Bio::Location::Split(3pm) User Contributed Perl Documentation Bio::Location::Split(3pm)
NAME
Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points)
SYNOPSIS
use Bio::Location::Split;
my $splitlocation = Bio::Location::Split->new();
$splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>1,
-end=>30,
-strand=>1));
$splitlocation->add_sub_Location(Bio::Location::Simple->new(-start=>50,
-end=>61,
-strand=>1));
my @sublocs = $splitlocation->sub_Location();
my $count = 1;
# print the start/end points of the sub locations
foreach my $location ( sort { $a->start <=> $b->start }
@sublocs ) {
printf "sub feature %d [%d..%d]
",
$count, $location->start,$location->end, "
";
$count++;
}
DESCRIPTION
This implementation handles locations which span more than one start/end location, or and/or lie on different sequences, and can work with
split locations that depend on the specific order of the sublocations ('join') or don't have a specific order but represent a feature
spanning noncontiguous sublocations ('order', 'bond').
Note that the order in which sublocations are added may be very important, depending on the specific split location type. For instance, a
'join' must have the sublocations added in the order that one expects to join the sublocations, whereas all other types are sorted based on
the sequence location.
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://redmine.open-bio.org/projects/bioperl/
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 _
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
Args : Optional sort order to be passed to sub_Location()
sub_Location
Title : sub_Location
Usage : @sublocs = $splitloc->sub_Location();
Function: Returns the array of sublocations making up this compound (split)
location. Those sublocations referring to the same sequence as
the root split location will be sorted by start position (forward
sort) or end position (reverse sort) and come first (before
those on other sequences).
The sort order can be optionally specified or suppressed by the
value of the first argument. The default is no sort.
Returns : an array of Bio::LocationI implementing objects
Args : Optionally 1, 0, or -1 for specifying a forward, no, or reverse
sort order
add_sub_Location
Title : add_sub_Location
Usage : $splitloc->add_sub_Location(@locationIobjs);
Function: add an additional sublocation
Returns : number of current sub locations
Args : list of Bio::LocationI implementing object(s) to add
splittype
Title : splittype
Usage : $splittype = $location->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set
is_single_sequence
Title : is_single_sequence
Usage : if($splitloc->is_single_sequence()) {
print "Location object $splitloc is split ".
"but only across a single sequence
";
}
Function: Determine whether this location is split across a single or
multiple sequences.
This implementation ignores (sub-)locations that do not define
seq_id(). The same holds true for the root location.
Returns : TRUE if all sublocations lie on the same sequence as the root
location (feature), and FALSE otherwise.
Args : none
guide_strand
Title : guide_strand
Usage : $str = $loc->guide_strand();
Function: Get/Set the guide strand. Of use only if the split type is
a 'join' (this helps determine the order of sublocation
retrieval)
Returns : value of guide strand (1, -1, or undef)
Args : new value (-1 or 1, optional)
LocationI methods
strand
Title : strand
Usage : $obj->strand($newval)
Function: For SplitLocations, setting the strand of the container
(this object) is a short-cut for setting the strand of all
sublocations.
In get-mode, checks if no sub-location is remote, and if
all have the same strand. If so, it returns that shared
strand value. Otherwise it returns undef.
Example :
Returns : on get, value of strand if identical between sublocations
(-1, 1, or undef)
Args : new value (-1 or 1, optional)
flip_strand
Title : flip_strand
Usage : $location->flip_strand();
Function: Flip-flop a strand to the opposite. Also switch Split strand
from undef to -1 or -1 to undef
Returns : None
Args : None
start
Title : start
Usage : $start = $location->start();
Function: get the starting point of the first (sorted) sublocation
Returns : integer
Args : none
end
Title : end
Usage : $end = $location->end();
Function: get the ending point of the last (sorted) sublocation
Returns : integer
Args : none
min_start
Title : min_start
Usage : $min_start = $location->min_start();
Function: get the minimum starting point
Returns : the minimum starting point from the contained sublocations
Args : none
max_start
Title : max_start
Usage : my $maxstart = $location->max_start();
Function: Get maximum starting location of feature startpoint
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 <,>, ^)
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
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 <,>, ^)
Returns : type of position coded as text
('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
Args : none
seq_id
Title : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
We override this here in order to propagate to all sublocations
which are not remote (provided this root is not remote either)
Returns : seq_id
Args : [optional] seq_id value to set
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 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 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 Bio::Location::CoordinatePolicyI implementing object.
Args : On set, a Bio::Location::CoordinatePolicyI implementing object.
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
perl v5.14.2 2012-03-02 Bio::Location::Split(3pm)