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Bio::Range.3pm

NAME

Bio::Range - Pure perl RangeI implementation

SYNOPSIS

   $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";
 
 

DESCRIPTION

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)
 
 

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://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email heikki-at-bioperl-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Constructors

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    : -strand (defaults to 0) and any two of (-start, -end, -length),
             the third will be calculated
 
 

unions

  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
 
 

Member variable access

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 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
 
 

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 an exception 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
 
 

Boolean Methods

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 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
 
 

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
 
 

Geometrical methods

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