function: This is a synonym of the element() method
	Status	: deprecated, will be removed in the next version

   PositionI-specific methods
   value
	Title	: value
	Usage	: my $pos = $position->value();
	Function: Get/Set the value for this position
	Returns : scalar, value
	Args	: [optional] new value to set

   numeric
	Title	: numeric
	Usage	: my $num = $position->numeric;
	Function: Read-only method that is guaranteed to return a numeric
		  representation of the start of this position.
	Returns : scalar numeric
	Args	: none to get the co-ordinate normally (see absolute() method), OR
		  Bio::Map::RelativeI to get the co-ordinate converted to be
		  relative to what this Relative describes.

   sortable
	Title	: sortable
	Usage	: my $num = $position->sortable();
	Function: Read-only method that is guaranteed to return a value suitable
		  for correctly sorting this kind of position amongst other positions
		  of the same kind on the same map. Note that sorting different kinds
		  of position together is unlikely to give sane results.
	Returns : numeric
	Args	: none

   relative
	 Title	 : relative
	 Usage	 : my $relative = $position->relative();
		   $position->relative($relative);
	 Function: Get/set the thing this Position's coordinates (numerical(), start(),
		   end()) are relative to, as described by a Relative object.
	 Returns : Bio::Map::RelativeI (default is one describing "relative to the
		   start of the Position's map")
	 Args	 : none to get, OR
		   Bio::Map::RelativeI to set

   absolute
	 Title	 : absolute
	 Usage	 : my $absolute = $position->absolute();
		   $position->absolute($absolute);
	 Function: Get/set how this Position's co-ordinates (numerical(), start(),
		   end()) are reported. When absolute is off, co-ordinates are
		   relative to the thing described by relative(). Ie. the value
		   returned by start() will be the same as the value you set start()
		   to. When absolute is on, co-ordinates are converted to be relative
		   to the start of the map.

		   So if relative() currently points to a Relative object describing
		   "relative to another position which is 100 bp from the start of
		   the map", this Position's start() had been set to 50 and absolute()
		   returns 1, $position->start() will return 150. If absolute() returns
		   0 in the same situation, $position->start() would return 50.

	 Returns : boolean (default 0)
	 Args	 : none to get, OR
		   boolean to set

   RangeI-based methods
   start
	 Title	 : start
	 Usage	 : my $start = $position->start();
		   $position->start($start);
	 Function: Get/set the start co-ordinate of this position.
	 Returns : the start of this position
	 Args	 : scalar numeric to set, OR
		   none to get the co-ordinate normally (see absolute() method), OR
		   Bio::Map::RelativeI to get the co-ordinate converted to be
		   relative to what this Relative describes.

   end
	 Title	 : end
	 Usage	 : my $end = $position->end();
		   $position->end($end);
	 Function: Get/set the end co-ordinate of this position.
	 Returns : the end of this position
	 Args	 : scalar numeric to set, OR
		   none to get the co-ordinate normally (see absolute() method), OR
		   Bio::Map::RelativeI to get the co-ordinate converted to be
		   relative to what this Relative describes.

   length
	 Title	 : length
	 Usage	 : $length = $position->length();
	 Function: Get the length of this position.
	 Returns : the length of this position
	 Args	 : none

   strand
	 Title	 : strand
	 Usage	 : $strand = $position->strand();
	 Function: Get the strand of this position; it is always 1 since maps to not
		   have strands.
	 Returns : 1
	 Args	 : none

   toString
	 Title	 : toString
	 Usage	 : print $position->toString(), "
";
	 Function: stringifies this range
	 Returns : a string representation of the range of this Position
	 Args	 : optional Bio::Map::RelativeI to have the co-ordinates reported
		   relative to the thing described by that Relative

RangeI-related methods
       These methods work by considering only the values of start() and end(), as modified by considering every such co-ordinate relative to the
       start of the map (ie. absolute(1) is set temporarily during the calculation), or any supplied Relative. For the boolean methods, when the
       comparison Position is on the same map as the calling Position, there is no point supplying a Relative since the answer will be the same as
       without. Relative is most useful when comparing Positions on different maps and you have a Relative that describes some special place on
       each map like 'the start of the gene', where the actual start of the gene relative to the start of the map is different for each map.

       The methods do not consider maps during their calculations - things on different maps can overlap/contain/intersect/etc. each other.

       The geometrical methods (intersect, union etc.) do things to the geometry of ranges, and return Bio::Map::PositionI compliant objects or
       triplets (start, stop, strand) from which new positions could be built. When a PositionI is made it will have a map transferred to it if
       all the arguments shared the same map.  If a Relative was supplied the result will have that same Relative.

