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

NAME
       Bio::Location::Fuzzy - Implementation of	a Location on a	Sequence which
       has unclear start and/or	end locations

SYNOPSIS
	   use Bio::Location::Fuzzy;
	   my $fuzzylocation = Bio::Location::Fuzzy->new(
							-start => '<30',
							-end   => 90,
							-location_type => '..');

	   print "location string is ",	$fuzzylocation->to_FTstring(), "\n";
	   print "location is of the type ", $fuzzylocation->location_type, "\n";

DESCRIPTION
       This module contains 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 and
       Swissprot.

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 _

   new
	Title	: new
	Usage	: my $fuzzyloc = Bio::Location::Fuzzy->new( @args);
	Function:
	Returns	:
	Args	: -start    => value for start	(initialize by superclass)
		  -end	    => value for end	(initialize by superclass)
		  -strand   => value for strand	(initialize by superclass)
		  -location_type => either ('EXACT','WITHIN','IN-BETWEEN',
				    'UNCERTAIN') OR ( 1,2,3,4)
		  -start_ext=> extension for start - defaults to 0,
		  -start_fuz=  fuzzy code for start can	be
			     ('EXACT','WITHIN','BETWEEN','BEFORE','AFTER',
			      'UNCERTAIN' ) OR
			     a value 1 - 5 corresponding to index+1 above
		  -end_ext=> extension for end - defaults to 0,
		  -end_fuz=  fuzzy code	for end	can be
			     ('EXACT','WITHIN','BETWEEN','BEFORE','AFTER',
			      'UNCERTAIN') OR
			     a value 1 - 5 corresponding to index+1 above

   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', 'UNCERTAIN')
	 Args	 : none

LocationI methods
   length
	 Title	 : length
	 Usage	 : $length = $fuzzy_loc->length();
	 Function: Get the length of this location.

		   Note	that the length	of a fuzzy location will always	depend
		   on the currently active interpretation of start and end. The
		   result will therefore vary for different CoordinatePolicy objects.

	 Returns : an integer
	 Args	 : none

   start
	 Title	 : start
	 Usage	 : $start = $fuzzy->start();
	 Function: get/set start of this range,	handling fuzzy_starts
	 Returns : a positive integer representing the start of	the location
	 Args	 : start location on set (can be fuzzy point string)

   end
	 Title	 : end
	 Usage	 : $end	= $fuzzy->end();
	 Function: get/set end of this range, handling fuzzy_ends
	 Returns : a positive integer representing the end of the range
	 Args	 : end location	on set (can be fuzzy string)

   min_start
	 Title	 : min_start
	 Usage	 : $min_start =	$fuzzy->min_start();
	 Function: get/set the minimum starting	point
	 Returns : the minimum starting	point from the contained sublocations
	 Args	 : integer or undef on set

   max_start
	 Title	 : max_start
	 Usage	 : my $maxstart	= $location->max_start();
	 Function: Get/set maximum starting location of	feature	startpoint
	 Returns : integer or undef if no maximum starting point.
	 Args	 : integer or undef on set

   start_pos_type
	 Title	 : start_pos_type
	 Usage	 : my $start_pos_type =	$location->start_pos_type();
	 Function: Get/set start position type.
	 Returns : type	of position coded as text
		   ('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN')
	 Args	 : a string on set

   min_end
	 Title	 : min_end
	 Usage	 : my $minend =	$location->min_end();
	 Function: Get/set minimum ending location of feature endpoint
	 Returns : integer or undef if no minimum ending point.
	 Args	 : integer or undef on set

   max_end
	 Title	 : max_end
	 Usage	 : my $maxend =	$location->max_end();
	 Function: Get/set maximum ending location of feature endpoint
	 Returns : integer or undef if no maximum ending point.
	 Args	 : integer or undef on set

   end_pos_type
	 Title	 : end_pos_type
	 Usage	 : my $end_pos_type = $location->end_pos_type();
	 Function: Get/set end position	type.
	 Returns : type	of position coded as text
		   ('BEFORE','AFTER','EXACT','WITHIN','BETWEEN','UNCERTAIN')
	 Args	 : a string on set

   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.

       See Bio::Location::CoordinatePolicyI

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

   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

   _fuzzypointdecode
	 Title	 : _fuzzypointdecode
	 Usage	 : ($type,$min,$max) = $self->_fuzzypointdecode('<5');
	 Function: Decode a fuzzy string.
	 Returns : A 3-element array consisting	of the type of location, the
		   minimum integer, and	the maximum integer describing the range
		   of coordinates this start or	endpoint refers	to. Minimum or
		   maximum coordinate may be undefined.
		 : Returns empty array on fail.
	 Args	 : fuzzypoint string

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

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

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