Bio::RangeI(3pm)					User Contributed Perl Documentation					  Bio::RangeI(3pm)

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 greater 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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Heikki Lehvaslaiho
       Email:  heikki-at-bioperl-dot-org

CONTRIBUTORS

       Juha Muilu (muilu@ebi.ac.uk) Sendu Bala (bix@sendu.me.uk) Malcolm Cook (mec@stowers-institute.org) Stephen Montgomery (sm8 at sanger.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	 : optionally 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	 : optionally 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	 : optionally 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 strandedness (-1, 0, +1)
	 Args	 : optionally 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
";

   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 = optional strand-testing arg ('strong', 'weak', 'ignore')
	 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 = optional strand-testing arg ('strong', 'weak', 'ignore')
	 Returns : true if the argument is totally 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	 : arg #1 = a range to compare this one to (mandatory)
		   arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
	 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, $end, $strand) = $r1->intersection($r2); OR
		  ($start, $end, $strand) = Bio::Range->intersection(@ranges); OR
		  my $containing_range = $r1->intersection($r2); OR
		  my $containing_range = Bio::Range->intersection(@ranges);
	Function: gives the range that is contained by all ranges
	Returns : undef if they do not overlap or if @ranges has only a
		  single range, else returns the range that they do
		  overlap. In scalar contex, the return value is an object of
		  the same class as the calling one. In array context the
		  return value is a three element array.
	Args	: arg #1 = [REQUIRED] a Bio::RangeI to compare this one to,
			   or an array ref of ranges
		  arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')

   union
	  Title   : union
	   Usage   : ($start, $end, $strand) = $r1->union($r2);
		   : ($start, $end, $strand) = Bio::Range->union(@ranges);
		     my $newrange = Bio::Range->union(@ranges);
	   Function: finds the minimal Range that contains all of the Ranges
	   Args    : a Range or list of Range objects

	   Returns : the range containing all of the range. In scalar contex,
		     the return value is an object of the same class as the
		     calling one. In array context the return value is a
		     three element array.

   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 containing the length unique to the calling
		  range, the length common to both, and the length unique to
		  the argument range
	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)

   offsetStranded
	   Title    : offsetStranded
	   Usage    : $rnge->ofsetStranded($fiveprime_offset, $threeprime_offset)
	   Function : destructively modifies RangeI implementing object to
		      offset its start and stop coordinates by values $fiveprime_offset and
		      $threeprime_offset (positive values being in the strand direction).
	   Args     : two integer offsets: $fiveprime_offset and $threeprime_offset
	   Returns  : $self, offset accordingly.

   subtract
	 Title	 : subtract
	 Usage	 : my @subtracted = $r1->subtract($r2)
	 Function: Subtract range r2 from range r1
	 Args	 : arg #1 = a range to subtract from this one (mandatory)
		   arg #2 = strand option ('strong', 'weak', 'ignore') (optional)
	 Returns : undef if they do not overlap or r2 contains this RangeI,
		   or an arrayref of Range objects (this is an array since some
		   instances where the subtract range is enclosed within this range
		   will result in the creation of two new disjoint ranges)

perl v5.14.2							    2012-03-02							  Bio::RangeI(3pm)