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