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Bio::Location::Split(3User Contributed Perl DocumentatiBio::Location::Split(3)

NAME
       Bio::Location::Split - Implementation of a Location on a Sequence which
       has multiple locations (start/end points)

SYNOPSIS
	   use Bio::Location::Split;

	   my $splitlocation = Bio::Location::Split->new();
	   $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>1,
								      -end=>30,
								      -strand=>1));
	   $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>50,
								      -end=>61,
								      -strand=>1));
	   my @sublocs = $splitlocation->sub_Location();

	   my $count = 1;
	   # print the start/end points of the sub locations
	   foreach my $location ( sort { $a->start <=> $b->start }
				  @sublocs ) {
	       printf "sub feature %d [%d..%d]\n",
		      $count, $location->start,$location->end, "\n";
	       $count++;
	   }

DESCRIPTION
       This implementation handles locations which span more than one
       start/end location, or and/or lie on different sequences, and can work
       with split locations that depend on the specific order of the
       sublocations ('join') or don't have a specific order but represent a
       feature spanning discontiguous sublocations ('order', 'bond').

       Note that the order in which sublocations are added may be very
       important, depending on the specific split location type.  For
       instance, a 'join' must have the sublocations added in the order that
       one expects to join the sublocations, whereas all other types are
       sorted based on the sequence location.

FEEDBACK
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to one
       of the Bioperl mailing lists.  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
       the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich
       Email jason-AT-bioperl_DOT_org

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

   each_Location
	Title	: each_Location
	Usage	: @locations = $locObject->each_Location($order);
	Function: Conserved function call across Location:: modules - will
		  return an array containing the component Location(s) in
		  that object, regardless if the calling object is itself a
		  single location or one containing sublocations.
	Returns : an array of Bio::LocationI implementing objects
	Args	: Optional sort order to be passed to sub_Location()

   sub_Location
	Title	: sub_Location
	Usage	: @sublocs = $splitloc->sub_Location();
	Function: Returns the array of sublocations making up this compound (split)
		  location. Those sublocations referring to the same sequence as
		  the root split location will be sorted by start position (forward
		  sort) or end position (reverse sort) and come first (before
		  those on other sequences).

		  The sort order can be optionally specified or suppressed by the
		  value of the first argument. The default is no sort.

	Returns : an array of Bio::LocationI implementing objects
	Args	: Optionally 1, 0, or -1 for specifying a forward, no, or reverse
		  sort order

   add_sub_Location
	Title	: add_sub_Location
	Usage	: $splitloc->add_sub_Location(@locationIobjs);
	Function: add an additional sublocation
	Returns : number of current sub locations
	Args	: list of Bio::LocationI implementing object(s) to add

   splittype
	 Title	 : splittype
	 Usage	 : $splittype = $location->splittype();
	 Function: get/set the split splittype
	 Returns : the splittype of split feature (join, order)
	 Args	 : splittype to set

   is_single_sequence
	 Title	 : is_single_sequence
	 Usage	 : if($splitloc->is_single_sequence()) {
		       print "Location object $splitloc is split ".
			     "but only across a single sequence\n";
		   }
	 Function: Determine whether this location is split across a single or
		   multiple sequences.

		   This implementation ignores (sub-)locations that do not define
		   seq_id(). The same holds true for the root location.

	 Returns : TRUE if all sublocations lie on the same sequence as the root
		   location (feature), and FALSE otherwise.
	 Args	 : none

   guide_strand
	 Title	 : guide_strand
	 Usage	 : $str = $loc->guide_strand();
	 Function: Get/Set the guide strand.  Of use only if the split type is
		   a 'join' (this helps determine the order of sublocation
			       retrieval)
	 Returns : value of guide strand (1, -1, or undef)
	 Args	 : new value (-1 or 1, optional)

LocationI methods
   strand
	Title	: strand
	Usage	: $obj->strand($newval)
	Function: For SplitLocations, setting the strand of the container
		  (this object) is a short-cut for setting the strand of all
		  sublocations.

