Bio RangeI
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Summary
Bio::RangeI - Range interface
Package variables
Globals (from "use vars" definitions)
%STRAND_OPTIONS
Included modules
Carp
integer
Inherit
Bio::Root::RootI
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)
Methods
BEGIN Code
_strong
No description
Code
_weak
No description
Code
_ignore
No description
Code
_testStrand()
No description
Code
startDescriptionCode
endDescriptionCode
lengthDescriptionCode
strandDescriptionCode
overlapsDescriptionCode
containsDescriptionCode
equalsDescriptionCode
intersectionDescriptionCode
unionDescriptionCode
overlap_extentDescriptionCode
disconnected_rangesDescriptionCode
offsetStrandedDescriptionCode
subtract()
No description
Code
Methods description
startcode    nextTop
  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)
endcodeprevnextTop
  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)
lengthcodeprevnextTop
  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)
strandcodeprevnextTop
  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)
overlapscodeprevnextTop
  Title   : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function: tests if $r2 overlaps $r1
Args : arg #1 = a range to compare this one to (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
Returns : true if the ranges overlap, false otherwise
containscodeprevnextTop
  Title   : contains
Usage : if($r1->contains($r2) { do stuff }
Function: tests whether $r1 totally contains $r2
Args : arg #1 = a range to compare this one to (mandatory)
alternatively, integer scalar to test
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
Returns : true if the argument is totally contained within this range
equalscodeprevnextTop
  Title   : equals
Usage : if($r1->equals($r2))
Function: test whether $r1 has the same start, end, length as $r2
Args : arg #1 = a range to compare this one to (mandatory)
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
Returns : true if they are describing the same range
intersectioncodeprevnextTop
 Title   : intersection
Usage : ($start, $end, $strand) = $r1->intersection($r2); OR
($start, $end, $strand) = Bio::Range->intersection(\@ranges); OR
my $containing_range = $r1->intersection($r2); OR
my $containing_range = Bio::Range->intersection(\@ranges);
Function: gives the range that is contained by all ranges
Returns : undef if they do not overlap or if @ranges has only a
single range, else returns the range that they do
overlap. In scalar contex, the return value is an object of
the same class as the calling one. In array context the
return value is a three element array.
Args : arg #1 = [REQUIRED] a Bio::RangeI to compare this one to,
or an array ref of ranges
arg #2 = optional strand-testing arg ('strong', 'weak', 'ignore')
unioncodeprevnextTop
   Title   : union
Usage : ($start, $end, $strand) = $r1->union($r2);
: ($start, $end, $strand) = Bio::Range->union(@ranges);
my $newrange = Bio::Range->union(@ranges);
Function: finds the minimal Range that contains all of the Ranges
Args : a Range or list of Range objects
Returns : the range containing all of the range. In scalar contex, the return value is an object of the same class as the calling one. In array context the return value is a three element array.
overlap_extentcodeprevnextTop
 Title   : overlap_extent
Usage : ($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_rangescodeprevnextTop
    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)
offsetStrandedcodeprevnextTop
    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.
Methods code
BEGINTop
BEGIN {
# STRAND_OPTIONS contains the legal values for the strand-testing options
%STRAND_OPTIONS = map { $_, '_' . $_ } ( 'strong', # ranges must have the same strand
'weak', # ranges must have the same strand or no strand
'ignore', # ignore strand information
);
}
_strongdescriptionprevnextTop
sub _strong {
    my ($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
}
_weakdescriptionprevnextTop
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
}
_ignoredescriptionprevnextTop
sub _ignore {
    return 1;
}

# works out what test to use for the strictness and returns true/false
# e.g. $r1->_testStrand($r2, 'strong')
}
_testStrand()descriptionprevnextTop
sub _testStrand() {
    my ($r1, $r2, $comp) = @_;
    return 1 unless $comp;
    my $func = $STRAND_OPTIONS{$comp};
    return $r1->$func($r2);
}
startdescriptionprevnextTop
sub start {
    shift->throw_not_implemented();
}
enddescriptionprevnextTop
sub end {
    shift->throw_not_implemented();
}
lengthdescriptionprevnextTop
sub length {
    shift->throw_not_implemented();
}
stranddescriptionprevnextTop
sub strand {
    shift->throw_not_implemented();
}
overlapsdescriptionprevnextTop
sub overlaps {
	my ($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() < $other->start()   )
				  ));
}
containsdescriptionprevnextTop
sub contains {
	my ($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 <= $self->end()); }
}
equalsdescriptionprevnextTop
sub equals {
    my ($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()   == $other->end()       );
}
intersectiondescriptionprevnextTop
sub intersection {
	my ($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; }
}
uniondescriptionprevnextTop
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' => $union_strand ); }
}
overlap_extentdescriptionprevnextTop
sub overlap_extent {
	my ($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);
	}
}
disconnected_rangesdescriptionprevnextTop
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;
}
offsetStrandeddescriptionprevnextTop
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 $self;
};
}
subtract()descriptionprevnextTop
sub subtract() {
   my ($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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
CONTRIBUTORSTop
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)
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Abstract methodsTop
These methods must be implemented in all subclasses.
Boolean MethodsTop
These methods return true or false. They throw an error if start and
end are not defined.
  $range->overlaps($otherRange) && print "Ranges overlap\n";
Geometrical methodsTop
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.
subtractTop
  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)