Bio::RangeI - Range interface


  #Do not run this module directly


This provides a standard BioPerl range interface that should be implemented by any object that wants to be treated as a range. This serves purely as an abstract base class for implementers and can not be instantiated.

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



Juha Muilu (


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

Abstract methods

These methods must be implemented in all subclasses.


  Title   : start
  Usage   : $start = $range->start();
  Function: get/set the start of this range
  Returns : the start of this range
  Args    : optionaly allows the start to be set
           using $range->start($start)


  Title   : end
  Usage   : $end = $range->end();
  Function: get/set the end of this range
  Returns : the end of this range
  Args    : optionaly allows the end to be set
            using $range->end($end)


  Title   : length
  Usage   : $length = $range->length();
  Function: get/set the length of this range
  Returns : the length of this range
  Args    : optionaly allows the length to be set
             using $range->length($length)


  Title   : strand
  Usage   : $strand = $range->strand();
  Function: get/set the strand of this range
  Returns : the strandidness (-1, 0, +1)
  Args    : optionaly allows the strand to be set
            using $range->strand($strand)

Boolean Methods

These methods return true or false. They throw an error if start and end are not defined.

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


  Title   : overlaps
  Usage   : if($r1->overlaps($r2)) { do stuff }
  Function: tests if $r2 overlaps $r1
  Args    : arg #1 = a range to compare this one to (mandatory)
            arg #2 = strand option ('strong', 'weak', 'ignore') (optional)
  Returns : true if the ranges overlap, false otherwise


  Title   : contains
  Usage   : if($r1->contains($r2) { do stuff }
  Function: tests whether $r1 totally contains $r2 
  Args    : arg #1 = a range to compare this one to (mandatory)
                     alternatively, integer scalar to test
            arg #2 = strand option ('strong', 'weak', 'ignore') (optional)
  Returns : true if the argument is totaly contained within this range


  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

Geometrical methods

These methods do things to the geometry of ranges, and return Bio::RangeI compliant objects or triplets (start, stop, 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    : arg #1 = a range to compare this one to (mandatory)
            arg #2 = strand option ('strong', 'weak', 'ignore') (optional)
  Returns : undef if they do not overlap, 
            or the range that they do overlap 
            (in an objectlike the calling one)


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


 Title   : overlap_extent
 Usage   : ($a_unique,$common,$b_unique) = $a->overlap_extent($b)
 Function: Provides actual amount of overlap between two different
 Example :
 Returns : array of values for 
           - the amount unique to a
           - the amount common to both
           - the amount unique to b
 Args    : a range