		  In get-mode, checks if no sub-location is remote, and if
		  all have the same strand. If so, it returns that shared
		  strand value. Otherwise it returns undef.

	Example :
	Returns : on get, value of strand if identical between sublocations
		  (-1, 1, or undef)
	Args	: new value (-1 or 1, optional)

   flip_strand
	 Title	 : flip_strand
	 Usage	 : $location->flip_strand();
	 Function: Flip-flop a strand to the opposite.	Also switch Split strand
		   from undef to -1 or -1 to undef
	 Returns : None
	 Args	 : None

   start
	 Title	 : start
	 Usage	 : $start = $location->start();
	 Function: get the starting point of the first (sorted) sublocation
	 Returns : integer
	 Args	 : none

   end
	 Title	 : end
	 Usage	 : $end = $location->end();
	 Function: get the ending point of the last (sorted) sublocation
	 Returns : integer
	 Args	 : none

   min_start
	 Title	 : min_start
	 Usage	 : $min_start = $location->min_start();
	 Function: get the minimum starting point
	 Returns : the minimum starting point from the contained sublocations
	 Args	 : none

   max_start
	 Title	 : max_start
	 Usage	 : my $maxstart = $location->max_start();
	 Function: Get maximum starting location of feature startpoint
	 Returns : integer or undef if no maximum starting point.
	 Args	 : none

   start_pos_type
	 Title	 : start_pos_type
	 Usage	 : my $start_pos_type = $location->start_pos_type();
	 Function: Get start position type (ie <,>, ^)
	 Returns : type of position coded as text
		   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
	 Args	 : none

   min_end
	 Title	 : min_end
	 Usage	 : my $minend = $location->min_end();
	 Function: Get minimum ending location of feature endpoint
	 Returns : integer or undef if no minimum ending point.
	 Args	 : none

   max_end
	 Title	 : max_end
	 Usage	 : my $maxend = $location->max_end();
	 Function: Get maximum ending location of feature endpoint
	 Returns : integer or undef if no maximum ending point.
	 Args	 : none

   end_pos_type
	 Title	 : end_pos_type
	 Usage	 : my $end_pos_type = $location->end_pos_type();
	 Function: Get end position type (ie <,>, ^)
	 Returns : type of position coded as text
		   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
	 Args	 : none

   seq_id
	 Title	 : seq_id
	 Usage	 : my $seqid = $location->seq_id();
	 Function: Get/Set seq_id that location refers to

		   We override this here in order to propagate to all sublocations
		   which are not remote (provided this root is not remote either)
	 Returns : seq_id
	 Args	 : [optional] seq_id value to set

   coordinate_policy
	 Title	 : coordinate_policy
	 Usage	 : $policy = $location->coordinate_policy();
		   $location->coordinate_policy($mypolicy); # set may not be possible
	 Function: Get the coordinate computing policy employed by this object.

		   See Bio::Location::CoordinatePolicyI for documentation about
		   the policy object and its use.

		   The interface *does not* require implementing classes to accept
		   setting of a different policy. The implementation provided here
		   does, however, allow to do so.

		   Implementors of this interface are expected to initialize every
		   new instance with a CoordinatePolicyI object. The implementation
		   provided here will return a default policy object if none has
		   been set yet. To change this default policy object call this
		   method as a class method with an appropriate argument. Note that
		   in this case only subsequently created Location objects will be
		   affected.

	 Returns : A Bio::Location::CoordinatePolicyI implementing object.
	 Args	 : On set, a Bio::Location::CoordinatePolicyI implementing object.

   to_FTstring
	 Title	 : to_FTstring
	 Usage	 : my $locstr = $location->to_FTstring()
	 Function: returns the FeatureTable string of this location
	 Returns : string
	 Args	 : none

   valid_Location
	Title	: valid_Location
	Usage	: if ($location->valid_location) {...};
	Function: boolean method to determine whether location is considered valid
		  (has minimum requirements for Simple implementation)
	Returns : Boolean value: true if location is valid, false otherwise
	Args	: none

perl v5.14.1			  2011-07-22	       Bio::Location::Split(3)
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