SYNOPSIS

#Do not run this module directly

DESCRIPTION

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 greater 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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

CONTRIBUTORS

Juha Muilu ([email protected]) Sendu Bala ([email protected]) Malcolm Cook ([email protected]) Stephen Montgomery (sm8 at sanger.ac.uk)

APPENDIX

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.

start

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

end

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

length

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

strand

  Title   : strand
  Usage   : $strand = $range->strand();
  Function: get/set the strand of this range
  Returns : the strandedness (-1, 0, +1)
  Args    : optionally 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";

overlaps

  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 = optional strand-testing arg ('strong', 'weak', 'ignore')
  Returns : true if the ranges overlap, false otherwise

contains

  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 = optional strand-testing arg ('strong', 'weak', 'ignore')
  Returns : true if the argument is totally contained within this range

equals

  Title   : equals
  Usage   : if($r1->equals($r2))
  Function: test whether $r1 has the same start, end, length as $r2
  Args    : arg #1 = a range to compare this one to (mandatory)
            arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
  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.

intersection

 Title   : intersection
 Usage   : ($start, $end, $strand) = $r1->intersection($r2); OR
           ($start, $end, $strand) = Bio::Range->intersection(\@ranges); OR
           my $containing_range = $r1->intersection($r2); OR
           my $containing_range = Bio::Range->intersection(\@ranges);
 Function: gives the range that is contained by all ranges
 Returns : undef if they do not overlap or if @ranges has only a
           single range, else returns the range that they do
           overlap. In scalar contex, the return value is an object of
           the same class as the calling one. In array context the
           return value is a three element array.
 Args    : arg #1 = [REQUIRED] a Bio::RangeI to compare this one to,
                    or an array ref of ranges
           arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')

union

   Title   : union
    Usage   : ($start, $end, $strand) = $r1->union($r2);
            : ($start, $end, $strand) = Bio::Range->union(@ranges);
              my $newrange = Bio::Range->union(@ranges);
    Function: finds the minimal Range that contains all of the Ranges
    Args    : a Range or list of Range objects
    Returns : the range containing all of the range. In scalar contex,
              the return value is an object of the same class as the
              calling one. In array context the return value is a
              three element array.

overlap_extent

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

disconnected_ranges

    Title   : disconnected_ranges
    Usage   : my @disc_ranges = Bio::Range->disconnected_ranges(@ranges);
    Function: finds the minimal set of ranges such that each input range
              is fully contained by at least one output range, and none of
              the output ranges overlap
    Args    : a list of ranges
    Returns : a list of objects of the same type as the input
              (conforms to RangeI)

offsetStranded

    Title    : offsetStranded
    Usage    : $rnge->ofsetStranded($fiveprime_offset, $threeprime_offset)
    Function : destructively modifies RangeI implementing object to
               offset its start and stop coordinates by values $fiveprime_offset and
               $threeprime_offset (positive values being in the strand direction).
    Args     : two integer offsets: $fiveprime_offset and $threeprime_offset
    Returns  : $self, offset accordingly.

subtract

  Title   : subtract
  Usage   : my @subtracted = $r1->subtract($r2)
  Function: Subtract range r2 from range r1
  Args    : arg #1 = a range to subtract from this one (mandatory)
            arg #2 = strand option ('strong', 'weak', 'ignore') (optional)
  Returns : undef if they do not overlap or r2 contains this RangeI,
            or an arrayref of Range objects (this is an array since some
            instances where the subtract range is enclosed within this range
            will result in the creation of two new disjoint ranges)