Bio::Location::Fuzzy(3User Contributed Perl DocumentatiBio::Location::Fuzzy(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 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
perl v5.14.1 2011-07-22 Bio::Location::Fuzzy(3)
