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Bio::Location::FuzzyLocationI.3pm

NAME

Bio::Location::FuzzyLocationI - Abstract interface of a Location on a Sequence which has unclear start/end location

SYNOPSIS

     # Get a FuzzyLocationI object somehow
     print "Fuzzy FT location string is ", $location->to_FTstring();
     print "location is of the type ", $location->loc_type, "\n";
 
 

DESCRIPTION

This interface encapsulates 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://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 _

LocationI methods

location_type

   Title   : loc_type
   Usage   : my $location_type = $location->location_type();
   Function: Get location type encoded as text
   Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
   Args    : none
 
 

Bio::LocationI methods

Bio::LocationI methods follow

min_start

   Title   : min_start
   Usage   : my $minstart = $location->min_start();
   Function: Get minimum starting location of feature startpoint   
   Returns : integer or undef if no maximum starting point.
   Args    : none
 
 

max_start

   Title   : max_start
   Usage   : my $maxstart = $location->max_start();
   Function: Get maximum starting location of feature startpoint  
   Returns : integer or undef if no maximum starting point.
   Args    : none
 
 

start_pos_type

   Title   : start_pos_type
   Usage   : my $start_pos_type = $location->start_pos_type();
   Function: Get start position type (ie <,>, ^) 
   Returns : type of position coded as text 
             ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
   Args    : none
 
 

min_end

   Title   : min_end
   Usage   : my $minend = $location->min_end();
   Function: Get minimum ending location of feature endpoint 
   Returns : integer or undef if no minimum ending point.
   Args    : none
 
 

max_end

   Title   : max_end
   Usage   : my $maxend = $location->max_end();
   Function: Get maximum ending location of feature endpoint 
   Returns : integer or undef if no maximum ending point.
   Args    : none
 
 

end_pos_type

   Title   : end_pos_type
   Usage   : my $end_pos_type = $location->end_pos_type();
   Function: Get end position type (ie <,>, ^) 
   Returns : type of position coded as text 
             ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
   Args    : none
 
 

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: returns the FeatureTable string of this location
   Returns : string
   Args    : none