Bio::Location::Fuzzy.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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