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Bio::Location::SplitLocationI.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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