/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Location::FuzzyLocationI

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:

https://github.com/bioperl/bioperl-live/issues

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 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.

to_FTstring

Title   : to_FTstring
Usage   : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args    : none