Bio::Location::Simple - Implementation of a Simple Location on a Sequence
use Bio::Location::Simple;
my $location = Bio::Location::Simple->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 exact location information
on a Sequence: '22' or '12..15' or '16^17'.
You can test the type of the location using
length() function () or
directly
location_type() which can one of two values: 'EXACT' or
'IN-BETWEEN'.
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
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Please direct usage questions or support issues to the mailing list:
[email protected]
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.
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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)
Note : If start is set but end is undefined, this now assumes that start
is the same as end but throws a warning (i.e. it assumes this is
a possible error). If start is undefined, this now throws an
exception.
Title : strand
Usage : $strand = $loc->strand();
Function: get/set the strand of this range
Returns : the strandedness (-1, 0, +1)
Args : optionally allows the strand to be set
: using $loc->strand($strand)
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 <,>, ^).
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 <,>, ^)
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' or 'IN-BETWEEN')
Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^'
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 : 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