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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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/ Email: heikki@ebi.ac.uk Juha Muilu (muilu@ebi.ac.uk) The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 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) 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 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)