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Bio::Location::Atomic(User Contributed Perl DocumentatBio::Location::Atomic(3)

NAME
       Bio::Location::Atomic - Implementation of a Atomic Location on a
       Sequence

SYNOPSIS
	   use Bio::Location::Atomic;

	   my $location = Bio::Location::Atomic->new(-start => 1, -end => 100,
						    -strand => 1 );

	   if( $location->strand == -1 ) {
	       printf "complement(%d..%d)\n", $location->start, $location->end;
	   } else {
	       printf "%d..%d\n", $location->start, $location->end;
	   }

DESCRIPTION
       This is an implementation of Bio::LocationI to manage simple location
       information on a Sequence.

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 _

   start
	 Title	 : start
	 Usage	 : $start = $loc->start();
	 Function: get/set the start of this range
	 Returns : the start of this range
	 Args	 : optionaly allows the start to be set
		 : using $loc->start($start)

   end
	 Title	 : end
	 Usage	 : $end = $loc->end();
	 Function: get/set the end of this range
	 Returns : the end of this range
	 Args	 : optionaly allows the end to be set
		 : using $loc->end($start)

   strand
	 Title	 : strand
	 Usage	 : $strand = $loc->strand();
	 Function: get/set the strand of this range
	 Returns : the strandidness (-1, 0, +1)
	 Args	 : optionaly allows the strand to be set
		 : using $loc->strand($strand)

   flip_strand
	 Title	 : flip_strand
	 Usage	 : $location->flip_strand();
	 Function: Flip-flop a strand to the opposite
	 Returns : None
	 Args	 : None

   seq_id
	 Title	 : seq_id
	 Usage	 : my $seqid = $location->seq_id();
	 Function: Get/Set seq_id that location refers to
	 Returns : seq_id (a string)
	 Args	 : [optional] seq_id value to set

   length
	Title	: length
	Usage	: $len = $loc->length();
	Function: get the length in the coordinate space this location spans
	Example :
	Returns : an integer
	Args	: none

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

   max_start
	 Title	 : max_start
	 Usage	 : my $maxstart = $location->max_start();
	 Function: Get maximum starting location of feature startpoint.

		   In this implementation this is exactly the same as min_start().

	 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 <,>, ^).

		   In this implementation this will always be 'EXACT'.

	 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

		   In this implementation this is exactly the same as min_end().

	 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 <,>, ^)

		   In this implementation this will always be 'EXACT'.

	 Returns : type of position coded as text
		   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
	 Args	 : none

   location_type
	 Title	 : location_type
	 Usage	 : my $location_type = $location->location_type();
	 Function: Get location type encoded as text
	 Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
	 Args	 : none

   is_remote
	Title	: is_remote
	Usage	: $self->is_remote($newval)
	Function: Getset for is_remote value
	Returns : value of is_remote
	Args	: newvalue (optional)

   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 - for
		  Simple locations, the return value is just itself.
	Args	:

   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

   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 L<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
		   L<Bio::Location::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 L<Bio::Location::CoordinatePolicyI> implementing object.
	 Args	 : On set, a L<Bio::Location::CoordinatePolicyI> implementing object.

       See Bio::Location::CoordinatePolicyI for more information

   trunc
	 Title	 : trunc
	       Usage   : $trunc_location = $location->trunc($start, $end, $relative_ori);
	       Function: To truncate a location and keep annotations and features
			 within the truncated segment intact.

						       This might do things differently where the truncation
						       splits the location in half.
	       CAVEAT  : As yet, this is an untested and unannounced method. Use
			 with caution!
	       Returns : A L<Bio::Location::Atomic> object.
	       Args    : The start and end position for the trunction, and the relative
			 orientation.

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