#
# BioPerl module for Bio::Range
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
# Copywright Matthew Pocock
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
=head1 NAME
Bio::Range - Pure perl RangeI implementation
=head1 SYNOPSIS
$range = Bio::Range->new(-start=>10, -end=>30, -strand=>+1);
$r2 = Bio::Range->new(-start=>15, -end=>200, -strand=>+1);
print join(', ', $range->union($r2)), "\n";
print join(', ', $range->intersection($r2)), "\n";
print $range->overlaps($r2), "\n";
print $range->contains($r2), "\n";
=head1 DESCRIPTION
This provides a pure perl implementation of the BioPerl range
interface.
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
greather 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 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Range;
use strict;
use Carp;
use integer;
use base qw(Bio::Root::Root Bio::RangeI);
=head1 Constructors
=head2 new
Title : new
Usage : $range = Bio::Range->new(-start => 100, -end=> 200, -strand = +1);
Function: generates a new Bio::Range
Returns : a new range
Args : -strand (defaults to 0) and any two of (-start, -end, -length),
the third will be calculated
=cut
sub new {
my ($caller, @args) = @_;
my $self = $caller->SUPER::new(@args);
my ($strand, $start, $end, $length) =
$self->_rearrange([qw(STRAND
START
END
LENGTH
)],@args);
$self->strand($strand || 0);
if(defined $start ) {
$self->start($start);
if(defined $end) {
$self->end($end);
} elsif(defined $length) {
$self->end($self->start()+ $length - 1);
}
} elsif(defined $end && defined $length ) {
$self->end($end);
$self->start($self->end() - $length + 1);
}
return $self;
}
=head2 unions
Title : unions
Usage : @unions = Bio::Range->unions(@ranges);
Function: generate a list of non-intersecting Bio::Range objects
from a list of Bio::Range objects which may intersect
Returns : a list of Bio::Range objects
Args : a list of Bio::Range objects
=cut
sub unions {
my ($class,@i) = @_;
my $i = 0;
my %i = map { $i++ => $_ } @i;
my $lastsize = scalar(keys %i);
do {
foreach my $j (sort { $i{$a}->start <=> $i{$b}->start } keys %i){
foreach my $k (sort { $i{$a}->start <=> $i{$b}->start } keys %i){
#it may have been replaced by a union under the key of
#the overlapping range, we are altering the hash in-place
next unless $i{$j};
next if $i{$k}->end < $i{$j}->start;
last if $i{$k}->start > $i{$j}->end;
if($i{$j}->overlaps($i{$k})){
my($start,$end,$strand) = $i{$j}->union($i{$k});
delete($i{$k});
$i{$j} = Bio::Range->new( -start => $start , -end => $end , -strand => $strand );
}
}
}
goto DONE if scalar(keys %i) == $lastsize;
$lastsize = scalar(keys %i);
#warn $lastsize;
} while(1);
DONE:
return values %i;
}
=head1 Member variable access
These methods let you get at and set the member variables
=head2 start
Title : start
Function : return or set the start co-ordinate
Example : $s = $range->start(); $range->start(7);
Returns : the value of the start co-ordinate
Args : optionally, the new start co-ordinate
Overrides: Bio::RangeI::start
=cut
sub start {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("'$value' is not an integer.\n")
unless $value =~ /^[-+]?\d+$/;
$self->{'start'} = $value;
}
return $self->{'start'};
}
=head2 end
Title : end
Function : return or set the end co-ordinate
Example : $e = $range->end(); $range->end(2000);
Returns : the value of the end co-ordinate
Args : optionally, the new end co-ordinate
Overrides: Bio::RangeI::end
=cut
sub end {
my ($self,$value) = @_;
if( defined $value) {
$self->throw("'$value' is not an integer.\n")
unless $value =~ /^[-+]?\d+$/;
$self->{'end'} = $value;
}
return $self->{'end'};
}
=head2 strand
Title : strand
Function : return or set the strandedness
Example : $st = $range->strand(); $range->strand(-1);
Returns : the value of the strandedness (-1, 0 or 1)
Args : optionally, the new strand - (-1, 0, 1) or (-, ., +).
Overrides: Bio::RangeI::strand
=cut
{
my %VALID_STRAND = (
-1 => -1,
0 => 0,
1 => 1,
'+' => 1,
'-' => -1,
'.' => 0
);
sub strand {
my $self = shift;
if(@_) {
my $val = shift;
if (exists $VALID_STRAND{$val}) {
$self->{'strand'} = $VALID_STRAND{$val};
} else {
$self->throw("Invalid strand: $val");
}
}
return $self->{'strand'};
}
}
=head2 length
Title : length
Function : returns the length of this range
Example : $length = $range->length();
Returns : the length of this range, equal to end - start + 1
Args : if you attempt to set the length an exception will be thrown
Overrides: Bio::RangeI::Length
=cut
sub length {
my $self = shift;
if(@_) {
confess ref($self), "->length() is read-only";
}
return $self->end() - $self->start() + 1;
}
=head2 toString
Title : toString
Function: stringifies this range
Example : print $range->toString(), "\n";
Returns : a string representation of this range
=cut
sub toString {
my $self = shift;
return "(${\$self->start}, ${\$self->end}) strand=${\$self->strand}";
}
=head1 Boolean Methods
These methods return true or false.
$range->overlaps($otherRange) && print "Ranges overlap\n";
=head2 overlaps
Title : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function : tests if $r2 overlaps $r1
Args : a range to test for overlap with
Returns : true if the ranges overlap, false otherwise
Inherited: Bio::RangeI
=head2 contains
Title : contains
Usage : if($r1->contains($r2) { do stuff }
Function : tests whether $r1 totally contains $r2
Args : a range to test for being contained
Returns : true if the argument is totally contained within this range
Inherited: Bio::RangeI
=head2 equals
Title : equals
Usage : if($r1->equals($r2))
Function : test whether $r1 has the same start, end, length as $r2
Args : a range to test for equality
Returns : true if they are describing the same range
Inherited: Bio::RangeI
=head1 Geometrical methods
These methods do things to the geometry of ranges, and return
triplets (start, end, strand) from which new ranges could be built.
=head2 intersection
Title : intersection
Usage : ($start, $stop, $strand) = $r1->intersection($r2)
Function : gives the range that is contained by both ranges
Args : a range to compare this one to
Returns : nothing if they do not overlap, or the range that they do overlap
Inherited: Bio::RangeI::intersection
=cut
=head2 union
Title : union
Usage : ($start, $stop, $strand) = $r1->union($r2);
: ($start, $stop, $strand) = Bio::Range->union(@ranges);
Function : finds the minimal range that contains all of the ranges
Args : a range or list of ranges
Returns : the range containing all of the ranges
Inherited: Bio::RangeI::union
=cut
1;