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

NAME

       Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has
       multiple locations (start/end points)

SYNOPSIS

         # get a SplitLocationI somehow
           print $splitlocation->start, "..", $splitlocation->end, "\n";
           my @sublocs = $splitlocation->sub_Location();

           my $count = 1;
           # print the start/end points of the sub locations
           foreach my $location ( sort { $a->start <=> $b->start }  @sublocs ) {
                       printf "sub feature %d [%d..%d]\n", $location->start,$location->end;
               $count++;
           }

DESCRIPTION

       This interface encapsulates the necessary methods for representing the location of a
       sequence feature that has more that just a single start/end pair.  Some examples of this
       are the annotated exons in a gene or the annotated CDS in a sequence file.

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 _

   sub_Location
        Title   : sub_Location
        Usage   : @locations = $feat->sub_Location();
        Function: Returns an array of LocationI objects
        Returns : An array
        Args    : none

   splittype
         Title   : splittype
         Usage   : $splittype = $fuzzy->splittype();
         Function: get/set the split splittype
         Returns : the splittype of split feature (join, order)
         Args    : splittype to set

   is_single_sequence
         Title   : is_single_sequence
         Usage   : if($splitloc->is_single_sequence()) {
                       print "Location object $splitloc is split ".
                             "but only across a single sequence\n";
                   }
         Function: Determine whether this location is split across a single or
                   multiple sequences.
         Returns : TRUE if all sublocations lie on the same sequence as the root
                   location (feature), and FALSE otherwise.
         Args    : none

Bio::LocationI methods

       Bio::LocationI inherited 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