Bio::Location::Simple(3pm)				User Contributed Perl Documentation				Bio::Location::Simple(3pm)

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)
", $location->start, $location->end;
	   } else {
	   printf "%d..%d
", $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://redmine.open-bio.org/projects/bioperl/

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	 : 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)
	 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	 : 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 <,>, ^).

	 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

perl v5.14.2							    2012-03-02						Bio::Location::Simple(3pm)