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Bio::Location::Atomic.3pm

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:

   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
 
 

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.