Bio Range
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Summary
Bio::Range - Pure perl RangeI implementation
Package variables
Privates (from "my" definitions)
%VALID_STRAND = ( -1 => -1, 0 => 0, 1 => 1, '+' => 1, '-' => -1, '.' => 0)
Included modules
Carp
integer
Inherit
Bio::RangeI Bio::Root::Root
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";
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 >= start and <= 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)
Methods
newDescriptionCode
unionsDescriptionCode
startDescriptionCode
endDescriptionCode
strandDescriptionCode
lengthDescriptionCode
toStringDescriptionCode
Methods description
newcode    nextTop
  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
unionscodeprevnextTop
 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
startcodeprevnextTop
  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
endcodeprevnextTop
  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
strandcodeprevnextTop
  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
lengthcodeprevnextTop
  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
toStringcodeprevnextTop
  Title   : toString
Function: stringifies this range
Example : print $range->toString(), "\n";
Returns : a string representation of this range
Methods code
newdescriptionprevnextTop
sub new {
  my ($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 $self;
}
unionsdescriptionprevnextTop
sub unions {
  my ($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 $lastsize;
} while(1); DONE: return values %i;
}
startdescriptionprevnextTop
sub start {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->throw("'$value' is not an integer.\n") 
	    unless $value =~ /^[-+]?\d+$/;
        $self->{'start'} = $value;
    }
    return $self->{'start'};
}
enddescriptionprevnextTop
sub end {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->throw("'$value' is not an integer.\n") 
	    unless $value =~ /^[-+]?\d+$/;
        $self->{'end'} = $value;
    }
    return $self->{'end'};
}
stranddescriptionprevnextTop
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'};
}
}
lengthdescriptionprevnextTop
sub length {
  my $self = shift;
  if(@_) {
    confess ref($self), "->length() is read-only";
  }
  return $self->end() - $self->start() + 1;
}
toStringdescriptionprevnextTop
sub toString {
  my $self = shift;
  return  "(${\$self->start}, ${\$self->end}) strand=${\$self->strand}";
}
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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
ConstructorsTop
Member variable accessTop
These methods let you get at and set the member variables
Boolean MethodsTop
These methods return true or false.
 $range->overlaps($otherRange) && print "Ranges overlap\n";
overlapsTop
  Title    : overlaps
Usage : if($r1->overlaps($r2)) { do stuff }
Function : tests if $r2 overlaps $r1
Args : a range to test for overlap with
Returns : true if the ranges overlap, false otherwise
Inherited: Bio::RangeI
containsTop
  Title    : contains
Usage : if($r1->contains($r2) { do stuff }
Function : tests whether $r1 totally contains $r2
Args : a range to test for being contained
Returns : true if the argument is totally contained within this range
Inherited: Bio::RangeI
equalsTop
  Title    : equals
Usage : if($r1->equals($r2))
Function : test whether $r1 has the same start, end, length as $r2
Args : a range to test for equality
Returns : true if they are describing the same range
Inherited: Bio::RangeI
Geometrical methodsTop
These methods do things to the geometry of ranges, and return
triplets (start, end, strand) from which new ranges could be built.
intersectionTop
  Title    : intersection
Usage : ($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
unionTop
  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