Bio::LocationI(3pm)					User Contributed Perl Documentation				       Bio::LocationI(3pm)

NAME

       Bio::LocationI - Abstract interface of a Location on a Sequence

SYNOPSIS

	   # get a LocationI somehow
	   printf( "start = %d, end = %d, strand = %s, seq_id = %s
",
		   $location->start, $location->end, $location->strand,
		   $location->seq_id);
	   print "location str is ", $location->to_FTstring(), "
";

DESCRIPTION

       This Interface defines the methods for a Bio::LocationI, an object which encapsulates a location on a biological sequence.  Locations need
       not be attached to actual sequences as they are stand alone objects.  LocationI objects are used by Bio::SeqFeatureI objects to manage and
       represent locations for a Sequence Feature.

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:

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

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 _

   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

   start
	 Title	 : start
	 Usage	 : $start = $location->start();
	 Function: Get the start coordinate of this location as defined by
		   the currently active coordinate computation policy. In
		   simple cases, this will return the same number as
		   min_start() and max_start(), in more ambiguous cases like
		   fuzzy locations the number may be equal to one or neither
		   of both.

		   We override this here from RangeI in order to delegate
		   'get' to a L<Bio::Location::CoordinatePolicy> implementing
		   object.  Implementing classes may also wish to provide
		   'set' functionality, in which case they *must* override
		   this method. The implementation provided here will throw
		   an exception if called with arguments.

	 Returns : A positive integer value.
	 Args	 : none

       See Bio::Location::CoordinatePolicy for more information

   end
	 Title	 : end
	 Usage	 : $end = $location->end();
	 Function: Get the end coordinate of this location as defined by the
		   currently active coordinate computation policy. In simple
		   cases, this will return the same number as min_end() and
		   max_end(), in more ambiguous cases like fuzzy locations
		   the number may be equal to one or neither of both.

		   We override this here from Bio::RangeI in order to delegate
		   'get' to a L<Bio::Location::CoordinatePolicy> implementing
		   object. Implementing classes may also wish to provide
		   'set' functionality, in which case they *must* override
		   this method. The implementation provided here will throw
		   an exception if called with arguments.

	 Returns : A positive integer value.
	 Args	 : none

       See Bio::Location::CoordinatePolicy and Bio::RangeI for more information

   min_start
	 Title	 : min_start
	 Usage	 : my $minstart = $location->min_start();
	 Function: Get minimum starting point of feature.

		   Note that an implementation must not call start() in this method.

	 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 point of feature.

		   Note that an implementation must not call start() in this method
		   unless start() is overridden such as not to delegate to the
		   coordinate computation policy object.

	 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 encoded as text

		   Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100),
		   'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with
		   their meaning best explained by their GenBank/EMBL location string
		   encoding in brackets.

	 Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
	 Args	 : none

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

   min_end
	 Title	 : min_end
	 Usage	 : my $minend = $location->min_end();
	 Function: Get minimum ending point of feature.

		   Note that an implementation must not call end() in this method
		   unless end() is overridden such as not to delegate to the
		   coordinate computation policy object.

	 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 point of feature.

		   Note that an implementation must not call end() in this method
		   unless end() is overridden such as not to delegate to the
		   coordinate computation policy object.

	 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 encoded as text.

		   Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100),
		   'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with
		   their meaning best explained by their GenBank/EMBL location string
		   encoding in brackets.

	 Returns : string ('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
	 Returns : seq_id (a string)
	 Args	 : [optional] seq_id value to set

   is_remote
	Title	: is_remote
	Usage	: $is_remote_loc = $loc->is_remote()
	Function: Whether or not a location is a remote location.

		  A location is said to be remote if it is on a different
		  'object' than the object which 'has' this
		  location. Typically, features on a sequence will sometimes
		  have a remote location, which means that the location of
		  the feature is on a different sequence than the one that is
		  attached to the feature. In such a case, $loc->seq_id will
		  be different from $feat->seq_id (usually they will be the
		  same).

		  While this may sound weird, it reflects the location of the
		  kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
		  feature tables.

	Example :
	Returns : TRUE if the location is a remote location, and FALSE otherwise
	Args	: Value to set to

   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

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

   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() for Splits

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

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