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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:

   http://bugzilla.bioperl.org/
 
 

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\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 = 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, $stop, $strand) = $r1->intersection($r2); OR
            ($start, $stop, $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
            the range that they do overlap (in the form of an object
             like the calling one, OR a three element array)
  Args    : arg #1 = [REQUIRED] a range 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, $stop, $strand) = $r1->union($r2);
             : ($start, $stop, $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 the form of an object like the calling one, OR
               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)