Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

SYNOPSIS

           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;
           }

DESCRIPTION

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

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 _

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

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

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

   flip_strand
         Title   : flip_strand
         Usage   : $location->flip_strand();
         Function: Flip-flop a strand to the opposite
         Returns : None
         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 (a string)
         Args    : [optional] seq_id value to set

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

   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 minimum starting point.
         Args    : none

   max_start
         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

   start_pos_type
         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

   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

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

         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 <,>, ^)

                   In this implementation this will always be 'EXACT'.

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

   location_type
         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

   is_remote
        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
                  same).

                  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

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

   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

   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 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 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

   trunc
         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
                         orientation.