--- name: "Bio::Location::SplitLocationI" section: "3pm" platform: "linux" package: "libbio-perl-perl" version: "1.7.8-1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Location::SplitLocationI" --- # Bio::Location::SplitLocationI(3pm) Abstract interface of a Location on a Sequence which has multiple locations (start/end points) ## 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, "\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. ## 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://github.com/bioperl/bioperl-live/issues ``` ## 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\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 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 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. ``` ### to\_FTstring ``` Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none ```