Provided by: libbio-perl-perl_1.7.6-3_all bug

NAME

       Bio::Location::Split - Implementation of a Location on a Sequence which has multiple
       locations (start/end points)

SYNOPSIS

           use Bio::Location::Split;

           my $splitlocation = Bio::Location::Split->new();
           $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>1,
                                                                      -end=>30,
                                                                      -strand=>1));
           $splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>50,
                                                                      -end=>61,
                                                                      -strand=>1));
           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",
                      $count, $location->start,$location->end, "\n";
               $count++;
           }

DESCRIPTION

       This implementation handles locations which span more than one start/end location, or
       and/or lie on different sequences, and can work with split locations that depend on the
       specific order of the sublocations ('join') or don't have a specific order but represent a
       feature spanning noncontiguous sublocations ('order', 'bond').

       Note that the order in which sublocations are added may be very important, depending on
       the specific split location type.  For instance, a 'join' must have the sublocations added
       in the order that one expects to join the sublocations, whereas all other types are sorted
       based on the sequence location.

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 _

   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()

   sub_Location
        Title   : sub_Location
        Usage   : @sublocs = $splitloc->sub_Location();
        Function: Returns the array of sublocations making up this compound (split)
                  location. Those sublocations referring to the same sequence as
                  the root split location will be sorted by start position (forward
                  sort) or end position (reverse sort) and come first (before
                  those on other sequences).

                  The sort order can be optionally specified or suppressed by the
                  value of the first argument. The default is no sort.

        Returns : an array of Bio::LocationI implementing objects
        Args    : Optionally 1, 0, or -1 for specifying a forward, no, or reverse
                  sort order

   add_sub_Location
        Title   : add_sub_Location
        Usage   : $splitloc->add_sub_Location(@locationIobjs);
        Function: add an additional sublocation
        Returns : number of current sub locations
        Args    : list of Bio::LocationI implementing object(s) to add

   splittype
         Title   : splittype
         Usage   : $splittype = $location->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.

                   This implementation ignores (sub-)locations that do not define
                   seq_id(). The same holds true for the root location.

         Returns : TRUE if all sublocations lie on the same sequence as the root
                   location (feature), and FALSE otherwise.
         Args    : none

   guide_strand
         Title   : guide_strand
         Usage   : $str = $loc->guide_strand();
         Function: Get/Set the guide strand.  Of use only if the split type is
                   a 'join' (this helps determine the order of sublocation
                               retrieval)
         Returns : value of guide strand (1, -1, or undef)
         Args    : new value (-1 or 1, optional)

LocationI methods

   strand
        Title   : strand
        Usage   : $obj->strand($newval)
        Function: For SplitLocations, setting the strand of the container
                  (this object) is a short-cut for setting the strand of all
                  sublocations.

                  In get-mode, checks if no sub-location is remote, and if
                  all have the same strand. If so, it returns that shared
                  strand value. Otherwise it returns undef.

        Example :
        Returns : on get, value of strand if identical between sublocations
                  (-1, 1, or undef)
        Args    : new value (-1 or 1, optional)

   flip_strand
         Title   : flip_strand
         Usage   : $location->flip_strand();
         Function: Flip-flop a strand to the opposite.  Also sets Split strand
                   to be consistent with the sublocation strands
                   (1, -1 or undef for mixed strand values)
         Returns : None
         Args    : None

   start
         Title   : start
         Usage   : $start = $location->start();
         Function: get the starting point of the first (sorted) sublocation
         Returns : integer
         Args    : none

   end
         Title   : end
         Usage   : $end = $location->end();
         Function: get the ending point of the last (sorted) sublocation
         Returns : integer
         Args    : none

   min_start
         Title   : min_start
         Usage   : $min_start = $location->min_start();
         Function: get the minimum starting point
         Returns : the minimum starting point from the contained sublocations
         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

   length
        Title   : length
        Usage   : $len = $loc->length();
        Function: get the length in the coordinate space this location spans
        Example :
        Returns : an integer
        Args    : none

   seq_id
         Title   : seq_id
         Usage   : my $seqid = $location->seq_id();
         Function: Get/Set seq_id that location refers to

                   We override this here in order to propagate to all sublocations
                   which are not remote (provided this root is not remote either)
         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

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