Bio::Location::Atomic(3)

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

SYNOPSIS
    use Bio::Location::Atomic;

    my $location = new Bio::Location::Atomic(-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

  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 _

  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   : $self->is_remote($newval)
 Function: Getset for is_remote value
 Returns : value of is_remote
 Args    : newvalue (optional)

  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

  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