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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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-orgAPPENDIX
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.