#
# BioPerl module for Bio::RangeI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copyright Matthew Pocock
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::RangeI - Range interface
=head1 SYNOPSIS
#Do not run this module directly
=head1 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 E<gt>= start and E<lt>= 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)
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Heikki Lehvaslaiho
Email: heikki-at-bioperl-dot-org
=head1 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)
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::RangeI;
use strict;
use Carp;
use integer;
use vars qw(%STRAND_OPTIONS);
use base qw(Bio::Root::RootI);
BEGIN {
# STRAND_OPTIONS contains the legal values for the strand-testing options
%STRAND_OPTIONS = map { $_, '_' . $_ }
(
'strong', # ranges must have the same strand
'weak', # ranges must have the same strand or no strand
'ignore', # ignore strand information
);
}
# utility methods
#
# returns true if strands are equal and non-zero
sub _strong {
my ($r1, $r2) = @_;
my ($s1, $s2) = ($r1->strand(), $r2->strand());
return 1 if $s1 != 0 && $s1 == $s2;
}
# returns true if strands are equal or either is zero
sub _weak {
my ($r1, $r2) = @_;
my ($s1, $s2) = ($r1->strand(), $r2->strand());
return 1 if $s1 == 0 || $s2 == 0 || $s1 == $s2;
}
# returns true for any strandedness
sub _ignore {
return 1;
}
# works out what test to use for the strictness and returns true/false
# e.g. $r1->_testStrand($r2, 'strong')
sub _testStrand() {
my ($r1, $r2, $comp) = @_;
return 1 unless $comp;
my $func = $STRAND_OPTIONS{$comp};
return $r1->$func($r2);
}
=head1 Abstract methods
These methods must be implemented in all subclasses.
=head2 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)
=cut
sub start {
shift->throw_not_implemented();
}
=head2 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)
=cut
sub end {
shift->throw_not_implemented();
}
=head2 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)
=cut
sub length {
shift->throw_not_implemented();
}
=head2 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)
=cut
sub strand {
shift->throw_not_implemented();
}
=head1 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";
=head2 overlaps
Title : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function: tests if $r2 overlaps $r1
Args : arg #1 = a range to compare this one to (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
Returns : true if the ranges overlap, false otherwise
=cut
sub overlaps {
my ($self, $other, $so) = @_;
$self->throw("start is undefined") unless defined $self->start;
$self->throw("end is undefined") unless defined $self->end;
$self->throw("not a Bio::RangeI object") unless defined $other &&
$other->isa('Bio::RangeI');
$other->throw("start is undefined") unless defined $other->start;
$other->throw("end is undefined") unless defined $other->end;
return
($self->_testStrand($other, $so)
and not (
($self->start() > $other->end() or
$self->end() < $other->start() )
));
}
=head2 contains
Title : contains
Usage : if($r1->contains($r2) { do stuff }
Function: tests whether $r1 totally contains $r2
Args : arg #1 = a range to compare this one to (mandatory)
alternatively, integer scalar to test
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
Returns : true if the argument is totally contained within this range
=cut
sub contains {
my ($self, $other, $so) = @_;
$self->throw("start is undefined") unless defined $self->start;
$self->throw("end is undefined") unless defined $self->end;
if(defined $other && ref $other) { # a range object?
$other->throw("Not a Bio::RangeI object: $other") unless $other->isa('Bio::RangeI');
$other->throw("start is undefined") unless defined $other->start;
$other->throw("end is undefined") unless defined $other->end;
return ($self->_testStrand($other, $so) and
$other->start() >= $self->start() and
$other->end() <= $self->end());
} else { # a scalar?
$self->throw("'$other' is not an integer.\n") unless $other =~ /^[-+]?\d+$/;
return ($other >= $self->start() and $other <= $self->end());
}
}
=head2 equals
Title : equals
Usage : if($r1->equals($r2))
Function: test whether $r1 has the same start, end, length as $r2
Args : arg #1 = a range to compare this one to (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
Returns : true if they are describing the same range
=cut
sub equals {
my ($self, $other, $so) = @_;
$self->throw("start is undefined") unless defined $self->start;
$self->throw("end is undefined") unless defined $self->end;
$other->throw("Not a Bio::RangeI object") unless $other->isa('Bio::RangeI');
$other->throw("start is undefined") unless defined $other->start;
$other->throw("end is undefined") unless defined $other->end;
return ($self->_testStrand($other, $so) and
$self->start() == $other->start() and
$self->end() == $other->end() );
}
=head1 Geometrical methods
These methods do things to the geometry of ranges, and return
Bio::RangeI compliant objects or triplets (start, stop, strand) from
which new ranges could be built.
