Bio::Range(3pm) 					User Contributed Perl Documentation					   Bio::Range(3pm)

NAME

       Bio::Range - Pure perl RangeI implementation

SYNOPSIS

	 $range = Bio::Range->new(-start=>10, -end=>30, -strand=>+1);
	 $r2 = Bio::Range->new(-start=>15, -end=>200, -strand=>+1);

	 print join(', ', $range->union($r2)), "
";
	 print join(', ', $range->intersection($r2)), "
";

	 print $range->overlaps($r2), "
";
	 print $range->contains($r2), "
";

DESCRIPTION

       This provides a pure perl implementation of the BioPerl range interface.

       Ranges are modeled as having (start, end, length, strand). They use Bio-coordinates - all points >= start and <= end are within the range.
       End is always greater-than or equal-to start, and length is greather than or equal to 1. The behaviour of a range is undefined if ranges
       with negative numbers or zero are used.

       So, in summary:

	 length = end - start + 1
	 end >= start
	 strand = (-1 | 0 | +1)

FEEDBACK

   Mailing Lists
       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 _

Constructors
   new
	 Title	 : new
	 Usage	 : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1);
	 Function: generates a new Bio::Range
	 Returns : a new range
	 Args	 : -strand (defaults to 0) and any two of (-start, -end, -length),
		   the third will be calculated

   unions
	Title	: unions
	Usage	: @unions = Bio::Range->unions(@ranges);
	Function: generate a list of non-intersecting Bio::Range objects
		  from a list of Bio::Range objects which may intersect
	Returns : a list of Bio::Range objects
	Args	: a list of Bio::Range objects

Member variable access
       These methods let you get at and set the member variables

   start
	 Title	  : start
	 Function : return or set the start co-ordinate
	 Example  : $s = $range->start(); $range->start(7);
	 Returns  : the value of the start co-ordinate
	 Args	  : optionally, the new start co-ordinate
	 Overrides: Bio::RangeI::start

   end
	 Title	  : end
	 Function : return or set the end co-ordinate
	 Example  : $e = $range->end(); $range->end(2000);
	 Returns  : the value of the end co-ordinate
	 Args	  : optionally, the new end co-ordinate
	 Overrides: Bio::RangeI::end

   strand
	 Title	  : strand
	 Function : return or set the strandedness
	 Example  : $st = $range->strand(); $range->strand(-1);
	 Returns  : the value of the strandedness (-1, 0 or 1)
	 Args	  : optionally, the new strand - (-1, 0, 1) or (-, ., +).
	 Overrides: Bio::RangeI::strand

   length
	 Title	  : length
	 Function : returns the length of this range
	 Example  : $length = $range->length();
	 Returns  : the length of this range, equal to end - start + 1
	 Args	  : if you attempt to set the length an exception will be thrown
	 Overrides: Bio::RangeI::Length

   toString
	 Title	 : toString
	 Function: stringifies this range
	 Example : print $range->toString(), "
";
	 Returns : a string representation of this range

Boolean Methods
       These methods return true or false.

	$range->overlaps($otherRange) && print "Ranges overlap
";

   overlaps
	 Title	  : overlaps
	 Usage	  : if($r1->overlaps($r2)) { do stuff }
	 Function : tests if $r2 overlaps $r1
	 Args	  : a range to test for overlap with
	 Returns  : true if the ranges overlap, false otherwise
	 Inherited: Bio::RangeI

   contains
	 Title	  : contains
	 Usage	  : if($r1->contains($r2) { do stuff }
	 Function : tests whether $r1 totally contains $r2
	 Args	  : a range to test for being contained
	 Returns  : true if the argument is totally contained within this range
	 Inherited: Bio::RangeI

   equals
	 Title	  : equals
	 Usage	  : if($r1->equals($r2))
	 Function : test whether $r1 has the same start, end, length as $r2
	 Args	  : a range to test for equality
	 Returns  : true if they are describing the same range
	 Inherited: Bio::RangeI

Geometrical methods
       These methods do things to the geometry of ranges, and return triplets (start, end, strand) from which new ranges could be built.

   intersection
	 Title	  : intersection
	 Usage	  : ($start, $stop, $strand) = $r1->intersection($r2)
	 Function : gives the range that is contained by both ranges
	 Args	  : a range to compare this one to
	 Returns  : nothing if they do not overlap, or the range that they do overlap
	 Inherited: Bio::RangeI::intersection

   union
	 Title	  : union
	 Usage	  : ($start, $stop, $strand) = $r1->union($r2);
		  : ($start, $stop, $strand) = Bio::Range->union(@ranges);
	 Function : finds the minimal range that contains all of the ranges
	 Args	  : a range or list of ranges
	 Returns  : the range containing all of the ranges
	 Inherited: Bio::RangeI::union

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