Bio::Range - Pure perl RangeI implementation 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) $range = new Bio::Range(-start=>10, -end=>30, -strand=>+1); $r2 = new Bio::Range(-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";

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://bio.perl.org/bioperl-bugs/ Email heikki@ebi.ac.uk The rest of the documentation details each of the object methods. Internal metho ds are usually preceded with a _

new
Title : new Usage : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1); Function: generates a new Bio::Range Returns : a new range Args : two of (-start, -end, '-length') - the third is calculated : -strand (defaults to 0) These methods let you get at and set the member variables

start
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

end
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

strand
Title : strand Function : return or set the strandidness Example : $st = $range->strand(); $range->strand(-1); Returns : the value of the strandedness (-1, 0 or 1) Args : optionaly, the new strand - (-1, 0, 1) or (-, ., +). Overrides: Bio::RangeI::Strand

length
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, and exeption will be thrown Overrides: Bio::RangeI::Length

toString
Title : toString Function: stringifies this range Example : print $range->toString(), "\n"; Returns : a string representation of this range These methods return true or false. $range->overlaps($otherRange) && print "Ranges overlap\n";

overlaps
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

contains
Title : contains Usage : if($r1->contains($r2) { do stuff } Function : tests wether $r1 totaly contains $r2 Args : a range to test for being contained Returns : true if the argument is totaly contained within this range Inherited: Bio::RangeI

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 Inherited: Bio::RangeI These methods do things to the geometry of ranges, and return triplets (start, end, strand) from which new ranges could be built.

intersection
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

union
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 to find the union of Returns : the range containing all of the ranges Inherited: Bio::RangeI::union