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://redmine.open-bio.org/projects/bioperl/

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 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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq