Provided by: libbio-perl-perl_1.7.2-3_all bug

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