--- name: "Bio::Location::Simple" 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::Simple" --- # Bio::Location::Simple(3pm) Implementation of a Simple Location on a Sequence ## NAME Bio::Location::Simple - Implementation of a Simple Location on a Sequence ## SYNOPSIS ``` use Bio::Location::Simple; my $location = Bio::Location::Simple->new( -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; } ``` ## DESCRIPTION This is an implementation of Bio::LocationI to manage exact location information on a Sequence: '22' or '12..15' or '16^17'. You can test the type of the location using **length()** function () or directly **location\_type()** which can one of two values: 'EXACT' or 'IN-BETWEEN'. ## 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 - Heikki Lehvaslaiho Email heikki-at-bioperl-dot-org ## APPENDIX 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 : optionally 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 : optionally allows the end to be set : using $loc->end($start) Note : If start is set but end is undefined, this now assumes that start is the same as end but throws a warning (i.e. it assumes this is a possible error). If start is undefined, this now throws an exception. ``` ### strand ``` Title : strand Usage : $strand = $loc->strand(); Function: get/set the strand of this range Returns : the strandedness (-1, 0, +1) Args : optionally 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 <,>, ^). 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 <,>, ^) 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' or 'IN-BETWEEN') Args : 'EXACT' or '..' or 'IN-BETWEEN' or '^' ``` ### 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 AL445212.9:83662..166657 which can be found in GenBank/EMBL feature tables. Example : Returns : TRUE if the location is a remote location, and FALSE otherwise Args : Value to set to ``` ### to\_FTstring ``` Title : to_FTstring Usage : my $locstr = $location->to_FTstring() Function: returns the FeatureTable string of this location Returns : string Args : none ``` ### valid\_Location ``` Title : valid_Location Usage : if ($location->valid_location) {...}; Function: boolean method to determine whether location is considered valid (has minimum requirements for Simple implementation) Returns : Boolean value: true if location is valid, false otherwise Args : none ```