Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::LocationI - Abstract interface of a Location on a Sequence

SYNOPSIS

           # get a LocationI somehow
           printf( "start = %d, end = %d, strand = %s, seq_id = %s\n",
                   $location->start, $location->end, $location->strand,
                   $location->seq_id);
           print "location str is ", $location->to_FTstring(), "\n";

DESCRIPTION

       This Interface defines the methods for a Bio::LocationI, an object which encapsulates a
       location on a biological sequence.  Locations need not be attached to actual sequences as
       they are stand alone objects.  LocationI objects are used by Bio::SeqFeatureI objects to
       manage and represent locations for a Sequence Feature.

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 _

   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')
         Args    : none

   start
         Title   : start
         Usage   : $start = $location->start();
         Function: Get the start coordinate of this location as defined by
                   the currently active coordinate computation policy. In
                   simple cases, this will return the same number as
                   min_start() and max_start(), in more ambiguous cases like
                   fuzzy locations the number may be equal to one or neither
                   of both.

                   We override this here from RangeI in order to delegate
                   'get' to a L<Bio::Location::CoordinatePolicy> implementing
                   object.  Implementing classes may also wish to provide
                   'set' functionality, in which case they *must* override
                   this method. The implementation provided here will throw
                   an exception if called with arguments.

         Returns : A positive integer value.
         Args    : none

       See Bio::Location::CoordinatePolicy for more information

   end
         Title   : end
         Usage   : $end = $location->end();
         Function: Get the end coordinate of this location as defined by the
                   currently active coordinate computation policy. In simple
                   cases, this will return the same number as min_end() and
                   max_end(), in more ambiguous cases like fuzzy locations
                   the number may be equal to one or neither of both.

                   We override this here from Bio::RangeI in order to delegate
                   'get' to a L<Bio::Location::CoordinatePolicy> implementing
                   object. Implementing classes may also wish to provide
                   'set' functionality, in which case they *must* override
                   this method. The implementation provided here will throw
                   an exception if called with arguments.

         Returns : A positive integer value.
         Args    : none

       See Bio::Location::CoordinatePolicy and Bio::RangeI for more information

   min_start
         Title   : min_start
         Usage   : my $minstart = $location->min_start();
         Function: Get minimum starting point of feature.

                   Note that an implementation must not call start() in this method.

         Returns : integer or undef if no minimum starting point.
         Args    : none

   max_start
         Title   : max_start
         Usage   : my $maxstart = $location->max_start();
         Function: Get maximum starting point of feature.

                   Note that an implementation must not call start() in this method
                   unless start() is overridden such as not to delegate to the
                   coordinate computation policy object.

         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 encoded as text

                   Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100),
                   'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with
                   their meaning best explained by their GenBank/EMBL location string
                   encoding in brackets.

         Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
         Args    : none

   flip_strand
         Title   : flip_strand
         Usage   : $location->flip_strand();
         Function: Flip-flop a strand to the opposite
         Returns : None
         Args    : None

   min_end
         Title   : min_end
         Usage   : my $minend = $location->min_end();
         Function: Get minimum ending point of feature.

                   Note that an implementation must not call end() in this method
                   unless end() is overridden such as not to delegate to the
                   coordinate computation policy object.

         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 point of feature.

                   Note that an implementation must not call end() in this method
                   unless end() is overridden such as not to delegate to the
                   coordinate computation policy object.

         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 encoded as text.

                   Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100),
                   'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with
                   their meaning best explained by their GenBank/EMBL location string
                   encoding in brackets.

         Returns : string ('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 (a string)
         Args    : [optional] seq_id value to set

   is_remote
        Title   : is_remote
        Usage   : $is_remote_loc = $loc->is_remote()
        Function: Whether or not a location is a remote location.

                  A location is said to be remote if it is on a different
                  'object' than the object which 'has' this
                  location. Typically, features on a sequence will sometimes
                  have a remote location, which means that the location of
                  the feature is on a different sequence than the one that is
                  attached to the feature. In such a case, $loc->seq_id will
                  be different from $feat->seq_id (usually they will be the
                  same).

                  While this may sound weird, it reflects the location of the
                  kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
                  feature tables.

        Example :
        Returns : TRUE if the location is a remote location, and FALSE otherwise
        Args    : Value to set to

   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 L<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
                   L<Bio::Location::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 L<Bio::Location::CoordinatePolicyI> implementing object.
         Args    : On set, a L<Bio::Location::CoordinatePolicyI> implementing object.

       See Bio::Location::CoordinatePolicyI for more information

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

   each_Location
        Title   : each_Location
        Usage   : @locations = $locObject->each_Location($order);
        Function: Conserved function call across Location:: modules - will
                  return an array containing the component Location(s) in
                  that object, regardless if the calling object is itself a
                  single location or one containing sublocations.
        Returns : an array of Bio::LocationI implementing objects
        Args    : Optional sort order to be passed to sub_Location() for Splits

   valid_Location
        Title   : valid_Location
        Usage   : if ($location->valid_location) {...};
        Function: boolean method to determine whether location is considered valid
                  (has minimum requirements for a specific LocationI implementation)
        Returns : Boolean value: true if location is valid, false otherwise
        Args    : none