Bio::Location
SplitLocationI
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Summary
Bio::SplitLocationI - Abstract interface of a Location on a Sequence
which has multiple locations (start/end points)
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# get a SplitLocationI somehow
print $splitlocation->start, "..", $splitlocation->end, "\n";
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]\n", $location->start,$location->end;
$count++;
}
Description
This interface encapsulates the necessary methods for representing the
location of a sequence feature that has more that just a single
start/end pair. Some examples of this are the annotated exons in a
gene or the annotated CDS in a sequence file.
Methods
Methods description
Title : is_single_sequence
Usage : if($splitloc->is_single_sequence()) {
print "Location object $splitloc is split ".
"but only across a single sequence\n";
}
Function: Determine whether this location is split across a single or
multiple sequences.
Returns : TRUE if all sublocations lie on the same sequence as the root
location (feature), and FALSE otherwise.
Args : none |
Title : splittype
Usage : $splittype = $fuzzy->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set |
Title : sub_Location
Usage : @locations = $feat->sub_Location();
Function: Returns an array of LocationI objects
Returns : An array
Args : none |
Methods code
sub is_single_sequence
{ my ($self) = @_;
$self->throw_not_implemented();} | sub splittype
{ my($self) = @_;
$self->throw_not_implemented();} | sub sub_Location
{ my ($self,@args) = @_;
$self->throw_not_implemented();} | General documentation
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://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| Bio::LocationI methods | Top |
Bio::LocationI inherited methods follow
Title : min_start
Usage : my $minstart = $location->min_start();
Function: Get minimum starting location of feature startpoint
Returns : integer or undef if no maximum starting point.
Args : none
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
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
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 : seq_id
Usage : my $seqid = $location->seq_id();
Function: Get/Set seq_id that location refers to
Returns : seq_id
Args : [optional] seq_id value to set
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.
Title : to_FTstring
Usage : my $locstr = $location->to_FTstring()
Function: returns the FeatureTable string of this location
Returns : string
Args : none