=head2 intersection
Title : intersection
Usage : ($start, $end, $strand) = $r1->intersection($r2); OR
($start, $end, $strand) = Bio::Range->intersection(\@ranges); OR
my $containing_range = $r1->intersection($r2); OR
my $containing_range = Bio::Range->intersection(\@ranges);
Function: gives the range that is contained by all ranges
Returns : undef if they do not overlap or if @ranges has only a
single range, else returns the range that they do
overlap. In scalar contex, the return value is an object of
the same class as the calling one. In array context the
return value is a three element array.
Args : arg #1 = [REQUIRED] a Bio::RangeI to compare this one to,
or an array ref of ranges
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
=cut
sub intersection {
my ($self, $given, $so) = @_;
$self->throw("missing arg: you need to pass in another feature") unless $given;
my @ranges;
if ($self eq "Bio::RangeI") {
$self = "Bio::Range";
$self->warn("calling static methods of an interface is deprecated; use $self instead");
}
if (ref $self) {
push(@ranges, $self);
}
ref($given) eq 'ARRAY' ? push(@ranges, @{$given}) : push(@ranges, $given);
#$self->throw("Need at least 2 ranges") unless @ranges >= 2;
# Rather than the above, I think the following is more consistent
return undef unless @ranges >= 2;
my $intersect;
while (@ranges > 0) {
unless ($intersect) {
$intersect = shift(@ranges);
$self->throw("Not an object: $intersect") unless ref($intersect);
$self->throw("Not a Bio::RangeI object: $intersect") unless $intersect->isa('Bio::RangeI');
$self->throw("start is undefined") unless defined $intersect->start;
$self->throw("end is undefined") unless defined $intersect->end;
}
my $compare = shift(@ranges);
$self->throw("Not an object: $compare") unless ref($compare);
$self->throw("Not a Bio::RangeI object: $compare") unless $compare->isa('Bio::RangeI');
$self->throw("start is undefined") unless defined $compare->start;
$self->throw("end is undefined") unless defined $compare->end;
return unless $compare->_testStrand($intersect, $so);
my @starts = sort {$a <=> $b} ($intersect->start(), $compare->start());
my @ends = sort {$a <=> $b} ($intersect->end(), $compare->end());
my $start = pop @starts; # larger of the 2 starts
my $end = shift @ends; # smaller of the 2 ends
my $intersect_strand; # strand for the intersection
if (defined($intersect->strand) && defined($compare->strand) && $intersect->strand == $compare->strand) {
$intersect_strand = $compare->strand;
}
else {
$intersect_strand = 0;
}
if ($start > $end) {
return;
}
else {
$intersect = $self->new(-start => $start,
-end => $end,
-strand => $intersect_strand);
}
}
if (wantarray()) {
return ($intersect->start, $intersect->end, $intersect->strand);
}
else {
return $intersect;
}
}
=head2 union
Title : union
Usage : ($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.
=cut
sub union {
my $self = shift;
my @ranges = @_;
if ($self eq "Bio::RangeI") {
$self = "Bio::Range";
$self->warn("calling static methods of an interface is deprecated; use $self instead");
}
if(ref $self) {
unshift @ranges, $self;
}
my @start = sort {$a<=>$b}
map( { $_->start() } @ranges);
my @end = sort {$a<=>$b}
map( { $_->end() } @ranges);
my $start = shift @start;
while( !defined $start ) {
$start = shift @start;
}
my $end = pop @end;
my $union_strand; # Strand for the union range object.
