Bio::Location::Atomic - Implementation of a Atomic Location on a Sequence use Bio::Location::Atomic; my $location = new Bio::Location::Atomic(-start => 1, -end => 100, -strand => 1 ); if( $location->strand == -1 ) { printf "complement(%d..%d)\n", $location->start, $location->end; } else { printf "%d..%d\n", $location->start, $location->end; } This is an implementation of Bio::LocationI to manage simple location information on a Sequence. 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 _

start
Title : start Usage : $start = $loc->start(); Function: get/set the start of this range Returns : the start of this range Args : optionaly allows the start to be set : using $loc->start($start)

end
Title : end Usage : $end = $loc->end(); Function: get/set the end of this range Returns : the end of this range Args : optionaly allows the end to be set : using $loc->end($start)

strand
Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandidness (-1, 0, +1) Args : optionaly allows the strand to be set : using $loc->strand($strand)

length
Title : length Usage : $len = $loc->length(); Function: get the length in the coordinate space this location spans Example : Returns : an integer Args : none

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 minimum starting point. Args : none

max_start
Title : max_start Usage : my $maxstart = $location->max_start(); Function: Get maximum starting location of feature startpoint. In this implementation this is exactly the same as min_start(). 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 <,>, ^). In this implementation this will always be 'EXACT'. 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 In this implementation this is exactly the same as min_end(). 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 <,>, ^) In this implementation this will always be 'EXACT'. Returns : type of position coded as text ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN') Args : none

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

is_remote
Title : is_remote Usage : $self->is_remote($newval) Function: Getset for is_remote value Returns : value of is_remote Args : newvalue (optional)

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 - for Simple locations, the return value is just itself. Args :

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