       Note that the strand-testing args are there for compatibility with the RangeI interface. They have no meaning when only using PositionI
       objects since maps do not have strands. Typically you will just set the argument to undef if you want to supply the argument after it.

   equals
	 Title	 : equals
	 Usage	 : if ($p1->equals($p2)) {...}
	 Function: Test whether $p1 has the same start, end, length as $p2.
	 Returns : true if they are describing the same position (regardless of map)
	 Args	 : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
			    one to (mandatory)
		   arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
		   arg #3 = optional Bio::Map::RelativeI to ask if the Positions
			    equal in terms of their relative position to the thing
			    described by that Relative

   less_than
	Title	: less_than
	Usage	: if ($position->less_than($other_position)) {...}
	Function: Ask if this Position ends before another starts.
	Returns : boolean
	Args	: arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
			   one to (mandatory)
		  arg #2 = optional Bio::Map::RelativeI to ask if the Position is less
			   in terms of their relative position to the thing described
			   by that Relative

   greater_than
	Title	: greater_than
	Usage	: if ($position->greater_than($other_position)) {...}
	Function: Ask if this Position starts after another ends.
	Returns : boolean
	Args	: arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
			   one to (mandatory)
		  arg #2 = optional Bio::Map::RelativeI to ask if the Position is
			   greater in terms of their relative position to the thing
			   described by that Relative

   overlaps
	 Title	 : overlaps
	 Usage	 : if ($p1->overlaps($p2)) {...}
	 Function: Tests if $p1 overlaps $p2.
	 Returns : True if the positions overlap (regardless of map), false otherwise
	 Args	 : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
			    one to (mandatory)
		   arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
		   arg #3 = optional Bio::Map::RelativeI to ask if the Positions
			    overlap in terms of their relative position to the thing
			    described by that Relative
		   arg #4 = optional minimum percentage length of the overlap before
			    reporting an overlap exists (default 0)

   contains
	 Title	 : contains
	 Usage	 : if ($p1->contains($p2)) {...}
	 Function: Tests whether $p1 totally contains $p2.
	 Returns : true if the argument is totally contained within this position
		   (regardless of map), false otherwise
	 Args	 : arg #1 = a Bio::RangeI (eg. a Bio::Map::Position) to compare this
			    one to, or scalar number (mandatory)
		   arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
		   arg #3 = optional Bio::Map::RelativeI to ask if the Position
			    is contained in terms of their relative position to the
			    thing described by that Relative

   intersection
	Title	: intersection
	Usage	: ($start, $stop, $strand) = $p1->intersection($p2)
		  ($start, $stop, $strand) = Bio::Map::Position->intersection(@positions);
		  $mappable = $p1->intersection($p2, undef, $relative);
		  $mappable = Bio::Map::Position->intersection(@positions);
	Function: gives the range that is contained by all ranges
	Returns : undef if they do not overlap, OR
		  Bio::Map::Mappable object who's positions are the
		  cross-map-calculated intersection of the input positions on all the
		  maps that the input positions belong to, OR, in list context, a three
		  element array (start, end, strand)
	Args	: arg #1 = [REQUIRED] a Bio::RangeI (eg. a Bio::Map::Position) to
			   compare this one to, or an array ref of Bio::RangeI
		  arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
		  arg #3 = optional Bio::Map::RelativeI to ask how the Positions
			   intersect in terms of their relative position to the thing
			   described by that Relative

   union
	Title	: union
	Usage	: ($start, $stop, $strand) = $p1->union($p2);
		  ($start, $stop, $strand) = Bio::Map::Position->union(@positions);
		  my $mappable = $p1->union($p2);
		  my $mappable = Bio::Map::Position->union(@positions);
	Function: finds the minimal position/range that contains all of the positions
	Returns : Bio::Map::Mappable object who's positions are the
		  cross-map-calculated union of the input positions on all the maps
		  that the input positions belong to, OR, in list context, a three
		  element array (start, end, strand)
	Args	: a Bio::Map::PositionI to compare this one to, or a list of such
		  OR
		  a single Bio::Map::PositionI or array ref of such AND a
		  Bio::Map::RelativeI to ask for the Position's union in terms of their
		  relative position to the thing described by that Relative

   overlap_extent
	Title	: overlap_extent
	Usage	: ($a_unique,$common,$b_unique) = $a->overlap_extent($b)
	Function: Provides actual amount of overlap between two different
		  positions
	Example :
	Returns : array of values containing the length unique to the calling
		  position, the length common to both, and the length unique to
		  the argument position
	Args	: a position

   disconnected_ranges
	Title	: disconnected_ranges
	Usage	: my @disc_ranges = Bio::Map::Position->disconnected_ranges(@ranges);
	Function: Creates the minimal set of positions such that each input position is
		  fully contained by at least one output position, and none of the
		  output positions overlap.
	Returns : Bio::Map::Mappable with the calculated disconnected ranges
	Args	: a Bio::Map::PositionI to compare this one to, or a list of such,
		  OR
		  a single Bio::Map::PositionI or array ref of such AND a
		  Bio::Map::RelativeI to consider all Position's co-ordinates in terms
		  of their relative position to the thing described by that Relative,
		  AND, optionally, an int for the minimum percentage of overlap that
		  must be present before considering two ranges to be overlapping
		  (default 0)

perl v5.14.2							    2012-03-02						  Bio::Map::PositionI(3pm)