Bio::Range - Pure perl RangeI implementation
$range = Bio::Range->new(-start=>10, -end=>30, -strand=>+1);
$r2 = Bio::Range->new(-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";
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)
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : new
Usage : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1);
Function: generates a new Bio::Range
Returns : a new range
Args : -strand (defaults to 0) and any two of (-start, -end, -length),
the third will be calculated
Title : unions
Usage : @unions = Bio::Range->unions(@ranges);
Function: generate a list of non-intersecting Bio::Range objects
from a list of Bio::Range objects which may intersect
Returns : a list of Bio::Range objects
Args : a list of Bio::Range objects
These methods let you get at and set the member variables
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
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
Title : strand
Function : return or set the strandedness
Example : $st = $range->strand(); $range->strand(-1);
Returns : the value of the strandedness (-1, 0 or 1)
Args : optionally, the new strand - (-1, 0, 1) or (-, ., +).
Overrides: Bio::RangeI::strand
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 an exception will be thrown
Overrides: Bio::RangeI::Length
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";
Title : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function : tests if $r2 overlaps $r1
Args : a range to test for overlap with
Returns : true if the ranges overlap, false otherwise
Inherited: Bio::RangeI
Title : contains
Usage : if($r1->contains($r2) { do stuff }
Function : tests whether $r1 totally contains $r2
Args : a range to test for being contained
Returns : true if the argument is totally contained within this range
Inherited: Bio::RangeI
Title : equals
Usage : if($r1->equals($r2))
Function : test whether $r1 has the same start, end, length as $r2
Args : a range to test for equality
Returns : true if they are describing the same range
Inherited: Bio::RangeI
These methods do things to the geometry of ranges, and return triplets (start,
end, strand) from which new ranges could be built.
Title : intersection
Usage : ($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
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
Returns : the range containing all of the ranges
Inherited: Bio::RangeI::union