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)