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BioPerl-1.007000_006
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Location::Split

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 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