The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.6.920
River stage two • 60 direct dependents • 65 total dependents
/ Bio::RangeI

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\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, $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)