Bio::Location::Split - Implementation of a Location on a Sequence which has multiple locations (start/end points) use Bio::Location::Split; my $splitlocation = new Bio::Location::Split(); $splitlocation->add_sub_Location(new Bio::Location::Simple(-start=>1, -end=>30, -strand=>1)); $splitlocation->add_sub_Location(new Bio::Location::Simple(-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]\n", $count, $location->start,$location->end, "\n"; $count++; } This implementation handles locations which span more than one start/end location, or and/or lie on different sequences. 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

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email jason@bioperl.org 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\n"; } 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

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)

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