LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::Utils::Interval

SYNOPSIS

  # let's get an interval spanning 9e5 bp and associated it with some data
  my $i1 = Bio::EnsEMBL::Utils::Interval->new(1e5, 1e6, { 'key1' => 'value1', 'key2' => 'value2' });

  # and another one which overlaps with the previous,
  # but with scalar associated data
  my $i2 = Bio::EnsEMBL::Utils::Interval->new(2e5, 3e5, 'a string' );

  warn "Empty interval(s)\n" if $i1->is_empty or $i2->is_empty;
  warn "Point interval(s)\n" if $i1->is_point or $i2->is_point;

  if ($i1->intersects($i2)) {
    print "I1 and I2 overlap\n";
  } else {
    print "I1 and I2 do not overlap\n";
  }

  # If an interval is defined with a start > end, then it is assumed
  # to be spanning the origin on a circular chromosome
  my $i3 = Bio::EnsEMBL::Utilities::Interval->new(1e5, 1e2);
  warn "Interval spans the origin" if $i3->spans_origin;

  etc.

DESCRIPTION

A class representing an interval defined on a genomic region. Instances of this class can store arbitrarily defined data. If created with start > end, then it is assumed that this interval is on a circular chromosome spanning the origin.

METHODS

new

  Arg [1]     : scalar $start
                The start coordinate of the region
  Arg [2]     : scalar $end
                The end coordinate of the region
  Arg [3]     : (optional) $data
                The data associated with the interval, can be anything
  Example     : my $i = Bio::EnsEMBL::Utils::Interval(1e2, 2e2, { 'key' => 'value' });
                my $i2 = Bio::EnsEMBL::Utilities::Interval(1e5, 1e2);
                $i->spans_origin # returns 0
                $i2->spans_origin # returns 1
  Description : Constructor. Creates a new instance
  Returntype  : Bio::EnsEMBL::Utils::Interval
  Exceptions  : Throws an exception if start and end are not defined.
  Caller      : general

start

  Arg []      : none
  Description : Returns the start coordinate of the region
  Returntype  : scalar
  Exceptions  : none
  Caller      : general

end

  Arg []      : none
  Description : Returns the end coordinate of the region
  Returntype  : scalar
  Exceptions  : none
  Caller      : general

data

  Arg []      : none
  Description : Returns the data associated with the region
  Returntype  : Any
  Exceptions  : none
  Caller      : general

spans_origin

  Arg []      : none
  Description : Returns whether this interval was created spanning zero
                (more particularly: if the interval was instantiated with start > end)
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

is_empty

  Arg []      : none
  Description : Returns whether or not the interval is empty
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

is_point

  Arg []      : none
  Description : Determines if the current interval is a single point
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

contains

  Arg [1]     : scalar, the point coordinate 
  Description : Determines if the current instance contains the query point
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

intersects

  Arg [1]     : An instance of Bio::EnsEMBL::Utils::Interval
  Description : Determines if the the instance intersects the given interval
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

is_right_of

  Arg [1]     : An instance of Bio::EnsEMBL::Utils::Interval or a scalar
  Description : Checks if this current interval is entirely to the right of a point
                or Interval.
                More formally, the method will return true, if for every point x from 
                the current interval the inequality x > point holds, where point
                is either a single scalar, or point is the end of another Interval.
                If spans_origin is true for either this Interval or an Interval
                passed in, then this method returns false.
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

is_left_of

  Arg [1]     : An instance of Bio::EnsEMBL::Utils::Interval or a scalar
  Description : Checks if this current interval is entirely to the left of a point
                or Interval.
                More formally, the method will return true, if for every point x from 
                the current interval the inequality x < point holds, where point
                is either a single scalar, or point is the start of another Interval.
                If spans_origin is true for either this Interval or an Interval
                passed in, then this method returns false
  Returntype  : boolean
  Exceptions  : none
  Caller      : general

cpanm Bio::EnsEMBL::CDS

perl -MCPAN -e shell
install Bio::EnsEMBL::CDS