Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence


           use Bio::Location::Atomic;

           my $location = Bio::Location::Atomic->new(-start => 1, -end => 100,
                                                    -strand => 1 );

           if( $location->strand == -1 ) {
               printf "complement(%d..%d)\n", $location->start, $location->end;
           } else {
               printf "%d..%d\n", $location->start, $location->end;


       This is an implementation of Bio::LocationI to manage simple location information on a


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       participation is much appreciated.
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AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

         Title   : start
         Usage   : $start = $loc->start();
         Function: get/set the start of this range
         Returns : the start of this range
         Args    : optionally allows the start to be set
                 : using $loc->start($start)

         Title   : end
         Usage   : $end = $loc->end();
         Function: get/set the end of this range
         Returns : the end of this range
         Args    : optionally allows the end to be set
                 : using $loc->end($start)

         Title   : strand
         Usage   : $strand = $loc->strand();
         Function: get/set the strand of this range
         Returns : the strandidness (-1, 0, +1)
         Args    : optionally allows the strand to be set
                 : using $loc->strand($strand)

         Title   : flip_strand
         Usage   : $location->flip_strand();
         Function: Flip-flop a strand to the opposite
         Returns : None
         Args    : None

         Title   : seq_id
         Usage   : my $seqid = $location->seq_id();
         Function: Get/Set seq_id that location refers to
         Returns : seq_id (a string)
         Args    : [optional] seq_id value to set

        Title   : length
        Usage   : $len = $loc->length();
        Function: get the length in the coordinate space this location spans
        Example :
        Returns : an integer
        Args    : none

         Title   : min_start
         Usage   : my $minstart = $location->min_start();
         Function: Get minimum starting location of feature startpoint
         Returns : integer or undef if no minimum starting point.
         Args    : none

         Title   : max_start
         Usage   : my $maxstart = $location->max_start();
         Function: Get maximum starting location of feature startpoint.

                   In this implementation this is exactly the same as min_start().

         Returns : integer or undef if no maximum starting point.
         Args    : none

         Title   : start_pos_type
         Usage   : my $start_pos_type = $location->start_pos_type();
         Function: Get start position type (ie <,>, ^).

                   In this implementation this will always be 'EXACT'.

         Returns : type of position coded as text
                   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
         Args    : none

         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

         Title   : max_end
         Usage   : my $maxend = $location->max_end();
         Function: Get maximum ending location of feature endpoint

                   In this implementation this is exactly the same as min_end().

         Returns : integer or undef if no maximum ending point.
         Args    : none

         Title   : end_pos_type
         Usage   : my $end_pos_type = $location->end_pos_type();
         Function: Get end position type (ie <,>, ^)

                   In this implementation this will always be 'EXACT'.

         Returns : type of position coded as text
                   ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
         Args    : none

         Title   : location_type
         Usage   : my $location_type = $location->location_type();
         Function: Get location type encoded as text
         Returns : string ('EXACT', 'WITHIN', 'IN-BETWEEN')
         Args    : none

        Title   : is_remote
        Usage   : $is_remote_loc = $loc->is_remote()
        Function: Whether or not a location is a remote location.

                  A location is said to be remote if it is on a different
                  'object' than the object which 'has' this
                  location. Typically, features on a sequence will sometimes
                  have a remote location, which means that the location of
                  the feature is on a different sequence than the one that is
                  attached to the feature. In such a case, $loc->seq_id will
                  be different from $feat->seq_id (usually they will be the

                  While this may sound weird, it reflects the location of the
                  kind of AL445212.9:83662..166657 which can be found in GenBank/EMBL
                  feature tables.

        Example :
        Returns : TRUE if the location is a remote location, and FALSE otherwise
        Args    : Value to set to

        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 - for
                  Simple locations, the return value is just itself.
        Args    :

         Title   : to_FTstring
         Usage   : my $locstr = $location->to_FTstring()
         Function: returns the FeatureTable string of this location
         Returns : string
         Args    : none

        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

         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 L<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
                   L<Bio::Location::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 L<Bio::Location::CoordinatePolicyI> implementing object.
         Args    : On set, a L<Bio::Location::CoordinatePolicyI> implementing object.

       See Bio::Location::CoordinatePolicyI for more information

         Title   : trunc
               Usage   : $trunc_location = $location->trunc($start, $end, $relative_ori);
               Function: To truncate a location and keep annotations and features
                         within the truncated segment intact.

                                                       This might do things differently where the truncation
                                                       splits the location in half.
               CAVEAT  : As yet, this is an untested and unannounced method. Use
                         with caution!
               Returns : A L<Bio::Location::Atomic> object.
               Args    : The start and end position for the trunction, and the relative