Bio::RangeI(3)

NAME
Bio::RangeI - Range interface

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 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://bio.perl.org/MailList.html             - About the mailing lists

  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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk

CONTRIBUTORS
Juha Muilu (muilu@ebi.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    : optionaly 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    : optionaly 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    : optionaly 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 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";

  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 = strand option ('strong', 'weak', 'ignore') (optional)
  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 = strand option ('strong', 'weak', 'ignore') (optional)
  Returns : true if the argument is totaly 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    : 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.

  intersection
  Title   : intersection
  Usage   : ($start, $stop, $strand) = $r1->intersection($r2)
            my $containing_range = $r1->intersection($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, OR a three element array)

  union
   Title   : union
    Usage   : ($start, $stop, $strand) = $r1->union($r2);
            : ($start, $stop, $strand) = Bio::RangeI->union(@ranges);
              my $newrange = 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
              (in an objectlike the calling one, OR a three element array)
=cut

sub union {
    my $self = shift;
    my @ranges = @_;
    if(ref $self) {
    unshift @ranges, $self;
    }

    my @start = sort {$a<=>$b}
    map( { $_->start() } @ranges);
    my @end   = sort {$a<=>$b}
    map( { $_->end()   } @ranges);

    my $start = shift @start;
    while( !defined $start ) {
        $start = shift @start;
    }

    my $end = pop @end;

    my $union_strand;  # Strand for the union range object.

    foreach(@ranges) {
        if(! defined $union_strand) {
            $union_strand = $_->strand;
            next;
        } else {
            if(not defined $_->strand or $union_strand ne $_->strand) {
                $union_strand = 0;
                last;
            }
        }
    }
    return undef unless $start or $end;
    if( wantarray() ) {
        return ( $start,$end,$union_strand);
    } else {
        return $self->new('-start' => $start,
                          '-end' => $end,
                          '-strand' => $union_strand
                          );
    }
}

  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 for
           - the amount unique to a
           - the amount common to both
           - the amount unique to b
 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)