Bio::Location::SplitLocationI(3p)

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