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

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

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(), "\n";
         Returns : a string representation of this range

Boolean Methods

       These methods return true or false.

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

   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