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Manual Reference Pages  -  BIO::LOCATION::FUZZYLOCATIONI (3)

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NAME

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

CONTENTS

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 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



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perl v5.20.3 BIO::LOCATION::FUZZYLOCATIONI (3) 2016-04-05

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