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Bio::Location::FuzzyLoUseroContributed Perl DoBio::Location::FuzzyLocationI(3)

NAME
       Bio::Location::FuzzyLocationI - Abstract	interface of a Location	on a
       Sequence	which has unclear start/end location

SYNOPSIS
	   # Get a FuzzyLocationI object somehow
	   print "Fuzzy	FT location string is ", $location->to_FTstring();
	   print "location is of the type ", $location->loc_type, "\n";

DESCRIPTION
       This interface encapsulates the necessary methods for representing a
       Fuzzy Location, one that	does not have clear start and/or end points.
       This will initially serve to handle features from Genbank/EMBL feature
       tables that are written as 1^100	meaning	between	bases 1	and 100	or
       <100..300 meaning it starts somewhere before 100.  Advanced
       implementations of this interface may be	able to	handle the necessary
       logic of	overlaps/intersection/contains/union.  It was constructed to
       handle fuzzy locations that can be represented in Genbank/EMBL.

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

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 _

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

Bio::LocationI methods
       Bio::LocationI methods follow

   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 maximum starting point.
	 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
	 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	one 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

perl v5.32.1			  2019-12-07  Bio::Location::FuzzyLocationI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX | LocationI methods | Bio::LocationI methods

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