foreach(@ranges) {
if(! defined $union_strand) {
$union_strand = $_->strand;
next;
} else {
if(not defined $_->strand or $union_strand ne $_->strand) {
$union_strand = 0;
last;
}
}
}
return unless $start or $end;
if( wantarray() ) {
return ( $start,$end,$union_strand);
} else {
return $self->new('-start' => $start,
'-end' => $end,
'-strand' => $union_strand
);
}
}
=head2 overlap_extent
Title : overlap_extent
Usage : ($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
=cut
sub overlap_extent{
my ($a,$b) = @_;
$a->throw("start is undefined") unless defined $a->start;
$a->throw("end is undefined") unless defined $a->end;
$b->throw("Not a Bio::RangeI object") unless $b->isa('Bio::RangeI');
$b->throw("start is undefined") unless defined $b->start;
$b->throw("end is undefined") unless defined $b->end;
if( ! $a->overlaps($b) ) {
return ($a->length,0,$b->length);
}
my ($au,$bu) = (0, 0);
if( $a->start < $b->start ) {
$au = $b->start - $a->start;
} else {
$bu = $a->start - $b->start;
}
if( $a->end > $b->end ) {
$au += $a->end - $b->end;
} else {
$bu += $b->end - $a->end;
}
my $intersect = $a->intersection($b);
if( ! $intersect ) {
warn("no intersection\n");
return ($au, 0, $bu);
} else {
my $ie = $intersect->end;
my $is = $intersect->start;
return ($au,$ie-$is+1,$bu);
}
}
=head2 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)
=cut
sub disconnected_ranges {
my $self = shift;
if ($self eq "Bio::RangeI") {
$self = "Bio::Range";
$self->warn("calling static methods of an interface is deprecated; use $self instead");
}
my @inranges = @_;
if(ref $self) {
unshift @inranges, $self;
}
my @outranges = (); # disconnected ranges
# iterate through all input ranges $inrange,
# adding each input range to the set of output ranges @outranges,
# provided $inrange does not overlap ANY range in @outranges
# - if it does overlap an outrange, then merge it
foreach my $inrange (@inranges) {
my $intersects = 0;
my @outranges_new = ();
my @intersecting_ranges = ();
# iterate through all @outranges, testing if it intersects
# current $inrange; if it does, merge and add to list
# of @intersecting_ranges, otherwise add $outrange to
# the new list of outranges that do NOT intersect
for (my $i=0; $i<@outranges; $i++) {
my $outrange = $outranges[$i];
my $intersection = $inrange->intersection($outrange);
if ($intersection) {
$intersects = 1;
my $union = $inrange->union($outrange);
push(@intersecting_ranges, $union);
}
else {
push(@outranges_new, $outrange);
}
}
@outranges = @outranges_new;
# @outranges now contains a list of non-overlapping ranges
# that do not intersect the current $inrange
if (@intersecting_ranges) {
if (@intersecting_ranges > 1) {
# this sf intersected > 1 range, which means that
# all the ranges it intersects should be joined
# together in a new range
my $merged_range =
$self->union(@intersecting_ranges);
push(@outranges, $merged_range);
}
else {
# exactly 1 intersecting range
push(@outranges, @intersecting_ranges);
}
}
else {
# no intersections found - new range
push(@outranges,
$self->new('-start'=>$inrange->start,
'-end'=>$inrange->end,
'-strand'=>$inrange->strand,
));
}
}
return @outranges;
}
=head2 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 : $self, offset accordingly.
=cut
sub offsetStranded {
my ($self, $offset_fiveprime, $offset_threeprime) = @_;
my ($offset_start, $offset_end) = $self->strand() eq -1 ? (- $offset_threeprime, - $offset_fiveprime) : ($offset_fiveprime, $offset_threeprime);
$self->start($self->start + $offset_start);
$self->end($self->end + $offset_end);
return $self;
};
=head2 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)
=cut
sub subtract() {
my ($self, $range, $so) = @_;
$self->throw("missing arg: you need to pass in another feature")
unless $range;
return unless $self->_testStrand($range, $so);
if ($self eq "Bio::RangeI") {
$self = "Bio::Range";
$self->warn("calling static methods of an interface is
deprecated; use $self instead");
}
$range->throw("Input a Bio::RangeI object") unless
$range->isa('Bio::RangeI');
my @sub_locations;
if ($self->location->isa('Bio::Location::SplitLocationI') ) {
@sub_locations = $self->location->sub_Location;
} else {
@sub_locations = $self;
}
my @outranges;
foreach my $sl (@sub_locations) {
if (!$sl->overlaps($range)) {
push(@outranges,
$self->new('-start' =>$sl->start,
'-end' =>$sl->end,
'-strand'=>$sl->strand,
));
next;
}
##Subtracts everything
if ($range->contains($sl)) {
next;
}
my ($start, $end, $strand) = $sl->intersection($range, $so);
##Subtract intersection from $self range
if ($sl->start < $start) {
push(@outranges,
$self->new('-start' =>$sl->start,
'-end' =>$start - 1,
'-strand'=>$sl->strand,
));
}
if ($sl->end > $end) {
push(@outranges,
$self->new('-start' =>$end + 1,
'-end' =>$sl->end,
'-strand'=>$sl->strand,
));
}
}
if (@outranges) {
return \@outranges;
}
return;
}
1;