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
            
          

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

            

              
              
Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.
            
          

NAME

Bio::EnsEMBL::Utils::Tree::Interval::Immutable

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.

METHODS

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
            
          

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
            
          

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