Ewan Birney


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


    use Bio::Location::Split;

    my $splitlocation = new Bio::Location::Split();
    $splitlocation->add_sub_Location(new Bio::Location::Simple(-start=>1,
    $splitlocation->add_sub_Location(new Bio::Location::Simple(-start=>50,
    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";


This implementation handles locations which span more than one start/end location, or and/or lie on different sequences.


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AUTHOR - Jason Stajich

Email jason@chg.mc.duke.edu


The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


 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 a forward sort.

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


 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


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


  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

LocationI methods


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


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


  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


  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


  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


  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


  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


  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


  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


  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

  Returns : A Bio::Location::CoordinatePolicyI implementing object.
  Args    : On set, a Bio::Location::CoordinatePolicyI implementing object.


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