Bio::EnsEMBL::Utils::Tree::Interval::Immutable Class Reference

Public Member Functions
public Bio::EnsEMBL::Utils::Tree::Interval::Immutable	new ()
public Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node	root ()
public An	query ()
protected	_query_point ()
protected	_range_query_left ()
protected	_range_query_right ()
public	in_order_traversal ()
protected	_in_order_traversal ()
protected	_divide_intervals ()
protected	_center ()
protected	_center_sorted ()
public	sort_by_begin ()
public	uniq ()

Detailed Description

Synopsis

# define a set of intervals to be added to the tree
my $intervals = [ Bio::EnsEMBL::Utils::Interval->new(121626874, 122092717),
          Bio::EnsEMBL::Utils::Interval->new(121637917, 121658918),
          Bio::EnsEMBL::Utils::Interval->new(122096077, 124088369) ];
 
# initialise the tree with the above intervals
my $tree = Bio::EnsEMBL::Utils::Tree::Interval::Immutable->new($intervals);
 
# point query
my $results = $tree->query(121779004);
if (scalar @$results) {
  print "Intervals contain 121779004\n";
}
 
# same query, but use interval query
my $results = $tree->query(121779004, 121779004);
if (scalar @$results) {
  print "Found containing interval: [", $result->[0]->start, ', ', $result->[0]->end, "\n";
}

Description

An implementation of an immutable interval tree. Immutable means the tree is
initialised with a fixed set of intervals at creation time. Intervals cannot
be added to or removed from the tree during its life cycle.

Implementation heavily inspired by https://github.com/tylerkahn/intervaltree-python

This implementation does not support Intervals having a start > end - i.e.
intervals spanning the origin of a circular chromosome.

Definition at line 47 of file Immutable.pm.

Member Function Documentation

_center()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_center

(

)

Undocumented method

Code:

_center_sorted()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_center_sorted

(

)

Undocumented method

Code:

_divide_intervals()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_divide_intervals

(

)

Undocumented method

Code:

_in_order_traversal()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_in_order_traversal

(

)

Undocumented method

Code:

_query_point()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_query_point

(

)

Undocumented method

Code:

_range_query_left()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_range_query_left

(

)

Undocumented method

Code:

_range_query_right()

protected Bio::EnsEMBL::Utils::Tree::Interval::Immutable::_range_query_right

(

)

Undocumented method

Code:

in_order_traversal()

public Bio::EnsEMBL::Utils::Tree::Interval::Immutable::in_order_traversal

(

)

Undocumented method

Code:

new()

public Bio::EnsEMBL::Utils::Tree::Interval::Immutable Bio::EnsEMBL::Utils::Tree::Interval::Immutable::new

(

)

  Arg [1]     : Arrayref of Bio::EnsEMBL::Utils::Interval instances
  Example     :

my $tree = Bio::EnsEMBL::Utils::Tree::Immutable([ $i1, $i2, $i3 ]);

  Description : Constructor. Creates a new immutable tree instance
  Returntype  : Bio::EnsEMBL::Utils::Tree::Interval::Immutable
  Exceptions  : none
  Caller      : general

Code:

query()

public An Bio::EnsEMBL::Utils::Tree::Interval::Immutable::query

(

)

  Arg [1]     : scalar, $start
                Where the query interval begins
  Arg [2]     : (optional) scalar, $end
                Where the query interval ends
  Example     :

my $results = $tree->query(121626874, 122092717);

  Description : Query the tree if its intervals overlap the interval whose start
                and end points are specified by the argument list.
                If end is not specified, it is assumed to be the same as start
                so effectively making a point query.
  Returntype  : An arrayref of Bio::EnsEMBL::Utils::Interval instances
  Exceptions  : none
  Caller      : general

Code:

root()

public Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node Bio::EnsEMBL::Utils::Tree::Interval::Immutable::root

(

)

  Arg []      : none
  Example     :

my $root = $tree->root();

  Description : Return the tree top node
  Returntype  : Bio::EnsEMBL::Utils::Tree::Interval::Immutable::Node
  Exceptions  : none
  Caller      : general

Code:

sort_by_begin()

public Bio::EnsEMBL::Utils::Tree::Interval::Immutable::sort_by_begin

(

)

Undocumented method

Code:

uniq()

public Bio::EnsEMBL::Utils::Tree::Interval::Immutable::uniq

(

)

Undocumented method

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Utils/Tree/Interval/Immutable.pm