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BioPerl-1.7.7
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Location::Atomic

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://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    : optionally 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    : optionally 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    : optionally 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 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

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.