| Bio::Location::SplitLocationI(3pm) | User Contributed Perl Documentation | Bio::Location::SplitLocationI(3pm) |
Bio::Location::SplitLocationI - Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
# 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++;
}
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.
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Please direct usage questions or support issues to the mailing list:
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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 : sub_Location Usage : @locations = $feat->sub_Location(); Function: Returns an array of LocationI objects Returns : An array Args : none
Title : splittype Usage : $splittype = $fuzzy->splittype(); Function: get/set the split splittype Returns : the splittype of split feature (join, order) Args : splittype to set
Title : is_single_sequence
Usage : if($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
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 one 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
| 2018-10-27 | perl v5.26.2 |