Provided by: libbio-perl-perl_1.7.2-3_all bug

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://github.com/bioperl/bioperl-live/issues

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\n";

   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)