Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence
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;
}
This is an implementation of Bio::LocationI to manage simple location
information on a Sequence.
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include a thorough description of the problem with code and data examples if
at all possible.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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)
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)
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)
Title : flip_strand
Usage : $location->flip_strand();
Function: Flip-flop a strand to the opposite
Returns : None
Args : None
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
Title : length
Usage : $len = $loc->length();
Function: get the length in the coordinate space this location spans
Example :
Returns : an integer
Args : none
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
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
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
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
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
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
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
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
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 :
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none
Title : valid_Location
Usage : if ($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
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
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.