Bio::Location::Fuzzy - Implementation of a Location on a Sequence which has
unclear start and/or end locations
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";
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.
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.
[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
[email protected]
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.
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
Email jason-at-bioperl-dot-org
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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
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
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
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)
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)
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
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
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
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
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
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
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
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
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
Title : valid_Location
Usage : if ($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
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