Bio::Location::Split.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 discontiguous 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:
   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 _

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 switch Split strand
             from undef to -1 or -1 to undef
   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
 
 

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