Provided by: libbio-perl-perl_1.6.923-1_all bug


       Bio::Range - Pure perl RangeI implementation


         $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";


       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)


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AUTHOR - Heikki Lehvaslaiho

       Email heikki-at-bioperl-dot-org


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _


         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

        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

         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

         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

         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

         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

         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";

         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

         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

         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.

         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

         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