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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Utils::Tree::Interval::Mutable::PP

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
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