Bio::Location::SplitLocationI(3pm) User Contributed Perl Documentation Bio::Location::SplitLocationI(3pm)
NAME
Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
SYNOPSIS
# get a SplitLocationI somehow
print $splitlocation->start, "..", $splitlocation->end, "
";
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]
", $location->start,$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.
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 _
sub_Location
Title : sub_Location
Usage : @locations = $feat->sub_Location();
Function: Returns an array of LocationI objects
Returns : An array
Args : none
splittype
Title : splittype
Usage : $splittype = $fuzzy->splittype();
Function: get/set the split splittype
Returns : the splittype of split feature (join, order)
Args : splittype to set
is_single_sequence
Title : is_single_sequence
Usage : if($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.
Returns : TRUE if all sublocations lie on the same sequence as the root
location (feature), and FALSE otherwise.
Args : none
Bio::LocationI methods
Bio::LocationI inherited methods follow
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 maximum starting point.
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
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
perl v5.14.2 2012-03-02 Bio::Location::SplitLocationI(3pm)