Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has unclear start and/or end locations use Bio::Location::Fuzzy; my $fuzzylocation = new Bio::Location::Fuzzy(-start => '<30', -end => 90, -location_type => '..'); print "location string is ", $fuzzylocation->to_FTstring(), "\n"; print "location is of the type ", $fuzzylocation->location_type, "\n"; 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. 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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $fuzzyloc = new Bio::Location::Fuzzy( @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', 'BETWEEN') OR ( 1,2,3) -start_ext=> extension for start - defaults to 0, -start_fuz= fuzzy code for start can be ( 'EXACT', 'WITHIN', 'BETWEEN', 'BEFORE', 'AFTER') 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') 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', 'BETWEEN') Args : none

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') 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') 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 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: Get/Set seq_id that location refers to Returns : seq_id Args : [optional] seq_id value to set

_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