/ 
Bio-EnsEMBL-112.0.0_58
River stage zero No dependents
/ Bio::EnsEMBL::Utils::Interval

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