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Man Pages


Manual Reference Pages  -  BIO::LOCATION::ATOMIC (3)

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NAME

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

CONTENTS

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://github.com/bioperl/bioperl-live/issues



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.



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