Bio::LocationI - Abstract interface of a Location on a Sequence # get a LocationI somehow printf( "start = %d, end = %d, strand = %s, seq_id = %s\n", $location->start, $location->end, $location->strand, $location->seq_id); print "location str is ", $location->to_FTstring(), "\n"; This Interface defines the methods for a Bio::LocationI, an object which encapsulates a location on a biological sequence. Locations need not be attached to actual sequences as they are stand alone objects. LocationI objects are used by Bio::SeqFeatureI objects to manage and represent locations for a Sequence Feature. 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 _

location_type
Title : location_type Usage : my $location_type = $location->location_type(); Function: Get location type encoded as text Returns : string ('EXACT', 'WITHIN', 'BETWEEN') Args : none

start
Title : start Usage : $start = $location->start(); Function: Get the start coordinate of this location as defined by the currently active coordinate computation policy. In simple cases, this will return the same number as min_start() and max_start(), in more ambiguous cases like fuzzy locations the number may be equal to one or neither of both. We override this here from RangeI in order to delegate 'get' to a L<Bio::Location::CoordinatePolicy> implementing object. Implementing classes may also wish to provide 'set' functionality, in which case they *must* override this method. The implementation provided here will throw an exception if called with arguments. Returns : A positive integer value. Args : none See Bio::Location::CoordinatePolicy for more information

end
Title : end Usage : $end = $location->end(); Function: Get the end coordinate of this location as defined by the currently active coordinate computation policy. In simple cases, this will return the same number as min_end() and max_end(), in more ambiguous cases like fuzzy locations the number may be equal to one or neither of both. We override this here from Bio::RangeI in order to delegate 'get' to a L<Bio::Location::CoordinatePolicy> implementing object. Implementing classes may also wish to provide 'set' functionality, in which case they *must* override this method. The implementation provided here will throw an exception if called with arguments. Returns : A positive integer value. Args : none See Bio::Location::CoordinatePolicy and Bio::RangeI for more information

min_start
Title : min_start Usage : my $minstart = $location->min_start(); Function: Get minimum starting point of feature. Note that an implementation must not call start() in this method. Returns : integer or undef if no minimum starting point. Args : none

max_start
Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting point of feature. Note that an implementation must not call start() in this method unless start() is overridden such as not to delegate to the coordinate computation policy object. 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 encoded as text Known valid values are 'BEFORE' (<5..100), 'AFTER' (>5..100), 'EXACT' (5..100), 'WITHIN' ((5.10)..100), 'BETWEEN', (5^6), with their meaning best explained by their GenBank/EMBL location string encoding in brackets. Returns : string ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none

min_end
Title : min_end Usage : my $minend = $location->min_end(); Function: Get minimum ending point of feature. Note that an implementation must not call end() in this method unless end() is overridden such as not to delegate to the coordinate computation policy object. 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 point of feature. Note that an implementation must not call end() in this method unless end() is overridden such as not to delegate to the coordinate computation policy object. 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 encoded as text. Known valid values are 'BEFORE' (5..<100), 'AFTER' (5..>100), 'EXACT' (5..100), 'WITHIN' (5..(90.100)), 'BETWEEN', (5^6), with their meaning best explained by their GenBank/EMBL location string encoding in brackets. Returns : string ('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 (a string) Args : [optional] seq_id value to set

is_remote
Title : is_remote Usage : $is_remote_loc = $loc->is_remote() Function: Whether or not a location is a remote location. A location is said to be remote if it is on a different 'object' than the object which 'has' this location. Typically, features on a sequence will sometimes have a remote location, which means that the location of the feature is on a different sequence than the one that is attached to the feature. In such a case, $loc->seq_id will be different from $feat->seq_id (usually they will be the same). While this may sound weird, it reflects the location of the kind of AB18375:450-900 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args :

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 L<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 L<Bio::Location::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 L<Bio::Location::CoordinatePolicyI> implementing object. Args : On set, a L<Bio::Location::CoordinatePolicyI> implementing object. See Bio::Location::CoordinatePolicyI for more information

to_FTstring
Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none

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() for Splits