Reference

Bio::Location::Split(3pm)

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

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

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