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::Tree::Interval::Mutable::PP

DESCRIPTION

Pure Perl fall back implementation of a mutable interval tree, uses augmented AVL binary balanced trees.

METHODS

new

  Arg []      : none
  Example     : my $tree = Bio::EnsEMBL::Utils::Tree::Mutable();
  Description : Constructor. Creates a new mutable tree instance
  Returntype  : Bio::EnsEMBL::Utils::Tree::Interval::Mutable::PP
  Exceptions  : none
  Caller      : general

root

  Arg []      : none
  Example     : my $root = $tree->root;
  Description : Returns the tree top node
  Returntype  : Bio::EnsEMBL::Utils::Tree::Interval::Mutable::Node
  Exceptions  : none
  Caller      : general

size

  Arg []      : none
  Example     : print "Tree size is ", $tree->size, "\n";
  Description : Return the size of the tree, i.e. the number of nodes
  Returntype  : scalar
  Exceptions  : none
  Caller      : general

insert

  Arg [1]     : Bio::EnsEMBL::Utils::Interval
                Interval to insert
  Example     : $tree->insert(Bio::EnsEMBL::Utils::Interval->new(10, 20, 'data'));
  Description : Insert an interval in the tree
  Returntype  : scalar (1), upon success
  Exceptions  : thrown if Interval spans origin (has start > end)
  Caller      : general

search

  Arg [1]     : scalar, $start
                the starting point of the interval to search
  Arg [2]     : scalar, $end
                the end point of the interval to search
  Example     : my $result = $tree->search(85, 100);
  Description : Search the intervals in the tree overlapping the query
  Returntype  : Arrayref of Bio::EnsEMBL::Utils::Interval instances
  Exceptions  : none
  Caller      : general

remove

  Arg [1]     : Bio::EnsEMBL::Utils::Interval
                The interval to remove from the tree
  Example     : $tree->remove($i);
  Description : Remove an interval from the tree
  Returntype  : scalar, 1 if removal is successful, 0 otherwise
  Exceptions  : none
  Caller      : general