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 = new Bio::Location::Fuzzy(-start => '<30',
-end => 90,
-loc_type => '.');
print "location string is ", $fuzzylocation->to_FTstring(), "\n";
print "location is of the type ", $fuzzylocation->loc_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.
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://bio.perl.org/MailList.html - About the mailing listsReporting 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://bio.perl.org/bioperl-bugs/AUTHOR - Jason Stajich
Email jason@chg.mc.duke.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
loc_type
Title : loc_type
Usage : my $location_type = $location->loc_type();
Function: Get location type encoded as text
Returns : string ('EXACT', 'WITHIN', 'BETWEEN')
Args : noneLocationI 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 : nonestart
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 setmax_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 setstart_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 setmin_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 setmax_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 setend_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 setseq_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 setcoordinate_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